@article {pmid39810263,
year = {2025},
author = {Nychas, E and Marfil-Sánchez, A and Chen, X and Mirhakkak, M and Li, H and Jia, W and Xu, A and Nielsen, HB and Nieuwdorp, M and Loomba, R and Ni, Y and Panagiotou, G},
title = {Discovery of robust and highly specific microbiome signatures of non-alcoholic fatty liver disease.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {10},
pmid = {39810263},
issn = {2049-2618},
mesh = {*Non-alcoholic Fatty Liver Disease/microbiology ; Humans ; *Gastrointestinal Microbiome/genetics ; Female ; Male ; Middle Aged ; Bacteria/classification/genetics/isolation & purification ; Machine Learning ; Metagenomics/methods ; Adult ; Obesity/microbiology ; Metagenome ; },
abstract = {BACKGROUND: The pathogenesis of non-alcoholic fatty liver disease (NAFLD) with a global prevalence of 30% is multifactorial and the involvement of gut bacteria has been recently proposed. However, finding robust bacterial signatures of NAFLD has been a great challenge, mainly due to its co-occurrence with other metabolic diseases.

RESULTS: Here, we collected public metagenomic data and integrated the taxonomy profiles with in silico generated community metabolic outputs, and detailed clinical data, of 1206 Chinese subjects w/wo metabolic diseases, including NAFLD (obese and lean), obesity, T2D, hypertension, and atherosclerosis. We identified highly specific microbiome signatures through building accurate machine learning models (accuracy = 0.845-0.917) for NAFLD with high portability (generalizable) and low prediction rate (specific) when applied to other metabolic diseases, as well as through a community approach involving differential co-abundance ecological networks. Moreover, using these signatures coupled with further mediation analysis and metabolic dependency modeling, we propose synergistic defined microbial consortia associated with NAFLD phenotype in overweight and lean individuals, respectively.

CONCLUSION: Our study reveals robust and highly specific NAFLD signatures and offers a more realistic microbiome-therapeutics approach over individual species for this complex disease. Video Abstract.},
}

*Non-alcoholic Fatty Liver Disease/microbiology
Humans
*Gastrointestinal Microbiome/genetics
Female
Male
Middle Aged
Bacteria/classification/genetics/isolation & purification
Machine Learning
Metagenomics/methods
Adult
Obesity/microbiology
Metagenome

@article {pmid39810137,
year = {2025},
author = {Zong, X and Wang, X and Yu, M and Wang, J and Li, C and Wang, B and Wang, Y},
title = {A reduction-secretion system contributes to roxarsone (V) degradation and efflux in Brevundimonas sp. M20.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {23},
pmid = {39810137},
issn = {1471-2180},
support = {S202410439004//National College Students Innovation and Entrepreneurship Training Program/ ; S202410439004//National College Students Innovation and Entrepreneurship Training Program/ ; },
abstract = {Roxarsone (V) (Rox(V)) is an organoarsenical compound that poses significant risks to aquatic ecosystems and various diseases. Reducing trivalent 3-amino-4-hydroxyphenylarsonic acid (HAPA(III)) offers a competitive advantage; however, it leads to localized arsenic contamination, which can disrupt the soil microbiome and impede plant growth. Three genes, BsntrA, arsC2, and BsexpA, encoding nitroreductase, arsenate reductase, and MFS transporter, respectively, were identified in the Rox(V)-resistant strain Brevundimonas sp. M20. A three-step approach, including nitroreduction, As(V) reduction, and HAPA(III) secretion, which is responsible for roxarsone(V) resistance, was subsequently confirmed. Moreover, the flavonoid compound baicalin occupied the HAPA(III) delivery space and grabbed the R127 residues via stronger interactions. This steric hindrance prevented the transportation of HAPA(III) by BsexpA to the extracellular space. These results demonstrate a new Rox(V) reduction pathway, providing a potential efflux pump inhibitor to trap more toxins.},
}

@article {pmid39809904,
year = {2025},
author = {Carril, P and Cordeiro, C and Silva, MS and Ngendahimana, E and Tenreiro, R and Cruz, C},
title = {Exploring the plant-growth promoting bacterium Herbaspirillum seropedicae as catalyst of microbiome remodeling and metabolic changes in wheat plants.},
journal = {Planta},
volume = {261},
number = {2},
pages = {36},
pmid = {39809904},
issn = {1432-2048},
support = {PD/BD/135249/2017//fundaçao ciencia e tecnologia/ ; },
mesh = {*Triticum/microbiology/metabolism/growth & development/genetics ; *Microbiota ; *Herbaspirillum/physiology/metabolism/genetics ; *Plant Roots/microbiology/metabolism/growth & development ; Soil Microbiology ; Metabolome ; RNA, Ribosomal, 16S/genetics ; Endophytes/physiology ; },
abstract = {Inoculation with the PGPB Herbaspirillum seropedicae shapes both the structure and putative functions of the wheat microbiome and causes changes in the levels of various plant metabolites described to be involved in plant growth and health. Plant growth promoting bacteria (PGPB) can establish metabolic imprints in their hosts, contributing to the improvement of plant health in different ways. However, while PGPB imprints on plant metabolism have been extensively characterized, much less is known regarding those affecting plant indigenous microbiomes, and hence it remains unknown whether both processes occur simultaneously. In this study, both 16S amplicon and ITS sequencing analyses were carried out to study both the structural as well as the putative functional changes in the seed-borne endophytic microbiome of wheat plants inoculated with the PGPB Herbaspirillum seropedicae strain RAM10. Concomitantly, Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) analyses were used to investigate the alterations in the root metabolome of PGPB-inoculated plants. PGPB inoculation led to marked differences in the composition of the root microbiome, accompanied by the differential enrichment of microorganisms with putative roles in both plant energy and nitrogen metabolism. In addition, metabolome analyses showed that the levels of 16 metabolites belonging to the phenylpropanoid, terpenoid, and unsaturated fatty acid families were significantly altered in PGPB-inoculated plants. These findings shed light on the interplay between PGPB, the plant and its associated microbiome, indicating that PGPB can act as the driving force mediating long-lasting changes in both the plant metabolome and the plant microbiome.},
}

*Triticum/microbiology/metabolism/growth & development/genetics
*Microbiota
*Herbaspirillum/physiology/metabolism/genetics
*Plant Roots/microbiology/metabolism/growth & development
Soil Microbiology
Metabolome
RNA, Ribosomal, 16S/genetics
Endophytes/physiology

@article {pmid39809790,
year = {2025},
author = {Chen, HC and Cheng, YC and Hsieh, ML and Lin, PJ and Wissel, EF and Steward, T and Chang, CMC and Coonen, J and Hacker, TA and Kamp, TJ and Hsieh, PCH},
title = {Gut microbiota modulation in cardiac cell therapy with immunosuppression in a nonhuman primate ischemia/reperfusion model.},
journal = {NPJ Regenerative medicine},
volume = {10},
number = {1},
pages = {2},
pmid = {39809790},
issn = {2057-3995},
support = {NHRI -EX112-11203SI//National Health Research Institutes (NHRI)/ ; },
abstract = {Gut microbiota affect transplantation outcomes; however, the influence of immunosuppression and cell therapy on the gut microbiota in cardiovascular care remains unexplored. We investigated gut microbiota dynamics in a nonhuman primate (NHP) cardiac ischemia/reperfusion model while under immunosuppression and receiving cell therapy with human induced pluripotent stem cell (hiPSC)-derived endothelial cells (EC) and cardiomyocytes (CM). Both immunosuppression and EC/CM co-treatment increased gut microbiota alpha diversity. Immunosuppression promoted anaerobes, such as Faecalibacterium, Streptococcus, Anaerovibrio and Dialister, and altered amino acid metabolism and nucleosides/nucleotides biosynthesis in host plasma. EC + CM cotreatment favors Phascolarctobacterium, Fusicatenibacter, Erysipelotrichaceae UCG-006, Veillonella and Mailhella. Remarkably, gut microbiota of the EC/CM co-treatment group resembled that of the pre-injury group, and the NHPs exhibited a metabolic shift towards amino acid and fatty acid/lipid biosynthesis in plasma following cell therapy. The interplay between shift in microbial community and host homeostasis during treatment suggests gut microbiome modulation could improve cell therapy outcomes.},
}

@article {pmid39809768,
year = {2025},
author = {Fahur Bottino, G and Bonham, KS and Patel, F and McCann, S and Zieff, M and Naspolini, N and Ho, D and Portlock, T and Joos, R and Midani, FS and Schüroff, P and Das, A and Shennon, I and Wilson, BC and O'Sullivan, JM and Britton, RA and Murray, DM and Kiely, ME and Taddei, CR and Beltrão-Braga, PCB and Campos, AC and Polanczyk, GV and Huttenhower, C and Donald, KA and Klepac-Ceraj, V},
title = {Early life microbial succession in the gut follows common patterns in humans across the globe.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {660},
pmid = {39809768},
issn = {2041-1723},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Infant ; *Feces/microbiology ; Female ; Metagenome ; Male ; Bifidobacterium/genetics/isolation & purification ; Infant, Newborn ; Faecalibacterium prausnitzii/genetics ; Child Development ; },
abstract = {Characterizing the dynamics of microbial community succession in the infant gut microbiome is crucial for understanding child health and development, but no normative model currently exists. Here, we estimate child age using gut microbial taxonomic relative abundances from metagenomes, with high temporal resolution (±3 months) for the first 1.5 years of life. Using 3154 samples from 1827 infants across 12 countries, we trained a random forest model, achieving a root mean square error of 2.56 months. We identified key taxonomic predictors of age, including declines in Bifidobacterium spp. and increases in Faecalibacterium prausnitzii and Lachnospiraceae. Microbial succession patterns are conserved across infants from diverse human populations, suggesting universal developmental trajectories. Functional analysis confirmed trends in key microbial genes involved in feeding transitions and dietary exposures. This model provides a normative benchmark of "microbiome age" for assessing early gut maturation that may be used alongside other measures of child development.},
}

Humans
*Gastrointestinal Microbiome/genetics
Infant
*Feces/microbiology
Female
Metagenome
Male
Bifidobacterium/genetics/isolation & purification
Infant, Newborn
Faecalibacterium prausnitzii/genetics
Child Development

@article {pmid39809763,
year = {2025},
author = {Armetta, J and Li, SS and Vaaben, TH and Vazquez-Uribe, R and Sommer, MOA},
title = {Metagenome-guided culturomics for the targeted enrichment of gut microbes.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {663},
pmid = {39809763},
issn = {2041-1723},
support = {NNF20CC0035580//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF17CO0028232//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF20CC0035580//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF17CO0028232//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF20CC0035580//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF17CO0028232//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF20CC0035580//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF17CO0028232//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; grant agreement No. 813781//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; grant agreement No. 813781//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; no. ALTF 137-2018//European Molecular Biology Organization (EMBO)/ ; no. GNT1166180//Department of Health | National Health and Medical Research Council (NHMRC)/ ; },
mesh = {*Gastrointestinal Microbiome/genetics/drug effects ; Humans ; *Metagenome ; *Phylogeny ; Culture Media/chemistry ; Bacteria/genetics/metabolism/classification ; Feces/microbiology ; Metagenomics/methods ; High-Throughput Nucleotide Sequencing ; Caffeine ; },
abstract = {The gut microbiome significantly impacts human health, yet cultivation challenges hinder its exploration. Here, we combine deep whole-metagenome sequencing with culturomics to selectively enrich for taxa and functional capabilities of interest. Using a modified commercial base medium, 50 growth modifications were evaluated, spanning antibiotics, physico-chemical conditions, and bioactive compounds. Whole-metagenome sequencing identified medium additives, like caffeine, that enhance taxa often associated with healthier subjects (e.g., Lachnospiraceae, Oscillospiraceae, Ruminococcaceae). We also explore the impact of modifications on the composition of cultured communities and establish a link between medium preference and microbial phylogeny. Leveraging these insights, we demonstrate that combinations of media modifications can further enhance the targeted enrichment of taxa and metabolic functions, such as Collinsella aerofaciens, or strains harboring biochemical pathways involved in dopamine metabolism. This streamlined, scalable approach unlocks the potential for selective enrichment, advancing microbiome research by understanding the impact of different cultivation parameters on gut microbes.},
}

*Gastrointestinal Microbiome/genetics/drug effects
Humans
*Metagenome
*Phylogeny
Culture Media/chemistry
Bacteria/genetics/metabolism/classification
Feces/microbiology
Metagenomics/methods
High-Throughput Nucleotide Sequencing
Caffeine

@article {pmid39809740,
year = {2025},
author = {Qu, Z and Liu, H and Yang, J and Zheng, L and Huang, J and Wang, Z and Xie, C and Zuo, W and Xia, X and Sun, L and Zhou, Y and Xie, Y and Lu, J and Zhu, Y and Yu, L and Liu, L and Zhou, H and Dai, L and Leung, EL},
title = {Selective utilization of medicinal polysaccharides by human gut Bacteroides and Parabacteroides species.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {638},
pmid = {39809740},
issn = {2041-1723},
mesh = {Humans ; *Bacteroides/genetics/metabolism ; *Gastrointestinal Microbiome/drug effects ; *Polysaccharides/metabolism ; *Bacteroidetes/genetics/metabolism ; Mannans/metabolism ; },
abstract = {Human gut Bacteroides and Parabacteroides species play crucial roles in human health and are known for their capacity to utilize diverse polysaccharides. Understanding how these bacteria utilize medicinal polysaccharides is foundational for developing polysaccharides-based prebiotics and drugs. Here, we systematically mapped the utilization profiles of 20 different medicinal polysaccharides by 28 human gut Bacteroides and Parabacteroides species. The growth profiles exhibited substantial variation across different bacterial species and medicinal polysaccharides. Ginseng polysaccharides promoted the growth of multiple Bacteroides and Parabacteroides species; in contrast, Dendrobium polysaccharides selectively promoted the growth of Bacteroides uniformis. This distinct utilization profile was associated with genomic variation in carbohydrate-active enzymes, rather than monosaccharides composition variation among medicinal polysaccharides. Through comparative transcriptomics and genetical manipulation, we validated that the polysaccharide utilization locus PUL34_Bu enabled Bacteroides uniformis to utilize Dendrobium polysaccharides (i.e. glucomannan). In addition, we found that the GH26 enzyme in PUL34_Bu allowed Bacteroides uniformis to utilize multiple plant-derived mannan. Overall, our results revealed the selective utilization of medicinal polysaccharide by Bacteroides and Parabacteroides species and provided insights into the use of polysaccharides in engineering the human gut microbiome.},
}

Humans
*Bacteroides/genetics/metabolism
*Gastrointestinal Microbiome/drug effects
*Polysaccharides/metabolism
*Bacteroidetes/genetics/metabolism
Mannans/metabolism

@article {pmid39809682,
year = {2025},
author = {Isali, I and Wong, TR and Tian, S},
title = {Best Practice Guidelines for Collecting Microbiome Samples in Research Studies.},
journal = {European urology focus},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.euf.2024.12.007},
pmid = {39809682},
issn = {2405-4569},
abstract = {Microbiome research has the potential to provide valuable information regarding the complex relationship between microbial communities and the human body. To help facilitate the translation of this potentially revolutionary research to clinical medicine, common guidelines and best practices are necessary. These guidelines should be based on the key findings of recent research in the field and address the primary areas of discrepancy in the previously published literature. Based on this review's findings, future microbiome research should adopt a consistent and clear approach to nomenclature, using standardized terminology to mitigate confusion. Additionally, only sample collection methods proven to reduce the risk of contamination should be utilized. While sample storage often creates difficulty in microbiome research, there are proven techniques that can improve results. With the wide array of research methodologies in the literature, standardization of metadata collection, kits, and analysis software could also be beneficial. Finally, documentation and records are critical in ensuring reproducibility, as is the case with all basic research. This brief review provides a foundation for evidence-based guidelines in microbiome research. PATIENT SUMMARY: This report outlines general guidelines and best practices for conducting microbiome research, which could significantly advance the field of medicine.},
}

@article {pmid39809651,
year = {2025},
author = {Liu, X and Meng, L and Song, W and Zhi, M and Wang, P and Liu, B and Du, M and Feng, Q},
title = {Efficacy of Toothpaste Containing Polylysine and Funme Peptide on Oral Microbiome and Oral Health.},
journal = {International dental journal},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.identj.2024.11.017},
pmid = {39809651},
issn = {1875-595X},
abstract = {OBJECTIVE: To evaluate the effect of the toothpaste containing ε-poly-L-lysine (ε-PL) and funme peptide (FP) as key components on oral microbial composition and oral health.

METHODS: An oral microbiome study was initially carried out to analyze the variation in the oral microbiota before and after use of antimicrobial peptide (AMP) toothpaste. Subsequently, a clinical trial was independently performed to assess the efficacy of AMP toothpaste by measuring the dental plaque index (PLI), volatile sulfur compounds (VSCs) levels, modified bleeding index (mBI), and bleeding on probing rate (BOP%).

RESULTS: The application of AMP toothpaste increased the α diversity and modified β diversity of oral microbiome across 3 oral niches. AMP toothpaste increased the relative abundance of the commensal oral microbes, and attenuated the abundance of pathogenic bacteria in gingivitis patients to normal levels. The clinical trial showed 44.33% and 12.29% reductions of PLI scores in the test and control groups, respectively, and the test group exhibited a more pronounced decrease in VSC levels. The test group recorded significant reductions in mBI and BOP% by 39.09% and 24.59%, respectively, exceeding the control group's reductions of 4.63% and -0.97% (P < .05).

CONCLUSION: The formulation of toothpaste with ε-PL and FP recalibrated the oral microbiome's diversity and abundance, and mitigated common oral health issues such as plaque, halitosis, and gingivitis while maintaining well safety.

CLINICAL RELEVANCE: Oral care products containing ε-PL and FP can be used as a new treatment for improving oral microbiota and oral diseases.},
}

@article {pmid39809345,
year = {2025},
author = {Gao, W and Li, F and Wu, T and Ji, L},
title = {Prognostic stratification of gastric cancer patients by intratumoral microbiota-mediated tumor immune microenvironment.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {107296},
doi = {10.1016/j.micpath.2025.107296},
pmid = {39809345},
issn = {1096-1208},
abstract = {Gastric cancer (GC) is a leading cause of cancer-related deaths worldwide, and therapeutic options for advanced GC are limited. Here, we observe that intratumoral microbiota controls chemokine expression, which in turn recruits immune cells into the tumor, and that immune infiltration is strongly associated with patient survival and disease attributes. Furthermore, microbiota regulation of chemokines is differentiated in GC patients with different survival risks. As seen in gastric tumors, in high-survival-risk patients, Pseudomonas regulates CCL4, CXCL9, CXCL10, and CXCL11 accumulation to recruit immune cells such as CD4[+] T cells, CD8[+] T cells, and M1 macrophages. In low-survival-risk patients, Leptospira regulates CCL4, CCL5, CXCL9, and CXCL10 accumulation to recruit multiple types of immune cells. An independent single-cell dataset of GC verified the relationship between chemokines and immune cells. What's more, chemokines, including CCL4, CCL5, CXCL9, CXCL10, and CXCL11, strongly influence the sensitivity of GC patients to potential drug candidates. This study demonstrates that intratumoral microbiota closely influences the gastric immune microenvironment and that this molding has prognostic heterogeneity, opening avenues for cancer prevention and therapy.},
}

@article {pmid39810228,
year = {2025},
author = {Schwenger, KJP and Copeland, JK and Ghorbani, Y and Chen, L and Comelli, EM and Guttman, DS and Fischer, SE and Jackson, TD and Okrainec, A and Allard, JP},
title = {Characterization of liver, adipose, and fecal microbiome in obese patients with MASLD: links with disease severity and metabolic dysfunction parameters.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {9},
pmid = {39810228},
issn = {2049-2618},
support = {MOP-126139/CAPMC/CIHR/Canada ; },
abstract = {BACKGROUND: Metabolic dysfunction-associated steatotic liver disease (MASLD) encompasses a range of histological findings from the generally benign simple steatosis to steatohepatitis (MASH) which can progress to fibrosis and cirrhosis. Several factors, including the microbiome, may contribute to disease progression.

RESULTS: Here, we demonstrate links between the presence and abundance of specific bacteria in the adipose and liver tissues, inflammatory genes, immune cell responses, and disease severity. Overall, in MASLD patients, we observed a generalized obesity-induced translocation of gut bacteria to hepatic and adipose tissues. We identified microbial patterns unique to more severely diseased tissues. Specifically, Enterococcus, Granulicatella, and Morganellaceae abundance is positively correlated with immune cell counts and inflammatory gene expression levels, and both genera are significantly enriched in MASH patients. Brevibacterium is enriched in adipose tissues of patients with liver fibrosis.

CONCLUSION: Together, these results provide further insight into the microbial factors that may be driving disease severity. Video Abstract.},
}

@article {pmid39809718,
year = {2025},
author = {Podder, I and Pesqué, D and Carrón, N and González Torres, PI and Pujol, RM and Giménez-Arnau, AM},
title = {Gut microbial alteration in chronic spontaneous urticaria unresponsive to second generation antihistamines and its correlation with disease characteristics- a cross-sectional case-control study.},
journal = {Clinical and translational allergy},
volume = {15},
number = {1},
pages = {e70027},
doi = {10.1002/clt2.70027},
pmid = {39809718},
issn = {2045-7022},
support = {EAACI Research fellowship program//European Academy of Allergy and Clinical Immunology/ ; },
abstract = {BACKGROUND: Gut microbial involvement has been speculated in chronic spontaneous urticaria (CSU). The aim of the study was to compare the gut microbiome composition and diversity in CSU patients uncontrolled with second-generation antihistamines (sgAHs) and healthy individuals, as well as to explore any association between gut microbiome and disease characteristics.

METHODS: A cross-sectional case-control study including 20 CSU patients unresponsive to standard doses of sgAHs, and 15 age-and-sex matched healthy controls was conducted. Clinico-demographic profile, laboratory investigations and stool analysis were conducted in all study participants. 16S RNA gene sequencing and DNA isolation was performed for all stool samples, followed by bioinformatic analysis.

RESULTS: The CSU patients (mean age 39.5 ± 9.3, M:F 1:4) and healthy controls (mean age 35 ± 13, M:F 1:2) were statistically comparable. The median (IQR) duration of CSU was 42 months (7-81). Concomitant angioedema and concomitant symptomatic dermographism were present in 30% and 20% CSU patients, respectively. At inclusion, 60% patients were receiving add-on omalizumab, while the remaining 40% were on up-dosed sgAHs. Stool microbial analysis revealed increased diversity and higher microbial richness in CSU patients compared with healthy individuals. CSU patients showed reduced load of short-chain fatty acid (SCFA) producing microbiota and increased load of opportunistic pathogens. The Firmicutes/Bacteroides (F/B) ratio was higher in CSU patients. Among CSU patients, higher Bacteroides and reduced Firmicutes count were associated with higher disease activity and poor control; however, there was no link with the type of therapy.

CONCLUSION: Gut microbial dysbiosis is seen in CSU and is linked with disease control.},
}

@article {pmid39809670,
year = {2025},
author = {Galeota-Sprung, B and Bhatt, AS and de la Fuente-Nunez, C},
title = {Microproteins: emerging roles as antibiotics.},
journal = {Trends in genetics : TIG},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tig.2024.12.004},
pmid = {39809670},
issn = {0168-9525},
abstract = {Recent advances in computational prediction and experimental techniques have detected previously unknown microproteins, particularly in the human microbiome. These small proteins, produced by diverse microbial species, are emerging as promising candidates for new antibiotics.},
}

@article {pmid39809570,
year = {2025},
author = {Bengtsson, MM and Helgesen, M and Wang, H and Fredriksen, S and Norderhaug, KM},
title = {Sea urchin intestinal bacterial communities depend on seaweed diet and contain nitrogen-fixing symbionts.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiaf006},
pmid = {39809570},
issn = {1574-6941},
abstract = {Kelp deforestation by sea urchin grazing is a widespread phenomenon globally, with vast consequences for coastal ecosystems. The ability of sea urchins to survive on a kelp diet of poor nutritional quality is not well understood and bacterial communities in the sea urchin intestine may play an important role in digestion. A no-choice feeding experiment was conducted with the sea urchin Strongylocentrotus droebachiensis, offering three different seaweeds as diet, including the kelp Saccharina latissima. Starved sea urchins served as experimental control. Amplicons of the 16S rRNA gene were analyzed from fecal pellets. One dominant symbiont (Psychromonas marina) accounted for 44% of all sequence reads and was especially abundant in the sea urchins fed seaweed diets. The starved and field captured sea urchins consistently displayed higher diversity than the seaweed-fed sea urchins. Cloning and sequencing of the nifH gene revealed diverse nitrogen fixers. We demonstrate that the sea urchin intestinal microbiome is dynamic, with bacterial communities that are plastic depending on diet and have the capacity for nitrogen fixation. This reflects the dietary flexibility of these sea urchins, and their intestinal microbiota could be a key component in understanding catastrophic kelp forest grazing events.},
}

@article {pmid39808928,
year = {2025},
author = {Ma, P and Du, Z and Zhang, Q and Sadowsky, M and Rosen, C},
title = {Effects of sewage sludge ash as a recycled phosphorus source on the soil microbiome.},
journal = {Current opinion in biotechnology},
volume = {92},
number = {},
pages = {103254},
doi = {10.1016/j.copbio.2024.103254},
pmid = {39808928},
issn = {1879-0429},
abstract = {Ash byproducts have been used as soil amendments to recycle nutrients and modify soil properties such as pH or density. Interest in these practices has continued with increasing emphasis on sustainability, particularly regarding phosphorus reuse from incinerated sewage sludge. Given recent advancements in microbial analyses, the impacts of these practices can now be studied from the soil microbiome perspective. Next-generation DNA sequencing technologies provide information about the taxonomic composition of bacterial, archaeal, and fungal communities in a complex environment like soil. In this review, we discuss the results of microbial analyses of soils amended with recycled ash products, including a pilot study of sewage sludge incinerator ash as a phosphorus source. These results indicated that changes in soil microbial community composition require high amounts of amendment for detectible effects. Future research efforts could include more focused investigations into phosphorus-related microorganisms, such as phosphorus-solubilizing bacteria or polyphosphate-accumulating organisms.},
}

@article {pmid39808540,
year = {2025},
author = {Zhao, C and Bao, L and Shan, R and Zhao, Y and Wu, K and Shang, S and Li, H and Liu, Y and Chen, K and Zhang, N and Ye, C and Hu, X and Fu, Y},
title = {Maternal Gut Inflammation Aggravates Acute Liver Failure Through Facilitating Ferroptosis via Altering Gut Microbial Metabolism in Offspring.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e2411985},
doi = {10.1002/advs.202411985},
pmid = {39808540},
issn = {2198-3844},
support = {32422086//National Natural Science Foundation of China/ ; 2023YFD1801100//National Key R&D Program of China/ ; 2023M741348//China Postdoctoral Science Foundation/ ; 2023SCZ17//Jilin Province Health Research Talents Special Project/ ; 2024CL04//Spring-Bud Plan Construction Project of China-Japan Union Hospital of Jilin University/ ; BX20230140//National Postdoctoral Program for Innovative Talents/ ; },
abstract = {Microbial transmission from mother to infant is important for offspring microbiome formation and health. However, it is unclear whether maternal gut inflammation (MGI) during lactation influences mother-to-infant microbial transmission and offspring microbiota and disease susceptibility. In this study, it is found that MGI during lactation altered the gut microbiota of suckling pups by shaping the maternal microbiota in the gut and mammary glands. MGI-induced changes in the gut microbiota of suckling pups lasted into adulthood, resulting in the exacerbation of acute liver failure (ALF) caused by acetaminophen (APAP) in offspring. Specifically, MGI reduced the abundance of Lactobacillus reuteri (L. reuteri) and its metabolite indole-3-acetic acid (IAA) level in adult offspring. L. reuteri and IAA alleviated ALF in mice by promoting intestinal IL-22 production. Mechanistically, IL-22 limits APAP-induced excessive oxidative stress and ferroptosis by activating STAT3. The intestinal abundances of L. reuteri and IAA are inversely associated with the progression of patients with ALF. Overall, the study reveals the role of MGI in mother-to-infant microbial transmission and disease development in offspring, highlighting potential strategies for intervention in ALF based on the IAA-IL-22-STAT3 axis.},
}

@article {pmid39808399,
year = {2025},
author = {Mafe, AN and Iruoghene Edo, G and Akpoghelie, PO and Gaaz, TS and Yousif, E and Zainulabdeen, K and Isoje, EF and Igbuku, UA and Opiti, RA and Garba, Y and Essaghah, AEA and Ahmed, DS and Umar, H},
title = {Probiotics and Food Bioactives: Unraveling Their Impact on Gut Microbiome, Inflammation, and Metabolic Health.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {39808399},
issn = {1867-1314},
abstract = {This review paper delves into the role of probiotics and food bioactives in influencing gut health and overall well-being, within the context of probiotics and food bioactives, emphasizing their roles in modulating inflammation, gut microbiota, and metabolic health. Probiotics are defined as live microorganisms that confer health benefits to the host, primarily through their impact on the gut microbiome; a complex community of microorganisms crucial for maintaining health. The review aims to elucidate how probiotics, incorporated into both traditional and modern food systems, can enhance gut health and address metabolic disorders. It examines the types of probiotics present in various foods and their mechanisms of action, including their effects on immune function and metabolic health. By exploring the links between probiotics and health outcomes such as digestive health, immune support, and mental health, the review identifies specific conditions where probiotics show significant promise. Hurldes such as inconsistencies in research findings, variability in probiotic strains, and dosages are addressed. The paper also suggests future research directions, including the potential for personalized probiotic interventions. The review concludes by summarizing key findings and emphasizing the critical role of probiotics in food systems for promoting overall health and mitigating metabolic diseases.},
}

@article {pmid39808113,
year = {2025},
author = {Mohamed-Noriega, K and Loya-Garcia, D and Vera-Duarte, GR and Morales-Wong, F and Ortiz-Morales, G and Navas, A and Graue-Hernandez, EO and Ramirez-Miranda, A},
title = {Ocular Rosacea: An Updated Review.},
journal = {Cornea},
volume = {},
number = {},
pages = {},
doi = {10.1097/ICO.0000000000003785},
pmid = {39808113},
issn = {1536-4798},
abstract = {PURPOSE: Ocular rosacea is a chronic inflammatory disorder affecting the ocular surface, often associated with cutaneous rosacea. This review aims to explore its pathogenesis, treatment approaches, and future directions for management.

METHODS: A review of current literature on the pathophysiology, clinical features, and treatment strategies of ocular rosacea in adults and children (pediatric blepharokeratoconjunctivitis) was conducted. Emerging research on immune dysregulation, microbiome alterations, and potential therapeutic targets was analyzed.

RESULTS: Ocular rosacea involves dysregulation of the immune and neurovascular systems, with toll-like receptor activation and complement system involvement leading to chronic ocular surface inflammation. Alterations in the ocular microbiome have been implicated in disease progression. Treatment strategies emphasize a stepwise approach, incorporating ocular and skin hygiene, lifestyle modifications, and pharmacological interventions. Recent advancements in understanding the disease mechanisms have led to the exploration of targeted therapies, including biologics and small-molecule inhibitors.

CONCLUSIONS: Ocular rosacea remains challenging to diagnose and treat, particularly in children (pediatric blepharokeratoconjunctivitis), often leading to delayed intervention and poor outcomes. A multidisciplinary approach, including new therapeutic options, holds promise for improving patient care. Further research into the genetic and molecular basis of ocular rosacea may enable more personalized treatments.},
}

@article {pmid39808000,
year = {2025},
author = {Li, X and Qin, Y and Yue, F and Lü, X},
title = {Comprehensive Analysis of Fecal Microbiome and Metabolomics Uncovered dl-Norvaline-Ameliorated Obesity-Associated Disorders in High-Fat Diet-Fed Obese Mice by Targeting the Gut Microbiota.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.4c06638},
pmid = {39808000},
issn = {1520-5118},
abstract = {Norvaline is a nonproteinogenic amino acid and an important food ingredient supplement for healthy food. In this study, dl-norvaline administration reduced body weight by more than 40% and improved glucose metabolism and energy metabolism in obese mice induced by a high-fat diet (HFD). Combination analysis of microbiome and metabolomics showed that dl-norvaline supplementation regulated gut bacteria structure, such as increasing beneficial bacteria (Mollicutes_RF39, Ruminococcaceae, Bacteroidaceae, Rikenellaceae, Lactobacillaceae, Clostridiaceae_1, uncultured_bacterium_f_Muribaculaceae, and Rikenellaceae_RC9_gut_group) and decreasing harmful bacteria (Fusobacteriia, Desulfovibrionales, Enterobacteriaceae, Burkholderiaceae, Helicobacteraceae, and Veillonellaceae) and modulated the metabolites involved in arachidonic acid metabolism, thus further promoting short-chain fatty acid production and improving gut barrier, thereby inflammatory responses and oxidative stress were ameliorated. In addition, the pseudogerm-free mouse model verified that dl-norvaline ameliorated obesity-associated disorders in HFD-fed obese mice by targeting gut microbiota. These results clarified that dl-norvaline may be promising for developing and innovating potential functional food products.},
}

@article {pmid39807898,
year = {2025},
author = {Forry, SP and Servetas, SL and Dootz, JN and Hunter, ME and Kralj, JG and Filliben, JJ and Jackson, SA},
title = {A sensitivity analysis of methodological variables associated with microbiome measurements.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0069624},
doi = {10.1128/spectrum.00696-24},
pmid = {39807898},
issn = {2165-0497},
abstract = {The experimental methods employed during metagenomic sequencing analyses of microbiome samples significantly impact the resulting data and typically vary substantially between laboratories. In this study, a full factorial experimental design was used to compare the effects of a select set of methodological choices (sample, operator, lot, extraction kit, variable region, and reference database) on the analysis of biologically diverse stool samples. For each parameter investigated, a main effect was calculated that allowed direct comparison both between methodological choices (bias effects) and between samples (real biological differences). Overall, methodological bias was found to be similar in magnitude to real biological differences while also exhibiting significant variations between individual taxa, even between closely related genera. The quantified method biases were then used to computationally improve the comparability of data sets collected under substantially different protocols. This investigation demonstrates a framework for quantitatively assessing methodological choices that could be routinely performed by individual laboratories to better understand their metagenomic sequencing workflows and to improve the scope of the datasets they produce.IMPORTANCEMethod-specific bias is a well-recognized challenge in metagenomic sequencing characterization of microbiome samples, but rigorous bias quantification is challenging. This report details a full factorial exploration of 48 experimental protocols by systematically varying microbiome sample, iterations of material production, laboratory personnel, DNA extraction kit, marker gene selection, and reference databases. Quantification of the biases associated with each parameter revealed similar magnitudes of variation arising from real biological differences and from varied analysis procedures. Furthermore, these measurement biases varied substantially with taxa, even between closely related genera. However, computational correction of method bias using a reference material was demonstrated that significantly harmonized metagenomic sequencing results collected using different analysis protocols.},
}

@article {pmid39807896,
year = {2025},
author = {Wu, L and Zhang, T and Luo, Z and Xiao, H and Wang, D and Wu, C and Fang, X and Li, J and Zhou, J and Miao, J and Tan, H and Wang, Y and Liu, Q and Huang, J},
title = {Impact of gut microbial diversity on egg production performance in chickens.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0192724},
doi = {10.1128/spectrum.01927-24},
pmid = {39807896},
issn = {2165-0497},
abstract = {UNLABELLED: Chickens are one of the most economically important poultry species, and their egg-laying performance is a crucial economic trait. The intestinal microbiome plays a significant role in the egg-laying performance. To clarify the diversity of chicken intestinal microbiota and its connection to egg-laying performance, this study utilized 16S rRNA sequencing technology to characterize the intestinal microbiomes of 101 chickens from 13 breeds with varying levels of egg production. The results reveal significant differences in gut microbiota structure among chicken groups with varying egg production levels. High egg-producing chickens showed significantly higher abundances of Firmicutes, Proteobacteria, and Lactobacillus, while low egg-producing chickens displayed greater microbial α-diversity and more complex community structures. These differences in gut microbiota influence key physiological functions, including nutrient absorption and hormone regulation through metabolic pathways, and directly affect egg production performance. The low and medium production groups partially overlapped on the principal coordinates analysis plot, whereas the high-production group was distinctly separate. This study provides a scientific basis and intestinal microbiome data for selecting probiotics related to high egg production in chickens.

IMPORTANCE: This study elucidates the critical role of gut microbiota in the egg-laying performance of chickens, a key economic indicator in the poultry industry. By employing 16S rRNA sequencing, we uncovered distinct microbial profiles associated with varying levels of egg production. High egg-producing chickens exhibit a higher abundance of specific bacterial taxa, such as Firmicutes and Proteobacteria, which are linked to enhanced nutrient absorption and metabolic efficiency. Conversely, lower and medium egg-producing chickens display greater microbial diversity, suggesting a more complex but less efficient gut ecosystem. Our findings provide valuable insights into the relationship between gut microbiota and egg production, offering a scientific foundation for the selection of probiotics that could potentially improve the egg-laying performance of chickens. This research not only advances our understanding of avian gut microbiology but also has practical implications for optimizing poultry farming practices and enhancing economic outcomes.},
}

@article {pmid39807875,
year = {2025},
author = {Schloss, PD},
title = {phylotypr: an R package for classifying DNA sequences.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0114424},
doi = {10.1128/mra.01144-24},
pmid = {39807875},
issn = {2576-098X},
abstract = {The phylotypr R package implements the popular naive Bayesian classification algorithm that is frequently used to classify 16S rRNA and other gene sequences to taxonomic lineages. A companion data package, phylotyprrefdata, also provides numerous versions of taxonomic databases from the Ribosomal Database Project, SILVA, and greengenes.},
}

@article {pmid39807869,
year = {2025},
author = {Sáenz, JS and Rios-Galicia, B and Seifert, J},
title = {Antiviral defense systems in the rumen microbiome.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0152124},
doi = {10.1128/msystems.01521-24},
pmid = {39807869},
issn = {2379-5077},
abstract = {The continuous interaction between phages and their respective hosts has resulted in the evolution of multiple bacterial immune mechanisms. However, the diversity and prevalence of antiviral defense systems in complex communities are still unknown. We therefore investigated the diversity and abundance of viral defense systems in 3,038 high-quality bacterial and archaeal genomes from the rumen. In total, 14,241 defense systems and 31,948 antiviral-related genes were identified. Those genes represented 114 unique system types grouped into 49 families. We observed a high prevalence of defense systems in the genomes. However, the number of defense systems, defense system families, and system density varied widely from genome to genome. Additionally, the number of defense system per genome correlated positively with the number of defense system families and the genome size. Restriction modification, Abi, and cas system families were the most common, but many rare systems were present in only 1% of the genomes. Antiviral defense systems are prevalent and diverse in the rumen, but only a few are dominant, indicating that most systems are rarely present. However, the collection of systems throughout the rumen may represent a pool of mechanisms that can be shared by different members of the community and modulate the phage-host interaction.IMPORTANCEPhages may act antagonistically at the cell level but have a mutualistic interaction at the microbiome level. This interaction shapes the structure of microbial communities and is mainly driven by the defense mechanism. However, the diversity of such mechanism is larger than previously thought. Because of that, we described the abundance and diversity of the antiviral defense system of a collection of genomes, metagenome-assembled genomes (MAGs) and isolates, from the rumen. While defense mechanisms seem to be prevalent among bacteria and archaea, only a few were common. This suggests that most of these defense mechanisms are not present in many rumen microbes but could be shared among different members of the microbial community. This is consistent with the "pan-immune system" model, which appears to be common across different environments.},
}

@article {pmid39807864,
year = {2025},
author = {Nakatsu, G and Ko, D and Michaud, M and Franzosa, EA and Morgan, XC and Huttenhower, C and Garrett, WS},
title = {Virulence factor discovery identifies associations between the Fic gene family and Fap2[+] fusobacteria in colorectal cancer microbiomes.},
journal = {mBio},
volume = {},
number = {},
pages = {e0373224},
doi = {10.1128/mbio.03732-24},
pmid = {39807864},
issn = {2150-7511},
abstract = {Fusobacterium is a bacterium associated with colorectal cancer (CRC) tumorigenesis, progression, and metastasis. Fap2 is a fusobacteria-specific outer membrane galactose-binding lectin that mediates Fusobacterium adherence to and invasion of CRC tumors. Advances in omics analyses provide an opportunity to profile and identify microbial genomic features that correlate with the cancer-associated bacterial virulence factor Fap2. Here, we analyze genomes of Fusobacterium colon tumor isolates and find that a family of post-translational modification enzymes containing Fic domains is associated with Fap2 positivity in these strains. We demonstrate that Fic family genes expand with the presence of Fap2 in the fusobacterial pangenome. Through comparative genomic analysis, we find that Fap2[+] Fusobacteriota are highly enriched with Fic gene families compared to other cancer-associated and human gut microbiome bacterial taxa. Using a global data set of CRC shotgun metagenomes, we show that fusobacterial Fic and Fap2 genes frequently co-occur in the fecal microbiomes of individuals with late-stage CRC. We further characterize specific Fic gene families harbored by Fap2[+] Fusobacterium animalis genomes and detect recombination events and elements of horizontal gene transfer via synteny analysis of Fic gene loci. Exposure of a F. animalis strain to a colon adenocarcinoma cell line increases gene expression of fusobacterial Fic and virulence-associated adhesins. Finally, we demonstrate that Fic proteins are synthesized by F. animalis as Fic peptides are detectable in F. animalis monoculture supernatants. Taken together, our study uncovers Fic genes as potential virulence factors in Fap2[+] fusobacterial genomes.IMPORTANCEAccumulating data support that bacterial members of the intra-tumoral microbiota critically influence colorectal cancer progression. Yet, relatively little is known about non-adhesin fusobacterial virulence factors that may influence carcinogenesis. Our genomic analysis and expression assays in fusobacteria identify Fic domain-containing genes, well-studied virulence factors in pathogenic bacteria, as potential fusobacterial virulence features. The Fic family proteins that we find are encoded by fusobacteria and expressed by Fusobacterium animalis merit future investigation to assess their roles in colorectal cancer development and progression.},
}

@article {pmid39807528,
year = {2025},
author = {Dobani, S and Kirsty Pourshahidi, L and Ternan, NG and McDougall, GJ and Pereira-Caro, G and Bresciani, L and Mena, P and Almutairi, TM and Crozier, A and Tuohy, KM and Del Rio, D and Gill, CIR},
title = {A review on the effects of flavan-3-ols, their metabolites, and their dietary sources on gut barrier integrity.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d4fo04721d},
pmid = {39807528},
issn = {2042-650X},
abstract = {Impairment of gut barrier integrity is associated with the pathogenesis of gastrointestinal diseases, including inflammatory bowel disease, colorectal cancer, and coeliac disease. While many aspects of diet have been linked to improved barrier function, (poly)phenols, a broad group of bioactive phytochemicals, are of potential interest. The (poly)phenolic sub-class, flavan-3-ols, have been investigated in some detail owing to their abundance in commonly consumed foods, including grapes, tea, apples, cocoa, berries, and nuts. This review summarises studies on the effects of flavan-3-ols, their microbiome-mediated metabolites, and food sources of these compounds, on gut barrier structure. Extensive evidence demonstrates that flavan-3-ol rich foods, individual flavan-3-ols (e.g., (epi)catechin, epi(gallo)catechin-3-O-gallate, and pro(antho)cyanidins), and their related microbiota-mediated metabolites, could be effective in protecting and restoring the integrity of the gut barrier. In this context, various endpoints are assessed, including transepithelial electrical resistance of the epithelial layer and expression of tight junction proteins and mucins, in ex vivo, in vitro, and animal models. The differences in bioactivity reported for barrier integrity are structure-function dependent, related to the (poly)phenolic source or the tested compound, as well as their dose, exposure time, and presence or absence of a stressor in the experimental system. Overall, these results suggest that flavan-3-ols and related compounds could help to maintain, protect, and restore gut barrier integrity, indicating that they might contribute to the beneficial properties associated with the intake of their dietary sources. However, rigorous and robustly designed human intervention studies are needed to confirm these experimental observations.},
}

@article {pmid39807439,
year = {2024},
author = {Lu, L and Yan, L and Sohrabi, A and Lindahl, K and Cederberg, S and Wang, R and Ye, W and Aleman, S and Sällberg Chen, M},
title = {The salivary microbiome and oral health status in HBeAg-negative chronic hepatitis B.},
journal = {Journal of dental sciences},
volume = {19},
number = {Suppl 1},
pages = {S17-S25},
pmid = {39807439},
issn = {2213-8862},
abstract = {BACKGROUND/PURPOSE: Dysbiosis of oral microbiota has been reported in late stage of chronic hepatitis B (CHB) infection with cirrhosis. CHB is characterized by the constant virus-induced liver injury which may lead to liver cirrhosis and hepatocellular carcinoma (HCC). However, some patients show normal liver function without antiviral treatment, associating with favourable prognosis. The oral microbiota composition and oral health status in these patients is unidentified.

MATERIALS AND METHODS: The study focuses on the composition of oral microbiota and oral health status in individuals with CHB and HBV vaccinees as controls. The CHB patients were hepatitis B 'e' antigen (HBeAg)-negative, with or without elevated liver enzyme increase at time of sampling, The 16S rRNA high-throughput sequencing and bioinformatic analysis were applied to investigate oral bacterial diversity, and oral examination including decay-missing-filled teeth (DMFT) index, probing depth (PD) and mucosal status was performed, along with oral health questionnaire, to assess the oral health status in CHB patients and healthy controls.

RESULTS: Our results indicate that their oral microbiome compositions are not significantly different though some have increased ALT/AST liver enzyme levels at the time of sampling, compared to the healthy control participants who are vaccinated e.g. protected from this viral disease. CHB patients here bore a good oral health status and life-style habits as comparing to healthy controls.

CONCLUSION: These findings suggest that a health-associated salivary microflora is present in CHB without severe liver injury. Continued regular dental health and lifestyle support in liver disease patients is therefore justified.},
}

@article {pmid39807321,
year = {2024},
author = {Gao, R and Yue, B and Lv, C and Geng, X and Yu, Z and Wang, H and Zhang, B and Ai, F and Wang, Z and Liu, D and Wang, Z and Chen, K and Dou, W},
title = {Targeted inhibition of Gus-expressing Enterococcus faecalis to promote intestinal stem cell and epithelial renovation contributes to the relief of irinotecan chemotoxicity by dehydrodiisoeugenol.},
journal = {Acta pharmaceutica Sinica. B},
volume = {14},
number = {12},
pages = {5286-5304},
pmid = {39807321},
issn = {2211-3835},
abstract = {Irinotecan (CPT11) chemotherapy-induced diarrhea affects a substantial cancer population due to β-glucuronidase (Gus) converting 10-O-glucuronyl-7-ethyl-10-hydroxycamptothecin (SN38G) to toxic 7-ethyl-10-hydroxycamptothecin (SN38). Existing interventions primarily address inflammation and Gus enzyme inhibition, neglecting epithelial repair and Gus-expressing bacteria. Herein, we discovered that dehydrodiisoeugenol (DDIE), isolated from nutmeg, alleviates CPT11-induced intestinal mucositis alongside a synergistic antitumor effect with CPT11 by improving weight loss, colon shortening, epithelial barrier dysfunction, goblet cells and intestinal stem cells (ISCs) loss, and wound-healing. The anti-mucositis effect of DDIE is gut microbiota-dependent. Analysis of microbiome profiling data from clinical patients and CPT11-induced mucositis mice reveals a strong correlation between CPT11 chemotoxicity and Gus-expressing bacteria, particularly Enterococcus faecalis (E. faecalis). DDIE counters CPT11-induced augmentation of E. faecalis, leading to decreased intestinal Gus and SN38 levels. The Partial Least Squares Path Model (PLS-PM) algorithm initially links E. faecalis to dysregulated epithelial renovation. This is further validated in a 3D intestinal organoid model, in which both SN38 and E. faecalis hinder the formation and differentiation of organoids. Interestingly, colonization of E. faecalis exacerbates CPT11-induced mucositis and disturbs epithelial differentiation. Our study unveils a microbiota-driven, epithelial reconstruction-mediated action of DDIE against mucositis, proposing the 'Gus bacteria-host-irinotecan axis' as a promising target for mitigating CPT11 chemotoxicity.},
}

@article {pmid39807021,
year = {2025},
author = {Zhang, YY and Chen, ST and Chen, G and Zhou, L and Zhou, GL and Yu, XY and Yuan, L and Deng, WQ and Wang, ZB and Li, J and Tu, YF and Zhang, DW and Li, Y and Sammad, A and Zhu, X and Yin, K},
title = {The Type III Secretion System (T3SS) of Escherichia Coli Promotes Atherosclerosis in Type 2 Diabetes Mellitus.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e2413296},
doi = {10.1002/advs.202413296},
pmid = {39807021},
issn = {2198-3844},
support = {2020GXNSFDA297011//Natural Science Foundation of Guangxi Zhuang Autonomous Region/ ; 2022GXNSFBA035664//Regional Science Fund/ ; 82370463//National Science Foundation of China/ ; 82060065//National Science Foundation of China/ ; 81970390//National Science Foundation of China/ ; 20210222-3//Guangxi Zhuang Autonomous Region Key Laboratory of Automatic Detecting Technology and Instruments, Guilin University of Electronic Technology/ ; },
abstract = {Large-scale studies indicate a strong relationship between the gut microbiome, type 2 diabetes mellitus (T2DM), and atherosclerotic cardiovascular disease (ASCVD). Here, a higher abundance of the type III secretion system (T3SS) virulence factors of Enterobacteriaceae/Escherichia-Shigella in patients with T2DM-related-ASCVD, which correlates with their atherosclerotic stenosis is reported. Overexpression of T3SS via Citrobacter rodentium (CR) infection in Apoe-/- T2DM mice exacerbated atherosclerotic lesion formation and increased gut permeability. Non-targeted metabolomic and proteomic analysis of mouse serum showed that T3SS caused abnormal glycerophospholipid metabolism in mice. Proteomics, RNA sequencing, and functional analyses showed that T3SS induced ferroptosis in intestinal epithelial cells, partly due to increased expression of ferritin heavy chains (FTH1). This findings first demonstrated that T3SS increases ferroptosis in intestinal epithelial cells, via disrupting the intestinal barrier and upregulation of phosphatidylcholine, thereby exacerbating T2DM-related ASCVD.},
}

@article {pmid39806633,
year = {2024},
author = {Yu, J and Lin, B and Zhang, Z and Chen, W and Lv, W and Zheng, L},
title = {Association between oral microbiome diversity and all-cause mortality: a longitudinal study of NHANES, 2009-2012.},
journal = {BMJ open},
volume = {14},
number = {12},
pages = {e087288},
doi = {10.1136/bmjopen-2024-087288},
pmid = {39806633},
issn = {2044-6055},
mesh = {Humans ; Male ; Female ; Adult ; *Nutrition Surveys ; Middle Aged ; Longitudinal Studies ; *Microbiota/genetics ; United States/epidemiology ; Mortality ; Mouth/microbiology ; Proportional Hazards Models ; Cause of Death ; Oral Health/statistics & numerical data ; },
abstract = {OBJECTIVE: The study investigates the association between oral microbiome diversity and all-cause mortality.

DESIGN: Population-based cohort study.

SETTING: US National Health and Nutrition Examination Survey (2009-2010 and 2011-2012).

PARTICIPANTS: A total of 8224 participants who had valid data on the oral microbiome diversity and survival through 31 December 2019 were included in this study.

Oral microbiome diversity was measured using the observed number of amplicon sequence variant (ASV) and grouped into quartiles. Cox proportional hazards regression models were used to estimate the HR and 95% CI for all-cause mortality according to the quartiles of ASV number, adjusted for potential confounders.

RESULTS: Among the 8224 participants (mean (SD) age: 42.0 (15.1) years; 49.9% male; 37.2% white, 23.8% black, 27.2% Hispanic and 11.8% other race/ethnicity), the median follow-up time was 108 months (IQR, 95-120 months) and 429 (5.2%) deaths were identified. Participants with a higher ASV number were more likely to be poor, non-Hispanic black or Hispanic, uninsured and current smokers, more likely to have poor self-rated oral health and periodontitis and less likely to use dental floss. However, compared with the lowest quartile of the ASV number, a suggestive association was observed for the second quartile (HR=0.80, 95% CI: 0.60 to 1.08), a significant reduction in all-cause mortality was observed for the third (HR=0.55, 95% CI: 0.37 to 0.82) and the fourth (HR=0.58, 95% CI: 0.38 to 0.89) quartile. The dose-response association for all-cause mortality risk was curvilinear; the protective association plateaued when the number of ASVs was larger than 120.

CONCLUSION: Despite being linked to greater socioeconomic disadvantages and poorer oral health, higher oral microbiome diversity was significantly associated with a substantial reduction in all-cause mortality.},
}

Humans
Male
Female
Adult
*Nutrition Surveys
Middle Aged
Longitudinal Studies
*Microbiota/genetics
United States/epidemiology
Mortality
Mouth/microbiology
Proportional Hazards Models
Cause of Death
Oral Health/statistics & numerical data

@article {pmid39806493,
year = {2025},
author = {Vartanian, M and Endres, KJ and Lee, YT and Friedrich, S and Meemken, MT and Schamarek, I and Rohde-Zimmermann, K and Schürfeld, R and Eisenberg, L and Hilbert, A and Beyer, F and Stumvoll, M and Sacher, J and Villringer, A and Christensen, JF and Witte, AV},
title = {Investigating the impact of microbiome-changing interventions on food decision-making: MIFOOD study protocol.},
journal = {BMC nutrition},
volume = {11},
number = {1},
pages = {8},
pmid = {39806493},
issn = {2055-0928},
support = {9294 / P30203//The Friedrich-Naumann-Foundation for Freedom/ ; 493646873 - MD-LEICS//Deutsche Forschungsgemeinschaft, DFG/ ; 464596826//Deutsche Forschungsgemeinschaft, DFG/ ; 209933838, CRC 1052/3, Project A1//Deutsche Forschungsgemeinschaft, DFG/ ; 209933838, CRC 1052/3, Project A1//Deutsche Forschungsgemeinschaft, DFG/ ; },
abstract = {BACKGROUND: Obesity is a multifactorial disease reaching pandemic proportions with increasing healthcare costs, advocating the development of better prevention and treatment strategies. Previous research indicates that the gut microbiome plays an important role in metabolic, hormonal, and neuronal cross-talk underlying eating behavior. We therefore aim to examine the effects of prebiotic and neurocognitive behavioral interventions on food decision-making and to assay the underlying mechanisms in a Randomized Controlled Trial (RCT).

METHOD: This study uses a parallel arm RCT design with a 26-week intervention period. We plan to enroll 90 participants (male/diverse/female) living with overweight or obesity, defined as either a Waist-to-Hip Ratio (WHR) ≥ 0.9 (male)/0.85 (diverse, female) or a Body Mass Index (BMI) ≥ 25 kg/m[2]. Key inclusion criteria are 18-60 years of age and exclusion criteria are type 2 diabetes, psychiatric disease, and Magnetic Resonance Imaging (MRI) contraindications. The interventions comprise either a daily supplementary intake of 30 g soluble fiber (inulin), or weekly neurocognitive behavioral group sessions, compared to placebo (equicaloric maltodextrin). At baseline and follow-up, food decision-making is assessed utilizing task-based MRI. Secondary outcome measures include structural MRI, eating habits, lifestyle factors, personality traits, and mood. Further, we obtain fecal and blood samples to investigate gut microbiome composition and related metabolites.

DISCUSSION: This study relies on expanding research suggesting that dietary prebiotics could improve gut microbiome composition, leading to beneficial effects on gut-brain signaling and higher-order cognitive functions. In parallel, neurocognitive behavioral interventions have been proposed to improve unhealthy eating habits and metabolic status. However, causal evidence on how these "bottom-up" and "top-down" processes affect food decision-making and neuronal correlates in humans is still scarce. In addition, microbiome, and gut-brain-axis-related mediating mechanisms remain unclear. The present study proposes a comprehensive approach to assess the effects of these gut-brain-related processes influencing food decision-making in overweight and obesity.

TRIAL REGISTRATION: ClinicalTrials.gov NCT05353504. Retrospectively registered on 29 April 2022.},
}

@article {pmid39808466,
year = {2023},
author = {Kolář, M},
title = {[Selected aspects of the human microbiome].},
journal = {Klinicka mikrobiologie a infekcni lekarstvi},
volume = {29},
number = {2},
pages = {46-51},
pmid = {39808466},
issn = {1211-264X},
abstract = {This review briefly defines the term microbiome and characterizes its importance in health and disease.},
}

@article {pmid39806479,
year = {2025},
author = {Rasuk, MC and Irazoqui, JM and Perez, MF and Pereyra, MM and Sineli, PE and Poehlein, A and Daniel, R and Dib, JR},
title = {Insights into the lemon (Citrus limon) epiphytic microbiome: impact of the biocontrol yeast Clavispora lusitaniae 146.},
journal = {BMC research notes},
volume = {18},
number = {1},
pages = {11},
pmid = {39806479},
issn = {1756-0500},
abstract = {BACKGROUND: Postharvest lemons are affected by several fungal infections, and as alternatives to chemical fungicides for combating these infections, different microbial biocontrol agents have been studied, with the Clavispora lusitaniae 146 strain standing out. Although strain 146 has proven to be an effective agent, the influence of a microbial biological control agent on the postharvest lemon microbiome has not been studied until now. Thus, this study aimed to evaluate how the epiphytic microbiome of postharvest lemons is affected by the application of the biocontrol yeast C. lusitaniae 146.

RESULTS: In terms of bacterial composition, the most abundant genera were Sphingomonas, Pelomonas, and Bacillus and no significant differences in the composition were detected between the treated and control samples. Among fungi, Clavispora was predominant not only in the treated samples but also in the control, and statistics indicated differences, suggesting its significant role in modulating the epiphytic community composition of lemon. Understanding fruit microbiomes is vital for effective disease control, and this study provides insights into the microbial composition of the surface of lemon and the role of C. lusitaniae 146.},
}

@article {pmid39806455,
year = {2025},
author = {Liu, Z and Yao, X and Chen, C and Zhao, Y and Dong, C and Sun, L and Zhao, J and Zhang, B and Yu, Z and Cheng, D and Zhu, L and Hu, B},
title = {Growth of microbes in competitive lifestyles promotes increased ARGs in soil microbiota: insights based on genetic traits.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {8},
pmid = {39806455},
issn = {2049-2618},
support = {22206166//National Natural Science Foundation of China/ ; 22193061//National Natural Science Foundation of China/ ; 22193061//National Natural Science Foundation of China/ ; 2020YFC1806903//National Key Research and Development Program of China/ ; 2023M733056//China Postdoctoral Science Foundation awards the fellowship/ ; ES202118//Open Project of State Key Laboratory of Urban Water Resource and Environment, Harbin Institute and Technology/ ; 2022HT0025//Zhejiang Province Ecological Environment Research and Results Promotion Project/ ; },
abstract = {BACKGROUND: The widespread selective pressure of antibiotics in the environment has led to the propagation of antibiotic resistance genes (ARGs). However, the mechanisms by which microbes balance population growth with the enrichment of ARGs remain poorly understood. To address this, we employed microcosm cultivation at different antibiotic (i.e., Oxytetracycline, OTC) stresses across the concentrations from the environmental to the clinical. Paired with shot-gun metagenomics analysis and quantification of bacterial growth, trait-based assessment of soil microbiota was applied to reveal the association between key ARG subtypes, representative bacterial taxa, and functional-gene features that drive the growth of ARGs.

RESULTS: Our results illuminate that resistome variation is closely associated with bacterial growth. A non-monotonic change in ARG abundance and richness was observed over a concentration gradient from none to 10 mg/l. Soil microbiota exposed to intermediate OTC concentrations (i.e., 0.1 and 0.5 mg/l) showed greater increases in the total abundance of ARGs. Community compositionally, the growth of representative taxa, i.e., Pseudomonadaceae was considered to boost the increase of ARGs. It has chromosomally carried kinds of multidrug resistance genes such as mexAB-oprM and mexCD-oprJ could mediate the intrinsic resistance to OTC. Streptomycetaceae has shown a better adaptive ability than other microbes at the clinical OTC concentrations. However, it contributed less to the ARGs growth as it represents a stress-tolerant lifestyle that grows slowly and carries fewer ARGs. In terms of community genetic features, the community aggregated traits analysis further indicates the enhancement in traits of resource acquisition and growth yield is driving the increase of ARGs abundance. Moreover, optimizations in energy production and conversion, alongside a streamlining of bypass metabolic pathways, further boost the growth of ARGs in sub-inhibitory antibiotic conditions.

CONCLUSION: The results of this study suggest that microbes with competitive lifestyles are selected under the stress of environmental sub-inhibitory concentrations of antibiotics and nutrient scarcity. They possess greater substrate utilization capacity and carry more ARGs, due to this they were faster growing and leading to a greater increase in the abundance of ARGs. This study has expanded the application of trait-based assessments in understanding the ecology of ARGs propagation. And the finding illustrated changes in soil resistome are accompanied by the lifestyle switching of the microbiome, which theoretically supports the ARGs control approach based on the principle of species competitive exclusion. Video Abstract.},
}

@article {pmid39806437,
year = {2025},
author = {Li, M and Liang, H and Zhang, J and Chen, J and Xu, S and Zhou, W and Ding, Q and Yang, Y and Zhang, Z and Yao, Y and Ran, C and Zhou, Z},
title = {Bacillus subtilis HGCC-1 improves growth performance and liver health via regulating gut microbiota in golden pompano.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {7},
pmid = {39806437},
issn = {2524-4671},
support = {32122088//National Natural Science Foundation of China/ ; 31925038//National Natural Science Foundation of China/ ; },
abstract = {Probiotics as green inputs have been reported to regulate metabolism and immunity of fish. However, the mechanisms by which probiotics improve growth and health of fish are unclear. Therefore, the aim of this study was to investigate the effect of Bacillus subtilis HGCC-1, an indigenous probiotic isolated from fish, on growth performance, host lipid metabolism, liver inflammation and gut microbiota of golden pompano. 160,000 golden pompanos with the initial body weight of 93.6 ± 5.0 g was randomly assigned to two dietary groups: Control and HGCC-1 (control diet supplemented with 0.3 g/kg Bacillus subtilis HGCC-1 fermentation product), and after three weeks of feeding, 26 golden pompanos were randomly collected from each group for gut microbiome and host phenotype analysis. Dietary supplementation with Bacillus subtilis HGCC-1 significantly promoted growth performance (P < 0.05) and enhanced feed utilization. Besides, HGCC-1 improved liver health and alleviated hepatic steatosis and inflammation. Furthermore, Bacillus subtilis HGCC-1 enhanced intestinal lipid absorption, promoted hepatic utilization of dietary fat by improving hepatic lipid uptake/transport and fatty acid β-oxidation to provide energy, and reduced hepatic TG level (P < 0.05), which may be the potential mechanism of Bacillus subtilis HGCC-1-mediated growth promotion. Finally, Bacillus subtilis HGCC-1 significantly altered the structure and function of gut microbiota (P < 0.05), leading to enrichment of beneficial taxa such as Bacillus (P < 0.0001) and increased of the ratio of "Functional Group 2/Functional Group 1" (P = 0.00092). Interestingly, the ratio of "Functional Group 2/Functional Group 1" was linked to the growth traits (Spearman, P < 0.05), while the intestinal abundance of Bacillus was correlated with serum TG in fish (Spearman, R = 0.47, P = 0.00091), suggesting a role of the intestinal microbiota in HGCC-1 mediated effect on growth and lipid metabolism. In summary, Bacillus subtilis HGCC-1 promotes growth performance, alleviate hepatic steatosis and enhances liver health via regulating gut microbiota in golden pompano, which ultimately showed as beneficial effect of fish growth and health.},
}

@article {pmid39806416,
year = {2025},
author = {Chen, L and Ye, Z and Li, J and Wang, L and Chen, Y and Yu, M and Han, J and Huang, J and Li, D and Lv, Y and Xiong, K and Tian, D and Liao, J and Seidler, U and Xiao, F},
title = {Gut bacteria Prevotellaceae related lithocholic acid metabolism promotes colonic inflammation.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {55},
pmid = {39806416},
issn = {1479-5876},
support = {81873556//National Natural Science Foundation of China/ ; 82170546//National Natural Science Foundation of China/ ; CCCF-QF-2022B67-3//China Crohn's & Colitis Foundation/ ; 2023B02//Tongji Hospital Fund/ ; },
abstract = {BACKGROUND: The conversion of primary bile acids to secondary bile acids by the gut microbiota has been implicated in colonic inflammation. This study investigated the role of gut microbiota related bile acid metabolism in colonic inflammation in both patients with inflammatory bowel disease (IBD) and a murine model of dextran sulfate sodium (DSS)-induced colitis.

METHODS: Bile acids in fecal samples from patients with IBD and DSS-induced colitis mice, with and without antibiotic treatment, were analyzed using ultraperformance liquid chromatography-mass spectrometry (UPLC-MS). The composition of the microbiota in fecal samples from IBD patients and DSS-colitis mice was characterized via Illumina MiSeq sequencing of the bacterial 16S rRNA gene V3-V4 region. Metagenomic profiling further identified metabolism-related gene signatures in stool samples from DSS-colitis mice. Histological analysis, quantitative PCR (qPCR) and Western Blotting were conducted on colonic samples from DSS-induced colitis mice to assess colonic inflammation, mucosal barrier integrity, and associated signaling pathways. The multivariate analysis of bile acids was conducted using Soft Independent Modelling of Class Analogy (SIMCA, Umetrics, Sweden). The relation between the relative abundance of specific phyla/genera and bile acid concentration was assess through Spearman's correlation analyses. Finally, lithocholic acid (LCA), the key bile acid, was administered via gavage to evaluate its effect on colonic inflammation and mucosal barrier integrity.

RESULTS: In patients with IBD, the composition of colonic bile acids and gut microbiota was altered. Moreover, changes in the gut microbiota further modulate the composition of bile acids in the intestine. As the gut microbiota continues to shift, the bile acid profile undergoes additional alterations. The aforementioned alterations were also observed in mice with DSS-induced colitis. The study revealed a correlation between dysbiosis of the gut microbiota and modifications in the profile of colonic bile acids, notably LCA observed in both patients with IBD and mice with DSS-induced colitis. Through multivariate analysis, LCA was identified as the key bile acid that significantly affects colonic inflammation and the integrity of mucosal barrier. Subsequent experiments confirmed that LCA supplementation effectively mitigated the inhibitory effects of gut microbiota on colitis progression in mice, primarily through the activation of the sphingosine-1-phosphate receptor 2 (S1PR2)/NF-κB p65 signaling pathway. Analysis of the microbiome and metagenomic data revealed changes in the gut microbiota, notably an increased abundance of an unclassified genus within the family Prevotellaceae in DSS-induced colitis mice. Furthermore, a positive correlation was observed between the relative abundance of Prevotellaceae and bile acid biosynthesis pathways, as well as colonic LCA level.

CONCLUSIONS: These findings suggest that LCA and its positively correlated gut bacteria, Prevotellaceae, are closely associated with intestinal inflammation. Targeting colonic inflammation may involve inhibiting LCA and members of the Prevotellaceae family as potential therapeutic strategies.},
}

@article {pmid39806400,
year = {2025},
author = {Park, H and Lynch, E and Tillman, A and Lewis, K and Jin, Z and Uhlemann, AC and Abrams, JA and Freedberg, DE},
title = {A phase 2 randomized, placebo-controlled trial of inulin for the prevention of gut pathogen colonization and infection among patients admitted to the intensive care unit for sepsis.},
journal = {Critical care (London, England)},
volume = {29},
number = {1},
pages = {21},
pmid = {39806400},
issn = {1466-609X},
support = {P30DK132710//Columbia Division of Digestive and Liver Disease/ ; P30DK132710//Columbia Division of Digestive and Liver Disease/ ; P30DK132710//Columbia Division of Digestive and Liver Disease/ ; PR181960//Department of Defense Peer Reviewed Medical Research Program/ ; PR181960//Department of Defense Peer Reviewed Medical Research Program/ ; },
abstract = {BACKGROUND: Patients admitted to the intensive care unit (ICU) often have gut colonization with pathogenic bacteria and such colonization is associated with increased risk for death and infection. We conducted a trial to determine whether a prebiotic would improve the gut microbiome to decrease gut pathogen colonization and decrease downstream risk for infection among newly admitted medical ICU patients with sepsis.

METHODS: This was a randomized, double-blind, placebo-controlled trial of adults who were admitted to the medical ICU for sepsis and were receiving broad-spectrum antibiotics. Participants were randomized 1:1:1 to placebo, inulin 16 g/day, or inulin 32 g/day which were given for seven days. The trial primary outcome was a surrogate measure for gut colonization resistance, namely the within-individual change from ICU admission to Day 3 in the relative abundance of short chain fatty acid (SCFA)-producing bacteria based on rectal swabs. Additional outcomes sought to evaluate the impact of inulin on the gut microbiome and downstream clinical effects.

RESULTS: Ninety participants were analyzed including 30 in each study group. There was no difference between study groups in the within-individual change in the relative abundance of SCFA-producing bacteria from ICU admission to ICU Day 3 (placebo: 0.0% change, IQR - 8·0% to + 7·4% vs. combined inulin: 0·0% change, IQR - 10·1% to + 4·8%; p = 0·91). At end-of-treatment on ICU Day 7, inulin did not affect SCFA-producer levels, microbiome diversity, or rates of gut colonization with pathogenic bacteria. After 30 days of clinical follow-up, inulin did not affect rates of death or clinical, culture-proven infection. Patients who died or developed culture-proven infections had lower relative abundance of SCFA-producing bacteria at ICU admission compared to those who did not (p = 0·03).

CONCLUSIONS: Prebiotic fiber had minimal impact on the gut microbiome in the ICU and did not improve clinical outcomes.

TRIAL REGISTRATION: Clinicaltrials.gov: NCT03865706.},
}

@article {pmid39806278,
year = {2025},
author = {Liu, Y and Chen, Z and Li, C and Sun, T and Luo, X and Jiang, B and Liu, M and Wang, Q and Li, T and Cao, J and Li, Y and Chen, Y and Kuai, L and Xiao, F and Xu, H and Cui, H},
title = {Associations between changes in the gut microbiota and liver cirrhosis: a systematic review and meta-analysis.},
journal = {BMC gastroenterology},
volume = {25},
number = {1},
pages = {16},
pmid = {39806278},
issn = {1471-230X},
support = {BJ-2024-091//National High Level Hospital Clinical Research Fund/ ; 82372314//National Natural Science Foundation of China/ ; 2021-I2M-1-050//CAMS Innovation Fund for Medical Sciences/ ; },
mesh = {*Liver Cirrhosis/microbiology ; *Gastrointestinal Microbiome ; Humans ; *Dysbiosis/microbiology ; Enterobacteriaceae/isolation & purification ; Streptococcaceae/isolation & purification ; Streptococcus/isolation & purification ; Proteobacteria/isolation & purification ; Veillonella/isolation & purification ; },
abstract = {OBJECTIVE: Summaries of the relationships between the microbiota and liver cirrhosis and their conclusions are not consistent. This study describes microbial differences in patients with liver cirrhosis by performing a meta-analysis.

METHODS: We searched PubMed, Embase, Web of Science, and the Cochrane Library and collected related articles published before March 10, 2024. Ratio of autochthonous to non-autochthonous taxa was calculated as the cirrhosis dysbiosis ratio (CDR). Using a random-effects model, the standard mean deviation (SMD) and 95% confidence interval (CI) were calculated. We subsequently performed subgroup, sensitivity, and publication bias analyses. cirrhosis dysbiosis ratio.

RESULTS: A total of 53 eligible papers including 5076 participants were included. The pooled estimates revealed a moderately significant reduction in gut microbiome richness in patients with liver cirrhosis compared with controls, including the Shannon, Chao1, observed species, ACE, and PD indices, but no significant difference was observed for the Simpson index. Over 80% of the studies reported significant differences in β diversity. Families Enterobacteriaceae and Pasteurellaceae, belonging to the phylum Proteobacteria, along with the family Streptococcaceae and the genera Haemophilus, Streptococcus, and Veillonella, were significantly associated with liver cirrhosis compared to the control group. In contrast, the healthy group exhibited a higher abundance of the class Clostridia, particularly the families Lachnospiraceae and Ruminococcaceae, which are known for their diversity and role as common gut commensals. Furthermore, the class Bacilli, predominantly represented by the genus Streptococcus, was markedly enriched in the cirrhosis group.

CONCLUSIONS: The microbiota richness of liver cirrhosis patients was lower than that of healthy controls. Alterations in gut microbiota linked to liver cirrhosis were characterized by a decrease in Lachnospiraceae, Ruminococcaceae, and Clostridia and an enrichment of Enterobacteriaceae, Pasteurellaceae, Streptococcaceae, Bacilli, and Streptococcus.},
}

*Liver Cirrhosis/microbiology
*Gastrointestinal Microbiome
Humans
*Dysbiosis/microbiology
Enterobacteriaceae/isolation & purification
Streptococcaceae/isolation & purification
Streptococcus/isolation & purification
Proteobacteria/isolation & purification
Veillonella/isolation & purification

@article {pmid39806201,
year = {2025},
author = {Japar, KV and Hariyanto, TI and Hamzah, DV and Prasetya, IB and Suastika, K},
title = {Probiotics Supplementation for Improving Glucolipid Parameters in Individuals with Prediabetes: A Systematic Review and Meta-Analysis of Randomized Trials.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {39806201},
issn = {1867-1314},
abstract = {The absence of suitable intervention significantly increases the likelihood of type 2 diabetes mellitus (T2DM) development in people with prediabetes. Recent statistical findings indicate that the gut microbiome might influences the development of insulin resistance. The objective of our study was to assess the efficacy and safety of probiotic supplementation in individuals diagnosed with prediabetes. A thorough search was carried out on the Cochrane Library, Medline, Scopus, and ClinicalTrials.gov databases until September 12th, 2024, using a mix of pertinent keywords. This review incorporates randomized clinical trials (RCTs) concerning the effect of probiotics for prediabetes. We used random-effect models to examine the mean difference (MD). A total of eight RCTs were incorporated. The results of our meta-analysis indicated that probiotics supplementation was associated with higher reduction in hemoglobin A1c (HbA1c) (MD -0.07% (95% CI -0.11, -0.03), p = 0.0005, I[2] = 0%) among individuals with prediabetes when compared to placebo. Other indicators such as total cholesterol, low-density lipoprotein cholesterol (LDL-C), high-density lipoprotein cholesterol (HDL-C), triglycerides (TG), and body mass index (BMI) did not differ significantly between probiotics and placebo. No significant difference was observed in the occurrence of adverse events (AEs) between the two groups. This study indicates the efficacy and safety of probiotics supplementation to improve the glycemic parameters in patients with prediabetes.},
}

@article {pmid39806046,
year = {2025},
author = {Sun, L and Liu, X and Zhou, L and Wang, H and Lian, C and Zhong, Z and Wang, M and Chen, H and Li, C},
title = {Shallow-water mussels (Mytilus galloprovincialis) adapt to deep-sea environment through transcriptomic and metagenomic insights.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {46},
pmid = {39806046},
issn = {2399-3642},
support = {42276153, 42106134, 42106100, 42030407//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {Animals ; *Mytilus/microbiology/genetics/immunology ; *Transcriptome ; *Microbiota ; Metagenomics ; Symbiosis/genetics ; Adaptation, Physiological/genetics ; Seawater/microbiology ; Metagenome ; },
abstract = {Recent studies have unveiled the deep sea as a rich biosphere, populated by species descended from shallow-water ancestors post-mass extinctions. Research on genomic evolution and microbial symbiosis has shed light on how these species thrive in extreme deep-sea conditions. However, early adaptation stages, particularly the roles of conserved genes and symbiotic microbes, remain inadequately understood. This study examined transcriptomic and microbiome changes in shallow-water mussels Mytilus galloprovincialis exposed to deep-sea conditions at the Site-F cold seep in the South China Sea. Results reveal complex gene expression adjustments in stress response, immune defense, homeostasis, and energy metabolism pathways during adaptation. After 10 days of deep-sea exposure, shallow-water mussels and their microbial communities closely resembled those of native deep-sea mussels, demonstrating host and microbiome convergence in response to adaptive shifts. Notably, methanotrophic bacteria, key symbionts in native deep-sea mussels, emerged as a dominant group in the exposed mussels. Host genes involved in immune recognition and endocytosis correlated significantly with the abundance of these bacteria. Overall, our analyses provide insights into adaptive transcriptional regulation and microbiome dynamics of mussels in deep-sea environments, highlighting the roles of conserved genes and microbial community shifts in adapting to extreme environments.},
}

Animals
*Mytilus/microbiology/genetics/immunology
*Transcriptome
*Microbiota
Metagenomics
Symbiosis/genetics
Adaptation, Physiological/genetics
Seawater/microbiology
Metagenome

@article {pmid39805887,
year = {2025},
author = {Al-Momani, H and Nelson, A and Al Balawi, H and Al Balawi, D and Aolymat, I and Khasawneh, AI and Tabl, H and Alsheikh, A and Zueter, AM and Pearson, J and Ward, C},
title = {Assessment of upper respiratory and gut bacterial microbiomes during COVID-19 infection in adults: potential aerodigestive transmission.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {1811},
pmid = {39805887},
issn = {2045-2322},
support = {593/61/2020//Deanship of Scientific Research, The Hashemite University/ ; },
mesh = {Humans ; *COVID-19/microbiology/virology/diagnosis ; Male ; *Gastrointestinal Microbiome ; Female ; Middle Aged ; Adult ; *SARS-CoV-2/isolation & purification ; *Feces/microbiology/virology ; Aged ; Saliva/microbiology/virology ; Sputum/microbiology/virology ; Respiratory System/microbiology/virology ; Gastroesophageal Reflux/microbiology/virology/complications ; RNA, Ribosomal, 16S/genetics ; Case-Control Studies ; },
abstract = {SARS-CoV-2 is the viral pathogen responsible for COVID-19. Although morbidity and mortality frequently occur as a result of lung disease, the gastrointestinal (GI) tract is recognized as a primary location for SARS-CoV-2. Connections and interactions between the microbiome of the gut and respiratory system have been linked with viral infections via what has been referred to as the 'gut-lung axis' with potential aerodigestive communication in health and disease. This research explored the relationship between the microbiomes of the upper respiratory and GI tracts in patients with COVID-19 and examined Extraesophageal reflux (EOR), a mechanism which could contribute to dysregulated communication between the GI and respiratory tract (as identified in COVID-19). 97 patients with a laboratory diagnosis of COVID-19 infection, and 50 age-matched controls were recruited and stool, saliva and sputum were obtained from each participant. ELISA Pepsin tests and Reflux Symptom Index scores (RSI) were conducted for EOR assessment. DNA sequencing of the V4 region of the 16 S rRNA gene was performed for microbiome analysis. No differences were observed between the fecal microbiome's alpha and Shannon diversity indices; however, a distinct microbial composition was observed in COVID-19 patients (when compared to the controls). The respiratory microbiota from individuals with COVID-19 demonstrated a statistically significant reduction in Shannon diversity and bacterial richness alongside an overall reduction in the prevalence of organisms from a typical healthy respiratory microbiome. Furthermore, the bacterial richness of the stool and sputum samples was significantly lower among COVID-19 patients admitted to ICU. A significantly higher RSI score and salivary pepsin level were detected among those with COVID-19. The data indicates that COVID-19 is associated with a dysregulation of both the gut and lung microbiome with a more marked perturbation in the lung, particularly among COVID-19 patients who had been admitted to the ICU. The presence of increased RSI scores, combined with elevated levels of Pepsin, suggests that increased micro-aspiration may occur, which is consistent with of under-recognized interactions between the GI and lung microbiomes in COVID-19 patients and requires additional study. Such studies would benefit from the insights provided by biological samples which reflect the continuum of the aerodigestive tract.},
}

Humans
*COVID-19/microbiology/virology/diagnosis
Male
*Gastrointestinal Microbiome
Female
Middle Aged
Adult
*SARS-CoV-2/isolation & purification
*Feces/microbiology/virology
Aged
Saliva/microbiology/virology
Sputum/microbiology/virology
Respiratory System/microbiology/virology
Gastroesophageal Reflux/microbiology/virology/complications
RNA, Ribosomal, 16S/genetics
Case-Control Studies

@article {pmid39805250,
year = {2024},
author = {Bortoluzzi, C and Ghanbari, M and Gonzáles, JC and Bohórquez, JO and Paredes, R and Mauri, Y and Lozano-Poveda, CA},
title = {Precision biotic as an effective replacement of hydrolyzed yeast and butyrate in antibiotic free diets of broiler chickens raised under field conditions.},
journal = {Poultry science},
volume = {104},
number = {2},
pages = {104664},
doi = {10.1016/j.psj.2024.104664},
pmid = {39805250},
issn = {1525-3171},
abstract = {A total of 1,436,000 Ross 380 AP broiler chicks were included in the experiment, which was conducted in two cycles with 20 houses per cycle and 35,900 birds per house. The objective was to evaluate, under field conditions, the impact of a precision biotic (PB) on the growth performance and cecal microbiome of broiler chickens, in comparison to enzymatically hydrolyzed yeast (EHY) and butyrate (BT) in an antibiotic-free diet. Each cycle consisted of six (6) houses under PB supplementation, and 14 houses under the regular dietary program used by the integration. Body weight (BW), feed intake (FI), and feed conversion ratio (FCR) were assessed at processing age, ranging from 39 to 45 d. Birds had ad libitum access to water and feed. On day 29, cecal content from 7 birds per house (42 birds per treatment) were collected for microbiome analysis by applying shotgun metagenomics approach. The performance data were analyzed by ANCOVA, house was considered as the experimental unit for growth performance (n = 20; P < 0.05), and the bird for microbiome analysis (n = 84; P < 0.05). Both treatment groups performed below the strain target in terms of BW, but better in terms of FCR. There were no significant differences (P > 0.05) between both groups on the growth performance, indicating that PB effectively replaced EHY and BT without compromising growth. However, significant functional changes were observed in the microbiome of birds fed PB, with enrichment in the pathways related to carbon and nitrogen metabolism. These changes were associated with an increased carbon metabolism index (P = 0.05), which can lead to higher endogenous short-chain fatty acids (SCFAs) production. Overall, by potentially increasing SCFA production by the intestinal microbiome, PB supported the growth performance of chickens similar to that achieved with EHY and BT.},
}

@article {pmid39805197,
year = {2025},
author = {Chen, G and Huang, T and Dai, Y and Huo, X and Xu, X},
title = {Effects of POPs-induced SIRT6 alteration on intestinal mucosal barrier function: A comprehensive review.},
journal = {Ecotoxicology and environmental safety},
volume = {289},
number = {},
pages = {117705},
doi = {10.1016/j.ecoenv.2025.117705},
pmid = {39805197},
issn = {1090-2414},
abstract = {Persistent organic pollutants (POPs) are pervasive organic chemicals with significant environmental and ecological ramifications, extending to adverse human health effects due to their toxicity and persistence. The intestinal mucosal barrier, a sophisticated defense mechanism comprising the epithelial layer, mucosal chemistry, and cellular immunity, shields the host from external threats and fosters a symbiotic relationship with intestinal bacteria. Sirtuin 6 (SIRT6), a sirtuin family member, is pivotal in genome and telomere stability, inflammation regulation, and metabolic processes. Result shows POPs have been implicated in the intestinal diseases, particularly in intestinal barrier dysfunction, through mechanisms such as cellular damage, epigenetic alterations, inflammation, microbiota changes, and metabolic disruptions. While the impact of SIRT6 expression changes on intestinal barrier functions has been reviewed, the mechanisms linking POPs to SIRT6 remain elusive. This review summarized the latest research results on the effects of POPs on intestinal barrier, discussed the role of SIRT6 from multiple mechanism perspectives, proposed new research directions on POPs, SIRT6 and intestinal health, and explored the therapeutic potential of SIRT6.},
}

@article {pmid39804942,
year = {2025},
author = {Gorstein, E and Aghdam, R and Solís-Lemus, C},
title = {HighDimMixedModels.jl: Robust high-dimensional mixed-effects models across omics data.},
journal = {PLoS computational biology},
volume = {21},
number = {1},
pages = {e1012143},
doi = {10.1371/journal.pcbi.1012143},
pmid = {39804942},
issn = {1553-7358},
abstract = {High-dimensional mixed-effects models are an increasingly important form of regression in which the number of covariates rivals or exceeds the number of samples, which are collected in groups or clusters. The penalized likelihood approach to fitting these models relies on a coordinate descent algorithm that lacks guarantees of convergence to a global optimum. Here, we empirically study the behavior of this algorithm on simulated and real examples of three types of data that are common in modern biology: transcriptome, genome-wide association, and microbiome data. Our simulations provide new insights into the algorithm's behavior in these settings, and, comparing the performance of two popular penalties, we demonstrate that the smoothly clipped absolute deviation (SCAD) penalty consistently outperforms the least absolute shrinkage and selection operator (LASSO) penalty in terms of both variable selection and estimation accuracy across omics data. To empower researchers in biology and other fields to fit models with the SCAD penalty, we implement the algorithm in a Julia package, HighDimMixedModels.jl.},
}

@article {pmid39804867,
year = {2025},
author = {Musyoki, VM and Mureithi, M and Heikinheimo, A and Maleche-Obimbo, E and Njaanake, K and Anzala, O},
title = {The impact of tuberculosis-induced hyperglycemia on pulmonary microbiota and airway mucus secretion in individuals not previously diabetic: A systematic review and meta-analysis protocol.},
journal = {PloS one},
volume = {20},
number = {1},
pages = {e0316810},
doi = {10.1371/journal.pone.0316810},
pmid = {39804867},
issn = {1932-6203},
mesh = {Humans ; *Systematic Reviews as Topic ; *Microbiota ; *Mucus/metabolism ; *Hyperglycemia/metabolism/microbiology ; *Lung/microbiology/metabolism ; Meta-Analysis as Topic ; Tuberculosis/microbiology/metabolism/complications/drug therapy ; Diabetes Mellitus, Type 2/complications/microbiology/metabolism ; Tuberculosis, Pulmonary/microbiology/metabolism/drug therapy/complications ; Mycobacterium tuberculosis ; },
abstract = {The lung environment harbours a community of microbes that play a significant role in health and disease, including innate protection against pathogenic microorganisms. Infection with Mycobacterium tuberculosis, psychological stress associated with the tuberculosis (TB) disease, and the metabolites from the rifampicin treatment regimen have been reported to induce hyperglycemia and consequently type 2 diabetes mellitus (T2DM) in individuals not previously diabetic. The high glucose concentration is proposed to alter the composition of the lung microbiota and airway homeostasis, exerting an influence on TB disease and treatment outcomes. In this systematic review, we propose to synthesize literature on TB-induced hyperglycemia and its impact on lung microbiota and secretion of airway mucus in individuals not previously diabetic. A systematic search will be carried out on PubMed, EMBASE, MEDLINE, PROQUEST, Cochrane, SCOPUS, and manually on Google Scholar and references of relevant articles to identify other studies. We will review published articles that include studies on TB-induced hyperglycemia, pulmonary microbiome, mucin secretion, and (or) airway surface liquid upon TB diagnosis and during treatment. The quality of the study articles will be assessed using the modified Newcastle-Ottawa Scale (NOS). Meta-analysis will be conducted using random effect model for heterogeneity to pool estimates on microbial diversity. Egger's test will be performed to explore any selective reporting bias. The findings of the systematic review and the meta-analysis will be reported as per the Preferred Reporting Items for Systematic Review and Meta-Analysis (PRISMA) protocol guidelines. This protocol was developed and uploaded onto the International Prospective Register of Systematic Reviews (PROSPERO) database, registration number: CRD42024482248.},
}

Humans
*Systematic Reviews as Topic
*Microbiota
*Mucus/metabolism
*Hyperglycemia/metabolism/microbiology
*Lung/microbiology/metabolism
Meta-Analysis as Topic
Tuberculosis/microbiology/metabolism/complications/drug therapy
Diabetes Mellitus, Type 2/complications/microbiology/metabolism
Tuberculosis, Pulmonary/microbiology/metabolism/drug therapy/complications
Mycobacterium tuberculosis

@article {pmid39804694,
year = {2025},
author = {Puller, V and Plaza Oñate, F and Prifti, E and de Lahondès, R},
title = {Impact of simulation and reference catalogues on the evaluation of taxonomic profiling pipelines.},
journal = {Microbial genomics},
volume = {11},
number = {1},
pages = {},
doi = {10.1099/mgen.0.001330},
pmid = {39804694},
issn = {2057-5858},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Computer Simulation ; Benchmarking ; Bacteria/classification/genetics ; Metagenomics/methods ; Microbiota/genetics ; },
abstract = {Microbiome profiling tools rely on reference catalogues, which significantly affect their performance. Comparing them is, however, challenging, mainly due to differences in their native catalogues. In this study, we present a novel standardized benchmarking framework that makes such comparisons more accurate. We decided not to customize databases but to translate results to a common reference to use the tools with their native environment. Specifically, we conducted two realistic simulations of gut microbiome samples, each based on a specific taxonomic profiler, and used two different taxonomic references to project their results, namely the Genome Taxonomy Database and the Unified Human Gastrointestinal Genome. To demonstrate the importance of using such a framework, we evaluated four established profilers as well as the impact of the simulations and that of the common taxonomic references on the perceived performance of these profilers. Finally, we provide guidelines to enhance future profiler comparisons for human microbiome ecosystems: (i) use or create realistic simulations tailored to your biological context (BC), (ii) identify a common feature space suited to your BC and independent of the catalogues used by the profilers and (iii) apply a comprehensive set of metrics covering accuracy (sensitivity/precision), overall representativity (richness/Shannon) and quantification (UniFrac and/or Aitchison distance).},
}

Humans
*Gastrointestinal Microbiome/genetics
Computer Simulation
Benchmarking
Bacteria/classification/genetics
Metagenomics/methods
Microbiota/genetics

@article {pmid39804518,
year = {2025},
author = {Claytor, JD and Lin, DL and Magnaye, KM and Guerrero, YS and Langelier, CR and Lynch, SV and El-Nachef, N},
title = {Effect of Fecal Microbiota Transplant on Antibiotic Resistance Genes Among Patients with Chronic Pouchitis.},
journal = {Digestive diseases and sciences},
volume = {},
number = {},
pages = {},
pmid = {39804518},
issn = {1573-2568},
abstract = {BACKGROUND: Pouchitis is common among patients with ulcerative colitis (UC) who have had colectomy with ileal pouch-anal anastomosis. Antibiotics are first-line therapy for pouch inflammation, increasing the potential for gut colonization with multi-drug resistant organisms (MDRO). Fecal microbial transplant (FMT) is being studied in the treatment of pouchitis and in the eradication of MDRO. Prior work using aerobic antibiotic culture disks suggests that some patients with chronic pouchitis may regain fluoroquinolone sensitivity after FMT. However, gut MDRO include anaerobic, fastidious organisms that are difficult to culture using traditional methods.

AIM: We aimed to assess whether FMT reduced the abundance of antibiotic resistance genes (ARG) or affected resistome diversity, evenness, or richness in patients with chronic pouchitis.

METHODS: We collected clinical characteristics regarding infections and antibiotic exposures for 18 patients who had previously been enrolled in an observational study investigating FMT as a treatment for pouchitis. Twenty-six pre- and post-FMT stool samples were analyzed using FLASH (Finding Low Abundance Sequences by Hybridization), a CRISPR/Cas9-based shotgun metagenomic sequence enrichment technique that detects acquired and chromosomal bacterial ARGs. Wilcoxon rank sum tests were used to assess differences in clinical characteristics, ARG counts, resistome diversity and ARG richness, pre- and post-FMT.

RESULTS: All 13 of the patients with sufficient stool samples for analysis had recently received antibiotics for pouchitis prior to a single endoscopic FMT. Fecal microbiomes of all patients had evidence of multi-drug resistance genes and ESBL resistance genes at baseline; 62% encoded fluoroquinolone resistance genes. A numerical decrease in overall ARG counts was noted post-FMT, but no statistically significant differences were noted (P = 0.19). Richness and diversity were not significantly altered. Three patients developed infections during the 5-year follow-up period, none of which were associated with MDRO.

CONCLUSION: Antibiotic resistance genes are prevalent among antibiotic-exposed patients with chronic pouchitis. FMT led to a numerical decrease, but no statistically significant change in ARG, nor were there significant changes in the diversity, richness, or evenness of ARGs. Further investigations to improve FMT engraftment and to optimize FMT delivery in patients with inflammatory pouch disorders are warranted.},
}

@article {pmid39804408,
year = {2025},
author = {Macdonald, JFH and Han, Y and Astafyeva, Y and Bergmann, L and Gurschke, M and Dirksen, P and Blümke, P and Schneider, YKH and Alawi, M and Lippemeier, S and Andersen, JH and Krohn, I},
title = {Exploring Tetraselmis chui microbiomes-functional metagenomics for novel catalases and superoxide dismutases.},
journal = {Applied microbiology and biotechnology},
volume = {109},
number = {1},
pages = {6},
pmid = {39804408},
issn = {1432-0614},
support = {AquaHealth FKZ 031B0945C//Bundesministerium für Bildung und Forschung/ ; SuReMetS FKZ 031B0944A//Bundesministerium für Bildung und Forschung/ ; },
mesh = {*Superoxide Dismutase/genetics/metabolism ; *Metagenomics ; *Antioxidants/metabolism ; *Catalase/metabolism/genetics ; *Microbiota ; Microalgae/genetics/enzymology ; Chlorophyta/genetics/enzymology ; Bacteria/genetics/enzymology/classification/isolation & purification ; },
abstract = {The focus on microalgae for applications in several fields, e.g. resources for biofuel, the food industry, cosmetics, nutraceuticals, biotechnology, and healthcare, has gained increasing attention over the last decades. In this study, we investigate the microbiome of the cultured microalga Tetraselmis chui (T. chui) to highlight their potential for health benefits. In this context, biomolecules like antioxidants play a crucial role in the well-being of living organisms as they metabolise harmful reactive oxygen species (ROS) to reduce oxidative stress. Impaired processing of ROS leads to damaged cells and increases the risk of cancer, inflammatory diseases, and diabetes, among others. Here, we identify, characterise, and test bacterial antioxidants derived from the T. chui microbiome metagenome dataset. We identified 258 genes coding for proteins with potential antioxidant activity. Of those, four novel enzymes are expressed and identified as two superoxide dismutases (SOD), TcJM_SOD2 and TcIK_SOD3, and two catalases (CAT), TcJM_CAT2 and TcIK_CAT3. Extensive analyses characterised all implemented enzymes as active even in concentrations down to 25 ng*ml[-1] for the SODs and 15 ng*ml[-1] for the CATs. Furthermore, sequence-based analyses assign TcJM_SOD2 and TcIK_SOD3 to iron superoxide dismutases (Fe SODs) and TcJM_CAT2 and TcIK_CAT3 to heme-containing catalases. These candidates are phylogenetically classified within the phylum Pseudomonadota. Regarding the biotechnological potential, a toxicity assay did not indicate any harmful effects. The introduced enzymes may benefit medical applications and expand the potential of microalgae microbiomes. KEY POINTS: • Omics-based discoveries of antioxidant enzymes from Tetraselmis chui microbiome • Two superoxide dismutases and two catalases are identified and tested for activity • Enzyme sensitivity highlights biotechnological potential of microalgae microbiomes.},
}

*Superoxide Dismutase/genetics/metabolism
*Metagenomics
*Antioxidants/metabolism
*Catalase/metabolism/genetics
*Microbiota
Microalgae/genetics/enzymology
Chlorophyta/genetics/enzymology
Bacteria/genetics/enzymology/classification/isolation & purification

@article {pmid39804239,
year = {2025},
author = {Quigley, EM},
title = {Small intestinal bacterial overgrowth: from malabsorption to misinterpretation.},
journal = {Minerva gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.23736/S2724-5985.24.03781-1},
pmid = {39804239},
issn = {2724-5365},
abstract = {Small intestinal bacterial overgrowth (SIBO) was originally described as a cause of maldigestion and malabsorption in situations where disruptions of intestinal anatomy or physiology favored the proliferation of bacteria normally confined to the colon. In this context, the pathogenesis of symptoms resulting from SIBO was well described. More recently, the concept of SIBO was extended to explain symptoms such as bloating, altered bowel habit and discomfort among individuals with irritable bowel syndrome and since then a whole host of gastrointestinal and extragastrointestinal disorders have been attributed to SIBO. In these more recent studies, the diagnosis of SIBO has been largely based on breath hydrogen testing; an approach that is subjected to misinterpretation. Here we critically assess the "modern" (as against the "classical") concept of SIBO and plead for caution in the application of breath tests, and those that employ lactulose as the substrate, in particular, to the diagnosis of this disorder. We look forward to the application of modern molecular microbiological techniques to the assessment of the small intestinal microbiome and metabolome and the delineation of what is truly normal.},
}

@article {pmid39804196,
year = {2025},
author = {Avery, EG and Haag, LM and McParland, V and Kedziora, SM and Zigra, GJ and Valdes, DS and Kirchner, M and Popp, O and Geisberger, S and Nonn, O and Karlsen, TV and N'Diaye, G and Yarritu, A and Bartolomaeus, H and Bartolomaeus, TUP and Tagiyeva, NA and Wimmer, MI and Haase, N and Zhang, YD and Wilhelm, A and Grütz, G and Tenstad, O and Wilck, N and Forslund, SK and Klopfleisch, R and Kühl, AA and Atreya, R and Kempa, S and Mertins, P and Siegmund, B and Wiig, H and Müller, DN},
title = {Intestinal interstitial fluid isolation provides novel insight into the human host-microbiome interface.},
journal = {Cardiovascular research},
volume = {},
number = {},
pages = {},
doi = {10.1093/cvr/cvae267},
pmid = {39804196},
issn = {1755-3245},
support = {DFG-SFB1449//Deutsche Forschungsgemeinschaft (DFG, German Research Foundation)/ ; 81Z0100110//Deutsches Zentrum für Herz-Kreislauf-Forschung/ ; //DZGIF (DZG Innovation Fund)/ ; 01EJ2202D//The German Ministry of Education and Research (BMBF)/ ; 262079//Research Council of Norway/ ; F-12546//Western Norway Regional Health Authority/ ; //Norwegian Health Association/ ; 852796//European Research Council under the European Union's Horizon 2020 research and innovation program/ ; //Corona Foundation in the German Stifterverband/ ; //Bundesministerium für Bildung und Forschung (BMBF) funding Multimodal Clinical Mass Spectrometry to Target Treatment Resistance (MSTARS)/ ; //Charité-Universitätsmedizin Berlin and the Berlin Institute of Health at Charité (BIH)/ ; },
abstract = {AIMS: The gastrointestinal (GI) tract is composed of distinct sub-regions, which exhibit segment-specific differences in microbial colonization and (patho)physiological characteristics. Gut microbes can be collectively considered as an active endocrine organ. Microbes produce metabolites, which can be taken up by the host and can actively communicate with the immune cells in the gut lamina propria with consequences for cardiovascular health. Variation in bacterial load and composition along the GI tract may influence the mucosal microenvironment and thus be reflected its interstitial fluid (IF). Characterization of the segment-specific microenvironment is challenging and largely unexplored because of lack of available tools.

METHODS AND RESULTS: Here, we developed methods, namely tissue centrifugation and elution, to collect IF from the mucosa of different intestinal segments. These methods were first validated in rats and mice, and the tissue elution method was subsequently translated for use in humans. These new methods allowed us to quantify microbiota-derived metabolites, mucosa-derived cytokines, and proteins at their site-of-action. Quantification of short-chain fatty acids showed enrichment in the colonic IF. Metabolite and cytokine analyses revealed differential abundances within segments, often significantly increased compared to plasma, and proteomics revealed that proteins annotated to the extracellular phase were site-specifically identifiable in IF. Lipopolysaccharide injections in rats showed significantly higher ileal IL-1β levels in IF compared to the systemic circulation, suggesting the potential of local as well as systemic effect.

CONCLUSION: Collection of IF from defined segments and the direct measurement of mediators at the site-of-action in rodents and humans bypasses the limitations of indirect analysis of faecal samples or serum, providing direct insight into this understudied compartment.},
}

@article {pmid39804080,
year = {2025},
author = {Kuhnert, P and Brodard, I and Jores, J},
title = {Complete genome sequence of the first Capnocytophaga canimorus strain isolated from a red fox (Vulpes vulpes) in Germany.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0122824},
doi = {10.1128/mra.01228-24},
pmid = {39804080},
issn = {2576-098X},
abstract = {The zoonotic pathogen Capnocytophaga canimorsus is part of the oral microbiome of dogs and cats. We report the genome sequence of strain KM3195_24, isolated from a red fox. It has a circular genome of 2,718,701 bp with a G + C content of 36%, 2,419 CDS, 3 rRNA operons, and 45 tRNAs.},
}

@article {pmid39803928,
year = {2025},
author = {Pandey, RP and Dhiman, R and Chang, CM},
title = {The potential of nanoencapsulated probiotics in the modulation of the gut microbiome.},
journal = {Nanomedicine (London, England)},
volume = {},
number = {},
pages = {1-4},
doi = {10.1080/17435889.2025.2452152},
pmid = {39803928},
issn = {1748-6963},
}

@article {pmid39803910,
year = {2025},
author = {Gong, W and Yu, H and You, W and Chen, Z and Wang, Y and Liu, C and Li, Y and Guan, S},
title = {The oral microbiota: new insight into intracranial aneurysms.},
journal = {Annals of medicine},
volume = {57},
number = {1},
pages = {2451191},
doi = {10.1080/07853890.2025.2451191},
pmid = {39803910},
issn = {1365-2060},
mesh = {*Intracranial Aneurysm/microbiology/immunology ; Humans ; *Dysbiosis/microbiology/immunology ; *Mouth/microbiology ; Microbiota/immunology/physiology ; Porphyromonas gingivalis/pathogenicity/immunology ; Inflammation/microbiology/immunology ; Gastrointestinal Microbiome/physiology/immunology ; Vascular Remodeling ; },
abstract = {BACKGROUND: Intracranial aneurysms (IAs) are a significant clinical concern, with detection rates increasing due to advances in imaging technologies. However, precise mechanisms underlying their pathophysiology remain incompletely understood. Recent evidence suggests a pivotal role of oral microbiota dysbiosis, particularly periodontal pathogens, in systemic inflammation that may contribute to IA development and rupture.

OBJECTIVE: This review aims to critically evaluate the association between oral microbiota dysbiosis and the pathogenesis of IAs, with a focus on the molecular and immunological mechanisms by which oral pathogens influence vascular pathology.

METHODS: We conducted a comprehensive analysis of the literature regarding the impact of oral microbial dysbiosis on IA pathophysiology, emphasizing the role of specific pathogenic species, such as Porphyromonas gingivalis. The review explores how these pathogens may mediate chronic inflammation through hematogenous spread, gut microbiome alterations, and neuroinflammatory processes, leading to vascular remodeling and cerebrovascular instability.

RESULTS: The findings suggest that oral microbial dysbiosis, particularly the presence of pathogenic bacteria, is implicated in the systemic inflammatory response that exacerbates the structural integrity of the cerebrovascular wall. Chronic inflammatory states induced by oral pathogens contribute to extracellular matrix degradation, impaired vascular remodeling, and an increased susceptibility to IA rupture.

CONCLUSIONS: The findings highlight the importance of maintaining oral microbiota homeostasis as a potential therapeutic target for preventing IAs. Interventions aimed at restoring oral microbial balance may represent a novel strategy for reducing the burden of IA formation and rupture, highlighting the need for an integrated approach to oral health and IAs prevention.},
}

*Intracranial Aneurysm/microbiology/immunology
Humans
*Dysbiosis/microbiology/immunology
*Mouth/microbiology
Microbiota/immunology/physiology
Porphyromonas gingivalis/pathogenicity/immunology
Inflammation/microbiology/immunology
Gastrointestinal Microbiome/physiology/immunology
Vascular Remodeling

@article {pmid39803897,
year = {2025},
author = {Carter, MM and Leatherwood, JL and Paris, BL and Moore, GE and George, JM and Martinez, RE and Karges, K and Cox, JR and Arnold, CE and Glass, KG and Bradbery, AN and Rodiles, A and Wickersham, TA},
title = {Influence of Saccharomyces cerevisiae CNCM I-1077 on the fecal pH, markers of gut permeability, fecal microbiota, and markers of systemic inflammation in sedentary horses fed a high-starch diet.},
journal = {Journal of animal science},
volume = {},
number = {},
pages = {},
doi = {10.1093/jas/skaf005},
pmid = {39803897},
issn = {1525-3163},
abstract = {Thirty mature Quarter Horse geldings were used in a completely randomized 32-d study to test the hypotheses that supplemental live Saccharomyces cerevisiae CNCM I-1077 improves apparent digestion, stabilizes the fecal pH, reduces gut permeability, maintains microbial communities, and decreases inflammation in horses fed a high-starch diet. Horses were stratified by body weight, age, and body condition score (BCS) to one of two treatments: concentrate formulated with 2g starch • kg BW-1 • meal-1 (CON; n=15) or the same concentrate top-dressed with 25g/d Saccharomyces cerevisiae CNCM I-1077 (SC; n=15; 8×108 CFU). Horses were fed individually in stalls every 12h. Between meals, horses were housed in dry lots with ad libitum access to water and Coastal bermudagrass hay. On d0 and 32, BW and BCS were recorded, and blood was collected before feeding and 2, 8, 16, and 24 h postmeal on d32 to analyze serum D-lactate. Fecal samples were collected on d0, 16, and 32 at 8, 16, and 24h post-meal for fecal pH and starch content. Intake and fecal production were recorded over 4-d to measure digestibility on d28-31. Whole blood total bacterial counts and 16S fecal microbiota rRNA sequencing were performed at d0, 16, and 32. Results revealed an increased ∆BW in SC horses compared with CON horses (P=0.03), with no change in BCS (P=0.97). D-lactate tended to be greater in SC horses on d32 at 16 and 24h post-meal compared with CON horses (P=0.10). Concentrations of TNFα and LogCCL2 decreased from d0 to d 32 regardless of dietary supplementation (P≤0.02). Fold change of percent reads from d0 in whole blood bacterial 16S rRNA did not differ between groups. Fecal starch was undetectable, and there were no differences in intake or apparent digestibility. Fecal pH tended (P=0.07) to be lower in CON at 0h on d32 (6.03 ± 0.06) than d16 (6.14 ± 0.06). Additionally, pH tended (P=0.09) to be lower in CON (6.03 ± 0.06) than SC (6.16 ± 0.06) at 0h on d32. Supplementation of Saccharomyces cerevisiae CNCM I-1077 maintained Bacteroidales and reduced acidosis-like bacteria like Streptococcus and potential pathogens like Enterobacteriaceae, Stenotrophomonas, and Rhodococcus at d16 (P<0.05). Further, supplementation increased fibrolytic bacteria at d32, such as Ruminococcus, Fibrobacter, and Succinivibrio (P<0.05). These results indicate Saccharomyces cerevisiae CNCM I-1077 increases BW and promotes a more diverse microbiome when hoses are fed ad libitum hay and a high-starch concentrate.},
}

@article {pmid39803564,
year = {2024},
author = {Lee, MT and Tan, X and Le, HH and Besler, K and Thompson, S and Harris-Tryon, T and Johnson, EL},
title = {Gut bacterial sphingolipid production modulates dysregulated skin lipid homeostasis.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.12.29.629238},
pmid = {39803564},
issn = {2692-8205},
abstract = {Sphingolipids are an essential lipid component of the skin barrier with alterations in skin sphingolipid composition associated with multiple skin disorders including psoriasis, atopic dermatitis, and ichthyosis. Contributions to skin sphingolipid abundance are not well characterized, thus the main method of modulating skin lipid levels is the topical application of creams rich with sphingolipids at the skin surface. Evidence that diet and gut microbiome function can alter skin biology proposes an intriguing potential for the modulation of skin lipid homeostasis through gut microbial metabolism, but potential mechanisms of action are not well understood. Sphingolipid synthesis by prominent gut microbes has been shown to affect intestinal, hepatic and immune functions with the potential for sphingolipid-producing bacteria to affect skin biology through altering skin sphingolipid levels. To address this question, we used bioorthogonal chemistry to label lipids from the sphingolipid-producing bacteria Bacteroides thetaiotaomicron and trace these lipids to the skin epidermis. Exposing mice to B. thetaiotaomicron strains mutant in the ability to produce sphingolipids resulted in significantly lower transfer of gut microbiome-derived lipids to the skin, while also altering skin biology and altering expression of skin barrier genes. Measurement of skin ceramide levels, a class of sphingolipids involved in skin barrier function, determined that skin sphingolipid levels were altered in the presence of gut sphingolipid-producing bacteria. Together this work demonstrates that gut bacterial lipids can transfer to the skin and provides a compelling avenue for modulating sphingolipid-dominant compartments of the skin using sphingolipid-producing bacteria of the gut microbiome.},
}

@article {pmid39803511,
year = {2024},
author = {Schulz, F and Yan, Y and Weiner, AKM and Ahsan, R and Katz, LA and Woyke, T},
title = {Protists as mediators of complex microbial and viral associations.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.12.29.630703},
pmid = {39803511},
issn = {2692-8205},
abstract = {Microbial eukaryotes (aka protists) are known for their important roles in nutrient cycling across different ecosystems. However, the composition and function of protist-associated microbiomes remains largely elusive. Here, we employ cultivation-independent single-cell isolation and genome-resolved metagenomics to provide detailed insights into underexplored microbiomes and viromes of over 100 currently uncultivable ciliates and amoebae isolated from diverse environments. Our findings reveal unique microbiome compositions and hint at an intricate network of complex interactions and associations with bacterial symbionts and viruses. We observed stark differences between ciliates and amoebae in terms of microbiome and virome compositions, highlighting the specificity of protist-microbe interactions. Over 115 of the recovered microbial genomes were affiliated with known endosymbionts of eukaryotes, including diverse members of the Holosporales, Rickettsiales, Legionellales, Chlamydiae, Dependentiae, and more than 250 were affiliated with possible host-associated bacteria of the phylum Patescibacteria. We also identified more than 80 giant viruses belonging to diverse viral lineages, of which some were actively expressing genes in single cell transcriptomes, suggesting a possible association with the sampled protists. We also revealed a wide range of other viruses that were predicted to infect eukaryotes or host-associated bacteria. Our results provide further evidence that protists serve as mediators of complex microbial and viral associations, playing a critical role in ecological networks. The frequent co-occurrence of giant viruses and diverse microbial symbionts in our samples suggests multipartite associations, particularly among amoebae. Our study provides a preliminary assessment of the microbial diversity associated with lesser-known protist lineages and paves the way for a deeper understanding of protist ecology and their roles in environmental and human health.},
}

@article {pmid39803498,
year = {2024},
author = {Arp, G and Jiang, A and Dufault-Thompson, K and Levy, S and Zhong, A and Wassan, JT and Grant, M and Li, Y and Hall, B and Jiang, X},
title = {Gut Bacteria Encode Reductases that Biotransform Steroid Hormones.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.10.04.616736},
pmid = {39803498},
issn = {2692-8205},
abstract = {The metabolism of steroids by the gut microbiome affects hormone homeostasis, impacting host development, mental health, and reproductive functions. In this study, we identify the Δ [4] -3-ketosteroid 5β-reductase, 3β-hydroxysteroid dehydrogenase/Δ [5-4] isomerase, and Δ [6] -3-ketosteroid reductase enzyme families encoded by common human gut bacteria. Through phylogenetic reconstruction and mutagenesis, We show that 5β-reductase and Δ [6] -3-ketosteroid reductase have evolved to specialize in converting diverse 3-keto steroid hormones into their 5β- and Δ [6] -reduced derivatives. We also find that the novel 3β-hydroxysteroid dehydrogenase/Δ [5-4] isomerase is fused with 5β-reductase in multiple species, streamlining the multi-step conversion of pregnenolone, a steroid hormone precursor, into epipregnanolone. Through metagenomic analysis, we reveal that these enzymes are prevalent in healthy populations, being enriched in females over males. These findings provide the molecular basis for studying microbial steroid metabolism in the gut, offering insights into its potential impact on hormonal health in hosts, especially in the context of women's health.},
}

@article {pmid39803475,
year = {2025},
author = {Queen, J and Cing, Z and Minsky, H and Nandi, A and Southward, T and Ferri, J and McMann, M and Iyadorai, T and Vadivelu, J and Roslani, A and Loke, MF and Wanyiri, J and White, JR and Drewes, JL and Sears, CL},
title = {Fusobacterium nucleatum is enriched in invasive biofilms in colorectal cancer.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.12.30.630810},
pmid = {39803475},
issn = {2692-8205},
abstract = {Fusobacterium nucleatum is an oral bacterium known to colonize colorectal tumors, where it is thought to play an important role in cancer progression. Recent advances in sequencing and phenotyping of F. nucleatum have revealed important differences at the subspecies level, but whether these differences impact the overall tumor ecology, and tumorigenesis itself, remain poorly understood. In this study, we sought to characterize Fusobacteria in the tumor microbiome of a cohort of individuals with CRC through a combination of molecular, spatial, and microbiologic analyses. We assessed for relative abundance of F. nucleatum in tumors compared to paired normal tissue, and correlated abundance with clinical and pathological features. We demonstrate striking enrichment of F. nucleatum and the recently discovered subspecies animalis clade 2 (Fna C2) specifically in colon tumors that have biofilms, highlighting the importance of complex community partnerships in the pathogenesis of this important organism.},
}

@article {pmid39803224,
year = {2025},
author = {Nami, Y and Barghi, A and Shahgolzari, M and Salehian, M and Haghshenas, B},
title = {Mechanism of Action and Beneficial Effects of Probiotics in Amateur and Professional Athletes.},
journal = {Food science & nutrition},
volume = {13},
number = {1},
pages = {e4658},
pmid = {39803224},
issn = {2048-7177},
abstract = {Probiotics are live microorganisms that, when administered in adequate amounts, provide health benefits to the host. According to the International Society of Sports Nutrition (ISSN), probiotic supplementation can optimize the health, performance, and recovery of athletes at all stages of their careers. Recent research suggests that probiotics can improve immune system functions, reduce gastrointestinal distress, and increase gut permeability in athletes. Additionally, probiotics may provide athletes with secondary health benefits that could positively affect athletic performance through enhanced recovery from fatigue, improved immune function, and maintenance of healthy gastrointestinal tract function. The integration of some probiotic strains into athletes' diets and the consumption of multi-strain compounds may lead to an improvement in performance and can positively affect performance-related aspects such as fatigue, muscle pain, body composition, and cardiorespiratory fitness. In summary, probiotics can be beneficial for athletes at all stages of their careers, from amateur to professional. This paper reviews the progress of research on the role of probiotic supplementation in improving energy metabolism and immune system functions, reducing gastrointestinal distress, and enhancing recovery from fatigue in athletes at different levels.},
}

@article {pmid39803193,
year = {2025},
author = {Lu, Z and Wang, Z and Jia, H and Meng, D and Wu, D},
title = {Captivity Reduces Diversity and Shifts Composition of the Great Bustard (Otis tarda dybowskii) Microbiome.},
journal = {Ecology and evolution},
volume = {15},
number = {1},
pages = {e70836},
pmid = {39803193},
issn = {2045-7758},
abstract = {Captivity offers protection for endangered species, but for bustards, captive individuals face a higher risk of disease and exhibit lower reintroduction success rates. Changes in the diversity of host bacterial and fungal microbiota may be a significant factor influencing reintroduction success. The great bustard (Otis tarda) is a globally recognized endangered bird species. Previous research on the gut microbiota of the great bustard has been limited, hindering effective conservation efforts. Therefore, this study utilized high-throughput sequencing of the 16S rRNA and Internal Transcribed Spacer (ITS) genes to compare the gut bacterial and fungal microbiota of great bustards in different environments. The results revealed a significant decline in alpha diversity and notable changes in microbial community structure in captive environments. Changes in diet and habitat are likely major factors contributing to these shifts. Consequently, managing rescued wild animals by increasing dietary diversity and exposure to natural environmental reservoirs may enhance the success rate of reintroduction efforts.},
}

@article {pmid39803189,
year = {2025},
author = {Llanwarne, F and Dobson, AJ},
title = {Covariation Between Microbiome Composition and Host Transcriptome in the Gut of Wild Drosophila melanogaster: A Re-Analysis.},
journal = {Ecology and evolution},
volume = {15},
number = {1},
pages = {e70853},
pmid = {39803189},
issn = {2045-7758},
abstract = {Gut microbiota are fundamental for healthy animal function, but the evidence that host function can be predicted from microbiota taxonomy remains equivocal, and natural populations remain understudied compared to laboratory animals. Paired analyses of covariation in microbiota and host parameters are powerful approaches to characterise host-microbiome relationships mechanistically, especially in wild populations of animals that are also lab models, enabling insight into the ecological basis of host function at molecular and cellular levels. The fruitfly Drosophila melanogaster is a preeminent model organism, amenable to field investigation by 'omic analyses. Previous work in wild male D. melanogaster guts analysed paired measurements of (A) bacterial diversity and abundance, measured by 16S amplicon sequencing; and (B) the host gut transcriptome, but no signature of covariation was detected. Here, we re-analyse those data comprehensively. We find orthogonal axes of microbial genera, which correspond to differential expression of host genes. The differentially expressed gene sets were enriched in functions including protein translation, mitochondrial respiration, immunity and reproduction. Each gene set had a distinct functional signature, suggesting that wild flies exhibit a range of distinct axes of functional variation, which correspond to orthogonal axes of microbiome variation. These findings lay a foundation to better connect ecology and functional genetics of a leading host-microbiome model.},
}

@article {pmid39802951,
year = {2024},
author = {Nie, Y and Schalper, KA and Chiang, A},
title = {Mechanisms of immunotherapy resistance in small cell lung cancer.},
journal = {Cancer drug resistance (Alhambra, Calif.)},
volume = {7},
number = {},
pages = {55},
pmid = {39802951},
issn = {2578-532X},
abstract = {Small-cell lung cancer (SCLC) is an aggressive neuroendocrine tumor with a poor prognosis. Although the addition of immunotherapy to chemotherapy has modestly improved outcomes, most patients rapidly develop resistance. Resistance to immunotherapy can be broadly categorized into primary resistance and acquired resistance, as proposed by the Society for Immunotherapy of Cancer (SITC) consensus definition. Primary resistance occurs in the setting of failure to respond to immune checkpoint inhibitors (ICIs), while acquired resistance develops after initial response. The mechanisms of acquired and primary resistance to ICI are not well understood in SCLC, denoting an area of critical unmet need. Both intrinsic and extrinsic mechanisms play significant roles in immunotherapy resistance. Intrinsic mechanisms include defects in antigen presentation, mutations in key genes, reduced tumor immunogenicity, and epigenetic alterations. Extrinsic mechanisms involve the tumor microenvironment (TME), which is a complex interplay of both tumor- and immunosuppressive immune cells, vasculature, and microbiome. An understanding of these resistance mechanisms is crucial for developing novel therapeutic strategies to advance effective immunotherapy in patients with SCLC, a critical area of unmet need.},
}

@article {pmid39802896,
year = {2024},
author = {Zong, Z and Zeng, W and Li, Y and Wang, M and Cao, Y and Cheng, X and Jin, Z and Mao, S and Zhu, X},
title = {Intratumor microbiota and colorectal cancer: Comprehensive and lucid review.},
journal = {Chinese journal of cancer research = Chung-kuo yen cheng yen chiu},
volume = {36},
number = {6},
pages = {683-699},
pmid = {39802896},
issn = {1000-9604},
abstract = {As a key component of tumor microenvironment, the microbiota has gradually played a key role in cancer research. Particularly in colorectal cancer, the specific population of microbiota within the tumor shows a strong association with the tumor type. Although the existence and potential role of microbiota in tumors have been recognized, the specific associations between the microbiota and tumor tissue and the mechanism of action still need to be further explored. This paper reviews the discovery, origin, and emerging role of the intratumor microbiota in the immune microenvironment and systematically outlines the oncogenic and metastasis-promoting strategies of the intratumor microbiota. Moreover, it comprehensively and holistically evaluates therapeutic strategies and prognostic performance on the basis of the intratumor microbiota, with the goal of providing strong support for future research and clinical practice.},
}

@article {pmid39802798,
year = {2024},
author = {Blank, RB and Bu, K and Chen, W and Cunningham, I and Sokolove, J and Lahey, L and Heguy, A and Medina, R and Ubeda, C and Nayak, RR and Hu, J and Cantor, A and Lee, J and Clemente, JC and Scher, JU},
title = {Multi-omic Biomarkers Distinguish Rheumatoid Arthritis in Discordant Monozygotic Twins.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.12.30.24319783},
pmid = {39802798},
abstract = {BACKGROUND: Although genetic factors have been identified in the pathogenesis of rheumatoid arthritis (RA), the concordance rate in monozygotic (MZ) twins is low, suggesting that other features contribute to disease development. Further, the relative contribution of such non-genetic elements in identical twins have not been characterized. Here, we aimed to measure differentiating host and microbial biomarkers of RA by studying MZ twins discordant for disease using a multi-omics approach.

METHODS: Eight pairs of MZ twins discordant for RA (n=16) were enrolled. Gut microbiome was assessed using shotgun metagenomic sequencing. Autoantibodies, cytokines, and other plasma proteins were measured in both plasma and feces. Levels of short and medium-chain fatty acids from serum and feces were quantified using gas chromatography mass spectrometry (GC-MS).

RESULTS: While overall microbiome diversity and composition did not significantly differ between twins, we observed a decrease in Blautia faecis in affected twins. Affected twins had higher concentrations of both fecal and plasma citrullinated and non-citrullinated autoantibodies, as well as significantly lower concentrations of fecal butyrate and propionate.

CONCLUSION: Multi-omics biomarkers differentiate MZ twins discordant for RA. Blautia faecis , which is associated with reduced inflammatory cytokine expression, was decreased in RA twins. Similarly, short-chain fatty acids, known to have immune modulatory effects, were decreased in affected twins, suggesting further bi-directional interactions between inflammation at the gut barrier and disease state. If confirmed in other cohorts, exhaustive multi-omics approaches may improve our understanding of RA pathogenesis and potentially contribute to novel diagnostics and co-adjuvant therapies.},
}

@article {pmid39802638,
year = {2025},
author = {Lin, Z and Li, T and Huang, F and Wu, M and Zhu, L and Zhou, Y and Ming, YA and Lu, Z and Peng, W and Gao, F and Zhu, Y},
title = {Comparison of diet and exercise on cardiometabolic factors in young adults with overweight/obesity: multiomics analysis and gut microbiota prediction, a randomized controlled trial.},
journal = {MedComm},
volume = {6},
number = {1},
pages = {e70044},
pmid = {39802638},
issn = {2688-2663},
abstract = {The optimal strategy for improving cardiometabolic factors (CMFs) in young obese individuals through diet and exercise remains unclear, as do the potential mechanisms. We conducted an 8-week randomized controlled trial to compare the effects of different interventions in youth with overweight/obesity. Gut microbes and serum metabolites were examined to identify regulating mechanisms. A total of 129 undergraduates were randomly assigned to fiber-rich (FR) diet, rope-skipping (RS), combined FR-RS and control groups. The results showed that single interventions were as effective as combined interventions in improving weight, waist circumference, body fat, and lipid profile compared with control group. Notably, the FR group further reduced low-density lipoprotein (LDL-C) and uric acid (UA) (all p < 0.05). Mediation analysis revealed four gut microbiota-metabolite-host axes in improving CMFs. Additionally, we used machine learning algorithms to further predict individual responses based on baseline gut microbiota composition, with specific microbial genera guiding targeted intervention selection. In conclusion, FR diet and/or RS were effective in improving CMFs, with the FR diet particular effectiveness in reducing LDL-C and UA levels. These benefits may drive by gut microbiome-metabolite-host interactions. Moreover, the predictability of gut microbiota composition supports making targeted decisions in selecting interventions. Trial Registration: NCT04834687.},
}

@article {pmid39802282,
year = {2025},
author = {Machado, AP and Adames, SM and Shatila, M and Aujla, P and Huey, R and Wang, Y and Thomas, A},
title = {Immune checkpoint inhibitor-associated gastrointestinal adverse events in patients with colorectal cancer.},
journal = {Annals of gastroenterology},
volume = {38},
number = {1},
pages = {72-79},
pmid = {39802282},
issn = {1108-7471},
abstract = {BACKGROUND: Immune checkpoint inhibitors (ICI) target microsatellite instability-high (MSI-H) tumors with success. The incidence and characteristics of ICI-related colitis (IMC) in patients with MSI-H colorectal cancers (CRC) are unclear.

METHODS: We performed a retrospective analysis of adult patients with CRC who received ICI between June 1, 2014, and December 31, 2022, including data on IMC observed up to 3 months after the last dose of ICI. Patients' demographics, oncologic profile, endoscopic features, treatment and clinical outcomes were evaluated.

RESULTS: Of 474 patients with CRC receiving ICI during our study period, 18 developed IMC (3.8%). The majority were Caucasian (88.8%), male (61.1%), and their median age was 69.5 years. Of these patients, 50% received combination therapy with anti-PD-1/L1 and CTLA-4; 66.6% had MSI-H colorectal cancer, 11.1% had a second cancer-melanoma, while 61.2% and 66.7% had grade 1-2 colitis and diarrhea respectively. Endoscopic evaluation was used in 5 patients, of whom 2 had ulcerative inflammation necessitating selective immunosuppressive therapy with biologics. Therapy was withheld in 61.1% because of toxicity; 41.4% and 5.8% were noted to have median Common Terminology Criteria for Adverse Events grade 2 liver and pancreas toxicity respectively. The majority of our cohort received steroid therapy.

CONCLUSIONS: The lower severity of IMC, compared to toxicity in other ICI-treated cancers, may be influenced by the tumor microenvironment in MSI-H colorectal cancer after ICI exposure. Larger prospective studies are necessary to determine the role of tumor biology and the gut microbiome in the disease profile and severity of IMC.},
}

@article {pmid39801834,
year = {2025},
author = {Bustamante, M and Mei, S and Daras, IM and van Doorn, GS and Falcao Salles, J and de Vos, MGJ},
title = {An eco-evolutionary perspective on antimicrobial resistance in the context of One Health.},
journal = {iScience},
volume = {28},
number = {1},
pages = {111534},
pmid = {39801834},
issn = {2589-0042},
abstract = {The One Health approach musters growing concerns about antimicrobial resistance due to the increased use of antibiotics in healthcare and agriculture, with all of its consequences for human, livestock, and environmental health. In this perspective, we explore the current knowledge on how interactions at different levels of biological organization, from genetic to ecological interactions, affect the evolution of antimicrobial resistance. We discuss their role in different contexts, from natural systems with weak selection, to human-influenced environments that impose a strong pressure toward antimicrobial resistance evolution. We emphasize the need for an eco-evolutionary approach within the One Health framework and highlight the importance of horizontal gene transfer and microbiome interactions for increased understanding of the emergence and spread of antimicrobial resistance.},
}

@article {pmid39801739,
year = {2024},
author = {Park, HJ and Yu, D and Hong, ST and Lee, J and Park, SJ and Park, MS and Lee, H and Kim, M and Cheon, YH and Lee, SG and Sohn, DH and Jun, JB and Kim, S and Lee, SI},
title = {Bifidobacterium longum RAPO Attenuates Dermal and Pulmonary Fibrosis in a Mouse Model of Systemic Sclerosis through Macrophage Modulation and Growth of Short-Chain Fatty Acid Producers.},
journal = {Immune network},
volume = {24},
number = {6},
pages = {e41},
pmid = {39801739},
issn = {1598-2629},
abstract = {Systemic sclerosis (SSc) is a complex autoimmune disease with an unclear etiology and no effective treatments. Recent research has suggested involvement of the microbiome in SSc pathogenesis. This study aimed to identify specific microbial species associated with SSc and explore their therapeutic potential. Serum Abs against 384 intestinal microbial species revealed a significant depletion in Abs against Bifidobacterium longum in patients with SSc compared to healthy controls. In a bleomycin-induced SSc mouse model, oral administration of B. longum strain RAPO attenuated skin and lung fibrosis, accompanied by reduced infiltration of inflammatory monocytes/macrophages and downregulation of pro-inflammatory cytokines and chemoattractant Ccl2 genes in lymph nodes and fibrotic tissues. B. longum RAPO treatment restored fecal microbial diversity and augmented short-chain fatty acid (SCFA)-producing bacteria in the gut, leading to increased fecal butyrate levels and upregulated SCFA receptor Gpr41 in the mesenteric lymph node. In vitro, B. longum RAPO and its culture supernatant suppressed the expressions of pro-inflammatory cytokine genes in macrophages and inhibited myofibroblast differentiation in fibroblasts. These findings highlight the probiotic potential of B. longum RAPO in preventing tissue fibrosis by modulating macrophage activity and promoting the growth of SCFA-producing bacteria, underscoring the therapeutic potential of microbial modulation in SSc.},
}

@article {pmid39801738,
year = {2024},
author = {Harmak, Z and Kone, AS and Ghouzlani, A and Ghazi, B and Badou, A},
title = {Beyond Tumor Borders: Intratumoral Microbiome Effects on Tumor Behavior and Therapeutic Responses.},
journal = {Immune network},
volume = {24},
number = {6},
pages = {e40},
pmid = {39801738},
issn = {1598-2629},
abstract = {The human body contains a diverse array of microorganisms, which exert a significant impact on various physiological processes, including immunity, and can significantly influence susceptibility to various diseases such as cancer. Recent advancements in metagenomic sequencing have uncovered the role of intratumoral microbiome, which covertly altered the development of cancer, the growth of tumors, and the response to existing treatments through multiple mechanisms. These mechanisms involve mainly DNA damage induction, oncogenic signaling pathway activation, and the host's immune response modulation. To explore novel therapeutic options and effectively target and regulate the intratumoral microbiome, a comprehensive understanding of these processes is indispensable. Here, we will explore various potential actions of the intratumoral microbiome concerning the initiation and progression of tumors. We will examine its impact on responses to chemotherapy, radiotherapy, and immunotherapy. Additionally, we will discuss the current state of knowledge regarding the use of genetically modified bacteria as a promising treatment option for cancer.},
}

@article {pmid39801684,
year = {2025},
author = {Moradzad, M and Ghaderi, D and Abdi, M and Sheikh Esmaili, F and Rahmani, K and Vahabzadeh, Z},
title = {Gut microbiota dysbiosis contributes to choline unavailability and NAFLD development.},
journal = {Journal of diabetes and metabolic disorders},
volume = {24},
number = {1},
pages = {37},
pmid = {39801684},
issn = {2251-6581},
abstract = {OBJECTIVES: Non-alcoholic fatty Liver Disease (NAFLD) poses a growing global health concern, yet its complex aetiology remains incompletely understood. Emerging evidence implicates the gut microbiome and choline metabolism in NAFLD pathogenesis. This study aims to elucidate the association of choline-consuming bacteria in gut microbiome with choline level.

METHODS: A population comprising 85 NAFLD patients and 30 healthy controls was selected. DNA extraction from stool samples was conducted using the FavorPrep™ Stool DNA Isolation Mini Kit, followed by polymerase chain reaction (PCR) detection of choline-consuming bacterial strains and quantitative PCR (qPCR) for Cut C gene expression. Choline content measurement was performed using fluorescence high-performance liquid chromatography (FL-HPLC).

RESULTS: Our findings revealed a significant reduction in choline levels among NAFLD patients compared to healthy controls. ROC curve analysis demonstrated choline levels and Cut C expression as a promising diagnostic tool for NAFLD, with high sensitivity and specificity. The microbial analysis identified specific choline-consuming bacteria enriched in NAFLD patients, notably Anarococcus Hydrogenalis and Clostridium asparagiforme. This was consistent with higher Cut C gene expression in patients compared to healthy individuals, which is responsible for encoding an enzyme to consume choline by these bacteria.

CONCLUSION: The current study gives a possible association between gut microbiota and the development of NAFLD, possibly due to an alteration in choline bioavailability. Further research is required to determine whether gut bacteria alter in the context of NAFLD or a change in their composition might lead to NAFLD progression, possibly via alternation in choline bioavailability.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s40200-024-01511-6.},
}

@article {pmid39801587,
year = {2025},
author = {Huang, X and Kang, J and Zhang, Y and Chen, X and Han, B},
title = {Initial abiotic factors as key drivers in core microbe assembly: Regulatory effects on flavor profiles in light-flavor Baijiu.},
journal = {Food chemistry: X},
volume = {25},
number = {},
pages = {101982},
pmid = {39801587},
issn = {2590-1575},
abstract = {Instability in initial abiotic factors of open solid-state fermentation systems can significantly alter Baijiu's flavor profile, but the mechanisms governing microbial interactions and flavor formation remain unclear. This study comprehensively monitored changes in abiotic factors, microbial communities, and flavor profiles across two distinct fermentation processes in a Baijiu distillery, which differed significantly in their management of initial abiotic factors. Our results revealed significant differences in abiotic factors between the two groups, including moisture, ethanol, acidity, glucose, and organic acid levels. The assembly of microbial communities in fermented grains was primarily driven by deterministic processes. The moisture content in the fermented grains positively affected the growth and metabolism of core microbiota. The rapid proliferation and metabolism of core microbes led to a rapid increase in the acidity of the fermented grains, alongside a significant accumulation of ethyl lactate. This study provides technical support and theoretical guidance for Baijiu production.},
}

@article {pmid39801488,
year = {2025},
author = {Santamaria, MP and Mathias-Santamaria, IF and Ferreira Bonafé, AC and Gonzalez, OA and Kirakodu, S and Monteiro, MF and Casarin, RCV and Shaddox, LM and Miguel, MMV},
title = {Microbiome and Inflammatory Biomarkers Associated With Palatal Wound Healing.},
journal = {Journal of periodontal research},
volume = {},
number = {},
pages = {},
doi = {10.1111/jre.13373},
pmid = {39801488},
issn = {1600-0765},
support = {//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; //Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; //Fundação de Amparo a Pesquisa do Estado de São Paulo/ ; //National Center for Advancing Translational Sciences, National Institutes of Health/ ; },
abstract = {AIM: The clinical outcomes of a variety of surgical procedures highly depend on tissue repair and show high variability among patients. There is a gap in the literature on how the host inflammatory response, the microbiome, and the interplay between them can influence oral mucosa healing. In this pilot study, we aimed to evaluate the microbiome and biomarkers profiles in patients who had desired versus undesired wound healing in the palatal mucosa.

METHODS: Seventeen patients underwent a free gingival graft (FGG) for socket preservation. Palatal wound closure (WC) and epithelization (EPT) were assessed clinically. Biofilm from the palatal wound was collected before the surgical procedure and 3, 7, 14, and 30 days postoperatively. The inflammatory exudate was sampled on Days 3 and 7. At 14 days posttreatment, patients were classified into two groups based on EPT rates: (1) undesired healing (UH) and (2) desired healing (DH).

RESULTS: No difference was observed in alfa diversity over time or between groups. In beta diversity, both UH and DH showed microbiome changes on Days 3-7 and 7, respectively, compared with the baseline (p = 0.01), returning to its initial condition 30 days later. There was a trend toward a different microbiome profile between groups on Day 7 (p = 0.08). Bacterium composition in DH showed a balance between healthy species and oral pathogens over time, whereas UH composition was characterized by microorganisms correlated with epithelium invasion/cytotoxicity; virulence factor upregulation; and oral diseases, such as periodontitis and aphthous stomatitis, until Day 30. UH showed an increase in IL-6, MCP-1, and MIP-1α over time, and DH showed a decrease in TIMP-1, IL-1β, and MIP-1α. On Days 3 and 7, MIP-1α and MMP-2 showed greater concentrations of DH in the intergroup assessment, and MCP-1 increased on Day 7 in UH.

CONCLUSION: Specific microbiome/inflammatory profiles are associated with DH and UH.

TRIAL REGISTRATION: NCT05171400.},
}

@article {pmid39801456,
year = {2025},
author = {Torozan, DA and Laczny, CC and Roomp, K and Wilmes, P and Fleckenstein, J and Schneider, JG},
title = {Metagenomic Profiling of Oral Microbiome Dynamics During Chemoradiotherapy in Head and Neck Squamous Cell Carcinoma Patients.},
journal = {Cancer medicine},
volume = {14},
number = {1},
pages = {e70589},
doi = {10.1002/cam4.70589},
pmid = {39801456},
issn = {2045-7634},
support = {863664//H2020 European Research Council/ ; },
mesh = {Humans ; Male ; *Chemoradiotherapy/adverse effects ; Female ; Middle Aged ; *Squamous Cell Carcinoma of Head and Neck/microbiology/therapy ; *Microbiota/radiation effects ; Aged ; *Metagenomics/methods ; *Head and Neck Neoplasms/microbiology/therapy ; *Saliva/microbiology ; Prospective Studies ; Mouth/microbiology ; Adult ; Case-Control Studies ; Metagenome ; },
abstract = {BACKGROUND: We explored the interaction between the oral microbiome and the development of radiation-induced mucositis in patients with head and neck squamous cell cancer (HNSCC) undergoing chemoradiotherapy (CRT). We prospectively studied the oral microbiome and compared it to healthy controls. Additionally, we compared patients with low-grade (LGM) vs. high-grade mucositis (HGM).

METHODS: Ten HNSCC patients scheduled for CRT were included. Saliva samples were characterized prior to, during, and nine months after CRT using metagenomic sequencing. We similarly characterized samples from seven healthy controls. We assessed alpha and beta diversity and examined abundances at different taxonomic levels between (sub)groups.

RESULTS: Patients exhibited significantly reduced alpha diversity compared to controls at all times (p ⟨ 0.05). Differential abundance of taxa between patients and controls was observed at baseline. In patients, the relative abundance of Staphylococcus aureus and Escherichia coli increased significantly during CRT. Capnocytophaga spp. was associated with the definitive CRT patients' subgroup. At baseline, two fungal families (Melampsoraceae and Herpotrichiellaceaea) were more abundant in patients who later developed HGM. No differentially abundant taxa were found between LGM vs. HGM during irradiation.

CONCLUSION: Our findings support the hypothesis that CRT, as well as HNSCC itself, influences the composition of the oral microbiome. Microbial markers found in patients who later developed HGM should be evaluated using independent cohorts to qualify their specific biomarker potential.},
}

Humans
Male
*Chemoradiotherapy/adverse effects
Female
Middle Aged
*Squamous Cell Carcinoma of Head and Neck/microbiology/therapy
*Microbiota/radiation effects
Aged
*Metagenomics/methods
*Head and Neck Neoplasms/microbiology/therapy
*Saliva/microbiology
Prospective Studies
Mouth/microbiology
Adult
Case-Control Studies
Metagenome

@article {pmid39801446,
year = {2025},
author = {Dong, A and Proctor, G and Zaric, S},
title = {Diagnostic Accuracy of Microbiome-Derived Biomarkers in Periodontitis: Systematic Review and Meta-Analysis.},
journal = {Journal of periodontal research},
volume = {},
number = {},
pages = {},
doi = {10.1111/jre.13377},
pmid = {39801446},
issn = {1600-0765},
support = {/AMS_/Academy of Medical Sciences/United Kingdom ; //China Scholarship Council/ ; },
abstract = {AIM: To evaluate the diagnostic accuracy of microbiome-derived biomarkers for periodontitis in oral fluids (saliva and subgingival samples).

METHODS: This systematic review followed PRISMA guidelines. Electronic searches were performed across multiple databases from December 2022 to November 2024. Subgroup analyses, divided into saliva and subgingival samples, were performed using the Random Effects Model (REM), while individual biomarker sensitivity and specificity were evaluated through the Bivariate Random-Effects Model (BREM).

RESULTS: Ten studies were included, stratified by sample type. In the saliva group, Porphyromonas gingivalis, Tannerella forsythia and Prevotella intermedia demonstrated the highest diagnostic accuracy, with sensitivities reaching 89.2%, 89.2% and 86.5%, and specificities of 94.6%, 86.5% and 83.8%, respectively, achieving AUC values above 0.80. Porphyromonas gingivalis was further analysed using BREM, with the Summary Receiver Operating Characteristic (SROC) curve indicating a combined sensitivity and specificity of 84.2% and 85.4%, with an AUC of 0.864. In the subgingival group, biomarkers such as endotoxin activity and combined bacterial biomarkers (5 bacterial species) displayed the highest diagnostic performance, with sensitivities of 90.6% and 85.1% and specificities of 87.9% and 100%, respectively, and AUC values of 0.93 and 0.88.

CONCLUSION: Microbiome-derived biomarkers show good clinical utility for improving diagnoses of periodontitis, offering high specificity and sensitivity. Future research should focus on standardising methodologies, increasing sample sizes, and including diverse populations to validate these findings, thereby improving diagnostic precision and facilitating the screening methods for the onset of periodontitis and dysbiotic activity.},
}

@article {pmid39801363,
year = {2025},
author = {Chevalier, C and Tournier, BB and Marizzoni, M and Park, R and Paquis, A and Ceyzériat, K and Badina, AM and Lathuiliere, A and Saleri, S and Cillis, F and Cattaneo, A and Millet, P and Frisoni, GB},
title = {Fecal Microbiota Transplantation (FMT) From a Human at Low Risk for Alzheimer's Disease Improves Short-Term Recognition Memory and Increases Neuroinflammation in a 3xTg AD Mouse Model.},
journal = {Genes, brain, and behavior},
volume = {24},
number = {1},
pages = {e70012},
doi = {10.1111/gbb.70012},
pmid = {39801363},
issn = {1601-183X},
support = {1216//Velux Stiftung/ ; },
mesh = {Animals ; *Fecal Microbiota Transplantation ; Mice ; *Alzheimer Disease/therapy/microbiology ; Humans ; Female ; *Gastrointestinal Microbiome ; Memory, Short-Term/physiology ; Neuroinflammatory Diseases/therapy/metabolism ; Disease Models, Animal ; Hippocampus/metabolism ; Aged ; },
abstract = {Human microbiota-associated murine models, using fecal microbiota transplantation (FMT) from human donors, help explore the microbiome's role in diseases like Alzheimer's disease (AD). This study examines how gut bacteria from donors with protective factors against AD influence behavior and brain pathology in an AD mouse model. Female 3xTgAD mice received weekly FMT for 2 months from (i) an 80-year-old AD patient (AD-FMT), (ii) a cognitively healthy 73-year-old with the protective APOEe2 allele (APOEe2-FMT), (iii) a 22-year-old healthy donor (Young-FMT), and (iv) untreated mice (Mice-FMT). Behavioral assessments included novel object recognition (NOR), Y-maze, open-field, and elevated plus maze tests; brain pathology (amyloid and tau), neuroinflammation (in situ autoradiography of the 18 kDa translocator protein in the hippocampus); and gut microbiota were analyzed. APOEe2-FMT improved short-term memory in the NOR test compared to AD-FMT, without significant changes in other behavioral tests. This was associated with increased neuroinflammation in the hippocampus, but no effect was detected on brain amyloidosis and tauopathy. Specific genera, such as Parabacteroides and Prevotellaceae_UGC001, were enriched in the APOEe2-FMT group and associated with neuroinflammation, while genera like Desulfovibrio were reduced and linked to decreased neuroinflammation. Gut microbiota from a donor with a protective factor against AD improved short-term memory and induced neuroinflammation in regions strategic to AD. The association of several genera with neuroinflammation in the APOEe2-FMT group suggests a collegial effect of the transplanted microbiome rather than a single-microbe driver effect. These data support an association between gut bacteria, glial cell activation, and cognitive function in AD.},
}

Animals
*Fecal Microbiota Transplantation
Mice
*Alzheimer Disease/therapy/microbiology
Humans
Female
*Gastrointestinal Microbiome
Memory, Short-Term/physiology
Neuroinflammatory Diseases/therapy/metabolism
Disease Models, Animal
Hippocampus/metabolism
Aged

@article {pmid39801018,
year = {2025},
author = {Zhang, T and Shi, J and Li, X and Liu, H and Wei, Y and Li, H},
title = {Pharyngeal Microbiome in Atopic Dermatitis: A 16S rRNA Sequencing Study.},
journal = {Experimental dermatology},
volume = {34},
number = {1},
pages = {e70031},
doi = {10.1111/exd.70031},
pmid = {39801018},
issn = {1600-0625},
support = {//Jiangsu Province Hospital of Chinese Medicine Foundation/ ; //National Natural Science Foundation of China/ ; //Natural Science Foundation of Jiangsu Province/ ; },
mesh = {Humans ; *Dermatitis, Atopic/microbiology ; *RNA, Ribosomal, 16S/genetics ; Male ; Female ; Adult ; *Microbiota ; *Pharynx/microbiology ; Young Adult ; Case-Control Studies ; Bacteria/genetics/classification ; Middle Aged ; Adolescent ; Phylogeny ; },
abstract = {While recent studies have demonstrated the involvement of the skin and gut microbiome in the pathogenesis of atopic dermatitis (AD), the influence of pharyngeal microbiota on AD remains unclear. This study aims to explore disparities in the composition of pharyngeal flora among AD patients and their potential role in the pathogenesis of AD. Between March and May 2023, 30 patients with AD at the outpatient department of Jiangsu Provincial Traditional Chinese Medicine Hospital were recruited, along with 20 healthy subjects, underwent 16S rRNA sequencing on pharyngeal swabs. Pharyngeal taxonomic biomarkers of AD were identified using linear discriminant analysis effect size (LEfSe), and phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt2) was employed to predict potential functional metabolic pathways of bacteria with differential abundance. Significant variations were observed in the microbiota composition between the two study groups. The Pharynx of AD patients exhibited a notably higher relative abundance of Granulicatella, Pseudomonas, and Acinetobacter compared to healthy volunteers. Conversely, the relative abundance of Prevotella, Porphyromonas, Campylobacter, Lactobacillaceae, Treponema, Megasphaera, Selenomonas, and Oribacterium was lower in AD patients. According to the metabolic functional enrichment annotations predicted by PICRUSt2, bacteria with differential abundance may be involved in the pathogenesis of AD through two metabolic pathways, namely chondroitin sulfate degradation and chitin derivatives degradation. AD patients displayed distinctive microbiota profiles compared to healthy controls. These findings imply a pivotal role of pharyngeal microbiota in the pathogenesis of AD, offering novel perspectives for AD treatment strategies.},
}

Humans
*Dermatitis, Atopic/microbiology
*RNA, Ribosomal, 16S/genetics
Male
Female
Adult
*Microbiota
*Pharynx/microbiology
Young Adult
Case-Control Studies
Bacteria/genetics/classification
Middle Aged
Adolescent
Phylogeny

@article {pmid39800869,
year = {2025},
author = {Zhang, H and Chen, A and Li, S and Chen, K and You, X and Bian, Y and Li, C and Liu, S and Huang, J and Zhang, S},
title = {Spatio-Temporal Change of Skin and Oral Microbiota: A Longitudinal Study of Microbial Diversity and Stability.},
journal = {Electrophoresis},
volume = {},
number = {},
pages = {},
doi = {10.1002/elps.202400160},
pmid = {39800869},
issn = {1522-2683},
support = {82371896//National Natural Science Foundation of China/ ; 82260335//National Natural Science Foundation of China/ ; },
abstract = {The human skin and oral cavity harbor complex microbial communities, which exist in dynamic equilibrium with the host's physiological state and the external environment. This study investigates the microbial atlas of human skin and oral cavities using samples collected over a 10-month period, aiming to assess how both internal and external factors influence the human microbiome. We examined bacterial community diversity and stability across various body sites, including palm and nasal skin, saliva, and oral epithelial cells, during environmental changes and a COVID-19 pandemic. The skin microbiome was confirmed to display spatial and temporal stability compared to the oral microbiome, particularly the oral epithelium, which was susceptible to changes in the host's physiological state and immune response. Moreover, significant differences in the microbial community structure among the 4 sample types were observed, and 87 distinct bacteria biomarkers were identified. The random forest prediction model achieved an overall prediction accuracy of 95.24% across the four types of samples studied. Additionally, nasal skin samples showed significant promise for individual identification through profiling the skin microbiota. These findings highlight the potential of skin and oral microbiota as forensic markers for inferring body sites and identifying individuals. In summary, despite facing limitations such as a small cohort size and the need for broader validation, this research provides an overall perspective and initial insights for refining experimental designs and conducting in-depth research in various microbial research fields.},
}

@article {pmid39800598,
year = {2025},
author = {Mariscal de Gante, L and Salanova, L and Valdivia Mazeyra, M and Serrano Pardo, R and Quiroga, B},
title = {Secondary hyperoxaluria: Cause and consequence of chronic kidney disease.},
journal = {Nefrologia},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.nefroe.2024.12.001},
pmid = {39800598},
issn = {2013-2514},
abstract = {Secondary hyperoxaluria is a metabolic disorder characterized by an increase in urinary oxalate excretion. The etiology may arise from an increase in the intake of oxalate or its precursors, decreased elimination at the digestive level, or heightened renal excretion. Recently, the role of the SLC26A6 transporter in the etiopathogenesis of this disease has been identified. This transporter is active at both the intestinal and renal levels, and its mechanism of action is disrupted during systemic inflammation and metabolic syndrome, which could explain the rising incidence of secondary hyperoxaluria in recent decades. Treatment includes hygienic dietary measures, and medications aimed at reducing intestinal absorption by increasing fecal excretion. Different immunomodulatory drugs, microbiome modifiers and SGLT2 inhibitors could constitute new therapeutic targets. Currently, specific treatments for secondary hyperoxaluria are lacking, making early diagnosis and preventive measures against kidney failure the main therapeutic strategies.},
}

@article {pmid39800212,
year = {2025},
author = {Li, P and Zhang, H and Chen, L and Gao, X and Hu, Y and Xu, Q and Liu, W and Chen, W and Chen, H and Yuan, S and Wang, M and Liu, S and Dai, M},
title = {Oral and Fecal Microbiota as Accurate Non-invasive Tools for Detection of Pancreatic Cancer in the Chinese Population.},
journal = {Cancer letters},
volume = {},
number = {},
pages = {217456},
doi = {10.1016/j.canlet.2025.217456},
pmid = {39800212},
issn = {1872-7980},
abstract = {Pancreatic cancer (PCA), a leading cause of cancer-related deaths, has limited non-invasive diagnostic methods. We aimed to identify oral and fecal microbiome biomarkers and construct diagnostic classifiers. Oral and fecal samples from 97 PCA patients and 90 healthy controls underwent 16S rRNA sequencing. Samples were randomly divided into training and validation cohorts in a 7:3 ratio. Random forest models were constructed using training cohort and validated internally and externally in Chinese, Japanese, and Spanish populations. Results revealed significant dysbiosis of the oral and fecal microbiota of PCA patients. Most of the differential taxa shared between oral and fecal samples showed similar changes. Relative abundances of Streptococcus in oral samples, and of Bifidobacterium, Klebsiella and Akkermansia in fecal samples, were enriched in PCA. The fecal Firmicutes to Bacteroidota ratio was higher in PCA patient samples. Oral and fecal microbiome classifiers based on the top 20 contributing genera were constructed, and internal validation showed that the area under the curve (AUC) values were 0.963 and 0.890, respectively. The fecal microbiome classifier performed well in the external Chinese population, with an AUC of 0.878, but poorly in the Japanese and Spanish populations. Furthermore, fecal microbiomes could predict metastasis status in PCA patients, with an AUC of 0.804. In conclusion, oral and fecal microbiota were dysbiotic in PCA patients. Fecal microbiome classifier provides a feasible, non-invasive, and cost-effective tool with high precision for PCA screening in China; oral microbiome classifier requires further validation in external populations sampled with the same simple and convenient methods.},
}

@article {pmid39799673,
year = {2025},
author = {Li, K and Rahman, SU and Rehman, A and Li, H and Hui, N and Khalid, M},
title = {Shaping rhizocompartments and phyllosphere microbiomes and antibiotic resistance genes: The influence of different fertilizer regimes and biochar application.},
journal = {Journal of hazardous materials},
volume = {487},
number = {},
pages = {137148},
doi = {10.1016/j.jhazmat.2025.137148},
pmid = {39799673},
issn = {1873-3336},
abstract = {Understanding the impact of different soil amendments on microbial communities and antibiotic resistance genes (ARGs) dissemination is crucial for optimizing agricultural practices and mitigating environmental risks. This study investigated the effects of different fertilizer regimes and biochar on plant-associated bacterial communities and ARGs dissemination. The biochar's structural and chemical characteristics were characterized using scanning electron microscopy (SEM) and Fourier-transform infrared (FTIR) spectroscopy, revealing a porous architecture with diverse functional groups. The presence of ARGs varied significantly across groups, with manure-treated samples exhibiting the greatest diversity and abundance, raising concerns about ARGs dissemination. Soil enzyme activities responded differently to treatments; manure significantly enhanced catalase, acid phosphatase, and urease activities, whereas saccharase was most responsive to chemical fertilizer. These differences are possibly responsible for the distinct microbiome structure associated with the plant's root system. The analysis of bacterial diversity and richness across rhizocompartments and the phyllosphere highlighted that manure-treated rhizospheres and phyllospheres displayed the highest species richness and diversity. Notably, Proteobacteria dominated across most treatments, with distinct shifts in bacterial phyla and genera influenced by manure and biochar applications. The LEfSe analysis identified key indicator genera specific to each group, indicating that both fertilizer type and biochar application significantly shape microbial community composition. Co-occurrence network analysis further demonstrated that manure and biochar treatments created unique microbial networks in the rhizosphere, rhizoplane, phyllosphere, and endosphere, highlighting the role of these amendments in modulating microbial interactions in plant-associated environments. These findings suggest that manure, while enhancing microbial diversity and soil enzyme activities, also increases ARGs, whereas biochar may not contribute to the spread of ARGs and fosters distinct microbial communities, offering valuable insights for sustainable agricultural practices.},
}

@article {pmid39799645,
year = {2025},
author = {Tromas, N and Goitom, E and Chin, T and Dinh, QT and Dorner, SM and Khawasik, OS and Cristescu, ME and Burnet, JB},
title = {Impact of grazing by multiple Daphnia species on wastewater bacterial communities.},
journal = {The Science of the total environment},
volume = {962},
number = {},
pages = {178364},
doi = {10.1016/j.scitotenv.2024.178364},
pmid = {39799645},
issn = {1879-1026},
abstract = {Understanding the dynamics of fecal bacterial communities is crucial for managing public health risks and protecting drinking water resources. While extensive research exists on how abiotic factors influence the survival of fecal microbial communities in water, less attention has been paid to the impact of predation by higher organisms, such as the widely distributed grazer Daphnia. Nevertheless, Daphnia plays a significant role in regulating bacterial communities in natural aquatic ecosystems, and recent studies highlighted its potential as a biofilter in alternative tertiary wastewater treatment systems. In this study, we investigated the influence of three different Daphnia species on a wastewater bacterial community, including fecal indicator bacterium E. coli. Using a microcosm setup to simulate the discharge of untreated sewage into surface water, we conducted in-depth analysis of bacterial community dynamics through sequencing the 16S rRNA gene. Our results revealed significant changes in microbial diversity and composition following exposure to Daphnia grazing, with variations observed among the three Daphnia species. D. pulicaria exerted the most pronounced impact on microbial diversity, followed by D. middendorffiana and D. mendotae. A total of 90 taxa exhibited significantly reduced relative abundance in the presence of Daphnia, with Firmicutes phylum being the most affected. At genus level, bacteria typically associated with wastewater (e.g., Zoogloea and Arcobacter) and gut microbiome constituents (e.g., Prevotella and Akkermansia) were notably affected by Daphnia exposure. The influence of Daphnia on bacterial community composition was most pronounced for D. pulicaria, while D. middendorffiana and D. mendotae primarily impacted community structure. Furthermore, we demonstrated that the microbial response to Daphnia exposure is phylogenetically conserved, potentially reflecting a grazing resistance or grazer feeding trait. Our findings shed new light on the role of Daphnia in controlling bacterial communities in polluted water bodies and underscore its potential as biofilter in wastewater treatment and reuse contexts.},
}

@article {pmid39800778,
year = {2025},
author = {Nyamota, R and Middlebrook, EA and Abkallo, HM and Akoko, J and Gakuya, F and Wambua, L and Ronoh, B and Lekolool, I and Mwatondo, A and Muturi, M and Bett, B and Fair, JM and Bartlow, AW},
title = {The Bacterial and pathogenic landscape of African buffalo (Syncerus caffer) whole blood and serum from Kenya.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {6},
pmid = {39800778},
issn = {2524-4671},
support = {HDTRA19-3-1960//USA, Defense Threat Reduction Agency/ ; },
abstract = {BACKGROUND: African buffalo (Syncerus caffer) is a significant reservoir host for many zoonotic and parasitic infections in Africa. These include a range of viruses and pathogenic bacteria, such as tick-borne rickettsial organisms. Despite the considerations of mammalian blood as a sterile environment, blood microbiome sequencing could become crucial for agnostic biosurveillance. This study investigated the blood microbiome of clinically healthy wild buffaloes in Kenya to determine its applicability in agnostic testing for bacteria in apparently healthy wild animals.

METHODS: Whole blood and serum samples were collected from 46 wild African buffalos from Meru National Park (30), Buffalo Springs (6) and Shaba (10) National Reserves in upper eastern Kenya. Total deoxyribonucleic acid (DNA) was extracted from these samples and subjected to amplicon-based sequencing targeting the 16 S rRNA gene. The bacteria operational taxonomic units (OTU) were identified to species levels by mapping the generated V12 and V45 regions of 16 S rRNA gene to the SILVA database. These OTU tables were used to infer the microbial abundance in each sample type and at the individual animal level. The sequences for the corresponding OTUs were also used to generate phylogenetic trees and thus infer evolution for the OTUs of interest.

RESULTS: Here, we demonstrate that buffaloes harbor many bacteria in their blood. We also report a diversity of 16 S rRNA gene sequences for Anaplasma and Mycoplasma from individual animals. By sequencing both whole blood and serum in triplicate for each animal, we provide evidence of the differences in detecting bacteria in both sample types.

CONCLUSIONS: Diverse bacteria, including some potential pathogens, can be found in the blood of clinically healthy wild African buffalo. Agnostic surveillance for such pathogens can be achieved through blood microbiome sequencing. However, considerations for the question being asked for the blood microbiome in wildlife will impact the choice for using whole blood or serum for sequencing.},
}

@article {pmid39800756,
year = {2025},
author = {Russell, D and Rajabal, V and Alfonzetti, M and van der Merwe, MM and Gallagher, RV and Tetu, SG},
title = {Seed banking impacts native Acacia ulicifolia seed microbiome composition and function.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {4},
pmid = {39800756},
issn = {2524-6372},
support = {CE200100029//Australian Research Council/ ; LP200200688//Australian Research Council/ ; CE200100029//Australian Research Council/ ; },
abstract = {BACKGROUND: Seed banks are a vital resource for preserving plant species diversity globally. However, seedling establishment and survival rates from banked seeds can be poor. Despite a growing appreciation for the role of seed-associated microbiota in supporting seed quality and plant health, our understanding of the effects of conventional seed banking processes on seed microbiomes remains limited. In this study we investigated the composition and functional potential of seed-associated bacterial epiphytes associated with stored and freshly collected seeds of a native plant, Acacia ulicifolia, using both 16S rRNA gene sequencing and culture-based approaches.

RESULTS: Seeds obtained from seed banking facilities were found to host significantly less diverse bacterial populations, with substantial reductions in both low-abundance taxa and in community members commonly identified in freshly collected A. ulicifolia seeds. Bacteria with key plant growth promoting traits including IAA production, ACC deaminase activity, phosphate solubilisation, siderophore activity, and nitrogen fixation were identified in seed epiphytic communities, but these beneficial traits were less prevalent in stored seed compared to fresh seeds.

CONCLUSION: Overall, these results suggest that epiphytic seed microbiomes may undergo significant changes during the storage process, selecting for bacteria tolerant to storage conditions, and potentially reducing the population of plant-growth promoting bacteria on seeds.},
}

@article {pmid39800090,
year = {2025},
author = {Grosserichter-Wagener, C and Looman, KIM and Beth, SA and Radjabzadeh, D and Gill, PA and Smit, KN and Duijts, L and Kiefte-de Jong, JC and Kraaij, R and Moll, HA and van Zelm, MC},
title = {A distinct immunophenotype in children carrying the Blautia enterotype: The generation R study.},
journal = {Clinical immunology (Orlando, Fla.)},
volume = {},
number = {},
pages = {110426},
doi = {10.1016/j.clim.2025.110426},
pmid = {39800090},
issn = {1521-7035},
abstract = {OBJECTIVE: Studies in mouse models and human adults have shown that the intestinal microbiota composition can affect peripheral immune cells. We here examined whether the gut microbiota compositions affect B and T-cell subsets in children.

METHODS: The intestinal microbiota was characterized from stool samples of 344 10-year-old children from the Generation R Study by performing 16S rRNA sequencing. Bray-Curtis dissimilarity was used to cluster distinct microbiome compositions (enterotypes). B-cell and T-cell phenotypes were defined by 11-color-flow cytometry. Linear regression models with adjustment for lifestyle and child characteristics were performed to determine associations between enterotypes and immune cell numbers.

RESULTS: Three enterotypes with distinct microbiota composition were found, characterized by high abundance of Prevotella, Bacteroides and Blautia. Children with the Blautia enterotype had decreased numbers of plasmablasts, CD4[+] central memory (Tcm) T cells and follicular T-helper cells (Tfh), while Th22 cells and CD4[+] effector memory (Tem) T cells, CD27[-]IgA[+] memory B cells and CD27[-]IgE[+] memory B cells, were increased in these children. In addition, in children with the Blautia enterotype CD4[+] Tcm cell numbers expressing the β7 integrin, which can pair with α4 to mediate intestinal were also lower, while CD4[+]β7[+] Tem cell numbers were higher than in the other enterotypes.

CONCLUSION: The Blautia enterotype showed features beneficial for human health. Enterotypes were associated with differences in memory B- and T-cell compartments. This study is unique in the detailed analysis of the B and T-cell compartment and the intestinal microbiome in a large generic pediatric cohort, enabling correction for child and maternal covariates. These outcomes could guide further studies about the impact of intestinal microbiome intervention, for instance through diet and microbiota metabolites such as short chain fatty acid production.},
}

@article {pmid39799656,
year = {2025},
author = {Chen, X and Zhou, Y and Mai, Z and Cheng, H and Wang, X},
title = {Mangroves increased the mercury methylation potential in the sediment by producing organic matters and altering microbial methylators community.},
journal = {The Science of the total environment},
volume = {962},
number = {},
pages = {178457},
doi = {10.1016/j.scitotenv.2025.178457},
pmid = {39799656},
issn = {1879-1026},
abstract = {Mangrove ecosystem has attracted global attention as a hotspot for mercury (Hg) methylation. Although numerous biotic and abiotic parameters have been reported to influence methylmercury (MeHg) production in sediments, the key factors determining the elevated MeHg levels in mangrove wetlands have not been well addressed. In this study, Hg levels in the sediments from different habitats (mudflats, mangrove fringe, and mangrove interior) in the Futian mangrove wetland were investigated, aiming to characterize the predominant factors affecting the MeHg production and distinguish the key microbial taxa responsible for Hg methylation. MeHg concentrations in the sediments from the mangrove interior (1.03 ± 0.34 ng g[-1] dw) were significantly higher than those in mudflats (0.26 ± 0.08 ng g[-1] dw) and mangrove fringe (0.45 ± 0.10 ng g[-1] dw). Mangrove vegetation also promoted the accumulation of organic matters in sediments, which stimulated the growth of methylators, ultimately leading to an elevated MeHg level in the sediment. The data from 16S sequencing and random forest analysis further indicated that the increased abundances of Desulfococcus and Desulfosarcina, which belong to complete-oxidizing microbes with acetyl-CoA pathway and are favored by mangrove vegetation, were the primary contributors to MeHg production. Besides, syntrophic partners of methylators (e.g. Syntrophus) also play a considerable role in MeHg production. The present findings provide a deep understanding of Hg-methylation in mangrove wetlands, and offers valuable insights into of the interactions between mangrove plants and soil microbiome in the presence of Hg contamination.},
}

@article {pmid39799515,
year = {2025},
author = {Jiang, Y and Liao, D and Zhu, Q and Lu, YY},
title = {PhyloMix: Enhancing microbiome-trait association prediction through phylogeny-mixing augmentation.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btaf014},
pmid = {39799515},
issn = {1367-4811},
abstract = {MOTIVATION: Understanding the associations between traits and microbial composition is a fundamental objective in microbiome research. Recently, researchers have turned to machine learning (ML) models to achieve this goal with promising results. However, the effectiveness of advanced ML models is often limited by the unique characteristics of microbiome data, which are typically high-dimensional, compositional, and imbalanced. These characteristics can hinder the models' ability to fully explore the relationships among taxa in predictive analyses. To address this challenge, data augmentation has become crucial. It involves generating synthetic samples with artificial labels based on existing data and incorporating these samples into the training set to improve ML model performance.

RESULTS: Here we propose PhyloMix, a novel data augmentation method specifically designed for microbiome data to enhance predictive analyses. PhyloMix leverages the phylogenetic relationships among microbiome taxa as an informative prior to guide the generation of synthetic microbial samples. Leveraging phylogeny, PhyloMix creates new samples by removing a subtree from one sample and combining it with the corresponding subtree from another sample. Notably, PhyloMix is designed to address the compositional nature of microbiome data, effectively handling both raw counts and relative abundances. This approach introduces sufficient diversity into the augmented samples, leading to improved predictive performance. We empirically evaluated PhyloMix on six real microbiome datasets across five commonly used ML models. PhyloMix significantly outperforms distinct baseline methods including sample-mixing-based data augmentation techniques like vanilla mixup and compositional cutmix, as well as the phylogeny-based method TADA. We also demonstrated the wide applicability of PhyloMix in both supervised learning and contrastive representation learning.

AVAILABILITY: The Apache licensed source code is available at (https://github.com/batmen-lab/phylomix).

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

@article {pmid39799378,
year = {2025},
author = {Sakhabutdinov, IT and Chastukhina, IB and Ryazanov, EA and Ponomarev, SN and Gogoleva, OA and Balkin, AS and Korzun, VN and Ponomareva, ML and Gorshkov, VY},
title = {Variability of microbiomes in winter rye, wheat, and triticale affected by snow mold: predicting promising microorganisms for the disease control.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {3},
pmid = {39799378},
issn = {2524-6372},
support = {23-16-00086//Russian Science Foundation/ ; 124050300040-5//Government assignment for the FRC Kazan Scientific Center of RAS/ ; },
abstract = {BACKGROUND: Snow mold caused by different psychrophilic phytopathogenic fungi is a devastating disease of winter cereals. The variability of the snow mold pathocomplex (the quantitative composition of snow mold fungi) has not been evaluated across different crops or different agrocenoses, and no microbial taxa have been predicted at the whole-microbiome level as potential effective snow mold control agents. Our study aimed to assess the variability of the snow mold pathocomplex in different winter cereal crops (rye, wheat, and triticale) in different agrocenoses following the peak disease progression and to arrange a hierarchical list of microbial taxa predicted to be the main candidates to prevent or, conversely, stimulate the development of snow mold pathogens.

RESULTS: The variability of microbiomes between different crops within a particular agrocenosis was largely determined by fungal communities, whereas the variability of microbiomes of a particular crop in different agrocenoses was largely determined by bacterial communities. The snow mold pathocomplex was the most "constant" in rye, with the lowest level of between-replicate variability and between-agrocenoses variability and (similar to the triticale snow mold pathocomplex) strong dominance of Microdochium over other snow mold fungi. The wheat snow mold pathocomplex was represented by different snow mold fungi, including poorly investigated Phoma sclerotioides. To predict snow mold-control microorganisms, a conveyor of statistical methods was formed and applied; this conveyor enables considering not only the correlation between the abundance of target taxa and a phytopathogen but also the stability and fitness of taxa within plant-associated communities and the reproducibility of the predicted effect of taxa under different conditions. This conveyor can be widely used to search for biological agents against various plant infectious diseases.

CONCLUSIONS: The top indicator microbial taxa for winter wheat and rye following the winter period were Ph. sclerotioides and Microdochium, respectively, both of which are causal agents of snow mold disease. Bacteria from the Cellulomonas, Lechevalieria, and Pseudoxanthomonas genera and fungi from the Cladosporium, Entimomentora, Pseudogymnoascus, and Cistella genera are prime candidates for testing their plant-protective properties against Microdochium-induced snow mold disease and for further use in agricultural practice.},
}

@article {pmid39799366,
year = {2025},
author = {Węsierska, E and Micek, P and Adamski, MG and Gondek, K and Lis, M and Trela, M and Wojtysiak, D and Kowal, J and Wyrobisz-Papiewska, A and Kunstman, G and Mosiołek, S and Smoroń, K},
title = {Changes in the intestinal microbiota of broiler chicken induced by dietary supplementation of the diatomite-bentonite mixture.},
journal = {BMC veterinary research},
volume = {21},
number = {1},
pages = {13},
pmid = {39799366},
issn = {1746-6148},
support = {BZ/4240/WHiBZ/2022//Test ordered by an individual poultry producer/ ; BZ/4240/WHiBZ/2022//Test ordered by an individual poultry producer/ ; BZ/4240/WHiBZ/2022//Test ordered by an individual poultry producer/ ; BZ/4240/WHiBZ/2022//Test ordered by an individual poultry producer/ ; BZ/4240/WHiBZ/2022//Test ordered by an individual poultry producer/ ; BZ/4240/WHiBZ/2022//Test ordered by an individual poultry producer/ ; BZ/4240/WHiBZ/2022//Test ordered by an individual poultry producer/ ; BZ/4240/WHiBZ/2022//Test ordered by an individual poultry producer/ ; BZ/4240/WHiBZ/2022//Test ordered by an individual poultry producer/ ; BZ/4240/WHiBZ/2022//Test ordered by an individual poultry producer/ ; BZ/4240/WHiBZ/2022//Test ordered by an individual poultry producer/ ; BZ/4240/WHiBZ/2022//Test ordered by an individual poultry producer/ ; },
mesh = {Animals ; *Chickens/microbiology ; *Gastrointestinal Microbiome/drug effects ; *Bentonite/pharmacology/administration & dosage ; *Dietary Supplements ; *Animal Feed/analysis ; *Diet/veterinary ; Diatomaceous Earth/pharmacology ; Bacteria/classification/drug effects/genetics ; },
abstract = {BACKGROUND: Diatomite is a source of biologically available silicon but in feed industry its insecticide and anti-caking properties have been also widely recognized. The aim of the study was to evaluate the effect of dietary diatomite-bentonite mixture (DBM) supplementation on the quantitative and qualitative composition of the bacterial microbiome of the broiler chicken gut. The trial was carried out on 960 Ross 308 broiler chickens divided into 2 experimental groups throughout the entire rearing period lasting 6 weeks. The birds were fed complete granulated diets without (group C) or with DBM (group E) in an amount of 1% from the 11 day of life. Two nutritionally balanced diets were used, tailored to the age of the broilers: a grower diet (from day 11 to 34) and a finisher diet (from day 35 to 42 of life).

RESULTS: Diatomite used in a mixture with bentonite significantly altered the microbiome. Restricting the description to species that comprise a minimum of 1% of all analyzed sequences, 36 species in group E (with diatomite) and 30 species in group C (without diatomite) were selected. Several bacteria species were identified in intestinal contents of chickens for the first time. Thirteen species occurred only in group E: Agathobaculum butyriciproducens, Anaerobutyricum hallii, Anaerobutyricum soehngenii, Blautia producta ATCC 27,340 = DSM 2950, Gordonibacter pamelaeae 7-10-1-b, Helicobacter pullorum NCTC 12,824, Lactobacillus crispatus, L. helveticus DSM 20,075 = CGMCC 1.1877, Mucispirillum schaedleri, Phascolarctobacterium faecium, Phocaeicola coprocola DSM 17,136, P. massiliensis, and Ruthenibacterium lactatiformans.

CONCLUSIONS: The findings highlight the intricate and potentially consequential relationship between diet, specifically diatomite-bentonite mixture supplementation, and gut microbiota composition.},
}

Animals
*Chickens/microbiology
*Gastrointestinal Microbiome/drug effects
*Bentonite/pharmacology/administration & dosage
*Dietary Supplements
*Animal Feed/analysis
*Diet/veterinary
Diatomaceous Earth/pharmacology
Bacteria/classification/drug effects/genetics

@article {pmid39799316,
year = {2025},
author = {Ruiz-Muñoz, M and Ontañón, I and Cobos, R and Calvo-Peña, C and Otero-Suárez, R and Ferreira, V and Roselló, J and Coque, JJR},
title = {The microbiota of cork and yellow stain as a model for a new route for the synthesis of chlorophenols and chloroanisoles from the microbial degradation of suberin and/or lignin.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {6},
pmid = {39799316},
issn = {2049-2618},
mesh = {*Lignin/metabolism ; *Chlorophenols/metabolism ; *Microbiota ; *Wine/microbiology/analysis ; *Anisoles/metabolism ; Fungi/metabolism/classification ; Parabens/metabolism ; Quercus/microbiology ; Bacteria/metabolism/classification ; Lipids ; },
abstract = {BACKGROUND: The main application of cork is the production of stoppers for wine bottles. Cork sometimes contains 2,4,6-trichloroanisole, a compound that, at a concentration of ng/L, produces an unpleasant musty odor that destroys the organoleptic properties of wine and results in enormous economic losses for wineries and cork industries. Cork can exhibit a defect known as yellow stain, which is associated with high levels of 2,4,6-trichloroanisole. We describe how the microbiota of cork and yellow stain define a novel mechanism that explains the formation of chlorophenols and chloroanisoles (including 2,4,6-trichloroanisole) from p-hydroxybenzoate produced during lignin and/or suberin breakdown.

RESULTS: Electron microscopy revealed that cork affected by yellow stain exhibited significant structural degradation. This deterioration was attributed to the presence of higher microbial populations compared to those found in standard cork. Cork microbiota is rich in filamentous fungi able to metabolize lignin. A metataxonomic analysis confirmed that yellow stain contained significantly greater populations of fungal species belonging to Absidia, Geomyces, Mortierella, Mucor, Penicillium, Pseudogymnoascus, Talaromyces, and Umbelopsis. It also contained significantly greater amounts of bacteria belonging to Enterobacterales, Streptosporangiales, Tepidisphaerales, Pseudomonas, and several members of Burkholderiaceae, particularly species of the Burkholderia-Caballeronia-Paraburkholderia group. The extraction of aromatic compounds from cork samples allowed the identification of several compounds typically observed following lignin depolymerization. Notably, p-hydroxybenzoic acid and phenol were detected. Two strains of the genus Streptomyces isolated from yellow stain were able to biotransform p-hydroxybenzoate into phenol in resting cell assays. Phenol could be efficiently chlorinated in vitro to produce 2,4,6-trichlorophenol by a fungal chloroperoxidase, an enzymatic activity commonly found in filamentous fungi isolated from cork. Finally, as has been widely demonstrated before, 2,4,6-trichlorophenol can be efficiently O-methylated to 2,4,6-trichloroanisole by many of fungi that inhabit cork.

CONCLUSIONS: Chlorophenols and chloroanisoles can be produced de novo in cork from p-hydroxybenzoate generated by the microbial biodegradation of lignin and/or suberin through the participation of different types of microorganisms present in cork. The natural origin of these compounds, which are of great interest for the chlorine cycle and represent a new source of environmental contamination that differs from that caused by human activity, is described. Video Abstract.},
}

*Lignin/metabolism
*Chlorophenols/metabolism
*Microbiota
*Wine/microbiology/analysis
*Anisoles/metabolism
Fungi/metabolism/classification
Parabens/metabolism
Quercus/microbiology
Bacteria/metabolism/classification
Lipids

@article {pmid39799280,
year = {2025},
author = {Tabardillo, JA and Juinio-Meñez, MA and Reitzel, AM and Ravago-Gotanco, R},
title = {Differences in gut microbial diversity and composition between growth phenotypes of farmed juvenile sandfish, Holothuria scabra.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {14},
pmid = {39799280},
issn = {1471-2180},
support = {ECWRG 2019-10-R//University of the Philippines/ ; ECWRG 2019-10-R//University of the Philippines/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; *Holothuria/microbiology/growth & development ; *RNA, Ribosomal, 16S/genetics ; *Aquaculture ; *Bacteria/classification/genetics/isolation & purification/growth & development ; *Feces/microbiology ; Phylogeny ; Biodiversity ; Phenotype ; DNA, Bacterial/genetics ; },
abstract = {BACKGROUND: The observed growth variability of different aquaculture species in captivity hinders its large-scale production. For the sandfish Holothuria scabra, a tropical sea cucumber species, there is a scarcity of information on its intestinal microbiota in relation to host growth, which could provide insights into the processes that affect growth and identify microorganisms with probiotic or biochemical potential that could improve current production strategies. To address this gap, this study used 16 S rRNA amplicon sequencing to characterize differences in gut and fecal microbiota among large and small juveniles reared in floating ocean nurseries.

RESULTS: We recovered 5915 amplicon sequence variants and diversity indices revealed significant differences between large and small juveniles (p < 0.05). Gut microbiota of large juveniles had lower bacterial diversity than its smaller counterparts. The genus cluster Burkholderia-Caballeronia-Paraburkholderia (BCP) is the most common and abundant taxa found in the gut for both size categories but less abundant in fecal samples. Small juveniles had a higher abundance of members from the Roseobacter clade (Rhodobacteriaceae) such as Ruegeria, Shimia, Psuedoruegeria and Marivita among others while the genus Schlegelella (Caldimonas) and Bosea were primarily found in larger juveniles. Predicted physiological functions identified signatures of metabolism, biosynthesis, and biodegradation pathways unique for each size category. Significant differences in diversity and composition were also exhibited between the pooled fecal and gut sample types.

CONCLUSIONS: The bacterial composition in the intestinal tract of the sandfish H. scabra is an important factor in the observed growth variability in aquaculture. The results show differences in diversity, composition and predicted physiological functions between the size groups, despite being from the same cohort and environment. It was also evident that the fecal microbiota differs from the gut and does not correspond to size category, warranting caution in using the fecal matter as a proxy to infer microbial composition and interactions in the gastrointestinal tract. Understanding the roles that these microorganisms play in sandfish growth could support the development of strategies to manage size variation in captive-bred sea cucumbers, or for the promotion and selection for faster-growing individuals.},
}

Animals
*Gastrointestinal Microbiome/genetics
*Holothuria/microbiology/growth & development
*RNA, Ribosomal, 16S/genetics
*Aquaculture
*Bacteria/classification/genetics/isolation & purification/growth & development
*Feces/microbiology
Phylogeny
Biodiversity
Phenotype
DNA, Bacterial/genetics

@article {pmid39799140,
year = {2025},
author = {Wu, C and Li, M and Chen, Z and Feng, S and Deng, Q and Duan, R and Liu, TC and Yang, L},
title = {Remote photobiomodulation ameliorates behavioral and neuropathological outcomes in a rat model of repeated closed head injury.},
journal = {Translational psychiatry},
volume = {15},
number = {1},
pages = {8},
pmid = {39799140},
issn = {2158-3188},
support = {32300959//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32100918//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {Animals ; Rats ; *Disease Models, Animal ; *Low-Level Light Therapy/methods ; Male ; *Head Injuries, Closed/complications/radiotherapy ; *Behavior, Animal ; *Rats, Sprague-Dawley ; Microglia ; Astrocytes ; Social Interaction ; },
abstract = {Repeated closed-head injuries (rCHI) from activities like contact sports, falls, military combat, and traffic accidents pose a serious risk due to their cumulative impact on the brain. Often, rCHI is not diagnosed until symptoms of irreversible brain damage appear, highlighting the need for preventive measures. This study assessed the prophylactic efficacy of remote photobiomodulation (PBM) targeted at the lungs against rCHI-induced brain injury and associated behavioral deficits. Utilizing the "Marmarou" weight-drop model, rCHI was induced in rats on days 0, 5, and 10. Remote PBM, employing an 808 nm continuous wave laser, was administered daily in 2-min sessions per lung side over 20 days. Behavioral deficits were assessed through three-chamber social interaction, forced swim, grip strength, open field, elevated plus maze, and Barnes maze tests. Immunofluorescence staining and 3D reconstruction evaluated neuronal damage, apoptosis, degeneration, and the morphology of microglia and astrocytes, as well as astrocyte and microglia-mediated excessive synapse elimination. Additionally, 16S rDNA amplicon sequencing analyzed changes in the lung microbiome following remote PBM treatment. Results demonstrated that remote PBM significantly improved depressive-like behaviors, motor dysfunction, and social interaction impairment while enhancing grip strength and reducing neuronal damage, apoptosis, and degeneration induced by rCHI. Analysis of lung microbiome changes revealed an enrichment of lipopolysaccharide (LPS) biosynthesis pathways, suggesting a potential link to neuroprotection. Furthermore, remote PBM mitigated hyperactivation of cortical microglia and astrocytes and significantly reduced excessive synaptic phagocytosis by these cells, highlighting its potential as a preventive strategy for rCHI with neuroprotective effects.},
}

Animals
Rats
*Disease Models, Animal
*Low-Level Light Therapy/methods
Male
*Head Injuries, Closed/complications/radiotherapy
*Behavior, Animal
*Rats, Sprague-Dawley
Microglia
Astrocytes
Social Interaction

@article {pmid39798925,
year = {2025},
author = {Aleksandrova, RR and Nieuwenhuis, LM and Karmi, N and Zhang, S and Swarte, JC and Björk, JR and Gacesa, R and Blokzijl, H and Connelly, MA and Weersma, RK and Lisman, T and Festen, EAM and de Meijer, VE and , },
title = {Gut microbiome dysbiosis is not associated with portal vein thrombosis in patients with end-stage liver disease: a cross-sectional study.},
journal = {Journal of thrombosis and haemostasis : JTH},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jtha.2024.12.036},
pmid = {39798925},
issn = {1538-7836},
abstract = {BACKGROUND: Portal vein thrombosis (PVT) is a common complication in patients with end-stage liver disease (ESLD). The portal vein in ESLD patients is proposedly an inflammatory vascular bed due to translocation of endotoxins and cytokines from the gut. We hypothesized that a pro-inflammatory gut microbiome and elevated trimethylamine N-oxide (TMAO), a driver of thrombosis, may contribute to PVT development.

OBJECTIVES: We investigated whether gut microbiome diversity, bacterial species, metabolic pathways, and TMAO levels are associated with PVT in ESLD patients.

METHODS: Fecal samples, plasma samples and data from ESLD patients and healthy controls were collected through the TransplantLines Biobank and Cohort Study. PVT was defined as a thrombus in the portal vein within a year prior to or after fecal sample collection. Fecal samples were analyzed using Shotgun Metagenomic Sequencing, and TMAO levels were measured in plasma using a Vantera® Clinical Analyzer.

RESULTS: 102 ESLD patients, of which 23 with PVT, and 246 healthy controls were included. No significant difference in gut microbiome diversity was found between patients with PVT and without PVT (P=0.18). Both ESLD groups had significantly lower alpha-diversity compared with controls. Bacteroides fragilis and three Clostridiales species were increased in patients with PVT compared to without PVT. TMAO levels between the three groups were not significantly different.

CONCLUSION: We observed profound differences in gut microbiota between ESLD patients and controls, but minimal differences between ESLD patients with or without PVT. In our cohort, a gut-derived pro-inflammatory state was not associated with presence of PVT in ESLD patients.},
}

@article {pmid39798661,
year = {2025},
author = {Liu, R and Wei, G and Yang, Y and Wang, J and Zhao, S and Zhang, B and Hao, X and Liu, K and Shao, Z},
title = {Discovery of potentially degrading microflora of different types of plastics based on long-term in-situ incubation in the deep sea.},
journal = {Environmental research},
volume = {},
number = {},
pages = {120812},
doi = {10.1016/j.envres.2025.120812},
pmid = {39798661},
issn = {1096-0953},
abstract = {Plastic waste that ends up in the deep sea is becoming an increasing concern. However, it remains unclear whether there is any microflora capable of degrading plastic within this vast ecosystem. In this study, we investigated the bacterial communities associated with different types of plastic-polyamide-nylon 4, 6 (PA), polyethylene (PE), polyethylene terephthalate (PET), and polystyrene (PS)-after one year of in situ incubation in the pelagic deep sea of the Western Pacific. The study was conducted via a submarine mooring system, anchored at four sites with water depths ranging from 1,167 to 1,735 meters in an area of seamounts. High-throughput 16S rRNA gene sequencing revealed distinct bacterial diversities associated with specific plastic types and locations. The family Gordoniaceae was enriched by PS and PE plastics, while the abundance of Methyloligellaceae was significantly increased in the presence of PET. In the case of PA, Bdellovibrionaceae was enriched. Additionally, all plastic types promoted the relative abundance of Rhodobacteraceae and Sulfurimonadaceae families. Plastics appeared to stimulate bacterial communities involved in nitrate and sulfur cycling in seawater, suggesting that nitrogen and sulfur potentially play significant roles in plastic degradation in deep-sea environments. The dominant family Kordiimonadaceae was identified as a significantly different taxon in non-plastic seawater. Furthermore, the addition of plastics enhanced negative interactions among the bacterial communities in the surrounding seawater, with Proteobacteria and Bdellovibrionota selected for the core microbiome. Overall, this in situ deep-sea incubation revealed the response of indigenous microflora to man-made polymeric materials and highlighted the bacterial communities that may be involved in plastic degradation in oceanic areas.},
}

@article {pmid39798621,
year = {2025},
author = {Heckmann, ND and Culler, M and Mont, MA and Lieberman, JR and Parvizi, J},
title = {Emerging Concepts in Periprosthetic Joint Infection Research: The Human Microbiome.},
journal = {The Journal of arthroplasty},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.arth.2025.01.001},
pmid = {39798621},
issn = {1532-8406},
abstract = {Microorganisms, including bacteria, fungi, and viruses, that reside on and within the human body are collectively known as the human microbiome. Dysbiosis, or disruption in the microbiome, has been implicated in several disease processes, including asthma, obesity, autoimmune diseases, and numerous other conditions. While the Human Microbiome Project (HMP) and the generation of descriptive studies it inspired established correlations between characteristic patterns in the composition of the microbiome and specific disease phenotypes, current research has begun to focus on elucidating the causal role of the microbiome in disease pathogenesis. Within the field of orthopaedic surgery, researchers have proposed the concept of a "gut-joint axis" by which the intestinal microbiome influences joint health and the development of diseases such as osteoarthritis and periprosthetic joint infection (PJI). It is theorized that intestinal dysbiosis increases gut permeability, leading to the translocation of bacteria and their metabolic products into the systemic circulation and the stimulation of proinflammatory response cascades throughout the body, including within the joints. While correlative studies have identified patterns of dysbiotic derangement associated with osteoarthritis and PJI, translational research is needed to clarify the precise mechanisms by which these changes influence disease processes. Additionally, an emerging body of literature has challenged the previously held belief that certain body sites are sterile and do not possess a microbiome, with studies identifying distinct microbial genomic signatures and a core microbiome that varies between anatomic sites. A more thorough characterization of the joint microbiome may have profound implications for our understanding of PJI pathogenesis and our ability to stratify patients based on risk. The purpose of this review was to outline our current understanding of the human microbiome, to describe the gut-joint axis and its role in specific pathologies, including PJI, and to highlight the potential of microbiome-based therapeutic interventions in the field of orthopaedics.},
}

@article {pmid39798533,
year = {2025},
author = {Mao, X and Yin, X and Yang, Y and Gao, F and Li, S and Shi, X and Deng, Y and Li, L and Leung, KMY and Zhang, T},
title = {Longitudinal metagenomic analysis on antibiotic resistome, mobilome, and microbiome of river ecosystems in a sub-tropical metropolitan city.},
journal = {Water research},
volume = {274},
number = {},
pages = {123102},
doi = {10.1016/j.watres.2025.123102},
pmid = {39798533},
issn = {1879-2448},
abstract = {Rivers play an important role as reservoirs and sinks for antibiotic resistance genes (ARGs). However, it remains underexplored for the resistome and associated mobilome in river ecosystems, and hosts of riverine ARGs particularly the pathogenic ones are rarely studied. This study for the first time conducted a longitudinal metagenomic analysis to unveil the resistome, mobilome, and microbiome in river water, by collecting samples from 16 rivers in Hong Kong over a three-year period and using both short-read and long-read sequencing. Results revealed that aminoglycoside, bacitracin, β-lactam, macrolide lincosamide-streptogramin, and sulfonamide were the predominant ARG types in the river water samples. Riverine ARGs exhibited high spatial variations in abundance and diversity. Environmental factors such as fecal coliform count, Escherichia coli count, 5-day biochemical oxygen demand (BOD5), dissolved oxygen (DO), and total organic carbon (TOC) had a significant correlation to the absolute concentrations of ARGs. Nanopore sequencing was used to reveal the physical genetic linkage of mobile genetic elements (MGEs) with ARGs in river water samples. The results showed that qacEdelta, transposase, integrase, and Tn916 had a high prevalence in ARG-carrying long reads. Host tracking using ARG-carrying reads identified 23 pathogenic bacteria species that harbored ARGs. Some ARGs were shared by different bacterial groups. This study presented a nuanced insight of resistome in river water by a longitudinal metagenomic analysis and deepened our understanding of common and divergent riverine antimicrobial resistant risk across the regional patterns.},
}

@article {pmid39798503,
year = {2024},
author = {Nagi, R and Kumar, SS and Sheth, M and Deshpande, A and Khan, J},
title = {Association between oral microbiome dysbiosis and Sjogren Syndrome. A systematic review of clinical studies.},
journal = {Archives of oral biology},
volume = {172},
number = {},
pages = {106167},
doi = {10.1016/j.archoralbio.2024.106167},
pmid = {39798503},
issn = {1879-1506},
abstract = {OBJECTIVES: This systematic review investigates the association of oral microbiome dysbiosis with Sjogren Syndrome (SS).

MATERIALS AND METHODS: Indexed databases (PubMed/Medline, EMBASE, OVID, Web of Science, and Scopus) were independently searched for relevant manuscripts published until August 2024. Clinical studies on oral microbial flora count and diversity in SS patients were included. Risk of bias across individual studies was performed using the Risk of Bias in Nonrandomized Studies of Interventions tool.

RESULTS: Out of the initial 295 studies, 15 clinical studies met the selection criteria. The protocols were similar across the studies but varied in diagnostic criteria for SS, salivary flow estimation methods, dental and periodontal status findings, and the type of oral microbes observed. Out of 15 studies, 14 showed an alteration in the oral microbiome and differences in microbial diversity in SS patients. Higher oral microbial counts of Prevotella, Viellonella, and Firmicutes in SS were reported, whereas a higher prevalence of caries-associated bacteria Streptococcus, Lactobacillus, and Viellonella was found in SS patients. Overall, the studies had a low risk of bias.

CONCLUSIONS: The findings of the present review have shown the existence of significant oral microbial dysbiosis and differences in microbial diversity in SS patients compared to healthy subjects. Future well-designed longitudinal studies are needed to validate the results.},
}

@article {pmid39798398,
year = {2025},
author = {Jokisch, F and Geyer, LJM and Janssen, KP},
title = {Liver regeneration in fatty liver disease: can metabolomics shed light on the contribution of the gut microbiome?.},
journal = {EBioMedicine},
volume = {112},
number = {},
pages = {105552},
doi = {10.1016/j.ebiom.2024.105552},
pmid = {39798398},
issn = {2352-3964},
}

@article {pmid39798223,
year = {2025},
author = {Larsson, SC and Ericson, U and Dekkers, KF and Arage, G and Rašo, LM and Sayols-Baixeras, S and Hammar, U and Baldanzi, G and Nguyen, D and Nielsen, HB and Holm, JB and Risérus, U and Michaëlsson, K and Sundström, J and Smith, JG and Engström, G and Ärnlöv, J and Orho-Melander, M and Fall, T and Ahmad, S},
title = {Meat intake in relation to composition and function of gut microbiota.},
journal = {Clinical nutrition (Edinburgh, Scotland)},
volume = {45},
number = {},
pages = {124-133},
doi = {10.1016/j.clnu.2024.12.034},
pmid = {39798223},
issn = {1532-1983},
abstract = {OBJECTIVE: Meat intake is suggested to affect gut microbiome composition and the risk of chronic diseases. We aimed to identify meat-associated gut microbiome features and their association with host factors.

DESIGN: Gut microbiota species were profiled by deep shotgun metagenomics sequencing in 9669 individuals. Intake of white meat, unprocessed red meat, and processed red meat was assessed using a food frequency questionnaire. The associations of meat intake with alpha-diversity and relative abundance of gut microbiota species were tested using linear regression models with adjustment for dietary fiber intake, body mass index, and other potential confounders. Meat-associated species were further assessed for association with enrichment of microbial gene function, meat-associated plasma metabolites, and clinical biomarkers.

RESULTS: Higher intake of processed red meat was associated with reduced alpha microbial diversity. White meat, unprocessed, and processed red meat intakes were associated with 36, 14, and 322 microbiota species, respectively. Species associated with processed red meat were enriched for bacterial pathways like amino acid degradation, while those negatively linked were enriched for pathways like homoacetogenesis. Furthermore, species positively associated with processed red meat were to a large extent associated with reduced trimethylamine N-oxide and glutamine levels but increased creatine and carnitine metabolites, fasting insulin and glucose, C-reactive protein, apolipoprotein A1, and triglyceride levels and higher blood pressure.

CONCLUSION: This largest to date population-based study on meat and gut microbiota suggests that meat intake, particularly processed red meat, may modify the gut microbiota composition, functional capacity, and health-related biomarkers.},
}

@article {pmid39798078,
year = {2025},
author = {Harindranath, S and Desai, D},
title = {Wearable technology in inflammatory bowel disease: current state and future direction.},
journal = {Expert review of medical devices},
volume = {},
number = {},
pages = {},
doi = {10.1080/17434440.2025.2453561},
pmid = {39798078},
issn = {1745-2422},
abstract = {INTRODUCTION: Wearables are electronic devices worn on the body to collect health data. These devices, like smartwatches and patches, use sensors to gather information on various health parameters. This review highlights current use and the potential benefit of wearable technology in patients with inflammatory bowel disease (IBD).

AREAS COVERED: In this review we explore the current use of wearable technology in healthcare and the studies applying this technology in patients with IBD. We also discuss the limitations of using digital health data in general and wearable technology in particular in the current clinical paradigm and predict a path forward in how to rationally and effectively apply this technology to improve the care of patients with IBD. A comprehensive search of all suitable studies was conducted using the databases of PubMed, MEDLINE, EMBASE, and Scopus from inception to August 2024.

EXPERT OPINION: Currently, wearable technology is applied in the monitoring of IBD and prediction of flares using devices and sensors. Future applications include early disease detection using biosensors, advanced data collection through ingestible devices, gut microbiome monitoring, and integration with machine learning. These advancements promise to revolutionize disease management, including IBD, by enabling early diagnosis, personalized treatment, and improved patient outcomes.},
}

@article {pmid39797944,
year = {2025},
author = {Zhang, Y and Yuan, F and Liu, Z and Huang, X and Hong, J and Chang, F and Wu, D},
title = {Rare constituents of the nasal microbiome contribute to the acute exacerbation of chronic rhinosinusitis.},
journal = {Inflammation research : official journal of the European Histamine Research Society ... [et al.]},
volume = {74},
number = {1},
pages = {14},
pmid = {39797944},
issn = {1420-908X},
support = {82000954//Natural Science Foundation of China/ ; Z201100006820086//Beijing Science and Technology Nova Program/ ; QML20190617//Beijing Hospitals Authority Youth Program/ ; XMLX202136//Beijing Hospitals Authority Clinical Medicine Development of Special Funding/ ; BYSYZD2023029//Key clinical projects of Peking University Third Hospital/ ; },
mesh = {Humans ; *Rhinitis/microbiology ; Male ; *Sinusitis/microbiology ; Female ; Middle Aged ; *Microbiota ; Adult ; Cross-Sectional Studies ; Chronic Disease ; RNA, Ribosomal, 16S/genetics ; Dysbiosis/microbiology ; Aged ; Bacteria/classification/genetics ; Prospective Studies ; Nasal Cavity/microbiology ; Rhinosinusitis ; },
abstract = {BACKGROUND: Dysbiosis of the nasal microbiome is considered to be related to the acute exacerbation of chronic rhinosinusitis (AECRS). The microbiota in the nasal cavity of AECRS patients and its association with disease severity has rarely been studied. This study aimed to characterize nasal dysbiosis in a prospective cohort of patients with AECRS.

METHODS: We performed a cross-sectional study of 28 patients with AECRS, 20 patients with chronic rhinosinusitis (CRS) without acute exacerbation (AE), and 29 healthy controls using 16S rRNA gene sequencing. Subjective and objective assessments of CRS disease severity during AE were also collected.

RESULTS: Compared to healthy controls and patients with CRS without AE, AECRS presented with a substantial decrease of the Corynebacterium_1 and a significant increase of Ralstonia and Acinetobacter at the genus level (LDA score > 2.0 [P < 0.05]). Furthermore, genera with a mean relative abundance (MRA) of less than 1% were defined as rare components based on published studies, then 29 genera with a substantial alteration in AECRS were rare constituents of the microbiome, of which 18 rare genera were highly associated with subjective and objective disease severity. Moreover, a combination of 15 genera could differentiate patients with AECRS with an area under the curve of 0.870 (95% CI = 0.784-0.955). Prediction of microbial functional pathways involved significantly enhanced lipopolysaccharide biosynthesis pathways and significantly decreased folate biosynthesis, sulfur relay system, and cysteine and methionine metabolism pathways in patients with AECRS.

CONCLUSIONS: The rare nasal microbiota (MRA < 1%) correlated with disease status and disease severity in patients with AECRS. The knowledge about the pattern of the nasal microbiome and its metabolomic pathway may contribute to the fundamental understanding of AECRS pathophysiology.},
}

Humans
*Rhinitis/microbiology
Male
*Sinusitis/microbiology
Female
Middle Aged
*Microbiota
Adult
Cross-Sectional Studies
Chronic Disease
RNA, Ribosomal, 16S/genetics
Dysbiosis/microbiology
Aged
Bacteria/classification/genetics
Prospective Studies
Nasal Cavity/microbiology
Rhinosinusitis

@article {pmid39797823,
year = {2025},
author = {Chen, B and Liu, M and Zhang, Z and Lv, B and Yu, Y and Zhang, Q and Xu, N and Yang, Z and Lu, T and Xia, S and Chen, J and Qian, H},
title = {Data-Driven Approach for Designing Eco-Friendly Heterocyclic Compounds for the Soil Microbiome.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.4c09664},
pmid = {39797823},
issn = {1520-5851},
abstract = {Soil microbiota plays crucial roles in maintaining the health, productivity, and nutrient cycling of terrestrial ecosystems. The persistence and prevalence of heterocyclic compounds in soil pose significant risks to soil health. However, understanding the links between heterocyclic compounds and microbial responses remains challenging due to the complexity of microbial communities and their various chemical structures. This study developed a machine-learning approach that integrates the properties of chemical structures with the diversity of soil bacteria and functions to predict the impact of heterocyclic compounds on the microbial community and improve the design of eco-friendly heterocyclic compounds. We screened the key chemical structures of heterocyclic compounds─particularly those with topological polar surface areas (<74.2 Å[2] or 111.3-154.1 Å[2]), carboxyl groups, and dissociation constant, which maintained high soil bacterial diversity and functions, revealing threshold effects where specific structural parameters dictated microbial responses. These eco-friendly compounds stabilize communities and increase beneficial carbon and nitrogen cycle functions. By applying these design parameters, we quantitatively assessed the eco-friendliness scores of 811 heterocyclic compounds, providing a robust foundation for guiding future applications. Our study disentangles the critical chemical structure-related properties that influence the soil microbial community and establishes a computational framework for designing eco-friendly compounds with ecological benefits from an ecological perspective.},
}