@article {pmid39831119,
year = {2024},
author = {Lenka, J and González-Tortuero, E and Kuba, S and Ferry, N},
title = {Bacterial community profiling and identification of bacteria with lignin-degrading potential in different gut segments of African palm weevil larvae (Rhynchophorus phoenicis).},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1401965},
doi = {10.3389/fmicb.2024.1401965},
pmid = {39831119},
issn = {1664-302X},
abstract = {The microbiota within the guts of insects plays beneficial roles for their hosts, such as facilitating digestion and extracting energy from their diet. The African palm weevil (APW) lives within and feeds on the high lignin-containing trunk of palm trees; therefore, their guts could harbour a large community of lignin-degrading microbes. In this study, we aimed to explore the bacterial community within the gut of the APW larvae, specifically with respect to the potential for lignin degradation in various gut segments as a first step to determining the viability of mining bacterial lignin-degrading enzymes for the bioconversion of lignocellulosic biomass to biofuels and biomaterials. Bacterial metagenomic DNA was extracted from the foregut, midgut, and hindgut of larvae of the APW, and the V3-V4 hypervariable region of the 16S rRNA gene was sequenced using the Illumina MiSeq platform. The generated data were analysed and taxonomically classified to identify the different bacterial phylotypes within the gut community cumulatively and per gut segment. We then determined the presence, diversity, and abundance of bacteria associated with lignin degradation within each larval gut compartment as a basis for suggesting the gut segment(s) where lignin degradation occurs the most. All sequences were classified and belonged to the bacterial kingdom. Firmicutes (54.3%) and Proteobacteria (42.5%) were the most dominant phyla within the gut, followed distantly by Bacteroidota (1.7%) and Actinobacteriota (1.4%). Enterococcus, Levilactobacillus, Lactococcus, Shimwellia, Megasphaera, Klebsiella, Pectinatus, Salmonella, Lelliotia, and Enterobacter constituted the most abundant genera found across all gut segments. The foregut and midgut had many similar genera, whilst the hindgut appeared unique. Overall, 29.5% of total gut bacteria comprising 21 genera were lignin degraders found predominantly in the Firmicutes and Proteobacteria phyla (56.8 and 39.5%, respectively), then moderately in Actinobacteriota (2.5%) and Bacteroidota (1.1%). The most abundant ligninolytic genera were Levilactobacillus (46.4%), Klebsiella (22.9%), Enterobacter (10.7%), Lactiplantibacillus (5.9%), Citrobacter (2.2%), Corynebacterium (1.8%), Paucilactobacillus (1.8%), Serratia (1.5%), Bacteroides (1.1%), and Leucobacter (1.0%) found in different amounts in different gut compartments. The foregut had the most diverse and highest abundance of lignin-degrading phylotypes, and we present reasons that point to the foregut as the main location for the depolymerization of lignin in the APW larval gut.},
}

@article {pmid39830903,
year = {2025},
author = {Cambray, GA and Kalinski, JJ},
title = {Microbial Characterization of a Zambian Honey Vinegar.},
journal = {Food science & nutrition},
volume = {13},
number = {1},
pages = {e4549},
doi = {10.1002/fsn3.4549},
pmid = {39830903},
issn = {2048-7177},
abstract = {Forest Fruits Organic Honey Vinegar (FFOHV) is a spontaneously fermented (yeast) and acetified (Acetic Acid Bacteria-AAB) Miombo Woodland honey vinegar developed in Zambia. Live vinegars containing live microbial cultures are marketed for their probiotic health benefits. The correlation between a well-developed gut microbiome and human health is well studied and fermented products such as live vinegar containing AAB contribute to a healthy gut microbiome. This study details a metagenomic analysis of stable, bottled FFOHV (Zambia) alongside two commercially available live vinegar products: Bragg Organic Apple Cider Vinegar (BOACV) and Nature's Source Apple Cider Vinegar (NSACV). FFOHV contained representatives of five bacterial and nine fungal genera, compared to BOACV with two bacterial and five fungal, and NSACV containing no bacterial and six fungal genera. FFOHV and BOACV showed a dominance of Komagataeibacter bacterial species. The dominant yeast was Vanrija humicola present in all three vinegar samples. FFOHV contained greater diversity of genera, with the notable species Monascus purpureus-a microbe that produces several health-enhancing compounds. The analysis showed that FFOHV is a microbially diverse product containing several potentially health-enhancing microbes. Graphical Abstract Text: This study presents a metagenomic analysis of Forest Fruits Organic Honey Vinegar (FFOHV) from Zambia, compared with two commercial live cider vinegars: Bragg Organic Apple Cider Vinegar (BOACV) and Nature's Source Apple Cider Vinegar (NSACV). FFOHV exhibited a richer microbial diversity, containing five bacterial and nine fungal genera, including the health-promoting species Monascus purpureus. Both FFOHV and BOACV were dominated by Komagataeibacter species, with Vanrija humicola as the prevalent yeast across all samples. This confirmed FFOHV's unique potential probiotic benefits.},
}

@article {pmid39830168,
year = {2024},
author = {Zhao, Y and Zhao, M and Zhang, W},
title = {Identification of a novel papillomavirus in oral swabs from giant pandas (Ailuropoda melanoleuca).},
journal = {Frontiers in veterinary science},
volume = {11},
number = {},
pages = {1457471},
doi = {10.3389/fvets.2024.1457471},
pmid = {39830168},
issn = {2297-1769},
abstract = {To fully characterize papillomavirus diversity in giant pandas (Ailuropoda melanoleuca), we identified a novel papillomavirus (named AmPV5, GenBank accession number MZ357114) in oral swabs from giant pandas with the help of viral metagenomics technology in this study. The complete circular genome of AmPV5 is 7,935 bp in length, with a GC content of 39.1%. It encodes five early genes (E1, E2, E4, E6, and E7), two late genes (L1 and L2), and features conserved zinc-binding domains (CXXC- (X)28/29-CXXC) in E6 and E7 genes. E7 protein has an LxCxE domain (pRB binding) in its N-terminal region. The nucleotide sequence of AmPV5 L1 gene shares < 70% identity with other related sequences available in the GenBank database. Phylogenetic analysis indicated that AmPV5 fell within the Lambdapapillomavirus genus but formed a monophyletic branch away from other papillomaviruses found in Ailuropoda melanoleuca, Canis, Felis catus, Panthera uncia, Enhydra lutris, and Procyon lotor. According to the International Committee on Taxonomy of Viruses (ICTV) classification guidelines, AmPV5 is classified as a new species within the Lambdapapillomavirus genus. The discovery provides valuable insights into the viral diversity in giant pandas and highlights the need for continued surveillance of wildlife pathogens. Future studies should explore the potential role of AmPV5 in the health and disease ecology of this endangered species.},
}

@article {pmid39830096,
year = {2025},
author = {Fei, C and Booker, A and Klass, S and Vidyarathna, NK and Ahn, SH and Mohamed, AR and Arshad, M and Glibert, PM and Heil, CA and Martínez Martínez, J and Amin, SA},
title = {Friends and foes: symbiotic and algicidal bacterial influence on Karenia brevis blooms.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycae164},
doi = {10.1093/ismeco/ycae164},
pmid = {39830096},
issn = {2730-6151},
abstract = {Harmful Algal Blooms (HABs) of the toxigenic dinoflagellate Karenia brevis (KB) are pivotal in structuring the ecosystem of the Gulf of Mexico (GoM), decimating coastal ecology, local economies, and human health. Bacterial communities associated with toxigenic phytoplankton species play an important role in influencing toxin production in the laboratory, supplying essential factors to phytoplankton and even killing blooming species. However, our knowledge of the prevalence of these mechanisms during HAB events is limited, especially for KB blooms. Here, we introduced native microbial communities from the GoM, collected during two phases of a Karenia bloom, into KB laboratory cultures. Using bacterial isolation, physiological experiments, and shotgun metagenomic sequencing, we identified both putative enhancers and mitigators of KB blooms. Metagenome-assembled genomes from the Roseobacter clade showed strong correlations with KB populations during HABs, akin to symbionts. A bacterial isolate from this group of metagenome-assembled genomes, Mameliella alba, alleviated vitamin limitations of KB by providing it with vitamins B1, B7 and B12. Conversely, bacterial isolates belonging to Bacteroidetes and Gammaproteobacteria, Croceibacter atlanticus, and Pseudoalteromonas spongiae, respectively, exhibited strong algicidal properties against KB. We identified a serine protease homolog in P. spongiae that putatively drives the algicidal activity in this isolate. While the algicidal mechanism in C. atlanticus is unknown, we demonstrated the efficiency of C. atlanticus to mitigate KB growth in blooms from the GoM. Our results highlight the importance of specific bacteria in influencing the dynamics of HABs and suggest strategies for future HAB management.},
}

@article {pmid39830095,
year = {2025},
author = {Junca, H and Steube, A and Mrowietz, S and Stallhofer, J and Vital, M and Dos Anjos Borges, LG and Pieper, DH and Stallmach, A},
title = {Bacterial and viral assemblages in ulcerative colitis patients following fecal microbiota and fecal filtrate transfer.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycae167},
doi = {10.1093/ismeco/ycae167},
pmid = {39830095},
issn = {2730-6151},
abstract = {Fecal microbiota filtrate transfer is discussed as a safe alternative to fecal microbiota transfer (FMT) to treat ulcerative colitis. We investigated modulation of viral and bacterial composition during fecal microbiota filtrate transfer followed by FMT in six patients with active ulcerative colitis (where clinical activity improved in three patients after filtrate transfer) and combined 16S ribosomal RNA gene amplicon sequencing with a virome analysis pipeline including fast viral particle enrichment and metagenome mapping to detect frequencies of 45,033 reference bacteriophage genomes. We showed that after antibiotic treatment and during filtrate transfer, the bacterial community typically adopted a stable composition distinct to that before antibiotic treatment, with no change toward a donor community. FMT in contrast typically changed the bacterial community to a community with similarity to donor(s). There were no indications of an establishment of predominant donor viruses during filtrate transfer but a remodeling of the virome. In contrast, the establishment of donor viruses during FMT correlated with the predicted hosts established during such transfer. Our approach warrants further investigation in a randomized trial to evaluate larger therapeutic interventions in a comparable and efficient manner.},
}

@article {pmid39829898,
year = {2025},
author = {Ni, M and Fan, Y and Liu, Y and Li, Y and Qiao, W and Davey, LE and Zhang, XS and Ksiezarek, M and Mead, E and Touracheau, A and Jiang, W and Blaser, MJ and Valdivia, RH and Fang, G},
title = {Epigenetic phase variation in the gut microbiome enhances bacterial adaptation.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.01.11.632565},
pmid = {39829898},
issn = {2692-8205},
abstract = {The human gut microbiome within the gastrointestinal tract continuously adapts to variations in diet, medications, and host physiology. A central strategy for genetic adaptation is epigenetic phase variation (ePV) mediated by bacterial DNA methylation, which can regulate gene expression, enhance clonal heterogeneity, and enable a single bacterial strain to exhibit variable phenotypic states. Genome-wide and site-specific ePV have been well characterized in human pathogens' antigenic variation and virulence factor production. However, the role of ePV in facilitating adaptation within the human microbiome remains poorly understood. Here, we comprehensively cataloged genome-wide and site-specific ePV in human infant and adult gut microbiomes. First, using long-read metagenomic sequencing, we detected genome-wide ePV mediated by complex structural variations of DNA methyltransferases, highlighting the ones associated with antibiotics or fecal microbiota transplantation. Second, we analyzed an extensive collection of public short-read metagenomic sequencing datasets, uncovering a greater prevalence of genome-wide ePV in the human gut microbiome. Third, we quantitatively detected site-specific ePVs using single-molecule methylation analysis to identify dynamic variations associated with antibiotic treatment or probiotic engraftment. Finally, we performed an in-depth assessment of an Akkermansia muciniphila isolate from an infant, highlighting that ePV can regulate gene expression and enhance the bacterial adaptive capacity by employing a bet-hedging strategy to increase tolerance to differing antibiotics. Our findings indicate that epigenetic modifications are a common and broad strategy used by bacteria in the human gut to adapt to their environment.},
}

@article {pmid39829854,
year = {2025},
author = {Ghazi, AR and Thompson, KN and Bhosle, A and Mei, Z and Yan, Y and Wang, F and Wang, K and Franzosa, EA and Huttenhower, C},
title = {Quantifying Metagenomic Strain Associations from Microbiomes with Anpan.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.01.06.631550},
pmid = {39829854},
issn = {2692-8205},
abstract = {Genetic and genomic variation among microbial strains can dramatically influence their phenotypes and environmental impact, including on human health. However, inferential methods for quantifying these differences have been lacking. Strain-level metagenomic profiling data has several features that make traditional statistical methods challenging to use, including high dimensionality, extreme variation among samples, and complex phylogenetic relatedness. We present Anpan, a set of quantitative methods addressing three key challenges in microbiome strain epidemiology. First, adaptive filtering designed to interrogate microbial strain gene carriage is combined with linear models to identify strain-specific genetic elements associated with host health outcomes and other phenotypes. Second, phylogenetic generalized linear mixed models are used to characterize the association of sub-species lineages with such phenotypes. Finally, random effects models are used to identify pathways more likely to be retained or lost by outcome-associated strains. We validated our methods by simulation, showing that we achieve more accurate effect size estimation and a lower false positive rate compared to alternative methodologies. We then applied our methods to a dataset of 1,262 colorectal cancer patients, identifying functionally adaptive genes and strong phylogenetic effects associated with CRC status, sometimes complementing and sometimes extending known species-level microbiome CRC biomarkers. Anpan's methods have been implemented as a publicly available R library to support microbial community strain and genetic epidemiology in a variety of contexts, environments, and phenotypes.},
}

@article {pmid39829744,
year = {2025},
author = {Tang, G and Carr, AV and Perez, C and Ramos Sarmiento, K and Levy, L and Lampe, JW and Diener, C and Gibbons, SM},
title = {Metagenomic estimation of absolute bacterial biomass in the mammalian gut through host-derived read normalization.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.01.07.631807},
pmid = {39829744},
issn = {2692-8205},
abstract = {Absolute bacterial biomass estimation in the human gut is crucial for understanding microbiome dynamics and host-microbe interactions. Current methods for quantifying bacterial biomass in stool, such as flow cytometry, qPCR, or spike-ins (i.e., adding cells or DNA from an organism not normally found in a sample), can be labor-intensive, costly, and confounded by factors like water content, DNA extraction efficiency, PCR inhibitors, and other technical challenges that add bias and noise. We propose a simple, cost-effective approach that circumvents some of these technical challenges: directly estimating bacterial biomass from metagenomes using bacterial-to-host (B:H) read ratios. We compare B:H ratios to the standard methods outlined above, demonstrating that B:H ratios are useful proxies for bacterial biomass in stool and possibly in other host-associated substrates. We show how B:H ratios can be used to track antibiotic treatment response and recovery in both mice and humans, which showed 403-fold and 45-fold reductions in bacterial biomass during antibiotic treatment, respectively. Our results indicate that host and bacterial metagenomic DNA fractions in human stool fluctuate longitudinally around a stable mean in healthy individuals, and the average host read fraction varies across healthy individuals by < 8-9 fold. B:H ratios offer a convenient alternative to other absolute biomass quantification methods, without the need for additional measurements, experimental design considerations, or machine learning algorithms, enabling retrospective absolute biomass estimates from existing stool metagenomic data.},
}

@article {pmid39828685,
year = {2025},
author = {Chen, Y and Yi, ZT and Yu, HL and Wu, XY and Wang, JP and Nie, C and Li, H and Li, SH and Yan, QL and He, TW and Chen, MC and Yang, XY and Wen, JY and Lv, LJ},
title = {Does preeclampsia impact the gut microbiota of preterm offspring during early infancy?.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {84},
pmid = {39828685},
issn = {1479-5876},
support = {2019A1515110389//Basic and Applied Basic Research Foundation of Guangdong Province/ ; },
mesh = {Humans ; Female ; *Gastrointestinal Microbiome ; *Pre-Eclampsia/microbiology ; Pregnancy ; Infant, Newborn ; *Infant, Premature ; Adult ; Feces/microbiology ; Biodiversity ; },
abstract = {Preeclampsia (PE) is a pregnancy complication characterized by high blood pressure and organ damage. This study investigates the differences in the gut microbiota between preterm neonates born to mothers with PE and those born to mothers without PE (PR), aiming to understand how maternal health conditions like PE influence neonatal gut microbiota. The early gut microbiota plays a crucial role in neonatal health, and disturbances in its development can have long-term consequences. Fecal samples were collected from preterm neonates of PE and PR mothers at 2 and 6 weeks postpartum and analyzed using shotgun metagenomic sequencing. We found that PE significantly affected the gut microbial composition of preterm neonates, particularly at 2 weeks postpartum. The gut microbial diversity in the PE_2 group was notably lower compared to the PR_2 group, with no significant difference observed between the PR_6 and PE_6 groups. At the phylum level, Firmicutes and Proteobacteria were predominant, with significant differences observed, particularly a lower abundance of Actinobacteria in the PE_2 group. At the genus level, Escherichia, Enterococcus, and Klebsiella were more prevalent in the PE_2 group, whereas Bifidobacterium and Cutibacterium dominated the PR_2 group. The gut virome analysis showed no significant differences among the groups. Functional analysis revealed distinct metabolic pathway activities across the groups, suggesting that early disturbances due to PE impact the establishment of healthy gut microbiota. These findings underscore the substantial influence of maternal health on the early development of the neonatal gut microbiota and highlight the potential long-term health consequences. Additionally, the differences in metabolic pathways further emphasize the impact of preeclampsia on gut microbiota functionality.},
}

Humans
Female
*Gastrointestinal Microbiome
*Pre-Eclampsia/microbiology
Pregnancy
Infant, Newborn
*Infant, Premature
Adult
Feces/microbiology
Biodiversity

@article {pmid39828574,
year = {2025},
author = {Ma, XY and A, XR and Ma, JD and Zhou, JW and Cheng, P and Tang, Y},
title = {[Differential analysis of intestinal flora in patients with hepatic blastomycosis based on second-generation sequencing].},
journal = {Zhonghua yu fang yi xue za zhi [Chinese journal of preventive medicine]},
volume = {59},
number = {1},
pages = {101-109},
doi = {10.3760/cma.j.cn112150-20240620-00487},
pmid = {39828574},
issn = {0253-9624},
support = {2022‑ZJ‑T01//Qinghai Province 2022 Innovation Platform Construction Special Project/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; Case-Control Studies ; *Feces/microbiology ; High-Throughput Nucleotide Sequencing ; Echinococcosis, Hepatic/microbiology ; Metagenomics/methods ; },
abstract = {Exploring the variability of the intestinal flora of patients with hepatic blastocysticercosis and searching for members of the intestinal microflora that may play a role in the disease process by means of macro-genome sequencing technology. A case-control study was used to include fecal samples from patients with hepatic vesicular schistosomiasis admitted to Qinghai Provincial People's Hospital between October 2023 and January 2024 and individuals attending health checkups. The experimental group (AE group) consisted of 10 patients with liver vesicular schistosomiasis and the control group (NC group) consisted of 9 individuals attending health checkups. Macrogenomic sequencing was performed on these two groups of samples using the Illumina Novaseq 6000 sequencing platform, using fastp (v0.20.1) to remove junctions, and bbmap (v38.93-0) to remove the hosted sequences, followed by sequence splicing using MEGAHIT (v1.2.9), and then using prodigal (v2.6.3) to The spliced scaffold was subjected to ORF prediction and translated into amino acid sequences, followed by the construction of a non-redundant gene set using MMSeqs2 (v13.45111), and finally compared with the non-redundant gene set using salmon (v1.8.0). Species were annotated by the non-redundant database, species abundance was calculated in each sample, and the two sets were tested using Wilcoxon rank sum test. Finally, the differences in intestinal flora between the two groups were statistically analyzed using linear discriminant analysis, and the correlation between the differential intestinal flora and clinical indicators was analyzed using redundancy analysis (RDA). The results showed that the effective data volume of each sample was distributed from 10.41 to 12.46 G. The number of ORFs in the de-redundantly constructed gene catalogue (non-redundant gene set) was 4 951 408, and the annotation rate of the non-redundant genes was 97.97% when compared with the NR database. The ages of the study subjects in the two groups were (44.78±4.58) years in the NC group and (42.90±10.44) years in the AE group, and the difference was not statistically significant (t=0.530, P=0.476). The two groups were matched for body mass index (BMI) (t=2.368, P=0.142), gender (χ[2]=0.200, P=0.655), and dietary habits. There was no statistically significant difference in alpha diversity in the AE group (ACE index, t=0.942; chao1 index, t=0.947; shannon index, t=0.813, the simpson's index, t=0.613, P>0.05), while beta diversity analysis showed significant differences in the overall structure of the two communities (Stress=0.054 5). A total of 120 species were annotated at the phylum level, of which two differed. While 1 736 species were annotated at the genus level, 69 were different, and 309 were different at the species level. The AE group ranked the top 6 in terms of abundance of Anaplasma, Escherichiaceae, Clostridium, Alternaria, Ruminalia, and Treponema spp. at the genus level; whereas, Segatella, Prevotella, E. faecalis, Rossella, and beneficial rod-shaped bacteria were more abundant in the NC group. There were differences in the abundance and diversity of intestinal flora between the two groups, and the structure of community composition was significantly different. Statistical results by linear discriminant analysis (LDA) showed that LDA scores >2 in the NC group included beneficial bacillus spp. and E. faecalis spp. in young infants, etc. LDA scores >2 in the AE group at the mid-species level included Clostridium polterococcus, unknown microorganisms in the genus Clostridium intestinalis, Hathaway's Henkett's bacillus, and Clostridium oryzae in the genus Clostridium refractory to culture and small Clostridium spp. in the AE group. Clostridium intestinalis. The RDA results showed a negative correlation between beneficial rod genera and liver function indices, and a positive correlation between Clostridium intestinalis genera and liver function indices. In conclusion, patients with hepatic blastomycosis have altered intestinal flora abundance and diversity, with significant structural changes in community composition and differences in several genera, including Mycobacterium anisopliae and Clostridium intestinalis, and imbalances in the intestinal flora may affect hepatic function by influencing intestinal metabolites and may have an impact on the development of hepatic blastomycosis, a finding that warrants further in-depth study.},
}

Humans
*Gastrointestinal Microbiome
Case-Control Studies
*Feces/microbiology
High-Throughput Nucleotide Sequencing
Echinococcosis, Hepatic/microbiology
Metagenomics/methods

@article {pmid39828197,
year = {2025},
author = {Lin, B and Zhang, Y and Hao, Y and Lu, M and Xiang, H and Ding, D and Niu, S and Li, K and Li, J and Huang, Z},
title = {Insights into nitrogen metabolism and humification process in aerobic composting facilitated by microbial inoculation.},
journal = {Environmental research},
volume = {},
number = {},
pages = {120894},
doi = {10.1016/j.envres.2025.120894},
pmid = {39828197},
issn = {1096-0953},
abstract = {To enhance the retention of compost nutrients, specifically in nitrogen metabolism and humification, compound microbial agents were added during the aerobic composting of bagasse pith and buffalo manure. The introduction of the microbial agent successfully colonized the mixture, boosted the degradation capacity of organic matter, and facilitated the formation of nitrogenous substances and humic substances (HSs). The incorporation of a composite microbial inoculum led to a substantial rise in total Kjeldahl nitrogen (TKN) by 62.04%, nitrate nitrogen (NO- 3-N) by 291.65%, and amino acid (AA) by 78.77%. Furthermore, this intervention resulted in achieving a humic acid (HA) to fulvic acid (FA) ratio of 1.64. Metagenomic sequencing revealed enhanced synergistic interactions among microorganisms through inoculation, increasing the abundance of functional genes related to nitrification and nitrogen fixation compared to the uninoculated control. Spearman correlation analysis identified unclassified_c__Deltaproteobacteria, unclassified_f__Planctomycetaceae, Chryseosolibacter, unclassified_f__Hyphomicrobiaceae as the principal producers of HA. This research provides insights into the interactions between nitrogen metabolism and humification in composting, aiming to effectively retain compost nutrients and support the long-term sustainability of agriculture.},
}

@article {pmid39828044,
year = {2025},
author = {Carluccio, M and Sabatino, R and Borgomaneiro, G and Cesare, AD and Rizzo, L},
title = {Bacterial community dynamics in a biofilm-based process after electro-assisted Fenton pre-treatment of real olive mill wastewater.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {132095},
doi = {10.1016/j.biortech.2025.132095},
pmid = {39828044},
issn = {1873-2976},
abstract = {In this work, the effect of the electro-assisted Fenton (EAF) process on the bacterial community of a moving bed biofilm reactor (MBBR) for olive mill wastewater (OMW) co-treatment with urban wastewater (UWW) was investigated. According to metagenomic analysis, pre-treatment by EAF, while removing total phenols (TPHs) up to 84 % ± 3 % and improving biodegradability of OMW from 0.38 to 0.62, led to the emergence of bacterial genera in the MBBR (R2) that were not detected under conditions without pre-treatment (R1). Indeed, in that condition, Candidatus Competibacter replaced Amaricoccus as dominant denitrifying bacteria. In both cases, the bacterial community composition matched with high simultaneous nitrification-denitrification efficiency (up to 98 %). Finally, Chlorobium (2.5-4.1 %), sulphate-reducing bacteria and Geobacter (up to 1.6 ± 0.4 %), anaerobic bacteria that utilise iron oxides, were observed exclusively with EAF application, suggesting potential for the development of new integrated microbial electrochemical systems.},
}

@article {pmid39827989,
year = {2025},
author = {Cheng, CK and Ye, L and Wang, Y and Wang, YL and Xia, Y and Wong, SH and Chen, S and Huang, Y},
title = {Exercised gut microbiota improves vascular and metabolic abnormalities in sedentary diabetic mice through gut‒vascular connection.},
journal = {Journal of sport and health science},
volume = {},
number = {},
pages = {101026},
doi = {10.1016/j.jshs.2025.101026},
pmid = {39827989},
issn = {2213-2961},
abstract = {BACKGROUND: Exercise elicits cardiometabolic benefits, reducing the risks of cardiovascular diseases and type 2 diabetes. This study aimed to investigate the vascular and metabolic effects of gut microbiota from exercise-trained donors on sedentary mice with type 2 diabetes and the potential mechanism.

METHODS: Leptin receptor-deficient diabetic (db/db) and nondiabetic (db/m[+]) mice underwent running treadmill exercise for 8 weeks, during which fecal microbiota transplantation (FMT) was parallelly performed from exercise-trained to sedentary diabetic (db/db) mice. Endothelial function, glucose homeostasis, physical performance, and vascular signaling of recipient mice were assessed. Vascular and intestinal stresses, including inflammation, oxidative stress, and endoplasmic reticulum (ER) stress, were investigated. RNA sequencing analysis on mouse aortic and intestinal tissues was performed. Gut microbiota profiles of recipient mice were evaluated by metagenomic sequencing.

RESULTS: Chronic exercise improved vascular and metabolic abnormalities in donor mice. Likewise, FMT from exercised donors retarded body weight gain and slightly improved grip strength and rotarod performance in recipient mice. Exercise-associated FMT enhanced endothelial function in different arteries, suppressed vascular and intestinal stresses, and improved glucose homeostasis in recipient mice, with noted microRNA-181b upregulation in aortas and intestines. Altered gut microbiota profiles and gut-derived factors (e.g., short-chain fatty acids and glucagon-like peptide-1) as well as improved intestinal integrity shall contribute to the cardiometabolic benefits, implying a gut‒vascular connection.

CONCLUSION: This proof-of-concept study indicates that exercised microbiota confers cardiometabolic benefits on sedentary db/db mice, extending the beneficial mechanism of exercise through gut‒vascular communication. The findings open up new therapeutic opportunities for cardiometabolic diseases and shed light on the development of exercise mimetics by targeting the gut microbiota.},
}

@article {pmid39827799,
year = {2025},
author = {Kuroda, K and Yamamoto, K and Isshiki, R and Tokizawa, R and Shiiba, C and Hino, S and Yamano, N and Usui, E and Miyakawa, T and Miura, T and Kamino, K and Tamaki, H and Nakayama, A and Narihiro, T},
title = {Metagenomic and metatranscriptomic analyses reveal uncharted microbial constituents responsible for polyhydroxybutyrate biodegradation in coastal waters.},
journal = {Journal of hazardous materials},
volume = {487},
number = {},
pages = {137202},
doi = {10.1016/j.jhazmat.2025.137202},
pmid = {39827799},
issn = {1873-3336},
abstract = {Polyhydroxybutyrate (PHB) has attracted attention as a representative polymer for biodegradable plastics produced by microorganisms. Since information regarding the fate of PHB released into the environment is limited, it is necessary to identify them based on metagenomic information. We estimated the PHB biodegradability in coastal water samples collected from 15 near shore sites around Japan using oxygen consumption as an indicator in laboratory-scale incubation experiments and conducted 16S rRNA gene-based microbial community profiling. The PHB-biodegradation-rate was significantly positively correlated with the diversity indices of the microbial community in seawater prior to incubation, indicating that seawater with higher diversity is more advantageous for biodegradation. We identified 41 operational taxonomic units exhibiting a significant positive correlation between their abundance and PHB-degradation-rates; these included several microorganisms with hitherto unreported PHB-degrading ability. Next, we analyzed gene expression patterns over incubation time using seawater samples employing metagenomic and metatranscriptomic approaches. Fifty-seven putative extracellular PHB/PHA depolymerase genes were found in 38 metagenomic bins and their expression changed with increasing biodegradation rates, indicating that PHB released into the marine environment is subject to degradation by phylogenetically diverse PHB-depolymerase-producing bacteria. These findings should contribute to expanding the knowledge on degradation of biodegradable plastics by complex marine microbial ecosystems.},
}

@article {pmid39827796,
year = {2025},
author = {He, LX and He, LY and Tang, YJ and Qiao, LK and Xu, MC and Zhou, ZY and Bai, H and Zhang, M and Ying, GG},
title = {Deciphering spread of quinolone resistance in mariculture ponds: Cross-species and cross-environment transmission of resistome.},
journal = {Journal of hazardous materials},
volume = {487},
number = {},
pages = {137198},
doi = {10.1016/j.jhazmat.2025.137198},
pmid = {39827796},
issn = {1873-3336},
abstract = {Mariculture is known to harbor antibiotic resistance genes (ARGs), which can be released into marine ecosystems via oceanic farming ponds, posing a public health concern. In this study, metagenomic sequencing was used to decipher the profiles of quinolone-resistant microbiomes and the mechanisms of quinolone resistance in sediment, seawater, and fish gill samples from five mariculture ponds. Residues of both veterinary-specific (enrofloxacin and sarafloxacin) and prohibited quinolones (ofloxacin, ciprofloxacin, pefloxacin, norfloxacin, and lomefloxacin) were detected. We identified a total of 285 subtypes of ARGs across all samples. Pathogens played a crucial role in the prevalence and distribution of these ARGs. Out of the annotated 629 bacterial species, 42 were identified as pathogenic, predominantly belonging to the Proteobacteria phylum. Notably, the Acinetobacter genus was prevalent in the gills and exhibited correlations with various ARGs. The presence of the plasmid-mediated quinolone resistance (PMQR) genes in various bacterial species and the identification of sulfonamide resistance genes across different samples indicated the potential for cross-species and cross-environment transmission of ARGs. Metagenomic binning revealed that Exiguobacterium harbored five ARGs (vanA, vanB, fexA, msr(G), mefF), while Shewanella carried six ARGs (blaOXA-436, adeF, qacl, ANT (2'')-Ia, dfrA1, rsmA). Mutations in gyrA and parC contributed to quinolone resistance in these multidrug-resistant Exiguobacterium and Shewanella. Our findings suggest a potential for ARG transmission across various bacterial species and environments in mariculture. This study emphasized the risk of resistance spread within the mariculture ecosystem.},
}

@article {pmid39827519,
year = {2025},
author = {Lin, W and Zhao, K and Wu, Q and Xu, F and Cui, L and Lin, H and Ye, C and Yu, X},
title = {Biofilms on pipelines shape the microbiome and antibiotic resistome in drinking water.},
journal = {Water research},
volume = {274},
number = {},
pages = {123136},
doi = {10.1016/j.watres.2025.123136},
pmid = {39827519},
issn = {1879-2448},
abstract = {Biofilms in the drinking water distribution system (DWDS) provide shelter for pathogens and antibiotic resistance genes (ARGs). However, how biofilms alter the microbiome and antibiotic resistome in tap water, as well as the precise quantitative evaluation of their health risks, remains unclear. Herein, biofilm reactors supplied with municipal drinking water were operated for 120 days. Metagenomic sequencing identified significant differences in microbial compositions among the biofilms, influent, and effluents. A total of 69-305 ARGs were detected in this DWDS, and ARG abundances increased in the biofilms (0.246-1.576 cpc) and effluents (0.309-0.503 cpc) compared to the influent (0.131 cpc). Metagenomic assembly pinpointed potential pathogenic ARG hosts such as Acinetobacter, Pseudomonas, and Escherichia. The co-occurrence of ARGs and mobile genetic elements indicated potential mobility, which was further supported by transformation assays demonstrating gene transfers at a frequency of 10[-6]. Furthermore, source tracking revealed that biofilms contributed high proportions (19 %-34 %) to the ARG profiles of effluents. The ARG risk scores increased from the influent (20.39) to the effluents (39.85-55.50), with highest level (55.50) in the cast iron effluent. Overall, this study provides novel insights into the impacts of biofilm growth on the microbiome and antibiotic resistome in tap water, along with their potential health risks in the DWDS.},
}

@article {pmid39827261,
year = {2025},
author = {Guccione, C and Patel, L and Tomofuji, Y and McDonald, D and Gonzalez, A and Sepich-Poore, GD and Sonehara, K and Zakeri, M and Chen, Y and Dilmore, AH and Damle, N and Baranzini, SE and Hightower, G and Nakatsuji, T and Gallo, RL and Langmead, B and Okada, Y and Curtius, K and Knight, R},
title = {Incomplete human reference genomes can drive false sex biases and expose patient-identifying information in metagenomic data.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {825},
pmid = {39827261},
issn = {2041-1723},
support = {P30 CA023100/CA/NCI NIH HHS/United States ; NIH/NIGMS T32GM007198//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; NIH Pioneer DP1AT010885//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; NCI U24CA248454//U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI)/ ; CDC award 75D301-22-C-14717//U.S. Department of Health & Human Services | Centers for Disease Control and Prevention (CDC)/ ; AGA Research Scholar Award AGA2022-13-05//AGA Research Foundation/ ; },
mesh = {Humans ; *Metagenomics/methods ; *Genome, Human ; Female ; Male ; Feces/microbiology ; High-Throughput Nucleotide Sequencing/methods ; Microbiota/genetics ; Metagenome/genetics ; Computational Biology/methods ; Skin/microbiology ; },
abstract = {As next-generation sequencing technologies produce deeper genome coverages at lower costs, there is a critical need for reliable computational host DNA removal in metagenomic data. We find that insufficient host filtration using prior human genome references can introduce false sex biases and inadvertently permit flow-through of host-specific DNA during bioinformatic analyses, which could be exploited for individual identification. To address these issues, we introduce and benchmark three host filtration methods of varying throughput, with concomitant applications across low biomass samples such as skin and high microbial biomass datasets including fecal samples. We find that these methods are important for obtaining accurate results in low biomass samples (e.g., tissue, skin). Overall, we demonstrate that rigorous host filtration is a key component of privacy-minded analyses of patient microbiomes and provide computationally efficient pipelines for accomplishing this task on large-scale datasets.},
}

Humans
*Metagenomics/methods
*Genome, Human
Female
Male
Feces/microbiology
High-Throughput Nucleotide Sequencing/methods
Microbiota/genetics
Metagenome/genetics
Computational Biology/methods
Skin/microbiology

@article {pmid39827180,
year = {2025},
author = {Van Goethem, MW and Bezuidt, OKI and Pierneef, R and Vikram, S and Hopkins, DW and Aspray, T and Hall, G and Woodborne, S and Hogg, ID and Northen, TR and Kong, W and Daffonchio, D and Cowan, DA and Van de Peer, Y and Delgado-Baquerizo, M and Makhalanyane, TP},
title = {Novel adaptive immune systems in pristine Antarctic soils.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {2368},
pmid = {39827180},
issn = {2045-2322},
support = {118981//National Research Foundation/ ; 118981//National Research Foundation/ ; 118981//National Research Foundation/ ; 118981//National Research Foundation/ ; 118981//National Research Foundation/ ; 118981//National Research Foundation/ ; 110717//South African National Antarctic Programme/ ; 110717//South African National Antarctic Programme/ ; 110717//South African National Antarctic Programme/ ; 110717//South African National Antarctic Programme/ ; 110717//South African National Antarctic Programme/ ; 110717//South African National Antarctic Programme/ ; },
mesh = {Antarctic Regions ; *Soil Microbiology ; *Phylogeny ; *CRISPR-Cas Systems ; Microbiota/genetics ; Metagenomics/methods ; Adaptive Immunity/genetics ; Genome, Bacterial ; Bacteria/genetics ; Prophages/genetics ; Metagenome ; },
abstract = {Antarctic environments are dominated by microorganisms, which are vulnerable to viral infection. Although several studies have investigated the phylogenetic repertoire of bacteria and viruses in these poly-extreme environments with freezing temperatures, high ultra violet irradiation levels, low moisture availability and hyper-oligotrophy, the evolutionary mechanisms governing microbial immunity remain poorly understood. Using genome-resolved metagenomics, we test the hypothesis that Antarctic poly-extreme high-latitude microbiomes harbour diverse adaptive immune systems. Our analysis reveals the prevalence of prophages in bacterial genomes (Bacteroidota and Verrucomicrobiota), suggesting the significance of lysogenic infection strategies in Antarctic soils. Furthermore, we demonstrate the presence of diverse CRISPR-Cas arrays, including Class 1 arrays (Types I-B, I-C, and I-E), alongside systems exhibiting novel gene architecture among their effector cas genes. Notably, a Class 2 system featuring type V variants lacks CRISPR arrays, encodes Cas1 and Cas2 adaptation module genes. Phylogenetic analysis of Cas12 effector proteins hints at divergent evolutionary histories compared to classified type V effectors and indicates that TnpB is likely the ancestor of Cas12 nucleases. Our findings suggest substantial novelty in Antarctic cas sequences, likely driven by strong selective pressures. These results underscore the role of viral infection as a key evolutionary driver shaping polar microbiomes.},
}

Antarctic Regions
*Soil Microbiology
*Phylogeny
*CRISPR-Cas Systems
Microbiota/genetics
Metagenomics/methods
Adaptive Immunity/genetics
Genome, Bacterial
Bacteria/genetics
Prophages/genetics
Metagenome

@article {pmid39827174,
year = {2025},
author = {Peng, Q and Lin, L},
title = {Comparative metagenomics reveals the metabolic flexibility of coastal prokaryotic microbiomes contributing to lignin degradation.},
journal = {Biotechnology for biofuels and bioproducts},
volume = {18},
number = {1},
pages = {9},
pmid = {39827174},
issn = {2731-3654},
support = {2023YFC3403500//National Key Research and Development Program of China/ ; 32370115//National Natural Science Foundation of China/ ; },
abstract = {Coastal wetlands are rich in terrestrial organic carbon. Recent studies suggest that microbial consortia play a role in lignin degradation in coastal wetlands, where lignin turnover rates are likely underestimated. However, the metabolic potentials of these consortia remain elusive. This greatly hinders our understanding of the global carbon cycle and the "bottom-up" design of synthetic consortia to enhance lignin conversion. Here, we developed two groups of lignin degrading consortia, L6 and L18, through the 6- and 18-month in situ lignin enrichments in the coastal East China Sea, respectively. Lignin degradation by L18 was 3.6-fold higher than L6. Using read-based analysis, 16S rRNA amplicon and metagenomic sequencing suggested that these consortia possessed varied taxonomic compositions, yet similar functional traits. Further comparative metagenomic analysis, based on metagenomic assembly, revealed that L18 harbored abundant metagenome-assembled genomes (MAGs) that encoded diverse and unique lignin degradation gene clusters (LDGCs). Importantly, anaerobic MAGs were significantly enriched in L18, highlighting the role of anaerobic lignin degradation. Furthermore, the generalist taxa, which possess metabolic flexibility, increased during the extended enrichment period, indicating the advantage of generalists in adapting to heterogenous resources. This study advances our understanding of the metabolic strategies of coastal prokaryotic consortia and lays a foundation for the design of synthetic communities for sustainable lignocellulose biorefining.},
}

@article {pmid39827146,
year = {2025},
author = {Angel, NZ and Sullivan, MJ and Alsheikh-Hussain, A and Fang, L and MacDonald, S and Pribyl, A and Wills, B and Tyson, GW and Hugenholtz, P and Parks, DH and Griffin, P and Wood, DLA},
title = {Metagenomics: a new frontier for routine pathology testing of gastrointestinal pathogens.},
journal = {Gut pathogens},
volume = {17},
number = {1},
pages = {4},
pmid = {39827146},
issn = {1757-4749},
abstract = {BACKGROUND: Accurate and comprehensive identification of enteropathogens, causing infectious gastroenteritis, is essential for optimal patient treatment and effective isolation processes in health care systems. Traditional diagnostic techniques are well established and optimised in low-cost formats. However, thorough testing for a wider range of causal agents is time consuming and remains limited to a subset of pathogenic organisms. Metagenomic next-generation sequencing (mNGS) allows the identification of all pathogens in a sample in a single test, without a reliance on culture or introduction of target selection bias. This study aims to determine the ability to routinely apply mNGS testing, in comparison to traditional culture or polymerase chain reaction (PCR) based tests, for the identification of causal pathogens for gastrointestinal infections.

RESULTS: The performance of mNGS, PCR and microscopy, culture and sensitivity (MCS) assays was established using 2,619 prospectively collected faecal samples from patients with symptomology indicative of infectious gastroenteritiss. Commonly experienced pathogens including Aeromonas spp, Campylobacter spp, Salmonella spp and Giardia spp, in single and co-infected patients, were used to establish test outcomes. When testing for these organisms, using the combined result from either or both PCR and MCS testing as the comparator, the mNGS assay had clinically acceptable sensitivity (89.2-100%). Further, the mNGS assay detected 14 additional enteropathogens, that were either not detected or not tested, by initial PCR/MCS testing.

CONCLUSIONS: The advantage of mNGS compared to other syndromic testing systems is the broad range of detectable targets and the ability to interrogate samples without clinician informed or assay specific bias. With the development of newer sequencing assays, it is now feasible to test for a wide range of target organisms in a sample using a single mNGS test. Overall, the mNGS based approach enabled pathogen detection that was comparable to conventional diagnostics and was shown to have the potential to be extended for the detection of many pathogens and genes of clinical interest. In conclusion, the mNGS assay offers an easy, sample to answer workflow with rapid detection of enteropathogens and has the potential to improve diagnosis, therapy and infection control precautions.},
}

@article {pmid39826761,
year = {2025},
author = {Zhou, Z and Liu, S and Saleem, M and Liu, F and Hu, R and Su, H and Dong, D and Luo, Z and Wu, Y and Zhang, Y and He, Z and Wang, C},
title = {Unraveling phase-dependent variations of viral community, virus-host linkage, and functional potential during manure composting process.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {132081},
doi = {10.1016/j.biortech.2025.132081},
pmid = {39826761},
issn = {1873-2976},
abstract = {The temporal dynamics of bacterial and fungal communities significantly impact the manure composting process, yet viral communities are often underexplored. Bulk metagenomes, viromes, metatranscriptomes, and metabolomes were integrated to investigate dynamics of double-stranded DNA (dsDNA) virus and virus-host interactions throughout a 63-day composting process. A total of 473 viral operational taxonomic units (vOTUs), predominantly Caudoviricetes, showed distinct phase-dependent differentiation. In phase I (initial-mesophilic), viruses targeted Gammaproteobacteria and Firmicutes, utilizing restriction-modification (RM) systems. In phase II (thermophilic-maturing), viruses infected Alphaproteobacteria, Chloroflexi, and Planctomycetes, employing CRISPR-Cas systems. Lysogenic and lytic viruses exerting differential effects on bacterial pathogens across phases. Additionally, six types of auxiliary metabolic genes (AMGs) related to galactose and cysteine metabolisms were identified. The homologous lineages of AMGs with bacterial genes, along with the significant temporal correlation observed between virus-host-metabolite interactions, underscore the critical yet often overlooked role of viral communities in modulating microbial metabolisms and pathogenesis within composting ecosystems.},
}

@article {pmid39826760,
year = {2025},
author = {Zhang, Z and Zhang, C and Yang, Y and Zhang, Z and Guo, K and Zhang, X and Qin, Z and Huang, J and Li, Y},
title = {Roles of nitrite in facilitating nitrogen and sulfur conversion in the hybrid bioreactor of Sulfate-reduced ammonium oxidation and anaerobic ammonium oxidation.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {132085},
doi = {10.1016/j.biortech.2025.132085},
pmid = {39826760},
issn = {1873-2976},
abstract = {The hybrid bioreactor combining sulfate-reducing ammonium oxidation (Sulfammox) and Anammox offered potential for simultaneous nitrogen and sulfur removal, but the removal efficiency and microbial mechanism remain unclear. This study demonstrated that in the hybrid bioreactor, the ammonium utilization rate (AUR) of Sulfammox increased by 5.42 times. The promotion of NO2[-] on nitrogen and sulfur conversion in Sulfammox could be attributed to: 1) Increasing extracellular polymers substance (EPS) accelerated the stratification of granule sludge; 2) Increasing the relative abundance of Candidatus Brocadia by 29.55 times and Candidatus Anammoxoglobus by 3.17 times; 3) Upregulating the expression of nitrification (amo, hao and nxr) and sulfur metabolism (sat, aprAB dsr and sox) genes, associated with the pathways NH4[+]→NH2OH → NO2[-]→NO3[-] and SO4[2-]→S[2-]→SO4[2-]. Moreover, Candida Brocadia sapporoensis emerged as a potential specie of Sulfammox, mediating nitrification by hao and nxr, and sulfate reduction by sat and aprAB, thereby enabling electron transfer between nitrogen and sulfur.},
}

@article {pmid39826606,
year = {2025},
author = {Hidalgo, KJ and Cueva, LG and Giachini, AJ and Schneider, MR and Soriano, AU and Baessa, MP and Martins, LF and Oliveira, VM},
title = {Long-term microbial functional responses in soil contaminated with biofuel/fossil fuel blends triggered by different bioremediation treatments.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {125685},
doi = {10.1016/j.envpol.2025.125685},
pmid = {39826606},
issn = {1873-6424},
abstract = {The use of biofuel blends with fossil fuels is widespread globally, raising concerns over novel contamination types in environments impacted by these mixtures. This study investigates the microbial functional in soils contaminated by biofuel and fossil fuel blends and subjected to various bioremediation treatments. Using metagenomic analysis, it was compared hydrocarbon degradation functional profiles across areas polluted with ethanol/gasoline and biodiesel/diesel blends. Results indicate that long-term natural attenuation areas exhibited distinct functional profiles compared to actively bioremediated areas. However, same hydrocarbon degradation genes were enriched across all areas, highlighting functional redundancy despite taxonomic variation in hydrocarbon-degrading microbes. Finally, several of the keystone species found were hydrocarbon degraders, such as members of the families Clostridiaceae and Comamonadaceae, representing potential targets for biostimulation in future remediation efforts. This long-term, field-scale study uniquely focuses on the functional profiles of microbial communities, offering new insights into the bioremediation of complex biofuel/fossil fuel contaminants in situ.},
}

@article {pmid39826254,
year = {2025},
author = {Oliveira de Farias, B and Saggioro, EM and Montenegro, KS and Magaldi, M and Oliveira Santos, HS and Pimenta, RL and Bianco, K and Clementino, MM},
title = {Degradation of plasmid-mediated resistance genes in poultry slaughterhouse wastewater employing a UV/H2O2 process: A metagenomic approach.},
journal = {Chemosphere},
volume = {372},
number = {},
pages = {144109},
doi = {10.1016/j.chemosphere.2025.144109},
pmid = {39826254},
issn = {1879-1298},
abstract = {Poultry slaughterhouse effluents are important hotspots for the spread of both antibiotic-resistant bacteria (ARBs) and antibiotic resistance genes (ARGs), contributing to the antimicrobial resistance (AMR). This study reports a novel investigation to assess the effects of UV/H2O2 treatment on the removal of metaplasmidome-mediated ARGs from poultry slaughterhouse effluents. The effluent samples were subjected at 0.005-0.15 mol L[-1] of H2O2 and pH conditions (3, 5, 7 and 9). Bacterial community (rrs 16S rRNA), Escherichia coli (uidA) antimicrobial resistance (sul1 and int1) and metagenomic plasmid DNA removal were assessed. The UV/H2O2 treatment employing H2O2 = 0.01 mol L[-1] at pH 3 resulted in decreased of several markers (uidA, sul1 and int1). A metaplasmidome indicated the persistence of Burkholderiales order. The UV/H2O2 process reduced plasmid-associated ARGs by 92.5% and 90.4% at pH 3 and 7, respectively. Persistent genes were mainly composed of genes associated with efflux pumps and resistance to beta-lactams and fluoroquinolones. These findings contribute to mitigate the spread of AMR in the agricultural sector, especially through the implementation of more efficient treatments, and reducing the use of antibiotics in livestock farming.},
}

@article {pmid39716651,
year = {2025},
author = {Xu, K and Liu, P and Qin, X and Wang, X and Shi, L and Wang, P and Wu, X and Xiao, H and Zhao, H and Zhong, Y and Zhang, C},
title = {Bacteriophage diversity and novelty revealed by metaviromic analysis of the gut virome in the medicinal Blaps rynchopetera.},
journal = {Microbial pathogenesis},
volume = {199},
number = {},
pages = {107249},
doi = {10.1016/j.micpath.2024.107249},
pmid = {39716651},
issn = {1096-1208},
mesh = {*Bacteriophages/genetics/isolation & purification/classification ; Animals ; *Genome, Viral ; *Virome ; *Gastrointestinal Microbiome ; *Coleoptera/virology ; *High-Throughput Nucleotide Sequencing ; Phylogeny ; DNA Viruses/genetics ; DNA, Viral/genetics ; Metagenomics ; },
abstract = {The medicinal beetle Blaps rynchopetera is recognized for its antibacterial, anti-inflammatory, and immune-regulating properties. This study utilized metaviromics technology to systematically characterize the viral community within the gut of B. rynchopetera through high-throughput sequencing of gut contents, with a specific focus on the composition of its bacteriophage community. The sequencing generated 15,394 contigs exceeding 200 bp, which were assembled into 577 viral operational taxonomic units. Among these, dsDNA viruses constituted 52.33%, ssDNA viruses 11.09%, and Nucleo-Cytoplasmic Large DNA Viruses 11.78%, with 24.80% remaining unknown. Bacteriophages were the predominant viral community members, comprising 65.86% of the total, mainly distributed among five families: Peduoviridae, Schitoviridae, Drexlerviridae, Autographiviridae, and Casjensviridae, with 40.21% of the bacteriophages belonging to unclassified genera. Deep genomic assembly yielded 34 complete bacteriophage sequences, including nine sequences lacking significant similarity to existing viral genomes in BLAST analysis. The remaining sequences were classified as follows: four in Stephanstirmvirinae, three in Schitoviridae, three in Peduoviridae, one in Autographiviridae, one in Guernseyvirinae, one in Herelleviridae, one in Gordonclarkvirinae, one in Chaseviridae, and one in Salmondvirus, while nine bacteriophages remained unclassified. The results indicate that the gut bacteriophage community of B. rynchopetera is diverse and species-rich, exhibiting distinct characteristics compared to bacteriophage communities from honey bees and mosquitoes. These findings lay a foundation for further investigation into virus-microbiota interactions and virus-host relationships within the gut of B. rynchopetera.},
}

*Bacteriophages/genetics/isolation & purification/classification
Animals
*Genome, Viral
*Virome
*Gastrointestinal Microbiome
*Coleoptera/virology
*High-Throughput Nucleotide Sequencing
Phylogeny
DNA Viruses/genetics
DNA, Viral/genetics
Metagenomics

@article {pmid39826029,
year = {2025},
author = {Reuben, RC and Torres, C},
title = {Integrating the milk microbiome signatures in mastitis: milk-omics and functional implications.},
journal = {World journal of microbiology & biotechnology},
volume = {41},
number = {2},
pages = {41},
pmid = {39826029},
issn = {1573-0972},
mesh = {*Milk/microbiology ; Animals ; *Microbiota ; Female ; *Metagenomics/methods ; *Mastitis/microbiology ; Mastitis, Bovine/microbiology ; Proteomics ; Humans ; Cattle ; Bacteria/classification/genetics/isolation & purification ; Dysbiosis/microbiology ; },
abstract = {Mammalian milk contains a variety of complex bioactive and nutritional components and microorganisms. These microorganisms have diverse compositions and functional roles that impact host health and disease pathophysiology, especially mastitis. The advent and use of high throughput omics technologies, including metagenomics, metatranscriptomics, metaproteomics, metametabolomics, as well as culturomics in milk microbiome studies suggest strong relationships between host phenotype and milk microbiome signatures in mastitis. While single omics studies have undoubtedly contributed to our current understanding of milk microbiome and mastitis, they often provide limited information, targeting only a single biological viewpoint which is insufficient to provide system-wide information necessary for elucidating the biological footprints and molecular mechanisms driving mastitis and milk microbiome dysbiosis. Therefore, integrating a multi-omics approach in milk microbiome research could generate new knowledge, improve the current understanding of the functional and structural signatures of the milk ecosystem, and provide insights for sustainable mastitis control and microbiome management.},
}

*Milk/microbiology
Animals
*Microbiota
Female
*Metagenomics/methods
*Mastitis/microbiology
Mastitis, Bovine/microbiology
Proteomics
Humans
Cattle
Bacteria/classification/genetics/isolation & purification
Dysbiosis/microbiology

@article {pmid39825576,
year = {2025},
author = {Fouché, J and Lebre, PH and Melville, HA and Cowan, DA},
title = {The Functional and Structural Succession of Mesic-Grassland Soil Microbiomes Beneath Decomposing Large Herbivore Carcasses.},
journal = {Environmental microbiology},
volume = {27},
number = {1},
pages = {e70022},
doi = {10.1111/1462-2920.70022},
pmid = {39825576},
issn = {1462-2920},
mesh = {*Soil Microbiology ; Animals ; *Microbiota ; *Herbivory ; *Grassland ; *Bacteria/classification/genetics/metabolism ; *RNA, Ribosomal, 16S/genetics ; Soil/chemistry ; Carbon/metabolism ; },
abstract = {Plant detritus is abundant in grasslands but decomposes slowly and is relatively nutrient-poor, whereas animal carcasses are labile and nutrient-rich. Recent studies have demonstrated that labile nutrients from carcasses can significantly alter the long-term soil microbial function at an ecosystem scale. However, there is a paucity of knowledge on the functional and structural response and temporal scale of soil microbiomes beneath large herbivore carcasses. This study compared microbiome functions and structures of soil beneath Connochaetes taurinus (hereafter 'wildebeest') carcasses at various postmortem intervals of decomposition to matched control samples over 18 months. Microbial functions were compared by their community-level physiological profiles determined by sole-carbon substrate utilisation and structures by metagenomic sequences using 16S rRNA gene markers. Overall metabolism and metabolic diversity remained increased and functionally dissimilar to control soils throughout the experimental period, with successive sole-carbon substrate utilisation observed. Conversely, diversity was initially reduced and structurally dissimilar from the control soil but recovered within the experimental period. The study contributes to the knowledge of carcass decomposition by investigating the long-term soil microbiome dynamics resulting from large herbivore carcasses decomposing in a mesic grassland. Microbial functional succession and ecologically relevant bacterial biomarkers of soil beneath the decomposing carcasses were identified for various postmortem intervals.},
}

*Soil Microbiology
Animals
*Microbiota
*Herbivory
*Grassland
*Bacteria/classification/genetics/metabolism
*RNA, Ribosomal, 16S/genetics
Soil/chemistry
Carbon/metabolism

@article {pmid39824927,
year = {2025},
author = {Prasad, BVV and Atmar, RL and Ramani, S and Palzkill, T and Song, Y and Crawford, SE and Estes, MK},
title = {Norovirus replication, host interactions and vaccine advances.},
journal = {Nature reviews. Microbiology},
volume = {},
number = {},
pages = {},
pmid = {39824927},
issn = {1740-1534},
abstract = {Human noroviruses (HuNoVs) are the leading cause of acute gastroenteritis worldwide in all age groups and cause significant disease and economic burden globally. To date, no approved vaccines or antiviral therapies are available to treat or prevent HuNoV illness. Several candidate vaccines are in clinical trials, although potential barriers to successful development must be overcome. Recently, significant advances have been made in understanding HuNoV biology owing to breakthroughs in virus cultivation using human intestinal tissue-derived organoid (or enteroid) cultures, advances in structural biology technology combined with epitope mapping and increased metagenomic sequencing. New and unexpected strain-specific differences in pandemic versus non-pandemic virus structures, replication properties and virus-host interactions, including host factors required for susceptibility to infection and pathogenesis, are discussed.},
}

@article {pmid39824780,
year = {2025},
author = {Wu, X and Peng, J and Malik, AA and Peng, Z and Luo, Y and Fan, F and Lu, Y and Wei, G and Delgado-Baquerizo, M and Liesack, W and Jiao, S},
title = {A Global Relationship Between Genome Size and Encoded Carbon Metabolic Strategies of Soil Bacteria.},
journal = {Ecology letters},
volume = {28},
number = {1},
pages = {e70064},
doi = {10.1111/ele.70064},
pmid = {39824780},
issn = {1461-0248},
support = {42122050//National Science Foundation for Excellent Young Scholars of China/ ; 42277307 & 41977038//National Natural Science Foundation of China/ ; 2021YFD1900500//National Key Research and Development Program of China/ ; },
mesh = {*Soil Microbiology ; *Carbon/metabolism ; *Bacteria/metabolism/genetics ; *Genome, Bacterial ; *Genome Size ; Gene Transfer, Horizontal ; Microbiota ; Biomass ; },
abstract = {Microbial traits are critical for carbon sequestration and degradation in terrestrial ecosystems. Yet, our understanding of the relationship between carbon metabolic strategies and genomic traits like genome size remains limited. To address this knowledge gap, we conducted a global-scale meta-analysis of 2650 genomes, integrated whole-genome sequencing data, and performed a continental-scale metagenomic field study. We found that genome size was tightly associated with an increase in the ratio between genes encoding for polysaccharide decomposition and biomass synthesis that we defined as the carbon acquisition-to-biomass yield ratio (A/Y). We also show that horizontal gene transfer played a major evolutionary role in the expanded bacterial capacities in carbon acquisition. Our continental-scale field study further revealed a significantly negative relationship between the A/Y ratio and soil organic carbon stocks. Our work demonstrates a global relationship between genome size and the encoded carbon metabolic strategies of soil bacteria across terrestrial microbiomes.},
}

*Soil Microbiology
*Carbon/metabolism
*Bacteria/metabolism/genetics
*Genome, Bacterial
*Genome Size
Gene Transfer, Horizontal
Microbiota
Biomass

@article {pmid39824489,
year = {2025},
author = {Yu, Z and Somasundaram, S and Yan, M},
title = {Rumen protozoa and viruses: New insights into their diversity and potential roles through omics lenses-A review.},
journal = {Journal of dairy science},
volume = {},
number = {},
pages = {},
doi = {10.3168/jds.2024-25780},
pmid = {39824489},
issn = {1525-3198},
abstract = {The rumen microbiome is essential for breaking down indigestible plant material, supplying ruminants with most of their metabolizable energy and protein. While research has primarily focused on bacteria and archaea, protozoa and viruses (phages) have only gained attention in recent years. Protozoa contribute to feed digestion and fermentation, but as predators, they regulate microbial populations by lysing large quantities of microbial cells (the primary protein source for ruminants) and influence the amount of microbial protein reaching the small intestines, along with other mechanisms of interactions. While rumen viruses (or phages) are abundant and diverse, they remain the least understood component of the rumen ecosystem. They can profoundly affect the rumen microbiome by directly lysing their hosts and reprogramming host metabolism through multiple mechanisms, including gene transfer and alteration of central carbon metabolism. Recent advances in omics technologies have deepened our understanding of these viruses, revealing their complex roles in rumen function. This review integrates current knowledge and recent discoveries from omics studies, highlighting the transformative impact of omics-based approaches. It also identifies critical knowledge gaps and outlines future research directions, including selective inhibition of rumen protozoa, development of phages as potential intervention tools to manage specific undesirable rumen microbes, and the causal impacts of rumen viruses on microbial dynamics and animal productivity.},
}

@article {pmid39824262,
year = {2025},
author = {Özdemir, A and Sarzhanov, F and Doğruman-Al, F and Gündoğdu, A and Nalbantoğlu, U and Yozgat, A and Yıldız, BD and Büyüktuncer, Z},
title = {Exploring the Complex Interplay of Blastocystis, Morbid Obesity, and Bariatric Surgery on Gut Microbial Dynamics.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {107306},
doi = {10.1016/j.micpath.2025.107306},
pmid = {39824262},
issn = {1096-1208},
abstract = {This study examines Blastocystis dynamics in 15 individuals undergoing sleeve gastrectomy. Molecular detection involved DNA extraction, RT-PCR, and sequencing, while 16S rRNA sequencing via Illumina MiSeq analyzed the intestinal microbiome. Statistical analysis through SPSS considered a significance level of p<0.05. Postoperative colonization of Blastocystis was observed in previously negative individuals, revealing subtypes and shifts in microbial taxa. Blastocystis-positive participants post-bariatric surgery showed a significant increase in Lachnospira, alongside higher abundances of Bacteroides, Oscillospira, Barnesiellaceae, and Rikenellaceae, with reduced Lactobacillus levels compared to Blastocystis-negative individuals. Collective analysis highlighted higher Clostridiales and RF32 in Blastocystis-positive post-surgery individuals, coupled with decreased Enterobacteriaceae. The study challenges previous notions, suggesting a complex interplay between Blastocystis, morbid obesity, and bariatric surgery. Despite limitations, including small sample sizes and absent gut microbiome diversity comparisons, this pioneering research calls for further investigation into the intricate mechanisms and implications for metabolic health. This study is registered at clinicaltrials.gov (NCT05085769).},
}

@article {pmid39824110,
year = {2025},
author = {Gou, Y and Liu, Y and Hu, A and Mao, G and Dong, R and Li, S and Liu, P and Liu, Y and Ji, M},
title = {Dissemination of genes associated with antibiotic resistance and bacterial virulence during ecosystem succession in two Tibetan glacier forefields.},
journal = {The Science of the total environment},
volume = {963},
number = {},
pages = {178514},
doi = {10.1016/j.scitotenv.2025.178514},
pmid = {39824110},
issn = {1879-1026},
abstract = {The release of pathogens and DNA from the cryosphere (glacier, permafrost, and, sea ice) has become a new threat to society and environment. Due to enhanced glacier retreat, the size of glacier forefields has greatly expanded. Herein, we used a combination of metagenomic and metatranscriptomic methods and adopted a sequence-based approach to investigate the distribution and changing patterns of virulence factor genes (VFGs) and antibiotic resistance genes (ARGs) in two glacier forefields. The forefields are separated by approximately 400 km located in the center and north of the Tibetan Plateau, which are used to demonstrate the gene dissemination capacity across short (10 m) and long (730 m) spatial transects. The results revealed a diverse range of actively transcribed VFGs and ARGs. The relative abundance of ARG reduced with ecosystem succession, while that of VFG was similar, suggesting that the ARG is under a stronger environmental selection pressure. VFGs and ARGs were dominated by those associated with adherence and vancomycin resistance, respectively. Notably, toxin production related genes were identified but a low abundance, indicating a low risk to health in glacier forefields. The dissemination risks were low for both VFGs and ARGs, which was strongly constrained by dispersal limitation. Additionally, the limited dissemination was mainly through vertical transmission, instead of horizontal transfer. In conclusion, the sequence-based approach revealed a low risk to health in recently deglaciated areas, with the risk of VFGs and ARGs being disseminated into downstream ecosystems remaining low.},
}

@article {pmid39824023,
year = {2025},
author = {Guo, X and Yu, P and Guo, J and Zhao, HP and Lai, CY},
title = {Viral auxiliary roles in hydrolytic and biosynthetic metabolism regulate prokaryotic microbial interactions in anaerobic digestion.},
journal = {Water research},
volume = {274},
number = {},
pages = {123140},
doi = {10.1016/j.watres.2025.123140},
pmid = {39824023},
issn = {1879-2448},
abstract = {Anaerobic digestion (AD) viruses have gained recognition as significant regulators of microbial interactions within AD communities, yet their ecological roles remain largely unexplored. In this study, we investigated the ecological roles of AD viruses in regulating microbial interactions among syntrophic hosts. We recovered 3921 diverse viral sequences from four full-scale anaerobic digesters and confirmed their widespread presence across 127 global metagenomic sampling sites (with >95 % sequence similarity), underscoring the ubiquity of prokaryotic viruses in AD-related systems. Through the construction of virus-prokaryote interactions (66.8 % validated at the transcriptional level) and analysis of viral-host transcriptional abundances, we identified significant associations between AD viruses and key processes, including hydrolysis, acidogenesis, and methanogenesis. Notably, polyvalent viruses were found to interact with both hydrolytic and fermentative communities. We further characterized viral auxiliary metabolism, hydrolytic substrate spectra, and microbial auxotrophy, showing that viruses not only could enhance the breakdown of complex substrates (e.g., cellulose, chitin, peptidoglycan) but also potentially supported the biosynthesis of essential nutrients (e.g., cysteine, methionine, heme, and cobalamin). These activities were proposed to regulate resource fluxes through alternating lysogenic and lytic cycles. Phylogenetic analysis of viral gene and horizontal gene transfer (HGT) identification suggest that AD viruses employ promiscuous infection on syntrophic hosts, potentially as an adaptive evolutionary strategy in the AD ecosystem. This study provides new insights into the ecological roles of AD viruses, highlighting their potential impact on the stability and functionality of AD systems.},
}

@article {pmid39823425,
year = {2025},
author = {Wang, F and Wang, X and Duan, J and Yang, S and Wei, J and Yang, S and Zheng, Q},
title = {The impact of straw and its post-pyrolysis incorporation on functional microbes and mineralization of organic carbon in yellow paddy soil.},
journal = {PloS one},
volume = {20},
number = {1},
pages = {e0314984},
doi = {10.1371/journal.pone.0314984},
pmid = {39823425},
issn = {1932-6203},
mesh = {*Soil Microbiology ; *Carbon/metabolism ; *Soil/chemistry ; *Charcoal/chemistry ; *Fertilizers ; Pyrolysis ; Oryza/growth & development/metabolism ; Carbon Cycle ; China ; },
abstract = {The impact of straw and biochar on carbon mineralization and the function of carbon cycle genes in paddy soil is important for soil nutrient management and the transformation of carbon pools. This research is based on a five-year field experiment with four treatments: no fertilizer application (CK); chemical fertilizer only (NPK); straw combined with chemical fertilizer (NPKS); and biochar combined with chemical fertilizer (NPKB). By integrating indoor mineralization culture with metagenomic approaches, we analyzed the response of organic carbon mineralization and carbon cycle genes in typical paddy soil from Guizhou Province, China, to different fertilization treatments. The result shows that the various fertilization treatments significantly increased the levels of soil organic carbon, dissolved organic carbon, microbial biomass carbon, and readily oxidizable organic carbon. The NPKS treatment increased the rate of soil organic carbon mineralization, whereas the NPKB treatment decreased it. Overall, the NPK and NPKB treatments increased the relative abundance of carbon fixation genes. The NPKS treatment increased the relative abundance of carbon degradation genes. The NPKS treatment increased the abundance of Proteobacteria, whereas the NPKB treatment decreased the abundance of Actinobacteria. Biochar after straw pyrolysis can reduce carbon loss and enhance sequestration of soil carbon, whereas straw decreases soil organic carbon stability, accelerating the transformation of soil carbon pools. Future research should encompass long-term impact assessments to comprehensively understand the enduring effects of these fertilization treatments on soil carbon mineralization and the function of carbon cycle genes.},
}

*Soil Microbiology
*Carbon/metabolism
*Soil/chemistry
*Charcoal/chemistry
*Fertilizers
Pyrolysis
Oryza/growth & development/metabolism
Carbon Cycle
China

@article {pmid39823339,
year = {2025},
author = {van der Loos, LM and Steinhagen, S and Stock, W and Weinberger, F and D'hondt, S and Willems, A and De Clerck, O},
title = {Low functional change despite high taxonomic turnover characterizes the Ulva microbiome across a 2000-km salinity gradient.},
journal = {Science advances},
volume = {11},
number = {3},
pages = {eadr6070},
doi = {10.1126/sciadv.adr6070},
pmid = {39823339},
issn = {2375-2548},
mesh = {*Ulva/genetics ; *Salinity ; *Microbiota ; Bacteria/genetics/classification/metabolism ; Metagenome ; Metagenomics/methods ; },
abstract = {The green seaweed Ulva relies on associated bacteria for morphogenesis and is an important model to study algal-bacterial interactions. Ulva-associated bacteria exhibit high turnover across environmental gradients, leading to the hypothesis that bacteria contribute to the acclimation potential of the host. However, the functional variation of these bacteria in relation to environmental changes remains unclear. We analyzed 91 Ulva samples across a 2000-kilometer Atlantic-Baltic Sea salinity gradient using metagenomic sequencing. Metabolic reconstruction of 639 metagenome-assembled genomes revealed widespread potential for carbon, nitrogen, sulfur, and vitamin metabolism. Although the R[2] value for salinity explained 70% of taxonomic variation, it accounted only for 17% of functional variation. The limited variation was attributed to typical high-salinity bacteria exhibiting enrichment in genes for thiamine, pyridoxal, and betaine biosynthesis, which likely contribute to stress mitigation and osmotic homeostasis in response to salinity variations. Our results emphasize the importance of functional profiling to understand the seaweed holobiont and its collective response to environmental change.},
}

*Ulva/genetics
*Salinity
*Microbiota
Bacteria/genetics/classification/metabolism
Metagenome
Metagenomics/methods

@article {pmid39823337,
year = {2025},
author = {Wu, D and Seshadri, R and Kyrpides, NC and Ivanova, NN},
title = {A metagenomic perspective on the microbial prokaryotic genome census.},
journal = {Science advances},
volume = {11},
number = {3},
pages = {eadq2166},
doi = {10.1126/sciadv.adq2166},
pmid = {39823337},
issn = {2375-2548},
mesh = {*Metagenomics/methods ; *Phylogeny ; *Archaea/genetics/classification ; *Bacteria/genetics/classification ; *Metagenome ; Humans ; Genome, Archaeal ; Genome, Bacterial ; Genome, Microbial ; },
abstract = {Following 30 years of sequencing, we assessed the phylogenetic diversity (PD) of >1.5 million microbial genomes in public databases, including metagenome-assembled genomes (MAGs) of uncultivated microbes. As compared to the vast diversity uncovered by metagenomic sequences, cultivated taxa account for a modest portion of the overall diversity, 9.73% in bacteria and 6.55% in archaea, while MAGs contribute 48.54% and 57.05%, respectively. Therefore, a substantial fraction of bacterial (41.73%) and archaeal PD (36.39%) still lacks any genomic representation. This unrepresented diversity manifests primarily at lower taxonomic ranks, exemplified by 134,966 species identified in 18,087 metagenomic samples. Our study exposes diversity hotspots in freshwater, marine subsurface, sediment, soil, and other environments, whereas human samples yielded minimal novelty within the context of existing datasets. These results offer a roadmap for future genome recovery efforts, delineating uncaptured taxa in underexplored environments and underscoring the necessity for renewed isolation and sequencing.},
}

*Metagenomics/methods
*Phylogeny
*Archaea/genetics/classification
*Bacteria/genetics/classification
*Metagenome
Humans
Genome, Archaeal
Genome, Bacterial
Genome, Microbial

@article {pmid39823335,
year = {2025},
author = {Santoro, EP and Cárdenas, A and Villela, HDM and Vilela, CLS and Ghizelini, AM and Duarte, GAS and Perna, G and Saraiva, JP and Thomas, T and Voolstra, CR and Peixoto, RS},
title = {Inherent differential microbial assemblages and functions associated with corals exhibiting different thermal phenotypes.},
journal = {Science advances},
volume = {11},
number = {3},
pages = {eadq2583},
doi = {10.1126/sciadv.adq2583},
pmid = {39823335},
issn = {2375-2548},
mesh = {*Anthozoa/microbiology/metabolism/physiology ; Animals ; *Microbiota ; *Phenotype ; Symbiosis ; Metagenomics/methods ; Bacteria/metabolism/genetics ; },
abstract = {Certain coral individuals exhibit enhanced resistance to thermal bleaching, yet the specific microbial assemblages and their roles in these phenotypes remain unclear. We compared the microbial communities of thermal bleaching-resistant (TBR) and thermal bleaching-sensitive (TBS) corals using metabarcoding and metagenomics. Our multidomain approach revealed stable distinct microbial compositions between thermal phenotypes. Notably, TBR corals were inherently enriched with microbial eukaryotes, particularly Symbiodiniaceae, linked to photosynthesis, and the biosynthesis of antibiotic and antitumor compounds and glycosylphosphatidylinositol-anchor proteins, crucial for cell wall regulation and metabolite exchange. In contrast, TBS corals were dominated by bacterial metabolic genes related to nitrogen, amino acid, and lipid metabolism. The inherent microbiome differences between TBR and TBS corals, already observed before thermal stress, point to distinct holobiont phenotypes associated to thermal bleaching resistance, offering insights into mechanisms underlying coral response to climate-induced stress.},
}

*Anthozoa/microbiology/metabolism/physiology
Animals
*Microbiota
*Phenotype
Symbiosis
Metagenomics/methods
Bacteria/metabolism/genetics

@article {pmid39823322,
year = {2025},
author = {Gebert, JT and Scribano, FJ and Engevik, KA and Huleatt, EM and Eledge, MR and Dorn, LE and Philip, AA and Kawagishi, T and Greenberg, HB and Patton, JT and Hyser, JM},
title = {Viroporin activity is necessary for intercellular calcium signals that contribute to viral pathogenesis.},
journal = {Science advances},
volume = {11},
number = {3},
pages = {eadq8115},
doi = {10.1126/sciadv.adq8115},
pmid = {39823322},
issn = {2375-2548},
mesh = {Animals ; *Rotavirus/pathogenicity ; Mice ; *Viral Nonstructural Proteins/metabolism/genetics ; *Calcium Signaling ; *Rotavirus Infections/virology/metabolism ; Calcium/metabolism ; Humans ; Viroporin Proteins/metabolism/genetics ; Glycoproteins/metabolism/genetics ; Toxins, Biological/metabolism ; Immunity, Innate ; Host-Pathogen Interactions ; Disease Models, Animal ; Cell Line ; },
abstract = {Viruses engage in a variety of processes to subvert host defenses and create an environment amenable to replication. Here, using rotavirus as a prototype, we show that calcium conductance out of the endoplasmic reticulum by the virus encoded ion channel, NSP4, induces intercellular calcium waves that extend beyond the infected cell and contribute to pathogenesis. Viruses that lack the ability to induce this signaling show diminished viral shedding and attenuated disease in a mouse model of rotavirus diarrhea. This implicates nonstructural protein 4 (NSP4) as a virulence factor and provides mechanistic insight into its mode of action. Critically, this signaling induces a transcriptional signature characteristic of interferon-independent innate immune activation, which is not observed in response to a mutant NSP4 that does not conduct calcium. This implicates calcium dysregulation as a means of pathogen recognition, a theme broadly applicable to calcium-altering pathogens beyond rotavirus.},
}

Animals
*Rotavirus/pathogenicity
Mice
*Viral Nonstructural Proteins/metabolism/genetics
*Calcium Signaling
*Rotavirus Infections/virology/metabolism
Calcium/metabolism
Humans
Viroporin Proteins/metabolism/genetics
Glycoproteins/metabolism/genetics
Toxins, Biological/metabolism
Immunity, Innate
Host-Pathogen Interactions
Disease Models, Animal
Cell Line

@article {pmid39822514,
year = {2024},
author = {Tan, L and Chen, B and Xu, Y and Wen, Z and Feng, B and Chen, D and Wang, X and Cui, X and Hu, D},
title = {Clinical value of metagenomic sequencing in system evaluation of potential donors and donor-derived infection in kidney transplantation.},
journal = {American journal of translational research},
volume = {16},
number = {12},
pages = {7707-7715},
doi = {10.62347/ZNKM3687},
pmid = {39822514},
issn = {1943-8141},
abstract = {OBJECTIVE: To explore the application and the clinical value of metagenomic sequencing in system evaluation of potential kidney donors, along with donor-derived infection in kidney transplantation.

METHODS: A prospective study was conducted on 40 voluntary renal donors in Ningbo Urology and Kidney Disease hospital from January 2021 to August 2023. The results of donor pathogen fed back by metagenomic sequencing were analyzed to understand the clinical significance of metagenomic sequencing in donor evaluation.

RESULTS: (1) Detection rate of pathogens. The probability of pathogens detected by traditional laboratories and metagenomic sequencing was 72.50% and 90.00%, respectively. Compared with traditional laboratory tests, metagenomic sequencing detected significantly more pathogens (P < 0.05). The percentage of co-infection of multiple pathogens detected by traditional laboratory tests (31.03%) in donors was significantly lower than that detected by metagenomic sequencing (88.89%) (P < 0.001). Traditional laboratory tests detected bacteria in 20 donors and fungi in 9 donors, but its performance on detecting viruses and mycoplasmas was limited. Metagenomic sequencing detected bacteria in 30 donors, fungi in 12 donors, viruses in 9 donors, and mycoplasmas in 9 donors. The positive rates of bacteria, viruses and mycoplasmas detected by metagenomic sequencing were significantly higher than those detected by traditional laboratory tests (P < 0.05). (2) Predictive value. The sensitivity, specificity, positive predictive value, and negative predictive value of metagenomic sequencing were 97.30%, 100.00%, 100% and 75.00%, respectively, while those of traditional laboratory tests were 78.39%, 100.00%, 100.00% and 27.27%, respectively. (3) The diagnostic efficiency of metagenomic sequencing was superior to that of traditional laboratory tests. (4) Time needed for result feedback. From specimen collection to the result feedback given to the clinician, the time required for traditional laboratory tests was longer than that for metagenomic sequencing, with significant differences (P < 0.001). In addition, the required time for traditional laboratory tests in detecting bacterial positivity was longer than that for metagenomic sequencing, with a statistically significant difference (P < 0.001).

CONCLUSION: This study probes into the application of metagenomic sequencing in the evaluation of donor pathogens, especially in negative samples detected by traditional laboratory tests. Our findings suggest that metagenomic sequencing can improve the sensitivity and specificity of diagnosis, increase the detection rate of pathogens, and minimize the turnover time.},
}

@article {pmid39822451,
year = {2024},
author = {Hazan, S and Bao, G and Vidal, A and Sfera, A},
title = {Gut Microbiome Alterations Following Oral Serum-Derived Bovine Immunoglobulin Administration in the Management of Dysbiosis.},
journal = {Cureus},
volume = {16},
number = {12},
pages = {e75884},
doi = {10.7759/cureus.75884},
pmid = {39822451},
issn = {2168-8184},
abstract = {INTRODUCTION: Inflammatory bowel disease (IBD) and irritable bowel syndrome (IBS) are chronic disorders of the gastrointestinal tract associated with gut microbiota dysbiosis and inflammation. Serum-derived bovine immunoglobulin (SBI) is used to manage IBS and IBD and has shown prebiotic-like effects in ex vivo models. Re-establishing a healthy gut microbiome with novel treatments like SBI could help treat the underlying causes of these diseases leading to higher and sustained patient response. The objective of this study was to assess whether supplementation with SBI would improve dysbiosis in IBD and IBS patients.

METHODS: This cross-sectional, single-site study had each participant serving as their own control. Stool samples from 18 patients with either IBS or IBD were analyzed before and after SBI administration. The relative abundance of bacterial diversity was assessed using metagenomic next-generation sequencing-based profiling.

RESULTS: Species diversity statistically significantly increased for measures of richness (Shannon index) (p < 0.0082) and evenness (Gini-Simpson index) (p < 0.0017). Phylum-level changes showed a 2.7-fold increase in Actinobacteria (p = 0.0181), 0.66-fold decrease in Bacteroidetes (p = 0.0401), and 0.38-fold decrease in Proteobacteria (p = 0.0071) after treatment with SBI. At the genus level, the relative abundances showed decreased Alistipes (p = 0.0121) and decreased Bacteroides (p = 0.0108) as well as increased Bifidobacterium (p = 0.0204), compared to pre-treatment levels. At the genus level, a 1.8-fold increase of Bifidobacterium breve (p = 0.0225) occurred upon treatment with SBI.

CONCLUSION: These findings confirm the prebiotic effects of SBI and suggest an additional mechanism of action in managing IBD and IBS symptoms. SBI re-establishes homeostasis in patients with IBD and IBS by decreasing Proteobacteria and increasing Bifidobacteria and species diversity. These insights highlight the promise of new therapeutic strategies for managing IBS and IBD by targeting dysbiosis and underscore the potential of personalized treatments based on a patient's gut microbiome profile.},
}

@article {pmid39821458,
year = {2025},
author = {Mathew, DE and Soni, A and Dhimmar, A and Gajjar, A and Parab, AS and Phakatkar, SS and Sahastrabudhe, H and Manohar, CS and Shinde, PB and Mantri, VA},
title = {Characterization, Bio-Prospection, and Comparative Metagenomics of Bacterial Communities Revealing the Predictive Functionalities in Wild and Cultured Samples of Industrially Important Red Seaweed Gracilaria dura.},
journal = {Current microbiology},
volume = {82},
number = {2},
pages = {85},
pmid = {39821458},
issn = {1432-0991},
support = {HCP 024//Council for Scientific and Industrial Research, India/ ; },
mesh = {*Gracilaria/microbiology ; *Metagenomics ; *Bacteria/genetics/classification/isolation & purification ; *Phylogeny ; Microbiota ; Seaweed/microbiology ; Metagenome ; Proteobacteria/genetics/isolation & purification/classification ; RNA, Ribosomal, 16S/genetics ; },
abstract = {The present study explores the microbial community associated with the industrially important red seaweed Gracilaria dura to determine the diversity and biotechnological potential through culture and metagenomics approaches. In the first part of the investigation, we isolated and characterized 75 bacterial morphotypes, with varied colony characteristics and metabolic diversity from the wild seaweed. Phylogenetic analysis identified isolates in Proteobacteria, Firmicutes, and Actinobacteria, with Bacillus sp. being prevalent. B. licheniformis and Streptomyces sp. were notable in producing important enzymes like L-asparaginase, and polysaccharide lyases. Antimicrobial activity was significant in 21% of isolates, effective against seaweed pathogens such as Vibrio and Xanthomonas. Rhodococcus pyridinivorans showed strong pyridine degradation, suggesting bioremediation potential. Several isolates exhibited phosphate solubilization and nitrate indicating the roles of bacteria as algal growth promoters and biocontrol agents. Subsequent metagenome analysis of wild and cultured samples provides insights into bacterial communities associated with G. dura, revealing their distribution and functional roles. Proteobacteria (~ 95%) dominated the communities, further bacterial groups involved in algal growth, carpospore liberation, stress resistance, biogeochemical cycles, and biomedical applications were identified. A notable difference in bacteriomes was observed between the samples, with 25% remaining stable. The samples are cultured in the lab to generate seedlings for farming and serve as germplasm storage during the monsoon season. Microbiome surveys are crucial for understanding the association of pathogens and the overall health of the seedlings, supporting successful seaweed farming. Our findings provide valuable insights into G. dura-associated microbial communities and their role in algal growth, which has aquacultural implications.},
}

*Gracilaria/microbiology
*Metagenomics
*Bacteria/genetics/classification/isolation & purification
*Phylogeny
Microbiota
Seaweed/microbiology
Metagenome
Proteobacteria/genetics/isolation & purification/classification
RNA, Ribosomal, 16S/genetics

@article {pmid39821111,
year = {2025},
author = {Mohammed, MM and Sekar, P and Al Jamal, J and Abu Taha, L and Bachir, A and Al Kawas, S},
title = {Comparative analysis of salivary antimicrobial resistance genes in dental students: A PCR and questionnaire study.},
journal = {PloS one},
volume = {20},
number = {1},
pages = {e0315450},
doi = {10.1371/journal.pone.0315450},
pmid = {39821111},
issn = {1932-6203},
mesh = {Humans ; Male ; Female ; *Saliva/microbiology ; Adult ; *Students, Dental ; Surveys and Questionnaires ; Young Adult ; Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Genes, Bacterial ; Bacteria/genetics ; DNA, Bacterial/genetics ; },
abstract = {INTRODUCTION: Antimicrobial resistance (AMR) is a major global healthcare challenge, with limited treatment options due to the decline in new antibiotics. The human oral cavity, home to diverse bacteria, is crucial for maintaining oral and systemic health. Recent studies suggest that saliva may serve as a reservoir for AMR genes. However, there is a lack of research on this topic in the UAE and most Middle Eastern countries. This study investigated the presence of AMR genes in saliva from forty 5th-year dental students and forty 1st-year dental students.

MATERIALS & METHODS: Demographic and health information was collected via a 28-question structured questionnaire. Real-Time PCR was used to detect a panel of preselected AMR genes in bacterial DNA from saliva samples.

RESULTS: Participants' ages ranged from 20 to 31 years, with 41 females and 39 males. The prevalence of AMR genes varied: blaCTX-M grp 1 (29%), blaCTX-M grp 9 (85%), blaCTX-M grp 8 (39%), blaOXA-48 (69%), blaKPC-1 (6%), blaVIM (49%), DHA (53%), ACC (25%), MOX (59%), armA (83%), and rmtB (63%). There were no significant differences in AMR gene prevalence between 5th-year and 1st-year students or between male and female students.

CONCLUSION: The study revealed a high occurrence of AMR genes in the oral microbiome. Comprehensive metagenomic analysis is recommended to further evaluate the prevalence and relative abundance of these genes in the UAE population. Establishing a database for these ARGs could aid in effective future monitoring.},
}

Humans
Male
Female
*Saliva/microbiology
Adult
*Students, Dental
Surveys and Questionnaires
Young Adult
Drug Resistance, Bacterial/genetics
Anti-Bacterial Agents/pharmacology
Genes, Bacterial
Bacteria/genetics
DNA, Bacterial/genetics

@article {pmid39820425,
year = {2025},
author = {Huang, H and Cheng, Z and Wang, Y and Qiao, G and Wang, X and Yue, Y and Gao, Q and Peng, S},
title = {Multi-omics dataset of individual variations in growth performance of large yellow croaker.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {90},
pmid = {39820425},
issn = {2052-4463},
mesh = {Animals ; *Perciformes/genetics/growth & development ; *Gastrointestinal Microbiome ; Metabolomics ; Transcriptome ; Metagenomics ; China ; Multiomics ; },
abstract = {Large yellow croaker (Larimichthys crocea) is a highly economically important marine fish species in China. However, substantial individual variations in growth performance have emerged as a limiting factor for the sustainable development of the large yellow croaker industry. Gut microbiota plays a crucial role in fish growth and development by regulating metabolic processes. To explore these dynamics, we employed metagenomics, transcriptomics, and untargeted metabolomics to comprehensively analyze the structure of the intestinal microbiome and its relationship with intestinal metabolism and host gene expression. We constructed association models for "gut microbiota-differentially expressed genes", "differentially expressed genes-metabolites," and "gut microbiota-metabolites." Sequencing data and LC-MS/MS raw data have been deposited in NCBI and MetaboLights databases for public access. Our findings offer critical insights into the molecular mechanisms underlying growth variations in L. crocea and provide valuable data for the selective breeding of improved strains.},
}

Animals
*Perciformes/genetics/growth & development
*Gastrointestinal Microbiome
Metabolomics
Transcriptome
Metagenomics
China
Multiomics

@article {pmid39819730,
year = {2025},
author = {Liu, X and Tang, Y and Chen, H and Liu, JX and Sun, HZ},
title = {Rumen DNA virome and its relationship with feed efficiency in dairy cows.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {14},
pmid = {39819730},
issn = {2049-2618},
support = {32322077//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Rumen/virology/microbiology ; Cattle ; *Virome ; *High-Throughput Nucleotide Sequencing ; *Animal Feed/virology ; Female ; DNA, Viral/genetics ; Metagenome ; Viruses/classification/genetics/isolation & purification ; },
abstract = {BACKGROUND: The rumen harbors a diverse virome that interacts with other microorganisms, playing pivotal roles in modulating metabolic processes within the rumen environment. However, the characterization of rumen viruses remains incomplete, and their association with production traits, such as feed efficiency (FE), has not been documented. In this study, rumen fluid from 30 Chinese Holstein dairy cows was analyzed using next-generation sequencing (NGS) and High-Fidelity (HiFi) sequencing to elucidate the rumen DNA virome profile and uncover potential viral mechanisms influencing FE.

RESULTS: Integrated NGS and HiFi sequencing enhanced the length, completeness, and resolution of viral operational taxonomic units (vOTUs) compared to NGS. A total of 6,922 vOTUs were identified, including 4,716 lytic and 1,961 temperate vOTUs. At the family level, lytic viruses were predominantly from Siphoviridae (30.35%) and Schitoviridae (23.93%), while temperate viruses were primarily Siphoviridae (67.21%). The study annotated 2,382 auxiliary metabolic genes (AMGs), comprising 1,752 lytic virus-associated AMGs across 51 functional categories and 589 temperate virus-associated AMGs across 29 categories. Additionally, 2,232 vOTU-host metagenome-assembled genome (hMAG) linkages were predicted, with Firmicutes_A (33.60%) and Bacteroidota (33.24%) being the most prevalent host phyla. Significant differences in viral populations were observed between high and low FE groups across multiple taxonomic levels (P < 0.05). Two pathways were proposed to explain how rumen viruses might modulate FE: (1) Lytic viruses could lyse beneficial host bacteria linked to favorable cattle phenotypes, such as vOTU1836 targeting Ruminococcaceae, resulting in diminished organic acid production and consequently lower FE; (2) AMG-mediated host metabolism modulation, exemplified by GT2 carried by vOTU0897, which may enhance Lachnospiraceae fermentation capacity, increasing organic acid production and thereby improving FE.

CONCLUSIONS: This study constructed a comprehensive rumen DNA virome profile for Holstein dairy cows, elucidating the structural and functional complexity of rumen viruses, the roles of AMGs, and vOTU-hMAG linkages. The integration of these data offers novel insights into the mechanisms by which rumen viruses may regulate nutrient utilization, potentially influencing FE in dairy cows. Video Abstract.},
}

Animals
*Rumen/virology/microbiology
Cattle
*Virome
*High-Throughput Nucleotide Sequencing
*Animal Feed/virology
Female
DNA, Viral/genetics
Metagenome
Viruses/classification/genetics/isolation & purification

@article {pmid39819379,
year = {2025},
author = {Terzin, M and Robbins, SJ and Bell, SC and Lê Cao, KA and Gruber, RK and Frade, PR and Webster, NS and Yeoh, YK and Bourne, DG and Laffy, PW},
title = {Gene content of seawater microbes is a strong predictor of water chemistry across the Great Barrier Reef.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {11},
pmid = {39819379},
issn = {2049-2618},
mesh = {*Seawater/microbiology ; *Coral Reefs ; *Bacteria/classification/genetics/isolation & purification ; *Metagenomics/methods ; *Microbiota/genetics ; Archaea/genetics/classification ; Salinity ; Seasons ; Synechococcus/genetics/classification ; },
abstract = {BACKGROUND: Seawater microbes (bacteria and archaea) play essential roles in coral reefs by facilitating nutrient cycling, energy transfer, and overall reef ecosystem functioning. However, environmental disturbances such as degraded water quality and marine heatwaves, can impact these vital functions as seawater microbial communities experience notable shifts in composition and function when exposed to stressors. This sensitivity highlights the potential of seawater microbes to be used as indicators of reef health. Microbial indicator analysis has centered around measuring the taxonomic composition of seawater microbial communities, but this can obscure heterogeneity of gene content between taxonomically similar microbes, and thus, microbial functional genes have been hypothesized to have more scope for predictive potential, though empirical validation for this hypothesis is still pending. Using a metagenomics study framework, we establish a functional baseline of seawater microbiomes across offshore Great Barrier Reef (GBR) sites to compare the diagnostic value between taxonomic and functional information in inferring continuous physico-chemical metrics in the surrounding reef.

RESULTS: Integrating gene-centric metagenomics analyses with 17 physico-chemical variables (temperature, salinity, and particulate and dissolved nutrients) across 48 reefs revealed that associations between microbial functions and environmental parameters were twice as stable compared to taxonomy-environment associations. Distinct seasonal variations in surface water chemistry were observed, with nutrient concentrations up to threefold higher during austral summer, explained by enhanced production of particulate organic matter (POM) by photoautotrophic picocyanobacteria, primarily Synechococcus. In contrast, nutrient levels were lower in winter, and POM production was also attributed to Prochlorococcus. Additionally, heterotrophic microbes (e.g., Rhodospirillaceae, Burkholderiaceae, Flavobacteriaceae, and Rhodobacteraceae) were enriched in reefs with elevated dissolved organic carbon (DOC) and phytoplankton-derived POM, encoding functional genes related to membrane transport, sugar utilization, and energy metabolism. These microbes likely contribute to the coral reef microbial loop by capturing and recycling nutrients derived from Synechococcus and Prochlorococcus, ultimately transferring nutrients from picocyanobacterial primary producers to higher trophic levels.

CONCLUSION: This study reveals that functional information in reef-associated seawater microbes more robustly associates with physico-chemical variables than taxonomic data, highlighting the importance of incorporating microbial function in reef monitoring initiatives. Our integrative approach to mine for stable seawater microbial biomarkers can be expanded to include additional continuous metrics of reef health (e.g., benthic cover of corals and macroalgae, fish counts/biomass) and may be applicable to other large-scale reef metagenomics datasets beyond the GBR. Video Abstract.},
}

*Seawater/microbiology
*Coral Reefs
*Bacteria/classification/genetics/isolation & purification
*Metagenomics/methods
*Microbiota/genetics
Archaea/genetics/classification
Salinity
Seasons
Synechococcus/genetics/classification

@article {pmid39818083,
year = {2025},
author = {Pandey, B and Pandey, AK and Bhardwaj, L and Dubey, SK},
title = {Biodegradation of acetaminophen: Current knowledge and future directions with mechanistic insights from omics.},
journal = {Chemosphere},
volume = {372},
number = {},
pages = {144096},
doi = {10.1016/j.chemosphere.2025.144096},
pmid = {39818083},
issn = {1879-1298},
abstract = {Acetaminophen (APAP), one of the most frequently used antipyretic and analgesic medications, has recently grown into a persistent organic contaminant of emerging concern due to its over-the-counter and widespread use. The excessive accumulation of APAP and its derivatives in various environmental matrices is threatening human health and the ecosystem. The complexity of APAP and its intermediates augments the need for adequate innovative and sustainable strategies for the remediation of contaminated environments. Bioremediation serves as an efficient, eco-friendly, cost-effective, and sustainable approach to mitigate the toxic impacts of APAP. The present review provides comprehensive insights into the ecotoxicity of APAP, its complex biodegradation pathways, and the various factors influencing biodegradation. The omics approaches viz., genomics/metagenomics, transcriptomics/metatranscriptomics, proteomics, and metabolomics have emerged as powerful tools for understanding the diverse APAP-degraders, degradation-associated genes, enzymatic pathways, and metabolites. The outcomes revealed amidases, deaminases, oxygenases, and dioxygenases as the lead enzymes mediating degradation via 4-aminophenol, hydroquinone, hydroxyquinol, 3-hydroxy-cis, cis-muconate, etc. as the major intermediates. Overall, a holistic approach with the amalgamation of omics aspects would accelerate the bioaugmentation processes and play a significant role in formulating strategies for remediating and reducing the heavy loads of acetaminophen from the environmental matrices.},
}

@article {pmid39817161,
year = {2024},
author = {Aththanayaka, AMMTB and Dayananda, BSWMTB and Ranasinghe, HAK and Amarasinghe, LD},
title = {Evolution of dirofilariasis diagnostic techniques from traditional morphological analysis to molecular-based techniques: a comprehensive review.},
journal = {Frontiers in parasitology},
volume = {3},
number = {},
pages = {1427449},
pmid = {39817161},
issn = {2813-2424},
abstract = {Dirofilariasis, caused by the nematode Dirofilaria spp., poses significant challenges in diagnosis due to its diverse clinical manifestations and complex life cycle. This comprehensive literature review focuses on the evolution of diagnostic methodologies, spanning from traditional morphological analyses to modern emerging techniques in the context of dirofilariasis diagnosis. The review traces the historical progression of diagnostic modalities, encompassing traditional approaches such as microscopic examination, serological tests (including ELISA and IFA), radiographic imaging, ultrasonography, and necropsy, which laid the foundation for subsequent advancements. The integration of molecular diagnostics marks a significant turning point in dirofilariasis diagnosis with the adoption of polymerase chain reaction (PCR) assays and real-time PCR (qPCR) facilitating enhanced sensitivity and specificity. Furthermore, recent strides in next-generation sequencing (NGS) technologies, including whole-genome sequencing (WGS), targeted sequencing (TS), metagenomic sequencing (MS), and RNA sequencing (transcriptome sequencing), have revolutionized the landscape of dirofilariasis diagnostics. Emerging techniques such as loop-mediated isothermal amplification (LAMP), digital PCR (dPCR), and digital microfluidics are also explored for their potential to augment diagnostic accuracy. The review addresses challenges associated with standardizing molecular protocols, tackling false positives/negatives, and discusses the advantages and limitations of each technique. By providing a comprehensive overview of dirofilariasis diagnostic strategies, from traditional to cutting-edge methods, this review aims to enhance understanding of the disease's diagnostic landscape. The insights gained have implications for improved disease management and guide future research endeavors toward refining diagnostic protocols and advancing therapeutic interventions.},
}

@article {pmid39816454,
year = {2025},
author = {Samanta, A and Sarma, MS},
title = {"Post-Kasai Portoenterostomy Cholangitis: What Have We Learnt So Far?".},
journal = {Journal of clinical and experimental hepatology},
volume = {15},
number = {3},
pages = {102471},
pmid = {39816454},
issn = {0973-6883},
abstract = {Post-Kasai portoenterostomy (KPE) cholangitis is one of the most common complications that has a negative impact on liver function and native liver survival. Early diagnosis and judicious empiric antimicrobial management are, therefore, important to prevent further liver damage and decompensation. However, there is no consensus regarding the standard definition of post-KPE cholangitis, and established guidelines on evaluation and management are also lacking. Metagenomic next-generation sequencing, a new molecular diagnostic technique, has the potential for detecting broader spectrum of pathogens, especially in blood culture-negative patients. Antibiotic prophylaxis to prevent cholangitis has been widely used, but questions over the choice of antibiotics, route of administration, and optimal duration remain unsettled. The available evidence on the efficacy of antibiotic prophylaxis in preventing cholangitis has shown conflicting results. This review offers a summary of the current research on advances in diagnostic approaches, including molecular techniques, and therapeutic challenges in managing intractable cholangitis.},
}

@article {pmid39816362,
year = {2024},
author = {Gong, Z and Ye, G and Xu, S and He, X},
title = {The characteristics of intestinal flora of Tibetan sheep in different regions at high altitude were revealed based on metagenomic technique.},
journal = {Heliyon},
volume = {10},
number = {14},
pages = {e34380},
pmid = {39816362},
issn = {2405-8440},
abstract = {Tibetan sheep play a vital role in the livelihoods of herders and are an important part of the ecosystem of the Tibetan Plateau. In order to study the characteristics of the gut microorganisms of Tibetan sheep at high altitude, this study employed macrogenomic techniques to analyse the diversity and differences in the gut flora of Tibetan sheep in different regions of high altitude and high cold. The results demonstrated that at the phylum level, the dominant phylum in the ileo-cecum segment of Tibetan sheep in Qilian, Henan and Gonghe counties was identical, namely Euryarchaeota, Firmicutes and Ascomycota. At the level of the archaebacterial genus, the dominant bacteria of the ileocecal segment of Tibetan sheep in Qilian County, Henan County and Gonghe County were Methanobrevibacter. At the level of bacterial genus, the dominant bacteria of Tibetan sheep ileocecal in Qilian County and Henan County were Bacteroides, while in Gonghe County, the dominant bacteria were Bifidobacterium. At the level of fungal genus, there were notable differences in the abundance of Tibetan sheep ileocecal genus across different regions. However, the abundance of cecum genus exhibited a more consistent trend across regions. From the perspective of functional prediction, the metabolic pathways enriched in the intestinal segments of Tibetan sheep in different regions were found to be identical, with the relative abundance of each functional gene also being essentially uniform. This result will provide a foundation for further research on the mechanism of action of gut microbes in ruminants at high altitude and alpine regions.},
}

@article {pmid39816186,
year = {2025},
author = {Tian, J and Wang, C and Song, P and You, Z and Jia, X and Li, X and Pang, F},
title = {Predictive Application Value of Metagenomic Next-Generation Sequencing in the Resistance of Carbapenem-Resistant Enterobacteriaceae.},
journal = {The Canadian journal of infectious diseases & medical microbiology = Journal canadien des maladies infectieuses et de la microbiologie medicale},
volume = {2025},
number = {},
pages = {6619016},
pmid = {39816186},
issn = {1712-9532},
abstract = {Objective: Although metagenomic next-generation sequencing (mNGS) technology has achieved notable outcomes in pathogen detection, there remains a gap in the research regarding its application in predicting the antibiotic resistance of pathogenic bacteria. This study aims to analyze the clinical application value of mNGS in predicting the resistance of carbapenem-resistant Enterobacteriaceae (CRE), as well as the relevant influencing factors, thereby providing valuable insights for clinical antimicrobial therapy. Methods: Nonduplicate isolates of Enterobacterales bacteria collected from Liaocheng People's Hospital from April 2023 to June 2024 were selected, and CRE bacteria were screened. mNGS was used to detect resistance genes, and the results were compared with those of polymerase chain reaction (PCR) to evaluate the specificity and sensitivity of gene detection. Furthermore, the performance of mNGS in identifying pathogenic microorganisms and predicting antibiotic resistance was assessed by comparing the sequencing results with those of antimicrobial susceptibility testing (AST). Results: A total of 46 isolates were confirmed as CRE through traditional AST and were further identified using the Vitek MS and Vitek 2 systems. The results indicated 27 isolates of Klebsiella pneumoniae, 14 isolates of Escherichia coli, 2 isolates of Enterobacter hormaechei, 2 isolates of Enterobacter cloacae, and 1 isolate of Citrobacter freundii. These isolates were subjected to both mNGS and PCR for detection. The calculation of the area under the receiver operating characteristic (ROC) curve demonstrated the reliability of mNGS in detecting resistance genes. Conclusion: mNGS demonstrated high sensitivity in predicting the presence of carbapenemase resistance genes in CRE, showing potential in early indication of isolate resistance information, thereby facilitating timely guidance for clinical treatment strategies.},
}

@article {pmid39816160,
year = {2025},
author = {Kaur, A and Russell, I and Liu, R and Holland, A and Bhandari, R and Potnis, N},
title = {Navigating Host Immunity and Concurrent Ozone Stress: Strain-Resolved Metagenomics Reveals Maintenance of Intraspecific Diversity and Genetic Variation in Xanthomonas on Pepper.},
journal = {Evolutionary applications},
volume = {18},
number = {1},
pages = {e70069},
pmid = {39816160},
issn = {1752-4571},
abstract = {The evolving threat of new pathogen variants in the face of global environmental changes poses a risk to a sustainable crop production. Predicting and responding to how climate change affects plant-pathosystems is challenging, as environment affects host-pathogen interactions from molecular to the community level, and with eco-evolutionary feedbacks at play. To address this knowledge gap, we studied short-term within-host eco-evolutionary changes in the pathogen, Xanthomonas perforans, on resistant and susceptible pepper in the open-top chambers (OTCs) under elevated Ozone (O3) conditions in a single growing season. We observed increased disease severity with greater variance on the resistant cultivar under elevated O3, yet no apparent change on the susceptible cultivar. Despite the dominance of a single pathogen genotype on the susceptible cultivar, the resistant cultivar supported a heterogeneous pathogen population. Altered O3 levels led to a strain turnover, with a relatively greater gene flux on the resistant cultivar. Both standing genetic variation and de novo parallel mutations contributed toward evolutionary modifications during adaptation onto the resistant cultivar. The presence of elevated O3, however, led to a relatively higher genetic polymorphism, with random and transient mutations. Population heterogeneity along with genetic variation, and the promotion of interdependency are mechanisms by which pathogen responds to stressors. While parallel mutations may provide clues to predicting long-term pathogen evolution and adaptive potential. And, a high proportion of transient mutations suggest less predictable pathogen evolution under climatic alterations. This knowledge is relevant as we study the risk of pathogen emergence and the mechanisms and constraints underlying long-term pathogen adaptation under climatic shifts.},
}

@article {pmid39813930,
year = {2025},
author = {Urbelienė, N and Gasparavičiūtė, R and Vaitekūnas, J and Meškienė, R and Valantinaitė, U and Kruopis, P and Gudiukaitė, R and Meškys, R},
title = {A screening method for polyester films-degrading microorganisms and enzymes.},
journal = {Journal of hazardous materials},
volume = {487},
number = {},
pages = {137177},
doi = {10.1016/j.jhazmat.2025.137177},
pmid = {39813930},
issn = {1873-3336},
abstract = {Enzymatic degradation of plastic pollution offers a promising environmentally friendly waste management strategy, however, suitable biocatalysts must be screened and developed. Traditional screening methods using soluble or solubilised polymers do not necessarily identify enzymes that are effective against solid or crystalline polymers. This study presents a simple, time-saving and cost-effective method for identifying microorganisms and enzymes capable of degrading polymeric films. The method was tested on polycaprolactone (PCL), polyethylene terephthalate (PET), polylactate (PLA) and polyhydroxybutyrate/polyhydroxyvalerate (PHB/PHV) films. It involves two steps: first, screening for PCL diol (PCLD)-degrading microorganisms on agar plates, and second, testing these microorganisms on polyester films. Using this screening method, over 100 PCLD-degrading microorganisms and 27 E. coli clones carrying genomic or metagenomic DNA fragments have been isolated. In addition, recombinant cutinases from Streptomyces scabiei and Thermobifida fusca have been tested. Approximately 66 % of the microorganisms forming halos on PCLD agar plates hydrolysed PCL and 6 % - the biaxially oriented PET film. In addition, five PLA- and four PHB/PHV-degrading esterases have been identified. The proposed method is effective for detecting both wild-type and recombinant microorganisms, as well as recombinant enzymes from in vitro transcription-translation reactions. Screening for thermostable and thermophilic enzymes, including those resistant to organic solvents or environmental inhibitors, is also easily implemented.},
}

@article {pmid39813892,
year = {2024},
author = {Su, R and Zhao, D and Zhang, X and Zhang, H and Cheng, J and Xu, L and Wu, QL and Zeng, J},
title = {Dissimilatory nitrate reduction pathways drive high nitrous oxide emissions and nitrogen retention under the flash drought in the largest freshwater lake in China.},
journal = {Water research},
volume = {274},
number = {},
pages = {123075},
doi = {10.1016/j.watres.2024.123075},
pmid = {39813892},
issn = {1879-2448},
abstract = {Flash drought (FD) events induced by climate change may disrupt the normal hydrological regimes of floodplain lakes and affect the plant-microbe mediated dissimilatory nitrate reduction (DNR), i.e., denitrification, anammox and dissimilatory nitrate reduction to ammonium (DNRA), thus having important consequences for nitrous oxide (N2O) emissions and nitrogen (N) retention. However, the responses of the DNR pathways in the floodplain lake to the record-breaking FD in 2022 in Yangtze River of China, as well as the underlying microbial mechanisms and feedbacks to climate change remain poorly understood. Here, we collected exposed sediments and Carex cinerascens-associated soils in the littoral wetlands of Poyang Lake during 2022 FD and the dry seasons prior to and after this event. The potential DNR rates and the synergistic metabolism of microbial guilds involved in DNR were investigated using [15]N isotope pairing technique, high-throughput and metagenomic sequencing. We found that the in situ N2O fluxes in the littoral wetlands were highest during the flash drought, especially in the exposed sediments. The potential DNRA rates were highest under flash drought conditions, and DNRA dominated the DNR for both exposed sediments (80.4 %) and Carex cinerascens-associated soils (57.5 %). Nutrients (i.e., N and P) and DNRA bacterial communities played a key role in producing the extremely high N2O fluxes from exposed sediments, which could be explained by the synergistic metabolism of DNRA bacteria and denitrifiers through the exchange of the key intermediates in DNR. Therefore, the climate change-induced flash drought promoted greater nitrous oxide emissions and N retention in the littoral wetlands of Poyang Lake, producing a greater flux of greenhouse gas emissions and elevating the risk of lake eutrophication. Hence, flash droughts reinforce a positive feedback between climate change and nitrous oxide emission from these aquatic ecosystems.},
}

@article {pmid39814151,
year = {2025},
author = {Qiao, XJ and Zhang, LY and Yuan, T and Wu, Y and Geng, Y and Li, Y and Li, B and Zhang, L and Zhuang, WQ and Yu, K},
title = {Mixotrophic anammox bacteria outcompete dissimilatory nitrate reduction and denitrifying bacteria in propionate-containing wastewater.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {132077},
doi = {10.1016/j.biortech.2025.132077},
pmid = {39814151},
issn = {1873-2976},
abstract = {Organic carbon can influence nitrogen removal during the anaerobic ammonia oxidation (anammox) process. Propionate, a common organic compound in pretreated wastewater, its impacts on mixotrophic anammox bacteria and the underlying mechanisms have not been fully elucidated. This study investigated the core metabolism and shift in behavior patterns of mixotrophic Candidatus Brocadia sapporoensis (AMXB) under long-term propionate exposure. Genome-resolved metagenomic analysis revealed that AMXB could convert nitrate generated by anammox bacteria to ammonium via the DNRA pathway, leveraging propionate as an electron donor. This recycled ammonium was then used to sustain the anammox process, thereby enhancing nitrogen removal efficiency. Notably, AMXB grew more efficiently than DNRA and denitrifying bacteria due to its more energy-efficient propionate metabolic pathway. This finding suggests that AMXB, as a mixotrophic anammox bacterium, has a competitive advantage in nitrogen metabolism in low C/N wastewater, contributing to efficient nitrogen removal.},
}

@article {pmid39814067,
year = {2025},
author = {Ji, J and Jung, S},
title = {PredCMB: Predicting changes in microbial metabolites based on the gene-metabolite network analysis of shotgun metagenome data.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btaf020},
pmid = {39814067},
issn = {1367-4811},
abstract = {MOTIVATION: Microbiota-derived metabolites significantly impact host biology, prompting extensive research on metabolic shifts linked to the microbiota. Recent studies have explored both direct metabolite analyses and computational tools for inferring metabolic functions from microbial shotgun metagenome data. However, no existing tool specifically focuses on predicting changes in individual metabolite levels, as opposed to metabolic pathway activities, based on shotgun metagenome data. Understanding these changes is crucial for directly estimating the metabolic potential associated with microbial genomic content.

RESULTS: We introduce PredCMB (Predicting Changes in Microbial metaBolites), a novel method designed to predict alterations in individual metabolites between conditions using shotgun metagenome data and enzymatic gene-metabolite networks. PredCMB evaluates differential enzymatic gene abundance between conditions and estimates its influence on metabolite changes. To validate this approach, we applied it to two publicly available datasets comprising paired shotgun metagenomics and metabolomics data from inflammatory bowel disease (IBD) cohorts and the cohort of gastrectomy for gastric cancer. Benchmark evaluations revealed that PredCMB outperformed a previous method by demonstrating higher correlations between predicted metabolite changes and experimentally measured changes. Notably, it identified metabolite classes exhibiting major alterations between conditions. By enabling the prediction of metabolite changes directly from shotgun metagenome data, PredCMB provides deeper insights into microbial metabolic dynamics than existing methods focused on pathway activity evaluation. Its potential applications include refining target metabolite selection in microbial metabolomic studies and assessing the contributions of microbial metabolites to disease pathogenesis.

AVAILABILITY: Freely available to non-commercial users at https://www.sysbiolab.org/predcmb.

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

@article {pmid39813953,
year = {2025},
author = {Knight, ME and Farkas, K and Wade, M and Webster, G and Pass, DA and Perry, W and Kille, P and Singer, A and Jones, DL},
title = {Wastewater-based analysis of antimicrobial resistance at UK airports: Evaluating the potential opportunities and challenges.},
journal = {Environment international},
volume = {195},
number = {},
pages = {109260},
doi = {10.1016/j.envint.2025.109260},
pmid = {39813953},
issn = {1873-6750},
abstract = {With 40 million annual passenger flights, airports are key hubs for microbial communities from diverse geographic origins to converge, mix, and distribute. Wastewater derived from airports and aircraft represent both a potential route for the global dispersion of antimicrobial resistant (AMR) organisms and an under-utilised resource for strengthening global AMR surveillance. This study investigates the abundance and diversity of antimicrobial resistance genes (ARGs) in wastewater samples collected from airport terminals (n = 132), aircraft (n = 25), and a connected wastewater treatment plant (n = 11) at three international airports in the UK (London Heathrow, Edinburgh and Bristol). A total of 76 ARGs were quantified using high throughput qPCR (HT-qPCR) while a subset of samples (n = 30) was further analysed by metagenomic sequencing. Our findings reveal that aircraft wastewater resistomes were compositionally distinct from those observed at airport terminals, despite their similar diversity. Notably, flights originating from Asia and Africa carried a higher number of unique ARGs compared to those from Europe and North America. However, clustering of the ARG profile displayed no overall association with geography. Edinburgh terminal and pumping station wastewater had compositionally comparable resistomes to that of the connected urban wastewater treatment plant, though further research is needed to determine the relative contributions of the local population and international travellers. This study provides the first comprehensive investigation of AMR in wastewater from both aircraft and terminals across multiple international airports. Our results highlight aircraft wastewater as a potential route for cross-border AMR transmission and a valuable tool for global AMR surveillance. However, the findings also underscore the limitations and need for standardised approaches for AMR monitoring in airport environments, to effectively mitigate the global spread of AMR and enhance public health surveillance strategies.},
}

@article {pmid39813926,
year = {2025},
author = {Qu, C and Tang, J and Liu, J and Wang, W and Song, F and Cheng, S and Tang, X and Tang, CJ},
title = {Quorum sensing-enhanced electron transfer in anammox consortia: A mechanism for improved resistance to variable-valence heavy metals.},
journal = {Journal of hazardous materials},
volume = {487},
number = {},
pages = {137130},
doi = {10.1016/j.jhazmat.2025.137130},
pmid = {39813926},
issn = {1873-3336},
abstract = {Quorum sensing (QS) is recognized for enhancing bacterial resistance against heavy metals by regulating the production of extracellular substances that hinder metal penetration into the intracellular environment. However, it remains unclear whether QS contributes to resistance by regulating electron transfer, thereby transforming metals from more toxic to less toxic forms. This study investigated the regulatory mechanism of acyl-homoserine lactone (AHL)-mediated QS on electron transfer under As(III) and Cr(VI) stress. Metagenomic binning results revealed that Candidatus Brocadia sinica serves as a major contributor to AHL production for regulating heavy metal resistance, while other symbiotic bacteria offer complementary resistance pathways. In these bacteria, the AHL synthesis gene htdS plays a pivotal role in QS regulation of electron transfer and heavy metal resistance. Experimental findings demonstrated that AHL increased the electron transport system activity by 19.8 %, and upregulated electron transfer gene expression by 1.1- to 6.9-fold. The enhanced electron transfer facilitated a 28.7 % increase in the transformation of As(III) to less toxic As(V) and monomethylarsonic acid, ultimately achieving efficient nitrogen removal under As(III) stress. This study expands our understanding of how QS strengthens bacterial resistance to heavy metals, offering novel strategies for enhancing nitrogen removal of anammox in heavy metal-contaminated environments.},
}

@article {pmid39813691,
year = {2024},
author = {Sumboh, JG and Agyenkwa-Mawuli, K and Schwinger, E and Donkor, IO and Akorli, J and Dwomoh, D and Ashong, Y and Osabutey, D and Ababio, FO and Nusbaum, O and Humphries, D and Cappello, M and Koram, KA and Kwofie, SK and Wilson, MD},
title = {Investigating Environmental Determinants of Hookworm Transmission using GPS Tracking and Metagenomics Technologies.},
journal = {The American journal of tropical medicine and hygiene},
volume = {},
number = {},
pages = {},
doi = {10.4269/ajtmh.24-0384},
pmid = {39813691},
issn = {1476-1645},
abstract = {To identify potential sources of hookworm infections in a Ghanaian community of endemicity that could be targeted to interrupt transmission, we tracked the movements of infected and noninfected persons to their most frequented locations. Fifty-nine participants (29 hookworm positives and 30 negatives) wore GPS trackers for 10 consecutive days. Their movement data were captured in real time and overlaid on a community grid map. Soil samples were collected and divided into two parts: one for determining the physical and chemical properties and the other for culture of helminth larvae. Soil parameters were determined using standard methods, and the number of larvae recovered from Baermann cultures (expressed as larvae per gram of soil) was recorded. We found no significant difference in the larval counts between sites of infected and noninfected participants (P = 0.59). Sandy-loam soil, pH, and effective cation exchange capacity were associated with high larval recovery counts (P <0.001), whereas nitrogen and clay content were associated with low counts (P <0.001). Genomic DNA was extracted from helminth larvae, and species were identified using metagenomic analysis of DNA sequences. The dominant helminth species identified were Panagrolaimus superbus, Parastrongyloides trichosuri, Trichuris trichiura (human whipworm), and Ancylostoma caninum (dog hookworm). Despite Necator americanus being the predominant species in the community, no larvae of this species were identified. This study, however, demonstrates the feasibility of applying molecular tools for identifying environmental factors and places associated with exposure to human and zoonotic helminths, including areas that may be targeted to break transmission in communities where infection is endemic.},
}

@article {pmid39813598,
year = {2025},
author = {Ren, M and Xia, Y and Pan, H and Zhou, X and Yu, M and Ji, F},
title = {Duodenal-jejunal bypass ameliorates MASLD in rats by regulating gut microbiota and bile acid metabolism through FXR pathways.},
journal = {Hepatology communications},
volume = {9},
number = {2},
pages = {},
doi = {10.1097/HC9.0000000000000615},
pmid = {39813598},
issn = {2471-254X},
mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; *Receptors, Cytoplasmic and Nuclear/metabolism ; Rats ; *Bile Acids and Salts/metabolism ; *Duodenum/surgery/metabolism/microbiology ; Male ; *Fecal Microbiota Transplantation ; Jejunum/surgery/metabolism ; Rats, Sprague-Dawley ; Disease Models, Animal ; Fatty Liver/metabolism ; Anti-Bacterial Agents/pharmacology ; Diet, High-Fat ; Gastric Bypass ; Insulin Resistance ; },
abstract = {BACKGROUND: Although bariatric and metabolic surgical methods, including duodenal-jejunal bypass (DJB), were shown to improve metabolic dysfunction-associated steatotic liver disease (MASLD) in clinical trials and experimental rodent models, their underlying mechanisms remain unclear. The present study therefore evaluated the therapeutic effects and mechanisms of action of DJB in rats with MASLD.

METHODS: Rats with MASLD were randomly assigned to undergo DJB or sham surgery. Rats were orally administered a broad-spectrum antibiotic cocktail (Abx) or underwent fecal microbiota transplantation to assess the role of gut microbiota in DJB-induced improvement of MASLD. Gut microbiota were profiled by 16S rRNA gene sequencing and metagenomic sequencing, and bile acids (BAs) were analyzed by BA-targeted metabolomics.

RESULTS: DJB alleviated hepatic steatosis and insulin resistance in rats with diet-induced MASLD. Abx depletion of bacteria abrogated the ameliorating effects of DJB on MASLD. Fecal microbiota transplantation from rats that underwent DJB improved MASLD in high-fat diet-fed recipients by reshaping the gut microbiota, especially by significantly reducing the abundance of Clostridium. This, in turn, suppressed secondary BA biosynthesis and activated the hepatic BA receptor, farnesoid X receptor. Inhibition of farnesoid X receptor attenuated the ameliorative effects of post-DJB microbiota on MASLD.

CONCLUSIONS: DJB ameliorates MASLD by regulating gut microbiota and BA metabolism through hepatic farnesoid X receptor pathways.},
}

Animals
*Gastrointestinal Microbiome/physiology
*Receptors, Cytoplasmic and Nuclear/metabolism
Rats
*Bile Acids and Salts/metabolism
*Duodenum/surgery/metabolism/microbiology
Male
*Fecal Microbiota Transplantation
Jejunum/surgery/metabolism
Rats, Sprague-Dawley
Disease Models, Animal
Fatty Liver/metabolism
Anti-Bacterial Agents/pharmacology
Diet, High-Fat
Gastric Bypass
Insulin Resistance

@article {pmid39812972,
year = {2025},
author = {de Oliveira, RVF and Garrido, LM and Padilla, G},
title = {Decontamination of DNA sequences from a Streptomyces genome for optimal genome mining.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {},
number = {},
pages = {},
pmid = {39812972},
issn = {1678-4405},
support = {001//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; 2015/17177-6//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; },
abstract = {Despite meticulous precautions, contamination of genomic DNA samples is not uncommon, which can significantly compromise the analysis of microorganisms' whole-genome sequencing data, thus affecting all subsequent analyses. Thanks to advancements in software and bioinformatics techniques, it is now possible to address this issue and prevent the loss of the entire dataset obtained in a contaminated whole-genome sequencing, where the DNA of another bacterium is present. In this study, it was observed that the sequencing reads from Streptomyces sp. BRB040, generated using the HiSeq System platform (Illumina Inc., San Diego, USA), were contaminated with the DNA of Bacillus licheniformis. To eliminate the contamination in Streptomyces sp. BRB040, a combination of tools available on the Galaxy platform and other web-based resources were used (MeDuSa and Blast). The contaminated reads were treated as a metagenome to isolate the genome of the contaminating organism. They were assembled using the metaSPAdes, resulting in a large scaffold of 4.187 Mb, which was identified as Bacillus licheniformis. After the identification of the contaminating organism, its genome was used as a filter to remove sequencing reads that could align using then Bowtie 2 software for this step. Once the contaminated reads were removed a new assembly was performed using the Unicycler software, yielding 117 contigs with a total size of 7.9 Mb. The completeness of this genome was assessed through BUSCO, resulting in a completeness of 95.9%. We also used an alternative tool (BBduk) to eliminate contaminated reads and the resulting assembly by Unicycler generated 85 contigs with a total size of 8.3 Mb and completeness of 99.5%. These results were better than the assembly obtained via SPAdes, which generated less complete genomes (maximum of 97.8% completeness) compared to Unicycler and which was unable to perform an adequate assembly of the data obtained from decontamination by BBduk. When compared with the uncontaminated BRB040 genome, which has a total size of 8.2 Mb and completeness of 99.8%, this pipeline revealed that the assembly performed with the decontaminated reads via BBduk presented better results, with completeness 0.3% lower than the reference. The genome mining of both genomes using antiSMASH 7.0 revealed the number of 24 Biosynthetic Gene Clusters (BGCs) for BBduk data as well as in the control assembly of the BRB040. In silico decontamination process allows the genome mining of BGCs despite the loss of nucleotides. These findings show that contamination can be effectively removed from a genome using readily available online tools, while preserving a dataset suitable for extracting valuable insights into the secondary metabolism of the target organism. This approach is particularly beneficial in scenarios where resequencing samples is not immediately feasible.},
}

@article {pmid39812647,
year = {2025},
author = {Selami, N and Zitouni-Haouar, FE and Zerouki, C and Aibeche, C and Draou, N and Khelil, O and Choubane, S and Maatallah, M and Madani, I and Ouenzar, K and Zemmour, A and Kerkoud, M and Mnasri, B and Moumen, B and Vriet, C and Djabeur, A},
title = {Pseudomonas retamae sp. nov., a novel endophytic bacterium with plant growth-promoting potential, isolated from root nodules of Retama monosperma in Northwestern Algeria.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {75},
number = {1},
pages = {},
doi = {10.1099/ijsem.0.006646},
pmid = {39812647},
issn = {1466-5034},
mesh = {*Pseudomonas/genetics/isolation & purification/classification ; *RNA, Ribosomal, 16S/genetics ; *Phylogeny ; Algeria ; *DNA, Bacterial/genetics ; *Nucleic Acid Hybridization ; *Endophytes/genetics/isolation & purification/classification ; *Multilocus Sequence Typing ; *Sequence Analysis, DNA ; *Bacterial Typing Techniques ; *Root Nodules, Plant/microbiology ; *Base Composition ; Genome, Bacterial ; Fatty Acids ; },
abstract = {A thorough polyphasic taxonomic study, integrating genome-based taxonomic approaches, was carried out to characterize the RB5[T] strain isolated from root nodules of Retama monosperma growing on the coastal dunes of Bousfer Beach (Oran, Algeria). The 16S rRNA gene sequence analysis revealed that strain RB5[T] had the highest similarity to Pseudomonas granadensis LMG27940[T] (98.94%) and Pseudomonas gozinkensis IzPS32d[T] (98.73%). Phylogenetic studies, including both 16S rRNA gene sequence and multilocus sequence analysis using 16S rRNA, gyrB and rpoD housekeeping genes, positioned RB5[T] in a distinct branch alongside its closest relative, P. granadensis LMG27940[T]. Phylogenomic analysis using the Bac120 marker set and Type (Strain) Genome Server confirmed the unique position of RB5[T] and its close relationship with P. granadensis LMG27940[T]. Similarly, genomic comparisons using average nucleotide identity based on blast (ANIb) and digital DNA-DNA hybridization (dDDH) revealed values of 92.85 and 59.3%, respectively, when compared with its closest relative, P. granadensis LMG27940[T]. Both values fall below the established species delimitation thresholds of 95-96% for ANIb and 70% for dDDH, providing strong genomic evidence that strain RB5[T] represents a novel species. Further average nucleotide identity comparisons with unclassified Pseudomonas spp. (384 genomes) and metagenomic-derived genomes from the Genome Taxonomy Database (GTDB) showed values between 84.27 and 89.2%, indicating that strain RB5[T] belongs to a unique evolutionary line. The genome of RB5[T], with a size of 6 311 310 bp and a G+C content of 60%, harbours several key genes associated with plant growth-promoting traits, making it a promising candidate for sustainable agriculture. Phenotypically, RB5[T] strain is an aerobic, rod-shaped, Gram-negative, non-spore-forming bacterium that is motile with a single polar flagellum. It grows under a wide range of temperature (4-42 °C) and pH (5-10) conditions and tolerates up to 6% (w/v) NaCl. The main cellular fatty acid composition of RB5[T] includes C16:0, C17:0 cyclo and the summed features 3 consisting of C16:1 ω7c/C16:1 ω6c. Based on the phylogenetic, phenotypic, chemotaxonomic and genome comparison analyses, strain RB5[T] was identified as a novel species of the genus Pseudomonas, for which the name Pseudomonas retamae sp. nov. is proposed. The type strain is RB5[T] (=DSM 117471[T]=LMG 33633[T]=CIP 112482[T]).},
}

*Pseudomonas/genetics/isolation & purification/classification
*RNA, Ribosomal, 16S/genetics
*Phylogeny
Algeria
*DNA, Bacterial/genetics
*Nucleic Acid Hybridization
*Endophytes/genetics/isolation & purification/classification
*Multilocus Sequence Typing
*Sequence Analysis, DNA
*Bacterial Typing Techniques
*Root Nodules, Plant/microbiology
*Base Composition
Genome, Bacterial
Fatty Acids

@article {pmid39812555,
year = {2025},
author = {Bell, PT and Baird, T and Goddard, J and Olagoke, OS and Burke, A and Subedi, S and Davey, TR and Anderson, J and Sarovich, DS and Price, EP},
title = {Evaluating the feasibility, sensitivity, and specificity of next-generation molecular methods for pleural infection diagnosis.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0196024},
doi = {10.1128/spectrum.01960-24},
pmid = {39812555},
issn = {2165-0497},
abstract = {Pleural infections are common and associated with substantial healthcare costs, morbidity, and mortality. Accurate diagnosis remains challenging due to low culture positivity rates, frequent polymicrobial involvement, and non-specific diagnostic biomarkers. Here, we undertook a prospective study examining the feasibility and performance of molecular methods for diagnosing suspected pleural infection. We prospectively characterized 26 consecutive clinically suspected pleural infections, and 10 consecutive patients with suspected non-infective pleural effusions, using shotgun metagenomics, bacterial metataxonomics, quantitative PCR, and conventional culture. Molecular methods exhibited excellent diagnostic performance, with each method identifying 54% (14 out of 26) positive cases among the pleural infection cohort, versus 38% (10 out of 26) with culture. Metagenomics and bacterial metataxonomics unveiled complex polymicrobial infections that were not captured by culture. Dominant microbes included streptococci (Streptococcus intermedius, Streptococcus pyogenes, and Streptococcus mitis), Prevotella spp. (Prevotella oris and Prevotella pleuritidis), staphylococci (S. aureus and S. saprophyticus), and Klebsiella pneumoniae. However, we encountered challenges that complicated pleural infection interpretation, including: (i) uncertainties regarding microbial pathogenicity and the impact of prior antibiotic therapy on diagnostic performance; (ii) lack of a clinical diagnostic gold-standard for molecular performance comparisons; (iii) potential microbial contamination during specimen collection or processing; and (iv) difficulties distinguishing background microbial noise from true microbial signal in low-biomass specimens. This pilot study demonstrates the potential utility and value of molecular methods in diagnosing pleural infection and highlights key concepts and challenges that should be addressed when designing larger prospective trials.IMPORTANCEConfident pleural infection diagnosis is often challenging due to low culture positivity rates, frequent polymicrobial involvement, and non-specific diagnostic biomarkers. Limitations of conventional diagnostic tests result in prolonged and inappropriately broad-spectrum antimicrobial use, encouraging antimicrobial resistance and leading to avoidable adverse effects. Here, we demonstrate the feasibility, utility, and challenges associated with the use of culture-independent molecular techniques for accurate pleural infection diagnosis in a real-world clinical setting. These data will help to inform the design of larger prospective clinical trials and identify potential obstacles to be overcome before next-generation sequencing technologies can be integrated into routine clinical practice.},
}

@article {pmid39812347,
year = {2025},
author = {Gustafson, KL and Rodriguez, TR and McAdams, ZL and Coghill, LM and Ericsson, AC and Franklin, CL},
title = {Failure of colonization following gut microbiota transfer exacerbates DSS-induced colitis.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2447815},
doi = {10.1080/19490976.2024.2447815},
pmid = {39812347},
issn = {1949-0984},
mesh = {Animals ; *Gastrointestinal Microbiome ; *Colitis/microbiology/chemically induced/pathology ; *Dextran Sulfate ; Mice ; *Disease Models, Animal ; *Mice, Inbred C57BL ; *Fecal Microbiota Transplantation ; Bacteria/classification/isolation & purification/genetics/metabolism ; Female ; Specific Pathogen-Free Organisms ; Feces/microbiology ; Inflammatory Bowel Diseases/microbiology ; Male ; },
abstract = {To study the impact of differing specific pathogen-free gut microbiomes (GMs) on a murine model of inflammatory bowel disease, selected GMs were transferred using embryo transfer (ET), cross-fostering (CF), and co-housing (CH). Prior work showed that the GM transfer method and the microbial composition of donor and recipient GMs can influence microbial colonization and disease phenotypes in dextran sodium sulfate-induced colitis. When a low richness GM was transferred to a recipient with a high richness GM via CH, the donor GM failed to successfully colonize, and a more severe disease phenotype resulted when compared to ET or CF, where colonization was successful. By comparing CH and gastric gavage for fecal material transfer, we isolated the microbial component of this effect and determined that differences in disease severity and survival were associated with microbial factors rather than the transfer method itself. Mice receiving a low richness GM via CH and gastric gavage exhibited greater disease severity and higher expression of pro-inflammatory immune mediators compared to those receiving a high richness GM. This study provides valuable insights into the role of GM composition and colonization in disease modulation.},
}

Animals
*Gastrointestinal Microbiome
*Colitis/microbiology/chemically induced/pathology
*Dextran Sulfate
Mice
*Disease Models, Animal
*Mice, Inbred C57BL
*Fecal Microbiota Transplantation
Bacteria/classification/isolation & purification/genetics/metabolism
Female
Specific Pathogen-Free Organisms
Feces/microbiology
Inflammatory Bowel Diseases/microbiology
Male

@article {pmid39810418,
year = {2025},
author = {Yu, H and Liu, S and Zhang, D and Hu, R and Chen, P and Liu, H and Zhou, Q and Tan, W and Hu, N and He, Z and Ding, D and Yan, Q},
title = {Specific Enrichment of arsM-Carrying Microorganisms with Nitrogen Fixation and Dissimilatory Nitrate Reduction Function Enhances Arsenic Methylation in Plant Rhizosphere Soil.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.4c10242},
pmid = {39810418},
issn = {1520-5851},
abstract = {Plants can recruit microorganisms to enhance soil arsenic (As) removal and nitrogen (N) turnover, but how microbial As methylation in the rhizosphere is affected by N biotransformation is not well understood. Here, we used acetylene reduction assay, arsM gene amplicon, and metagenome sequencing to evaluate the influence of N biotransformation on As methylation in the rhizosphere of Vetiveria zizanioides, a potential As hyperaccumulator. V. zizanioides was grown in mining soils (MS) and artificial As-contaminated soils (AS) over two generations in a controlled pot experiment. Results showed that the content of dimethylarsinic acid in the rhizosphere was significantly positively correlated with the rate of N fixation and the activity of nitrite reductase. The As-methylating species (e.g., Flavisolibacter and Paraflavitalea) were significantly enriched in the root-associated compartments in the second generation of MS and AS. Notably, higher abundance of genes involved in N fixation (nifD, nifK) and dissimilatory nitrate reduction to ammonium (narG/H, nirB/D/K/S) was detected in the second generation of MS than in the first generation. The metabolic pathway analysis further demonstrated that N fixing-stimulative and DNRA-stimulative As-methylating species could provide ammonium to enhance the synthesis of S-adenosyl-l-methionine, serving as methyl donors for soil As methylation. This study highlights two important N conversion-stimulative As-methylating pathways and has important implications for enhancing phytoremediation in As-contaminated soils.},
}

@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 {pmid39810145,
year = {2025},
author = {Xiang, H and Zhang, L and Yang, L and Cai, M and Ma, Y and Zhang, Y},
title = {Asymptomatic lung abscess of aspergillus in a female without previous lung diseases or immunocompromise: a case report.},
journal = {BMC infectious diseases},
volume = {25},
number = {1},
pages = {66},
pmid = {39810145},
issn = {1471-2334},
support = {BRWEP2024W042180101//Beijing Research Ward Excellence Program/ ; },
mesh = {Humans ; Female ; Adult ; *Lung Abscess/microbiology/drug therapy/diagnosis ; *Aspergillus/isolation & purification/genetics ; *Pulmonary Aspergillosis/diagnosis/microbiology/drug therapy ; *Antifungal Agents/therapeutic use ; Tomography, X-Ray Computed ; Voriconazole/therapeutic use ; Lung/microbiology/diagnostic imaging/pathology ; },
abstract = {BACKGROUND: Chronic pulmonary abscess usually results from bacterial or mycobacterium infection, but rarely from aspergillosis. Chronic pulmonary aspergillosis is usually found in a person with structural lung disease or immunocompromise. Here, we report a case of chronic lung abscess of aspergillosis without immunocompromise, structural lung diseases or even clinical symptoms.

CASE PRESENTATION: A 43-year-old female was found a mass shadow with central liquid anechoic area in the apical posterior segment of the left upper lung lobe by chest computerized tomography for 1 month, but had no any systematic or respiratory complaints. The percutaneous abscess puncture was performed and 30 milliliters of yellow purulent fluid were aspirated from the liquid anechoic area. Then Aspergillus terreus was detected by both fluid culture and metagenomics next-generation sequencing. Interestingly, this patient had no history of tuberculosis or chronic pulmonary diseases. Other immunocompromised conditions were also denied through history inquest and laboratory tests. Ultimately, the catheterization and drainage of the lung abscess and 6 months of antifungal therapy with standard dose of voriconazole brought the woman a favorable outcome.

CONCLUSION: Aspergillus lung abscess can occasionally occur in a person without pre-existent lung cavity and immune suppression, which is prone to misdiagnosis because of the rarity and the symptom-free.},
}

Humans
Female
Adult
*Lung Abscess/microbiology/drug therapy/diagnosis
*Aspergillus/isolation & purification/genetics
*Pulmonary Aspergillosis/diagnosis/microbiology/drug therapy
*Antifungal Agents/therapeutic use
Tomography, X-Ray Computed
Voriconazole/therapeutic use
Lung/microbiology/diagnostic imaging/pathology

@article {pmid39809974,
year = {2025},
author = {Jia, W and Chan, JC and Wong, TY and Fisher, EB},
title = {Diabetes in China: epidemiology, pathophysiology and multi-omics.},
journal = {Nature metabolism},
volume = {},
number = {},
pages = {},
pmid = {39809974},
issn = {2522-5812},
abstract = {Although diabetes is now a global epidemic, China has the highest number of affected people, presenting profound public health and socioeconomic challenges. In China, rapid ecological and lifestyle shifts have dramatically altered diabetes epidemiology and risk factors. In this Review, we summarize the epidemiological trends and the impact of traditional and emerging risk factors on Chinese diabetes prevalence. We also explore recent genetic, metagenomic and metabolomic studies of diabetes in Chinese, highlighting their role in pathogenesis and clinical management. Although heterogeneity across these multidimensional areas poses major analytic challenges in classifying patterns or features, they have also provided an opportunity to increase the accuracy and specificity of diagnosis for personalized treatment and prevention. National strategies and ongoing research are essential for improving diabetes detection, prevention and control, and for personalizing care to alleviate societal impacts and maintain quality of life.},
}

@article {pmid39809928,
year = {2025},
author = {Lai, LM and Chen, QG and Liu, Y and Zhao, R and Cao, ML and Yuan, L},
title = {The value of metagenomic next-generation sequencing in the diagnosis of fever of unknown origin.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {1963},
pmid = {39809928},
issn = {2045-2322},
support = {20242BAB20430//the Natural Science Foundation of Jiangxi Province/ ; 2021B723//the Science and Technology Program of Jiangxi Traditional Chinese Medicine/ ; },
mesh = {Humans ; *Fever of Unknown Origin/diagnosis/microbiology ; *High-Throughput Nucleotide Sequencing/methods ; Male ; *Metagenomics/methods ; Female ; Retrospective Studies ; Middle Aged ; Adult ; Aged ; Sensitivity and Specificity ; Young Adult ; Adolescent ; Metagenome ; Aged, 80 and over ; },
abstract = {Fever of unknown origin (FUO) caused by infection is a disease state characterized by complex pathogens and remains a diagnostic dilemma. Metagenomic next-generation sequencing (mNGS) technology is a promising diagnostic tool for identifying pathogenic microbes of FUO caused by infection. Little is known about the clinical impact of mNGS in the etiological diagnosis of FUO. This study focuses on the value of mNGS in the etiologic diagnosis of FUO by diagnostic performance, further clarifying the value of mNGS in clinical management. In a single-centre retrospective cohort study, 263 FUO patients who underwent both mNGS and culture at the First Affiliated Hospital of Nanchang University were enrolled from December 2020 to February 2023. The sensitivity and specificity of culture and mNGS were analyzed based on the final clinical diagnosis as the gold standard to assess the diagnostic value of mNGS in FUO cases. Among the 263 patients, 69.96%(184/263) cases were diagnosed as infectious diseases, of which lower respiratory tract infections were the most common, accounting for 53.26%(98/184). 30.04%(79/263) cases had a diagnosis of non-infectious disease. From these cases, mNGS identified 150 true-positive cases, 21 false-positive cases, 58 true-negative cases, and 34 false-negative cases. The sensitivity of mNGS in infection diagnosis was much higher than that of culture [81.52%(150/184) vs. 47.28%(87/184)], but the specificity was the opposite[73.42%(58/79) vs. 84.81%(67/79)]. mNGS had a receiver operating characteristic (ROC) curve of 0.775 for infectious disease, which was significantly higher than that of culture (0.661, P < 0.05). mNGS detection revealed that bacteria were the most commonly identified potential pathogens. The top causative pathogens identified were Acinetobacter baumannii. Of the 263 patients with FUO, clinical management of 48.67% (128/263) patients was positively affected by mNGS, and 51.33% (135/263) patients were not affected by mNGS(P = 0.1074). To sum up, infectious diseases are the principal cause of FUO. mNGS could significantly improve the detected pathogen spectrum of FUO caused by infection. However, the FUO disease spectrum is relatively broad, including a large number of non-infectious diseases. Therefore, Further investigation is warranted into the specific clinical scenarios for which mNGS may offer the greatest clinical diagnostic value.},
}

Humans
*Fever of Unknown Origin/diagnosis/microbiology
*High-Throughput Nucleotide Sequencing/methods
Male
*Metagenomics/methods
Female
Retrospective Studies
Middle Aged
Adult
Aged
Sensitivity and Specificity
Young Adult
Adolescent
Metagenome
Aged, 80 and over

@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 {pmid39809266,
year = {2025},
author = {Wang, D and Jiang, Y and Jiang, J and Pan, Y and Yang, Y and Fang, X and Liang, L and Li, H and Dong, Z and Fan, S and Ma, D and Zhang, XS and Li, H and He, Y and Li, N},
title = {Gut microbial GABA imbalance emerges as a metabolic signature in mild autism spectrum disorder linked to overrepresented Escherichia.},
journal = {Cell reports. Medicine},
volume = {},
number = {},
pages = {101919},
doi = {10.1016/j.xcrm.2024.101919},
pmid = {39809266},
issn = {2666-3791},
abstract = {Gut microbiota (GM) alterations have been implicated in autism spectrum disorder (ASD), yet the specific functional architecture remains elusive. Here, employing multi-omics approaches, we investigate stool samples from two distinct cohorts comprising 203 children with mild ASD or typical development. In our screening cohort, regression-based analysis for metabolomic profiling identifies an elevated γ-aminobutyric acid (GABA) to glutamate (Glu) ratio as a metabolic signature of ASD, independent of age and gender. In the validating cohort, we affirm the GABA/Glu ratio as an ASD diagnostic indicator after adjusting for geography, age, gender, and specific food-consuming frequency. Integrated analysis of metabolomics, 16S rRNA sequencing, and metagenomics reveals a correlation between overrepresented Escherichia and disrupted GABA metabolism. Furthermore, we observe social behavioral impairments in weaning mice transplanted with E. coli, suggesting a potential link to ASD symptomatology. Collectively, these findings provide insights into potential diagnostic and therapeutic strategies aimed at evaluating and restoring gut microbial neurotransmitter homeostasis.},
}

@article {pmid39809157,
year = {2024},
author = {Xu, H and Liu, Y and Niu, H and Cai, X and Zhan, F},
title = {Characteristics, symptoms, and outcomes of patients with Vibrio vulnificus infection in Hainan, China: A retrospective study.},
journal = {Medicine},
volume = {103},
number = {47},
pages = {e40706},
doi = {10.1097/MD.0000000000040706},
pmid = {39809157},
issn = {1536-5964},
mesh = {Humans ; Male ; *Vibrio Infections/epidemiology/diagnosis/therapy ; Female ; Retrospective Studies ; Middle Aged ; China/epidemiology ; Aged ; *Vibrio vulnificus/isolation & purification ; Adult ; Anti-Bacterial Agents/therapeutic use ; },
abstract = {With global temperatures on the rise and an expanding seafood trade, infections by Vibrio vulnificus, particularly in warm coastal areas like Hainan, China, are increasingly prevalent. These bacteria are notorious for causing grave infections with a high fatality rate. This study aims to dissect the clinical features, laboratory findings, treatment modalities, and patient outcomes associated with V vulnificus infections in Hainan Province. The medical records and clinical data of intensive care unit patients from Hainan General Hospital were retrospectively analyzed. Conventional sequencing and metagenomic sequencing were used to identify V vulnificus. The study involved 10 patients (9 males and 1 female) with a median age of 60.5 years, predominantly fishermen, with infections mainly occurring between May and October. Of note, 2 cases were linked to plant-related injuries. The typical manifestations included fever, pain, swelling, hemorrhagic vesicles, septic shock, and multi-organ dysfunction. It was found that delayed hospital admissions were associated with elevated Sequential Organ Failure Assessment and Acute Physiology and Chronic Health Evaluation II scores and increased mortality. Laboratory results indicated a robust inflammatory response, and interventions comprised antibiotic therapy and surgical procedures. A mortality rate of 50% was recorded. Vigilance for V vulnificus infections is crucial in coastal locales. The study endorses immediate and assertive treatment strategies, including the use of targeted antibiotics and surgical interventions, to enhance patient survival rates. A call for heightened awareness, intensified surveillance, and expanded research is essential to combat this life-threatening condition.},
}

Humans
Male
*Vibrio Infections/epidemiology/diagnosis/therapy
Female
Retrospective Studies
Middle Aged
China/epidemiology
Aged
*Vibrio vulnificus/isolation & purification
Adult
Anti-Bacterial Agents/therapeutic use

@article {pmid39808116,
year = {2024},
author = {Zárate, A and Díaz-González, L and Taboada, B},
title = {VirDetect-AI: a residual and convolutional neural network-based metagenomic tool for eukaryotic viral protein identification.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {1},
pages = {},
doi = {10.1093/bib/bbaf001},
pmid = {39808116},
issn = {1477-4054},
mesh = {*Metagenomics/methods ; *Neural Networks, Computer ; *Viral Proteins/genetics ; Humans ; Viruses/genetics/classification ; Genome, Viral ; Animals ; Eukaryota/genetics ; Artificial Intelligence ; Metagenome ; Algorithms ; },
abstract = {This study addresses the challenging task of identifying viruses within metagenomic data, which encompasses a broad array of biological samples, including animal reservoirs, environmental sources, and the human body. Traditional methods for virus identification often face limitations due to the diversity and rapid evolution of viral genomes. In response, recent efforts have focused on leveraging artificial intelligence (AI) techniques to enhance accuracy and efficiency in virus detection. However, existing AI-based approaches are primarily binary classifiers, lacking specificity in identifying viral types and reliant on nucleotide sequences. To address these limitations, VirDetect-AI, a novel tool specifically designed for the identification of eukaryotic viruses within metagenomic datasets, is introduced. The VirDetect-AI model employs a combination of convolutional neural networks and residual neural networks to effectively extract hierarchical features and detailed patterns from complex amino acid genomic data. The results demonstrated that the model has outstanding results in all metrics, with a sensitivity of 0.97, a precision of 0.98, and an F1-score of 0.98. VirDetect-AI improves our comprehension of viral ecology and can accurately classify metagenomic sequences into 980 viral protein classes, hence enabling the identification of new viruses. These classes encompass an extensive array of viral genera and families, as well as protein functions and hosts.},
}

*Metagenomics/methods
*Neural Networks, Computer
*Viral Proteins/genetics
Humans
Viruses/genetics/classification
Genome, Viral
Animals
Eukaryota/genetics
Artificial Intelligence
Metagenome
Algorithms

@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 {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 {pmid39807156,
year = {2025},
author = {Song, H and Tithi, SS and Brown, C and Aylward, FO and Jensen, R and Zhang, L},
title = {Virseqimprover: an integrated pipeline for viral contig error correction, extension, and annotation.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e18515},
pmid = {39807156},
issn = {2167-8359},
mesh = {*Genome, Viral/genetics ; *Metagenomics/methods ; *Software ; Contig Mapping/methods ; Molecular Sequence Annotation/methods ; Computational Biology/methods ; },
abstract = {Despite the recent surge of viral metagenomic studies, it remains a significant challenge to recover complete virus genomes from metagenomic data. The majority of viral contigs generated from de novo assembly programs are highly fragmented, presenting significant challenges to downstream analysis and inference. To address this issue, we have developed Virseqimprover, a computational pipeline that can extend assembled contigs to complete or nearly complete genomes while maintaining extension quality. Virseqimprover first examines whether there is any chimeric sequence based on read coverage, breaks the sequence into segments if there is, then extends the longest segment with uniform depth of coverage, and repeats these procedures until the sequence cannot be extended. Finally, Virseqimprover annotates the gene content of the resulting sequence. Results show that Virseqimprover has good performances on correcting and extending viral contigs to their full lengths, hence can be a useful tool to improve the completeness and minimize the assembly errors of viral contigs. Both a web server and a conda package for Virseqimprover are provided to the research community free of charge.},
}

*Genome, Viral/genetics
*Metagenomics/methods
*Software
Contig Mapping/methods
Molecular Sequence Annotation/methods
Computational Biology/methods

@article {pmid39807079,
year = {2025},
author = {Björnberg, A and Nestor, D and Peker, N and Sinha, B and Couto, N and Rossen, J and Sundqvist, M and Mölling, P},
title = {Critical Steps in Shotgun Metagenomics-Based Diagnosis of Bloodstream Infections Using Nanopore Sequencing.},
journal = {APMIS : acta pathologica, microbiologica, et immunologica Scandinavica},
volume = {133},
number = {1},
pages = {e13511},
doi = {10.1111/apm.13511},
pmid = {39807079},
issn = {1600-0463},
mesh = {Humans ; *Metagenomics/methods ; *Nanopore Sequencing/methods ; *DNA, Bacterial/genetics/blood ; Bacteremia/diagnosis/microbiology ; Reproducibility of Results ; },
abstract = {Shotgun metagenomics offers a broad detection of pathogens for rapid blood stream infection of pathogens but struggles with often low numbers of pathogens combined with high levels of human background DNA in clinical samples. This study aimed to develop a shotgun metagenomics protocol using blood spiked with various bacteria and to assess bacterial DNA extraction efficiency with human DNA depletion. The Blood Pathogen Kit (Molzym) was used to extract DNA from EDTA-whole blood (WB) and plasma samples, using contrived blood specimens spiked with bacteria for shotgun metagenomics diagnostics via Oxford Nanopore sequencing and PCR-based library preparation. Results showed that bacterial reads were higher in WB than plasma. Differences for Staphylococcus aureus and Streptococcus pneumoniae were more pronounced compared to Escherichia coli. Plasma samples exhibited better method reproducibility, with more consistent droplet digital PCR results for human DNA. The study found that extraction was more efficient for Gram-positive bacteria than Gram-negative, suggesting that the human DNA depletion exerts a negative effect on Gram-negative bacteria. Overall, shotgun metagenomics needs further optimisation to improve bacterial DNA recovery and enhance pathogen detection sensitivity. This study highlights some critical steps in the methodology of shotgun metagenomic-based diagnosis of blood stream infections using Nanopore sequencing.},
}

Humans
*Metagenomics/methods
*Nanopore Sequencing/methods
*DNA, Bacterial/genetics/blood
Bacteremia/diagnosis/microbiology
Reproducibility of Results

@article {pmid39806507,
year = {2025},
author = {Zhang, D and Cao, Y and Dai, B and Zhang, T and Jin, X and Lan, Q and Qian, C and He, Y and Jiang, Y},
title = {The virome composition of respiratory tract changes in school-aged children with Mycoplasma pneumoniae infection.},
journal = {Virology journal},
volume = {22},
number = {1},
pages = {10},
pmid = {39806507},
issn = {1743-422X},
support = {No. Q202342//Scientific Research Program of Wuxi Health Commission/ ; No. 32201990//National Natural Science Foundation of China/ ; No. BK20210461//Natural Science Foundation of Jiangsu Province of China/ ; No. SBQN22013//Hospital-level project of Northern Jiangsu People's Hospital/ ; },
abstract = {BACKGROUND: Mycoplasma pneumoniae (MP) is a common pathogen for respiratory infections in children. Previous studies have reported respiratory tract microbial disturbances associated with MP infection (MPI); however, since the COVID-19 pandemic, respiratory virome data in school-aged children with MPI remains insufficient. This study aims to explore the changes in the respiratory virome caused by MPI after the COVID-19 pandemic to enrich local epidemiological data.

METHODS: Clinical samples from 70 children with MPI (70 throat swab samples and 70 bronchoalveolar lavage fluid (BALF) samples) and 78 healthy controls (78 throat swab samples) were analyzed using viral metagenomics. Virus reads were calculated and normalized using MEGAN.6, followed by statistical analysis.

RESULTS: Principal Coordinate Analysis (PCoA) showed that viral community diversity is a significant difference between disease cohorts and healthy controls. After MPI, the number of virus species in the upper respiratory tract (URT) increased obviously, and the abundance of families Poxviridae, Retroviridae, and Iridoviridae, which infect vertebrates, rose evidently, particularly the species BeAn 58,085 virus (BAV). Meanwhile, phage alterations in the disease cohorts were predominantly characterized by increased Myoviridae and Ackermannviridae families and decreased Siphoviridae and Salasmaviridae families (p < 0.01). In addition, some new viruses, such as rhinovirus, respirovirus, dependoparvovirus, and a novel gemykibvirus, were also detected in the BALF of the disease cohort.

CONCLUSIONS: This cross-sectional research highlighted the respiratory virome characteristics of school-aged children with MPI after the COVID-19 outbreak and provided important epidemiological information. Further investigation into the impact of various microorganisms on diseases will aid in developing clinical treatment strategies.},
}

@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 {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 {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 {pmid39805953,
year = {2025},
author = {Daruka, L and Czikkely, MS and Szili, P and Farkas, Z and Balogh, D and Grézal, G and Maharramov, E and Vu, TH and Sipos, L and Juhász, S and Dunai, A and Daraba, A and Számel, M and Sári, T and Stirling, T and Vásárhelyi, BM and Ari, E and Christodoulou, C and Manczinger, M and Enyedi, MZ and Jaksa, G and Kovács, K and van Houte, S and Pursey, E and Pintér, L and Haracska, L and Kintses, B and Papp, B and Pál, C},
title = {ESKAPE pathogens rapidly develop resistance against antibiotics in development in vitro.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {39805953},
issn = {2058-5276},
abstract = {Despite ongoing antibiotic development, evolution of resistance may render candidate antibiotics ineffective. Here we studied in vitro emergence of resistance to 13 antibiotics introduced after 2017 or currently in development, compared with in-use antibiotics. Laboratory evolution showed that clinically relevant resistance arises within 60 days of antibiotic exposure in Escherichia coli, Klebsiella pneumoniae, Acinetobacter baumannii and Pseudomonas aeruginosa, priority Gram-negative ESKAPE pathogens. Resistance mutations are already present in natural populations of pathogens, indicating that resistance in nature can emerge through selection of pre-existing bacterial variants. Functional metagenomics showed that mobile resistance genes to antibiotic candidates are prevalent in clinical bacterial isolates, soil and human gut microbiomes. Overall, antibiotic candidates show similar susceptibility to resistance development as antibiotics currently in use, and the corresponding resistance mechanisms overlap. However, certain combinations of antibiotics and bacterial strains were less prone to developing resistance, revealing potential narrow-spectrum antibacterial therapies that could remain effective. Finally, we develop criteria to guide efforts in developing effective antibiotic candidates.},
}

@article {pmid39805403,
year = {2025},
author = {Wolf, PG and Welsh, C and Binion, B and Dai, H and Oliveira, ML and Hamm, A and Goldberg, S and Buobu, PS and Schering, T and Vergis, S and Kessee, N and Gomez, SL and Yazici, C and Maienschein-Cline, M and Byrd, DA and Gaskins, HR and Ridlon, J and Mutlu, E and Greening, C and Tussing-Humphreys, L},
title = {Secondary bile acid derivatives are contributors to the fecal bile acid pool and associated with bile acid modulating nutrients.},
journal = {The Journal of nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tjnut.2024.12.035},
pmid = {39805403},
issn = {1541-6100},
abstract = {OBJECTIVE: Accumulation of hydrophobic bile acids is linked with cancer development. However, derivatives of deoxycholic acid (DCA) and lithocholic acid (LCA) produced via bacterial metabolism may mitigate the proinflammatory and cytotoxic effects of hydrophobic bile acids. The impact of diet on secondary bile acid (BA) derivative production has not been determined. Therefore, associations between BA modulating nutrients and the composition of secondary BAs and their derivatives were investigated.

METHODS: Stool and blood were collected from 138 participants aged 45-75 years that self-identified as Black or non-Hispanic White. BAs were extracted from stool and serum and quantified using LC/ESI-MS/MS. Energy, macronutrients, micronutrients, and specific dietary nutrients were estimated from two 24-hour diet recalls. The abundance of genes for microbial BA metabolism were assessed from stool metagenomes. Kendall's tau correlation and regression-based modeling was performed to determine associations between BA categories, microbial genes, and select energy adjusted dietary variables (alcohol, calcium, coffee, fiber, fat, protein).

RESULTS: Participants had a mean age of 60 years and a mean BMI of 31 kg/m[2]. BA derivatives were present in all participant stools, with lagodeoxycholic acid being the most abundant derivative quantified. Analysis of stool microbial metagenomes revealed the presence of genes for secondary BA derivative production in all participants. Protein is positively associated with the accumulation of secondary BAs. Monounsaturated fatty acids were negatively associated with high abundant derivatives of deoxycholic acid in regression models. Total fiber and coffee intake were positively correlated with increased conversion of BAs to derivatives. Race and smoking status were significant predictors of associations between dietary variables and BA derivatives.

CONCLUSIONS: Protein, monounsaturated fatty acids, total fiber and coffee were significantly associated with concentrations of secondary BAs and their derivatives. Future work should account for social and structural influences on dietary intake and its relationship with BA elicited cancer risk.},
}

@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 {pmid39805166,
year = {2025},
author = {Memon, FU and Zhu, Y and Cui, Y and Feng, X and Ahmad, S and Zeng, P and Nabi, F and Hao, D and Huang, Z and Tettamanti, G and Tian, L},
title = {Gut microbial communities and transcriptional profiles of black soldier fly (Hermitia illucens) larvae fed on fermented sericulture waste.},
journal = {Waste management (New York, N.Y.)},
volume = {194},
number = {},
pages = {158-168},
doi = {10.1016/j.wasman.2025.01.011},
pmid = {39805166},
issn = {1879-2456},
abstract = {Sericulture waste poses significant challenges to industrial and environmental safety. Black soldier fly larvae (BSFL) offer a promising solution for organic waste management by converting it into insect protein. This study aimed to develop a microbial fermented method for utilizing sericulture waste to feed BSFL and explore the underlying mechanisms. Our results showed that all fermented sericulture waste groups had positive effects on body weight, survival rate, substrate consumption rate, and substrate conversion rate. Metagenomic analysis revealed a notable increase in the abundances of commensal genera, including Sedimentibacter, Clostridium, Enterococcus, Bacteroides, and Bacillus, in the gut of BSFL fed on sericulture waste fermented with the most effective combination of microbial strains (B. subtilis, B. licheniformis, and E. faecalis). In contrast, BSFL reared on unfermented sericulture waste exhibited higher abundances of potentially pathogenic and harmful genera, including Providencia, Klebsiella, Escherichia, Brucella, and Enterobacter. Clusters of orthologous genes (COG) analysis indicated that altered microbial communities in the fermented group mainly participated in metabolic pathways, defense mechanism, and signal transduction mechanism. Transcriptome analysis further revealed that the upregulated genes were functionally associated with key metabolic pathways and immune mechanisms in the fermented group. These findings underscore the pivotal role of selected microbial fermentation in utilizing sericulture waste as BSFL feed, providing a sustainable solution for organic waste management.},
}

@article {pmid39805015,
year = {2025},
author = {Chuckran, PF and Estera-Molina, K and Nicolas, AM and Sieradzki, ET and Dijkstra, P and Firestone, MK and Pett-Ridge, J and Blazewicz, SJ},
title = {Codon bias, nucleotide selection, and genome size predict in situ bacterial growth rate and transcription in rewetted soil.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {122},
number = {3},
pages = {e2413032122},
doi = {10.1073/pnas.2413032122},
pmid = {39805015},
issn = {1091-6490},
support = {SCW1632//U.S. Department of Energy (DOE)/ ; DE-SC0020163//U.S. Department of Energy (DOE)/ ; DE-SC0016247//U.S. Department of Energy (DOE)/ ; SCW1589//U.S. Department of Energy (DOE)/ ; SCW1421//U.S. Department of Energy (DOE)/ ; },
mesh = {*Soil Microbiology ; *Bacteria/genetics/classification/growth & development ; *Codon Usage ; *Soil/chemistry ; *Genome Size ; Metagenome ; Codon/genetics ; Genome, Bacterial ; Transcription, Genetic ; Nucleotides/genetics ; },
abstract = {In soils, the first rain after a prolonged dry period represents a major pulse event impacting soil microbial community function, yet we lack a full understanding of the genomic traits associated with the microbial response to rewetting. Genomic traits such as codon usage bias and genome size have been linked to bacterial growth in soils-however, often through measurements in culture. Here, we used metagenome-assembled genomes (MAGs) with [18]O-water stable isotope probing and metatranscriptomics to track genomic traits associated with growth and transcription of soil microorganisms over one week following rewetting of a grassland soil. We found that codon bias in ribosomal protein genes was the strongest predictor of growth rate. We also found higher growth rates in bacteria with smaller genomes, suggesting that reduced genome size enables a faster response to pulses in soil bacteria. Faster transcriptional upregulation of ribosomal protein genes was associated with high codon bias and increased nucleotide skew. We found that several of these relationships existed within phyla, indicating that these associations between genomic traits and activity could be generalized characteristics of soil bacteria. Finally, we used publicly available metagenomes to assess the distribution of codon bias across a pH gradient and found that microbial communities in higher pH soils-which are often more water limited and pulse driven-have higher codon usage bias in their ribosomal protein genes. Together, these results provide evidence that genomic characteristics affect soil microbial activity during rewetting and pose a potential fitness advantage for soil bacteria where water and nutrient availability are episodic.},
}

*Soil Microbiology
*Bacteria/genetics/classification/growth & development
*Codon Usage
*Soil/chemistry
*Genome Size
Metagenome
Codon/genetics
Genome, Bacterial
Transcription, Genetic
Nucleotides/genetics

@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 {pmid39804671,
year = {2025},
author = {Broderick, CM and Benucci, GMN and Bachega, LR and Miller, GD and Evans, SE and Hawkes, CV},
title = {Long-term climate establishes functional legacies by altering microbial traits.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf005},
pmid = {39804671},
issn = {1751-7370},
abstract = {Long-term climate history can influence rates of soil carbon cycling but the microbial traits underlying these legacy effects are not well understood. Legacies may result if historical climate differences alter the traits of soil microbial communities, particularly those associated with carbon cycling and stress tolerance. However, it is also possible that contemporary conditions can overcome the influence of historical climate, particularly under extreme conditions. Using shotgun metagenomics, we assessed the composition of soil microbial functional genes across a mean annual precipitation gradient that previously showed evidence of strong climate legacies in soil carbon flux and extracellular enzyme activity. Sampling coincided with recovery from a regional, multi-year severe drought, allowing us to document how the strength of climate legacies varied with contemporary conditions. We found increased investment in genes associated with resource cycling with historically higher precipitation across the gradient, particularly in traits related to resource transport and complex carbon degradation. This legacy effect was strongest in seasons with the lowest soil moisture, suggesting that contemporary conditions-particularly, resource stress under water limitation-influences the strength of legacy effects. In contrast, investment in stress tolerance did not vary with historical precipitation, likely due to frequent periodic drought throughout the gradient. Differences in the relative abundance of functional genes explained over half of variation in microbial functional capacity-potential enzyme activity-more so than historical precipitation or current moisture conditions. Together, these results suggest that long-term climate can alter the functional potential of soil microbial communities, leading to legacies in carbon cycling.},
}

@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 {pmid39803536,
year = {2025},
author = {Kettenburg, G and Ranaivoson, HC and Andrianianina, A and Andry, S and Henry, AR and Davis, RL and Laboune, F and Longtine, ER and Godbole, S and Horigan, S and Ruhs, EC and Raharinosy, V and Randriambolamanantsoa, TH and Lacoste, V and Heraud, JM and Dussart, P and Douek, DC and Brook, CE},
title = {Picornaviridae and Caliciviridae diversity in Madagascar fruit bats is driven by cross-continental genetic exchange.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.12.31.630946},
pmid = {39803536},
issn = {2692-8205},
abstract = {Bats are reservoir hosts for numerous well-known zoonotic viruses, but their broader virus-hosting capacities remain understudied. Picornavirales are an order of enteric viruses known to cause disease across a wide range of mammalian hosts, including Hepatitis A in humans and foot-and-mouth disease in ungulates. Host-switching and recombination drive the diversification of Picornavirales worldwide. Divergent Caliciviridae and Picornaviridae (families within the Picornavirales) have been described in bats across mainland Africa, but surveillance for these viruses has been rare in the Southwest Indian Ocean Islands. Bats live in close proximity to and are consumed widely as a food source by humans in Madagascar, providing opportunities for zoonotic transmission. Prior work in Madagascar has described numerous evolutionarily divergent bat viruses, some with zoonotic potential. Using metagenomic Next Generation Sequencing of urine and fecal samples obtained from three species of endemic Malagasy fruit bats (Eidolon dupreanum , Pteropus rufus , and Rousettus madagascariensis), we recovered 13 full-length and 37 partial-length genomic sequences within the order Picornavirales (36 Picornaviridae and 14 Caliciviridae sequences), which we identify and describe here. We find evidence that genetic exchange between mainland African bat and Madagascar bat Picornavirales likely shaped the diversification patterns of these novel sequences through recombination events between closely related Picornavirales ; thus far, high host fidelity appears to have limited these viruses from spilling over into other species.},
}

@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 {pmid39802822,
year = {2025},
author = {French, RK and Anderson, S and Cain, K and Digby, A and Greene, TC and Miskelly, CM and Muller, CG and Taylor, MW and Recovery Team, K and Geoghegan, JL and Holmes, EC},
title = {Diversity and cross-species transmission of viruses in a remote island ecosystem: implications for wildlife conservation.},
journal = {Virus evolution},
volume = {11},
number = {1},
pages = {veae113},
pmid = {39802822},
issn = {2057-1577},
abstract = {The ability of viruses to emerge in new species is influenced by aspects of host biology and ecology, with some taxa harbouring a high diversity and abundance of viruses. However, how these factors shape virus diversity at the ecosystem scale is often unclear. To better understand the pattern and determinants of viral diversity within an ecosystem, and to describe the novel avian viruses infecting an individual avian community, we performed a metagenomic snapshot of the virome from the entire avian community on remote Pukenui/Anchor Island in Aotearoa New Zealand. Through total RNA sequencing of 18 bird species, we identified 50 avian viruses from 9 viral families, of which 96% were novel. Of note, passerines (perching birds) exhibited high viral abundance and diversity, with viruses found across all nine viral families identified. We also identified numerous viruses infecting seabirds on the Island, including megriviruses, hepaciviruses, and hepatoviruses, while parrots exhibited an extremely low diversity of avian viruses. Within passerines, closely related astroviruses and hepatoviruses, and multiple identical hepe-like viruses, were shared among host species. Phylogenetic reconciliation analysis of these viral groups revealed a mixture of co-divergence and cross-species transmission, with virus host-jumping relatively frequent among passerines. In contrast, there was no evidence for recent cross-species virus transmission in parrots or seabirds. The novel pegiviruses and a flavivirus identified here also pose intriguing questions regarding their origins, pathogenicity, and potential impact on vertebrate hosts. Overall, these results highlight the importance of understudied remote island ecosystems as refugia for novel viruses, as well as the intricate interplay between host ecology and behaviour in shaping viral communities.},
}

@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 {pmid39802519,
year = {2025},
author = {Yan, C and Qiu, J and Pan, X and Huang, X and Pan, L and Wang, C and Mao, M},
title = {Mixed Pulmonary Infection, Asthma, and Nephrotic Syndrome in a Patient Diagnosed with Selective IgA Deficiency: A Case Report.},
journal = {Journal of inflammation research},
volume = {18},
number = {},
pages = {127-132},
pmid = {39802519},
issn = {1178-7031},
abstract = {Patients with selective IgA deficiency could have various clinical presentations ranging from asymptomatic to severe respiratory or gastrointestinal tract infection, as well as autoimmune disease and allergic reactions. Selective IgA deficiency is relatively common in Caucasians, but it is rare in the Asian population, meaning it could be easily missed in the clinic. In this study, we report a 26-year-old man with a history of asthma and nephrotic syndrome. He presented with symptoms of pulmonary infection, and his condition quickly deteriorated to respiratory failure that required endotracheal intubation and mechanical ventilation. Sputum smear; sputum, blood, and bronchoalveolar lavage fluid culture; and metagenomic sequencing examination identified multiple mixed pathogens, including Mycobacterium chelonae-abscessus, Pseudomonas aeruginosa, Candida parapsilosis, Acinetobacter baumannii, and Klebsiella cepacia. Finally, he was diagnosed with selective IgA deficiency after a laboratory test detected an extremely low serum IgA level (<0.06 g/L). The patient died of septic shock and multiorgan failure despite aggressive management with a combination of antibiotics and supportive care. We report this case to remind clinicians about this rare disease in the Asian population. Patients with multisystem illnesses that are related to immune dysregulation, such as asthma or nephrotic syndrome, should be tested for immune system disorder. Rare and mixed pathogens should be considered during antibiotic selection in patients with selective IgA deficiency.},
}

@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 {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 {pmid39800795,
year = {2025},
author = {Pagac, MP and Davient, B and Plado, LA and Lam, HYI and Lee, SM and Ravikrishnan, A and Chua, WLE and Muralidharan, S and Sridharan, A and Irudayaswamy, AS and Srinivas, R and Wearne, S and Mohamed Naim, AN and Ho, EXP and Ng, HQA and Kwah, JS and Png, E and Bendt, AK and Wenk, MR and Torta, F and Nagarajan, N and Common, J and Chong, YS and Tham, EH and Shek, LP and Loo, EXL and Chambers, J and Yew, YW and Loh, M and Dawson, TL},
title = {Life stage impact on the human skin ecosystem: lipids and the microbial community.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {13},
pmid = {39800795},
issn = {2055-5008},
mesh = {Humans ; *Skin/microbiology ; Female ; Adult ; *Microbiota ; *Oxylipins/metabolism ; *Lipid Metabolism ; *Lipidomics/methods ; Child ; Malassezia ; Keratinocytes/microbiology/metabolism ; Middle Aged ; Male ; Metagenomics/methods ; Sebum/metabolism ; Interleukin-6/metabolism ; Interleukin-1beta/metabolism ; Aged ; Coculture Techniques ; Adolescent ; Bacteria/classification/metabolism/genetics/isolation & purification ; Young Adult ; Host Microbial Interactions ; Ecosystem ; },
abstract = {Sebaceous free fatty acids are metabolized by multiple skin microbes into bioactive lipid mediators termed oxylipins. This study investigated correlations between skin oxylipins and microbes on the superficial skin of pre-pubescent children (N = 36) and adults (N = 100), including pre- (N = 25) and post-menopausal females (N = 25). Lipidomics and metagenomics revealed that Malassezia restricta positively correlated with the oxylipin 9,10-DiHOME on adult skin and negatively correlated with its precursor, 9,10-EpOME, on pre-pubescent skin. Co-culturing Malassezia with keratinocytes demonstrated a link between 9,10-DiHOME and pro-inflammatory cytokines IL-1β and IL-6 production. We also observed strong correlations between other skin oxylipins and microbial taxa, highlighting life stage differences in sebum production and microbial community composition. Our findings imply a complex host-microbe communication system mediated by lipid metabolism occurring on human skin, warranting further research into its role in skin health and disease and paving the way towards novel therapeutic targets and treatments.},
}

Humans
*Skin/microbiology
Female
Adult
*Microbiota
*Oxylipins/metabolism
*Lipid Metabolism
*Lipidomics/methods
Child
Malassezia
Keratinocytes/microbiology/metabolism
Middle Aged
Male
Metagenomics/methods
Sebum/metabolism
Interleukin-6/metabolism
Interleukin-1beta/metabolism
Aged
Coculture Techniques
Adolescent
Bacteria/classification/metabolism/genetics/isolation & purification
Young Adult
Host Microbial Interactions
Ecosystem