@article {pmid39907344, year = {2025}, author = {Cuong, NC and Hung, NV and Linh, TK and Loi, NTT and Tung, QN and Tuyen, DT and Anh, DTN}, title = {Structure of fungal community and culturable fungi on the discolored surfaces of pine storage boxes in the tropical region in Dong Nai, Vietnam.}, journal = {Brazilian journal of biology = Revista brasleira de biologia}, volume = {84}, number = {}, pages = {e289015}, doi = {10.1590/1519-6984.289015}, pmid = {39907344}, issn = {1678-4375}, mesh = {Vietnam ; *Fungi/classification/isolation & purification/genetics ; *Wood/microbiology ; *Pinus/microbiology ; Tropical Climate ; Mycobiome ; }, abstract = {Wood and wood-based materials are commonly used for storage, but their surfaces are prone to biodegradation by microorganisms, especially fungi. This study focuses on the microbial communities on pine wood storage boxes treated with an anti-termite and mold solution in a tropical region in Dong Nai, Vietnam. We isolated 13 fungal strains from these surfaces and classified them into six genera: Rhizopus, Aspergillus, Fusarium, Curvularia, Penicillium, and Trichoderma. Enzyme activity tests revealed that strains Curvularia eragrostidis TD4.2 and Aspergillus sydowii TD5 were the most effective producers of cellulase, amylase, and laccase. Shotgun metagenomics analysis of the biological sample of the discolored surface of pine storage boxes indicated that Ascomycota was the dominant phylum, with Dothideomycetes and Sordariomycetes as the prevalent class. Aureobasidium (0.33%) and Chaetomium (1.1%) were the most abundant genera in the Dothideomycetes and Sordariomycetes, respectively. This research illustrates the complexity of microbial communities on wood surfaces, providing insights into the fungal dynamics affecting wooden storage materials in tropical climates.}, }
@article {pmid39907343, year = {2025}, author = {Alifia, L and Zulaika, E and Soeprijanto, S and Hamzah, A and Luqman, A}, title = {Microbial diversity and biotechnological potential of mangrove leaf litter in Kebun Raya Mangrove, Surabaya, Indonesia.}, journal = {Brazilian journal of biology = Revista brasleira de biologia}, volume = {84}, number = {}, pages = {e288968}, doi = {10.1590/1519-6984.288968}, pmid = {39907343}, issn = {1678-4375}, mesh = {Indonesia ; *Plant Leaves/microbiology ; *Rhizophoraceae/microbiology ; *Avicennia/microbiology ; Biodiversity ; Bacteria/classification/genetics/isolation & purification ; Wetlands ; }, abstract = {Mangrove ecosystems play a crucial role in maintaining ecological balance with leaf litter serving as an important substrate for diverse microbial communities. This study investigates the microbial communities inhabiting leaf litter from four different mangrove species: Rhizophora apiculata, Rhizophora stylosa, Sonneratia caseolaris, and Avicennia marina collected from Kebun Raya Mangrove, Surabaya, Indonesia. Using metagenomic sequencing, we revealed that Proteobacteria were predominant, followed by Chlorobi and Actinobacteria in the samples. Interestingly, we detected notable populations of anaerobic bacteria, including genus of Chlorobaculum and Allochromatium. Metagenomic analyses exhibited high levels of adaptation to stressors, evidenced by the prevalence of genes conferring resistance to antibiotics (e.g., beta-lactams, tetracyclines), heavy metals (e.g., chromium, arsenic), and hydrocarbons. Furthermore, the metagenomic analysis revealed the presence of genes involved in the biosynthesis of polyunsaturated fatty acids (PUFAs), antimicrobial compounds, and plant growth-promoting activities. These findings highlight the potential of mangrove leaf litter as a reservoir of beneficial microbes with diverse biotechnological applications, including bioremediation, nutraceuticals, pharmaceuticals, and agriculture.}, }
@article {pmid39906212, year = {2024}, author = {Xi, Z and Chen, J and Wang, L and Lu, A}, title = {Characteristics of lower respiratory microbiota in children's refractory Mycoplasma pneumoniae pneumonia pre- and post-COVID-19 era.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1438777}, pmid = {39906212}, issn = {2235-2988}, mesh = {Humans ; *Microbiota ; *COVID-19/immunology/microbiology ; Male ; Female ; Child ; Child, Preschool ; *Pneumonia, Mycoplasma/microbiology ; Mycoplasma pneumoniae/genetics/isolation & purification ; SARS-CoV-2 ; Infant ; High-Throughput Nucleotide Sequencing ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Drug Resistance, Bacterial ; RNA, Ribosomal, 23S/genetics ; Respiratory System/microbiology/virology ; }, abstract = {INTRODUCTION: Little was known about the characteristics of low respiratory tract (LRT) microbiota of refractory M. pneumoniae pneumonia (RMPP) in children before and after the COVID-19 pandemic.
METHODS: Forty-two children diagnosed with RMPP in 2019 (Y2019 group) and 33 children diagnosed with RMPP in 2023 (Y2023 group), entered into the study. The characteristics of the clinical findings were examined, and the LRT microbiota was analyzed by metagenomic next generation sequencing.
RESULTS: The ratio of consolidate, atelectasis, lung necrosis, and erythema multiforme in Y2023 group was significantly higher than that in Y2019 (P<0.05). Mycoplasmoides pneumoniae was the top species of the LRT microbiota in both groups. The rate of macrolide resistance MP in Y2023 was significantly higher than that in Y2019 (P<0.05), and the mutant site was all 23S rRNA A2063G. There were no significant differences in α-diversity and β-diversity of LRT microbiota between Y2019 and Y2023 group. Trichoderma citrinoviride, Canine mastadenovirus A, Ralstonia pickettii, Lactococcus lactis, Pseudomonas aeruginosa were the biomarkers of LRT microbiota in children with RMPP of Y2023. The abundance of Mycoplasmoides pneumoniae positively correlated with the levels of D-dimer and LDH, negatively correlated with the counts of CD3[+] T cells, CD8[+] T cells, CD19[+] B cells and CD16[+]CD56[+] NK cells.
DISCUSSION: Our study showed that high abundance of MP was correlated with the severity of RMPP and decrease of immune cells. Trichoderma citrinoviride, Canine mastadenovirus A, Ralstonia pickettii, Lactococcus lactis, Pseudomonas aeruginosa were the biomarkers in microbiota of LRT in children with RMPP post COVID-19 era.}, }
@article {pmid39905573, year = {2025}, author = {Armstrong, E and Liu, R and Pollock, J and Huibner, S and Udayakumar, S and Irungu, E and Ngurukiri, P and Muthoga, P and Adhiambo, W and Yegorov, S and Kimani, J and Beattie, T and Coburn, B and Kaul, R}, title = {Quantitative profiling of the vaginal microbiota improves resolution of the microbiota-immune axis.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {39}, pmid = {39905573}, issn = {2049-2618}, support = {Canada Graduate Scholarship/CAPMC/CIHR/Canada ; Vanier Canada Graduate Scholarship/CAPMC/CIHR/Canada ; PJT-180629/CAPMC/CIHR/Canada ; MR/R023182/1//Medical Research Council and the UK Foreign, Commonwealth and Development Office/ ; }, mesh = {Humans ; Female ; *Vagina/microbiology/immunology ; *Vaginosis, Bacterial/microbiology/immunology ; Kenya ; *Microbiota ; Adult ; *Sex Workers ; *Bacterial Load ; Bacteria/classification/genetics/isolation & purification ; Young Adult ; Interleukin-1alpha/metabolism ; Cytokines/metabolism ; Metagenomics/methods ; RNA, Ribosomal, 16S/genetics ; Lactobacillus/isolation & purification ; }, abstract = {BACKGROUND: The composition of the vaginal microbiota is closely linked to adverse sexual and reproductive health outcomes, due in part to effects on genital immunology. Compositional approaches such as metagenomic sequencing provide a snapshot of all bacteria in a sample and have become the standard for characterizing the vaginal microbiota, but only provide microbial relative abundances. We hypothesized that the addition of absolute abundance data would provide a more complete picture of host-microbe interactions in the female genital tract.
RESULTS: We analyzed cervicovaginal secretions from 196 female sex workers in Kenya and found that bacterial load was elevated among women with diverse, bacterial vaginosis (BV)-type microbiota and lower among women with Lactobacillus predominance. Bacterial load was also positively associated with proinflammatory cytokines, such as IL-1α, and negatively associated with chemokines, such as IP-10. The associations between bacterial load and immune factors differed across bacterial community states, but L. crispatus predominance was the only microbial community where higher bacterial load was not associated with higher proinflammatory cytokines. Total vaginal bacterial load was also a stronger predictor of the genital immune environment than BV by Nugent score, the current clinical standard, in the Kenya-based cohort and in a Uganda-based confirmatory cohort.
CONCLUSIONS: Our results suggest that total vaginal bacterial load is at least as strong a predictor of the genital immune milieu as current BV clinical diagnostic tools, supporting exploration of the vaginal bacterial load as a predictor of adverse reproductive and sexual health outcomes. Video Abstract.}, }
@article {pmid39905490, year = {2025}, author = {Molina-Pardines, C and Haro-Moreno, JM and Rodriguez-Valera, F and López-Pérez, M}, title = {Extensive paralogism in the environmental pangenome: a key factor in the ecological success of natural SAR11 populations.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {41}, pmid = {39905490}, issn = {2049-2618}, support = {PRE2021-098122//Ministerio de Economía y Competitividad/ ; PID2020-118052GB-I00//Ministerio de Economía y Competitividad/ ; 2021/PER/00020//Ministerio de Universidades/ ; }, mesh = {*Metagenomics/methods ; Mediterranean Sea ; *Genetic Variation ; Microbiota/genetics ; Genome, Bacterial ; Metagenome ; Phylogeny ; Seawater/microbiology ; }, abstract = {BACKGROUND: The oceanic microbiome is dominated by members of the SAR11 clade. Despite their abundance, challenges in recovering the full genetic diversity of natural populations have hindered our understanding of the eco-evolutionary mechanisms driving intra-species variation. In this study, we employed a combination of single-amplified genomes and long-read metagenomics to recover the genomic diversity of natural populations within the SAR11 genomospecies Ia.3/VII, the dominant group in the Mediterranean Sea.
RESULTS: The reconstruction of the first complete genome within this genomospecies revealed that the core genome represents a significant proportion of the genome (~ 81%), with highly divergent areas that allow for greater strain-dependent metabolic flexibility. The flexible genome was concentrated in small regions, typically containing a single gene, and was located in equivalent regions within the genomospecies. Each variable region was associated with a specific set of genes that, despite exhibiting some divergence, maintained equivalent biological functionality within the population. The environmental pangenome is large and enriched in genes involved in nutrient transport, as well as cell wall synthesis and modification, showing an extremely high degree of functional redundancy in the flexible genome (i.e. paralogisms).
CONCLUSIONS: This genomic architecture promotes polyclonality, preserving genetic variation within the population. This, in turn, mitigates intraspecific competition and enables the population to thrive under variable environmental conditions and selective pressures. Furthermore, this study demonstrates the power of long-read metagenomics in capturing the full genetic diversity of environmental SAR11 populations, overcoming the limitations of second-generation sequencing technologies in genome assembly. Video Abstract.}, }
@article {pmid39905038, year = {2025}, author = {Qu, Q and Dou, Q and Xiang, Z and Yu, B and Chen, L and Fan, Z and Zhao, X and Yang, S and Zeng, P}, title = {Population-level gut microbiome and its associations with environmental factors and metabolic disorders in Southwest China.}, journal = {NPJ biofilms and microbiomes}, volume = {11}, number = {1}, pages = {24}, pmid = {39905038}, issn = {2055-5008}, mesh = {*Gastrointestinal Microbiome ; Humans ; China ; *Metabolic Diseases/microbiology/etiology ; *Feces/microbiology ; *Metagenomics/methods ; Female ; Male ; Middle Aged ; Diet ; Adult ; Bacteria/classification/genetics/isolation & purification ; Life Style ; Socioeconomic Factors ; }, abstract = {Gut microbiota affects host health and disease. Large-scale cohorts have explored the interactions between the microbiota, host, and environment to reveal the disease-associated microbiota variation. A population-level gut metagenomic cohort is still rare in China. Here, we performed metagenomic sequencing on fecal samples from the CMEC Microbiome Project in Southwest China. In this study, we identified host socioeconomics, diet, lifestyle, and medical measurements that were significantly associated with microbiome function and composition. We revealed extensive novel associations between the host microbiome and common metabolic disorders. Our results provide new insight into associations of gut microbiota with metabolic disorders so as to support the translation of gut microbiome findings into potential clinical practice.}, }
@article {pmid39904998, year = {2025}, author = {Boulton, W and Salamov, A and Grigoriev, IV and Calhoun, S and LaButti, K and Riley, R and Barry, K and Fong, AA and Hoppe, CJM and Metfies, K and Oetjen, K and Eggers, SL and Müller, O and Gardner, J and Granskog, MA and Torstensson, A and Oggier, M and Larsen, A and Bratbak, G and Toseland, A and Leggett, RM and Moulton, V and Mock, T}, title = {Metagenome-assembled-genomes recovered from the Arctic drift expedition MOSAiC.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {204}, pmid = {39904998}, issn = {2052-4463}, mesh = {Arctic Regions ; *Metagenome ; Oceans and Seas ; Expeditions ; Ecosystem ; Ice Cover/microbiology ; }, abstract = {The Multidisciplinary Observatory for Study of the Arctic Climate (MOSAiC) expedition consisted of a year-long drifting survey of the Central Arctic Ocean. The ecosystems component of MOSAiC included the sampling of molecular data, with metagenomes collected from a diverse range of environments. The generation of metagenome-assembled-genomes (MAGs) from metagenomes are a starting point for genome-resolved analyses. This dataset presents a catalogue of MAGs recovered from a set of 73 samples from MOSAiC, including 2407 prokaryotic and 56 eukaryotic MAGs, as well as annotations of a near complete eukaryotic MAG using the Joint Genome Institute (JGI) annotation pipeline. The metagenomic samples are from the surface ocean, chlorophyll maximum, mesopelagic and bathypelagic, within leads and under-ice ocean, as well as melt ponds, ice ridges, and first- and second-year sea ice. This set of MAGs can be used to benchmark microbial biodiversity in the Central Arctic Ocean, compare individual strains across space and time, and to study changes in Arctic microbial communities from the winter to summer, at a genomic level.}, }
@article {pmid39903340, year = {2025}, author = {Yan, Z and Zheng, Z and Cao, L and Zhu, Z and Zhou, C and Sun, Q and Tang, B and Zhao, G}, title = {Altered gut microbiome and serum metabolome profiles associated with essential tremor.}, journal = {Metabolic brain disease}, volume = {40}, number = {2}, pages = {118}, pmid = {39903340}, issn = {1573-7365}, support = {U20A20355//National Natural Science Foundation of China/ ; WKJ-ZJ-ZZ08//Major Health Science and Technology Program of Zhejiang Province/ ; LZ23H090004//Key Projects of Zhejiang Provincial Natural Science Fund/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Metabolome ; *Essential Tremor/blood/microbiology ; Male ; Female ; Middle Aged ; Aged ; Dysbiosis/blood ; Lipid Metabolism/physiology ; }, abstract = {The genetic predisposition and environmental factors both trigger the complex neurological dyskinesia of essential tremor (ET). Gut dysbiosis may facilitate the occurrence and development of neurological diseases. Therefore, it is worth exploring the inner connections between gut microbiota and ET. First, the gut microbiota of 19 ET patients and 21 healthy controls (HCs) were analysed with metagenomics approach. Second, the potential linkages between gut microbiome and serum metabolome profiles were explored by integrative analysis. The gut microbiota disorders were present in ET patients. The LEfSe method showed a significant decrease in Bacteroides. The functional analysis revealed that there were differences in gut microbial apoptosis, retinol metabolism, and steroid hormone biosynthesis pathways. The levels of various lipids and lipid-like molecules alter in serum of ET patients, which correlated with altered gut microbial abundance, indicating the alterations in lipid metabolism involved in apoptosis pathway in ET. All of these data point to the gut dysbiosis in ET, and some changed gut microbial species were linked to abnormalities in blood lipid metabolism, which open up new avenues for investigation into the pathophysiology of ET.}, }
@article {pmid39844349, year = {2025}, author = {Fonseca de Souza, L and Oliveira, HG and Pellegrinetti, TA and Mendes, LW and Bonatelli, ML and Dumaresq, ASR and Sinatti, VVC and Pinheiro, JB and Azevedo, JL and Quecine, MC}, title = {Co-inoculation with Bacillus thuringiensis RZ2MS9 and rhizobia improves the soybean development and modulates soil functional diversity.}, journal = {FEMS microbiology ecology}, volume = {101}, number = {2}, pages = {}, doi = {10.1093/femsec/fiaf013}, pmid = {39844349}, issn = {1574-6941}, support = {2021/12378-4//FAPESP/ ; 166644/2020-0//National Council for Scientific and Technological Development/ ; 69242/2018-8//H.G.O./ ; 22.1.08498.01.0//T.A.P./ ; }, mesh = {*Glycine max/microbiology/growth & development ; *Soil Microbiology ; *Bacillus thuringiensis/genetics/growth & development ; *Soil/chemistry ; Rhizobium/genetics ; Quorum Sensing ; Microbiota ; Phosphorus/metabolism ; Biodiversity ; }, abstract = {Despite the beneficial effects of plant growth-promoting rhizobacteria on agriculture, understanding the consequences of introducing foreign microbes into soil taxonomic and functional diversity is necessary. This study evaluated the effects co-inoculation of soybean with Bacillus thuringiensis (Bt) RZ2MS9 and commercial rhizobia on the natural microbial community structure and functional potential. Our results indicated that soybean development was positively influenced by co-inoculation, plants exhibited greater height and a higher number of pods, and no reductions in productivity estimates. Soil prokaryotic diversity and community structure remained unchanged by Bt RZMS9 inoculation or co-inoculation with rhizobia 147 days after sowing. However, functional diversity was influenced by sole Bt inoculation, potentially due to community quorum sensing disruption by N-acyl homoserine lactone hydrolases. The genes enriched by co-inoculation were mostly related to soil phosphorus cycling, with gcd showing the most pronounced increase. The nifA genes increased when rhizobia alone were inoculated, suggesting that this pathway could be affected by Bt RZ2MS9 inoculation. This study demonstrates the synergistic activity of rhizobia and Bt RZ2MS9 on soybean development, without significantly interfering with natural microbial community, presenting a promising approach for sustainable crop management.}, }
@article {pmid39832809, year = {2025}, author = {Miebach, J and Green, D and Strittmatter, M and Mallinger, C and Le Garrec, L and Zhang, QY and Foucault, P and Kunz, C and Gachon, CMM}, title = {Importance, structure, cultivability, and resilience of the bacterial microbiota during infection of laboratory-grown Haematococcus spp. by the blastocladialean pathogen Paraphysoderma sedebokerense: evidence for a domesticated microbiota and its potential for biocontrol.}, journal = {FEMS microbiology ecology}, volume = {101}, number = {2}, pages = {}, doi = {10.1093/femsec/fiaf011}, pmid = {39832809}, issn = {1574-6941}, support = {BB/P027806/1//UK Research and Innovation/ ; H2020-BG1-2016//Horizon Europe/ ; //MNHN/ ; }, mesh = {*Microbiota ; *Chlorophyta/microbiology/growth & development ; *Bacteria/genetics/classification/growth & development/isolation & purification ; Ascomycota/genetics/growth & development/physiology ; Metagenomics ; Biological Control Agents ; }, abstract = {Industrial production of the unicellular green alga Haematococcus lacustris is compromised by outbreaks of the fungal pathogen Paraphysoderma sedebokerense (Blastocladiomycota). Here, using axenic algal and fungal cultures and antibiotic treatments, we show that the bacterial microbiota of H. lacustris is necessary for the infection by P. sedebokerense and that its modulation affects the outcome of the interaction. We combined metagenomics and laboratory cultivation to investigate the diversity of the bacterial microbiota associated to three Haematococcus species and monitor its change upon P. sedebokerense infection. We unveil three types of distinct, reduced bacterial communities, which likely correspond to keystone taxa in the natural Haematococcus spp. microbiota. Remarkably, the taxonomic composition and functionality of these communities remained stable during infection. The major bacterial taxa identified in this study have been cultivated by us or others, paving the way to developing synthetic communities to experimentally explore interactions within this tripartite system. We discuss our results in the light of emerging evidence concerning the structuring and domestication of plant and animal microbiota, thus providing novel experimental tools and a new conceptual framework necessary to enable the engineering of Haematococcus spp. microbiota toward the biocontrol of P. sedebokerense.}, }
@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 = {419}, number = {}, pages = {132081}, doi = {10.1016/j.biortech.2025.132081}, pmid = {39826761}, issn = {1873-2976}, mesh = {*Composting/methods ; *Manure/virology ; Bacteria/genetics ; Metagenome ; Virome ; }, 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 {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 = {16}, number = {2}, pages = {e0373224}, doi = {10.1128/mbio.03732-24}, pmid = {39807864}, issn = {2150-7511}, support = {//Cancer Research UK (CRUK)/ ; R01CA154426//HHS | NIH | National Cancer Institute (NCI)/ ; }, mesh = {Humans ; *Virulence Factors/genetics ; *Colorectal Neoplasms/microbiology/genetics/pathology ; Bacterial Proteins/genetics/metabolism ; Gastrointestinal Microbiome/genetics ; Fusobacterium/genetics/pathogenicity/metabolism ; Multigene Family ; Genome, Bacterial ; Lectins/genetics/metabolism ; Fusobacteria/genetics/metabolism/pathogenicity ; }, 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 {pmid39798223, year = {2025}, author = {Larsson, SC and Ericson, U and Dekkers, KF and Arage, G and Rašo, LM and Sayols-Baixeras, S and Hammar, U and Baldanzi, G and Nguyen, D and Nielsen, HB and Holm, JB and Risérus, U and Michaëlsson, K and Sundström, J and Smith, JG and Engström, G and Ärnlöv, J and Orho-Melander, M and Fall, T and Ahmad, S}, title = {Meat intake in relation to composition and function of gut microbiota.}, journal = {Clinical nutrition (Edinburgh, Scotland)}, volume = {45}, number = {}, pages = {124-133}, doi = {10.1016/j.clnu.2024.12.034}, pmid = {39798223}, issn = {1532-1983}, mesh = {*Gastrointestinal Microbiome/physiology ; Humans ; Male ; Female ; Middle Aged ; Adult ; Diet/methods/statistics & numerical data ; Meat/microbiology ; Aged ; Red Meat/microbiology ; Metagenomics/methods ; Biomarkers/blood ; }, abstract = {OBJECTIVE: Meat intake is suggested to affect gut microbiome composition and the risk of chronic diseases. We aimed to identify meat-associated gut microbiome features and their association with host factors.
DESIGN: Gut microbiota species were profiled by deep shotgun metagenomics sequencing in 9669 individuals. Intake of white meat, unprocessed red meat, and processed red meat was assessed using a food frequency questionnaire. The associations of meat intake with alpha-diversity and relative abundance of gut microbiota species were tested using linear regression models with adjustment for dietary fiber intake, body mass index, and other potential confounders. Meat-associated species were further assessed for association with enrichment of microbial gene function, meat-associated plasma metabolites, and clinical biomarkers.
RESULTS: Higher intake of processed red meat was associated with reduced alpha microbial diversity. White meat, unprocessed, and processed red meat intakes were associated with 36, 14, and 322 microbiota species, respectively. Species associated with processed red meat were enriched for bacterial pathways like amino acid degradation, while those negatively linked were enriched for pathways like homoacetogenesis. Furthermore, species positively associated with processed red meat were to a large extent associated with reduced trimethylamine N-oxide and glutamine levels but increased creatine and carnitine metabolites, fasting insulin and glucose, C-reactive protein, apolipoprotein A1, and triglyceride levels and higher blood pressure.
CONCLUSION: This largest to date population-based study on meat and gut microbiota suggests that meat intake, particularly processed red meat, may modify the gut microbiota composition, functional capacity, and health-related biomarkers.}, }
@article {pmid39719199, year = {2025}, author = {Qi, Y and Fu, R and Yan, C and Liu, X and Liu, N}, title = {Enrichment of a heterotrophic nitrifying and aerobic denitrifying bacterial consortium: Microbial community succession and nitrogen removal characteristics and mechanisms.}, journal = {Bioresource technology}, volume = {419}, number = {}, pages = {132013}, doi = {10.1016/j.biortech.2024.132013}, pmid = {39719199}, issn = {1873-2976}, mesh = {*Denitrification ; *Nitrification ; *Nitrogen/metabolism ; Aerobiosis ; *Heterotrophic Processes ; *Microbial Consortia/physiology ; Bacteria/metabolism ; }, abstract = {This study cultivated a bacterial consortium (S60) from landfill leachate that exhibited effective heterotrophic nitrification and aerobic denitrification (HN-AD) properties. Under aerobic conditions, the removal of NH4[+]-N reached 100 % when the S60 consortium utilised NH4[+]-N either as the sole nitrogen source or in combination with NO2[-]-N and NO3[-]-N. Optimal HN-AD performance was achieved with sodium acetate as a carbon source and a pH of 7.0-8.0, dissolved oxygen concentration of 4.0-5.0 mg/L, and a C/N ratio of 10. Furthermore, the presence of functional genes (amoA, hao, napA, nirK, nirS, nosZ), hydroxylamine oxidase, nitrate reductase, and nitrite reductase was confirmed in the S60 consortium. Drawing from these findings, two HN-AD pathways were delineated: NH4[+]-N → NH2OH → NO2[-]-N → NO3[-]-N → NO2[-]-N → NO → N2O → N2 and NH4[+]-N → NH2OH → N2O → N2. Metagenomic binning analysis of the S60 consortium uncovered complete pathways for dissimilatory nitrate reduction and denitrification within Halomonas, Zobellella, Stutzerimonas, Marinobacter, and Pannonibacter. These findings offer new insights into the application of HN-AD bacteria and their collaborative nitrogen removal in environments with varying nitrogen sources.}, }
@article {pmid39702789, year = {2025}, author = {Kaur, S and Patel, BCK and Collen, A and Malhotra, R}, title = {The microbiome and the eye: a new era in ophthalmology.}, journal = {Eye (London, England)}, volume = {39}, number = {3}, pages = {436-448}, pmid = {39702789}, issn = {1476-5454}, mesh = {Humans ; *Microbiota/physiology ; *Eye Diseases/microbiology/therapy ; *Ophthalmology ; *Gastrointestinal Microbiome/physiology ; Eye/microbiology ; Fecal Microbiota Transplantation ; }, abstract = {The human microbiome has progressively been recognised for its role in various disease processes. In ophthalmology, complex interactions between the gut and distinct ocular microbiota within each structure and microenvironment of the eye has advanced our knowledge on the multi-directional relationships of these ecosystems. Increasingly, studies have shown that modulation of the microbiome can be achieved through faecal microbiota transplantation and synbiotics producing favourable outcomes for ophthalmic diseases. As ophthalmologists, we are obliged to educate our patients on measures to cultivate a healthy gut microbiome through a range of holistic measures. Further integrative studies combining microbial metagenomics, metatranscriptomics and metabolomics are necessary to fully characterise the human microbiome and enable targeted therapeutic interventions.}, }
@article {pmid39487079, year = {2025}, author = {Williams, AD and Leung, VW and Tang, JW and Hidekazu, N and Suzuki, N and Clarke, AC and Pearce, DA and Lam, TT}, title = {Ancient environmental microbiomes and the cryosphere.}, journal = {Trends in microbiology}, volume = {33}, number = {2}, pages = {233-249}, doi = {10.1016/j.tim.2024.09.010}, pmid = {39487079}, issn = {1878-4380}, mesh = {*Microbiota ; *Metagenomics ; *Environmental Microbiology ; Permafrost/microbiology ; Ice ; Bacteria/genetics/classification/isolation & purification ; Computational Biology/methods ; }, abstract = {In this review, we delineate the unique set of characteristics associated with cryosphere environments (namely, ice and permafrost) which present both challenges and opportunities for studying ancient environmental microbiomes (AEMs). In a field currently reliant on several assumptions, we discuss the theoretical and empirical feasibility of recovering microbial nucleic acids (NAs) from ice and permafrost with varying degrees of antiquity. We also summarize contamination control best practices and highlight considerations for the latest approaches, including shotgun metagenomics, and downstream bioinformatic authentication approaches. We review the adoption of existing software and provide an overview of more recently published programs, with reference to their suitability for AEM studies. Finally, we summarize outstanding challenges and likely future directions for AEM research.}, }
@article {pmid39901058, year = {2025}, author = {Richardson, M and Zhao, S and Lin, L and Sheth, RU and Qu, Y and Lee, J and Moody, T and Ricaurte, D and Huang, Y and Velez-Cortes, F and Urtecho, G and Wang, HH}, title = {SAMPL-seq reveals micron-scale spatial hubs in the human gut microbiome.}, journal = {Nature microbiology}, volume = {10}, number = {2}, pages = {527-540}, pmid = {39901058}, issn = {2058-5276}, support = {MCB-2025515//National Science Foundation (NSF)/ ; DGE-1644869//National Science Foundation (NSF)/ ; DGE-1644869//National Science Foundation (NSF)/ ; DGE-1644869//National Science Foundation (NSF)/ ; 2R01AI132403, 1R01DK118044, 1R01EB031935, 1R21AI146817//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; N00014-18-1-2237//United States Department of Defense | United States Navy | ONR | Office of Naval Research Global (ONR Global)/ ; 1016691//Burroughs Wellcome Fund (BWF)/ ; HR0011-23-2-0001//United States Department of Defense | Defense Advanced Research Projects Agency (DARPA)/ ; W911NF-22-2-0210//United States Department of Defense | United States Army | U.S. Army Research, Development and Engineering Command | Army Research Office (ARO)/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Metagenomics/methods ; *Bacteria/genetics/classification/isolation & purification ; High-Throughput Nucleotide Sequencing/methods ; Feces/microbiology ; Inulin/metabolism ; RNA, Ribosomal, 16S/genetics ; Metagenome ; }, abstract = {The local arrangement of microbes can profoundly impact community assembly, function and stability. However, our understanding of the spatial organization of the human gut microbiome at the micron scale is limited. Here we describe a high-throughput and streamlined method called Split-And-pool Metagenomic Plot-sampling sequencing (SAMPL-seq) to capture spatial co-localization in a complex microbial consortium. The method obtains microbial composition of micron-scale subcommunities through split-and-pool barcoding. SAMPL-seq analysis of the healthy human gut microbiome identified bacterial taxa pairs that consistently co-occurred both over time and across multiple individuals. These co-localized microbes organize into spatially distinct groups or 'spatial hubs' dominated by Bacteroidaceae, Ruminococcaceae and Lachnospiraceae families. Using inulin as a dietary perturbation, we observed reversible spatial rearrangement of the gut microbiome where specific taxa form new local partnerships. Spatial metagenomics using SAMPL-seq can unlock insights into microbiomes at the micron scale.}, }
@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 = {13}, number = {2}, pages = {e0069624}, doi = {10.1128/spectrum.00696-24}, pmid = {39807898}, issn = {2165-0497}, mesh = {*Metagenomics/methods ; *Feces/microbiology ; Humans ; *Microbiota/genetics ; *Bacteria/genetics/classification/isolation & purification ; Sequence Analysis, DNA/methods ; Gastrointestinal Microbiome/genetics ; High-Throughput Nucleotide Sequencing/methods ; Metagenome ; DNA, Bacterial/genetics ; }, 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 {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 = {10}, number = {2}, pages = {313-331}, pmid = {39805953}, issn = {2058-5276}, mesh = {*Anti-Bacterial Agents/pharmacology ; Humans ; *Microbial Sensitivity Tests ; Pseudomonas aeruginosa/drug effects/genetics/growth & development ; Drug Resistance, Bacterial/genetics ; Mutation ; Escherichia coli/drug effects/genetics/growth & development ; Metagenomics ; Gastrointestinal Microbiome/drug effects ; Acinetobacter baumannii/drug effects/genetics/growth & development ; Klebsiella pneumoniae/drug effects/genetics/growth & development ; Drug Resistance, Multiple, Bacterial/genetics ; Gram-Negative Bacteria/drug effects/genetics ; }, 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 {pmid39794474, year = {2025}, author = {Yin, Q and da Silva, AC and Zorrilla, F and Almeida, AS and Patil, KR and Almeida, A}, title = {Ecological dynamics of Enterobacteriaceae in the human gut microbiome across global populations.}, journal = {Nature microbiology}, volume = {10}, number = {2}, pages = {541-553}, pmid = {39794474}, issn = {2058-5276}, support = {MR/W016184/1//RCUK | Medical Research Council (MRC)/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; *Enterobacteriaceae/genetics/classification/isolation & purification ; Metagenome ; Enterobacteriaceae Infections/microbiology ; Feces/microbiology ; Machine Learning ; }, abstract = {Gut bacteria from the Enterobacteriaceae family are a major cause of opportunistic infections worldwide. Given their prevalence among healthy human gut microbiomes, interspecies interactions may play a role in modulating infection resistance. Here we uncover global ecological patterns linked to Enterobacteriaceae colonization and abundance by leveraging a large-scale dataset of 12,238 public human gut metagenomes spanning 45 countries. Machine learning analyses identified a robust gut microbiome signature associated with Enterobacteriaceae colonization status, consistent across health states and geographic locations. We classified 172 gut microbial species as co-colonizers and 135 as co-excluders, revealing a genus-wide signal of colonization resistance within Faecalibacterium and strain-specific co-colonization patterns of the underexplored Faecalimonas phoceensis. Co-exclusion is linked to functions involved in short-chain fatty acid production, iron metabolism and quorum sensing, while co-colonization is linked to greater functional diversity and metabolic resemblance to Enterobacteriaceae. Our work underscores the critical role of the intestinal environment in the colonization success of gut-associated opportunistic pathogens with implications for developing non-antibiotic therapeutic strategies.}, }
@article {pmid39745426, year = {2025}, author = {Gulyaeva, A and Liu, L and Garmaeva, S and Kruk, M and Weersma, RK and Harmsen, HJM and Zhernakova, A}, title = {Identification and characterization of Faecalibacterium prophages rich in diversity-generating retroelements.}, journal = {Microbiology spectrum}, volume = {13}, number = {2}, pages = {e0106624}, doi = {10.1128/spectrum.01066-24}, pmid = {39745426}, issn = {2165-0497}, mesh = {*Prophages/genetics/isolation & purification ; *Retroelements ; Humans ; *Metagenomics ; Genome, Viral/genetics ; Gastrointestinal Microbiome ; Computational Biology/methods ; Host Specificity ; Bacteriophages/genetics/classification/isolation & purification/physiology ; Genome, Bacterial/genetics ; Phylogeny ; Genetic Variation ; }, abstract = {Metagenomics has revealed the incredible diversity of phages within the human gut. However, very few of these phages have been subjected to in-depth experimental characterization. One promising method of obtaining novel phages for experimental characterization is through induction of the prophages integrated into the genomes of cultured gut bacteria. Here, we developed a bioinformatic approach to prophage identification that builds on prophage genomic properties, existing prophage-detecting software, and publicly available virome sequencing data. We applied our approach to 22 strains of bacteria belonging to the genus Faecalibacterium, resulting in identification of 15 candidate prophages, and validated the approach by demonstrating the activity of five prophages from four of the strains. The genomes of three active phages were identical or similar to those of known phages, while the other two active phages were not represented in the Viral RefSeq database. Four of the active phages possessed a diversity-generating retroelement (DGR), and one retroelement had two variable regions. DGRs of two phages were active at the time of the induction experiments, as evidenced by nucleotide variation in sequencing reads. We also predicted that the host range of two active phages may include multiple bacterial species. Finally, we noted that four phages were less prevalent in the metagenomes of inflammatory bowel disease patients compared to a general population cohort, a difference mainly explained by differences in the abundance of the host bacteria. Our study highlights the utility of prophage identification and induction for unraveling phage molecular mechanisms and ecological interactions.IMPORTANCEWhile hundreds of thousands of phage genomes have been discovered in metagenomics studies, only a few of these phages have been characterized experimentally. Here, we explore phage characterization through bioinformatic identification of prophages in genomes of cultured bacteria, followed by prophage induction. Using this approach, we detect the activity of five prophages in four strains of commensal gut bacteria Faecalibacterium. We further note that four of the prophages possess diversity-generating retroelements implicated in rapid mutation of phage genome loci associated with phage-host and phage-environment interactions and analyze the intricate patterns of retroelement activity. Our study highlights the potential of prophage characterization for elucidating complex molecular mechanisms employed by the phages.}, }
@article {pmid39716679, year = {2025}, author = {Bai, X and Wu, J and Zhang, B and Zhao, H and Tian, F and Wang, B}, title = {Metagenomics reveals functional profiles of soil nitrogen and phosphorus cycling under different amendments in saline-alkali soil.}, journal = {Environmental research}, volume = {267}, number = {}, pages = {120686}, doi = {10.1016/j.envres.2024.120686}, pmid = {39716679}, issn = {1096-0953}, mesh = {*Phosphorus/analysis ; *Soil Microbiology ; *Soil/chemistry ; *Nitrogen/metabolism ; *Metagenomics ; China ; Manure/microbiology ; Nitrogen Cycle ; Fertilizers/analysis ; Salinity ; Alkalies/chemistry ; Microbiota ; }, abstract = {High salinity, low fertility and poor structure in saline-alkali soils led to nutrient cycling slow and microbial activity loss. The application of amendments has proven effective in enhancing soil nutrients, which significantly affects soil nitrogen and phosphorus cycling process. However, the specific impact of different amendments on the microbial functional potential related to nutrient cycling in saline-alkali soils remains unclear. Hence, metagenomics sequencing was used to investigate soil microbial communities and nitrogen and phosphorus cycling genes in response to different amendments, and to examine the influence of soil physicochemical properties on functional genes in the Hetao irrigation district of China. The results showed that amendments application enriched the Proteobacteria abundance, while inhibiting oligotrophic groups such as Chloroflexi. Compared to the control (CK), the combined application of desulfurization gypsum and cattle manure (DC) notably increased nasA (assimilatory nitrate reduction) and nirB (dissimilatory nitrate reduction), as well as phoD and phoA genes (organic P mineralization). Furthermore, soil AK and AP were primary factors affecting microbial communities and N and P cycling genes. Overall, this study offers valuable insights into soil nitrogen and phosphorus cycling genes and their interactions in response to different amendments, where the application of amendments affects nitrogen and phosphorus cycling by altering soil nutrient availability.}, }
@article {pmid39701354, year = {2025}, author = {Liu, J and Zhou, M and Zhou, L and Dang, R and Xiao, L and Tan, Y and Li, M and Yu, J and Zhang, P and Hernández, M and Lichtfouse, E}, title = {Methane production related to microbiota in dairy cattle feces.}, journal = {Environmental research}, volume = {267}, number = {}, pages = {120642}, doi = {10.1016/j.envres.2024.120642}, pmid = {39701354}, issn = {1096-0953}, mesh = {Animals ; *Methane/metabolism/biosynthesis ; Cattle ; *Feces/microbiology ; *Archaea/metabolism/genetics ; Bacteria/metabolism/genetics/classification ; Microbiota ; Dairying ; }, abstract = {Methane (CH4) emission from livestock feces, led by ruminants, shows a profound impact on global warming. Despite this, we have almost no information on the syntrophy of the intact microbiome metabolisms, from carbohydrates to the one-carbon units, covering multiple stages of ruminant development. In this study, syntrophic effects of polysaccharide degradation and acetate-producing bacteria, and methanogenic archaea were revealed through metagenome-assembled genomes from water saturated dairy cattle feces. Although CH4 is thought to be produced by archaea, more edges, nodes, and balanced interaction types revealed by network analysis provided a closed bacteria-archaea network. The CH4 production potential and pathways were further evaluated through dynamic, thermodynamic and [13]C stable isotope analysis. The powerful CH4 production potential benefited from the metabolic flux: classical polysaccharides, soluble sugar (glucose, galactose, lactose), acetate, and CH4 produced via typical acetoclastic methanogenesis. In comparison, a cooperative model dominated by hydrogenotrophic methanogenic archaea presented a weak ability to generate CH4. Our findings comprehensively link carbon and CH4 metabolism paradigm to specific microbial lineages which are shaped related to developmental stages of the dairy cattle, directing influencing global warming from livestock and waste treatment.}, }
@article {pmid39670752, year = {2025}, author = {Peterson, D and Weidenmaier, C and Timberlake, S and Gura Sadovsky, R}, title = {Depletion of key gut bacteria predicts disrupted bile acid metabolism in inflammatory bowel disease.}, journal = {Microbiology spectrum}, volume = {13}, number = {2}, pages = {e0199924}, doi = {10.1128/spectrum.01999-24}, pmid = {39670752}, issn = {2165-0497}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Bile Acids and Salts/metabolism ; *Inflammatory Bowel Diseases/microbiology/metabolism ; *Feces/microbiology ; *Clostridium/genetics/metabolism/isolation & purification ; Animals ; Mice ; Bacteria/classification/genetics/metabolism/isolation & purification ; Operon ; Metagenomics ; Metagenome ; }, abstract = {The gut microbiome plays a key role in bile acid (BA) metabolism, where a diversity of metabolic products contribute to human health and disease. In particular, Inflammatory Bowel Disease (IBD) is characterized by a low concentration of secondary bile acids (SBAs), whose transformation from primary bile acids (PBAs) is an essential function performed solely by gut bacteria. BA-transformation activity mediated by the bile acid inducible (bai) operon has been functionally characterized in the genus Clostridium, and homologous bai gene sequences have been found in metagenome-assembled genomes (MAGs) belonging to other taxa in the human gut, but it is unclear which species of bai-carrying bacteria perform physiologically significant amounts of bile acid transformation in healthy and sick individuals. Here, we analyzed hundreds of stool samples with paired metagenomic and metabolomic data from IBD patients and controls and found that the abundance of the bai operon in metagenomic samples was highly predictive of that sample's high- or low-SBA metabolic state. We further found that bai genes from the Clostridium species best characterized as BA transformers were more prevalent in IBD patients than in non-IBD controls, while bai genes from uncharacterized taxa known only from MAGs were much more physiologically relevant in non-IBD samples. These un-isolated clades of BA-transforming bacteria merit further research; as beyond their prevalence in the human population, we found some cases in which they engrafted in IBD patients who had undergone fecal microbiota transplantation and experienced a clinical response.IMPORTANCEIn this paper, we identify specific bacteria that perform an important metabolic function in the human gut and demonstrate that in the guts of a large subset of patients with IBD, these bacteria are missing and the function is defective. This is a rare example where the correlation between the absence of specific bacteria and the dysfunction of metabolism is directly observed, not in mice nor in the lab, but in physiologic microbial communities in the human gut. Our results point to a path for studying how a small but important set of bacteria is affected by conditions in the IBD gut and perhaps to the development of interventions to mitigate the loss of these bacteria in IBD.}, }
@article {pmid39665565, year = {2025}, author = {Gao, X and Liang, H and Hu, T and Zou, Y and Xiao, L}, title = {Cultivated genome references for protein database construction and high-resolution taxonomic annotation in metaproteomics.}, journal = {Microbiology spectrum}, volume = {13}, number = {2}, pages = {e0175524}, doi = {10.1128/spectrum.01755-24}, pmid = {39665565}, issn = {2165-0497}, support = {No. 32100009//MOST | National Natural Science Foundation of China (NSFC)/ ; No.XMHT20220104017//Shenzhen Municipal Science and Technology Innovation Council | Shenzhen Key Laboratory Fund ()/ ; }, mesh = {*Proteomics/methods ; *Metagenomics/methods ; *Databases, Protein ; *Gastrointestinal Microbiome/genetics ; Bacterial Proteins/genetics/metabolism ; Peptides/genetics/metabolism ; Molecular Sequence Annotation ; Genome, Bacterial/genetics ; Metagenome ; Bacteria/genetics/classification ; }, abstract = {Metaproteomics offers a profound understanding of the functional dynamics of the gut microbiome, which is crucial for personalized healthcare strategies. The selection of an appropriate database is a critical step for the identification of peptides and proteins, as well as for the provision of accurate taxonomic and functional annotations. The matched metagenomic-derived database is considered to be the best, but its limitations include the identification of low-abundance organisms and taxonomic resolution. Herein, we constructed a protein database (DBCGR2) based on Cultivated Genome Reference 2 (CGR2) and developed a complete peptide-centric analysis workflow for database searching and for the annotation of taxonomy and function. This workflow was subsequently appraised in comparison with metagenomics-derived databases for the analysis of metaproteomic data. Our findings suggested that the performance of DBCGR2 in identification was comparable with metagenomics-derived databases with improvement in identification rates of peptides from low-abundance species. The database searching results could be fully annotated using the pepTaxa taxonomic annotation approach developed in this study, and the taxonomic resolution was enhanced to strain level. Additionally, the results demonstrated that the sensitivity of functional annotation could be enhanced by employing DBCGR2. Overall, the DBCGR2 combined with pepTaxa can be considered an alternative for metaproteomic data analysis with superior analysis performances.IMPORTANCEMass spectrometry-based metaproteomics offers a profound understanding of the gut microbial taxonomy and functionality. The databases utilized in the analysis of metaproteomic data are crucial, as they determine the identification of proteins that can be recognized and linked to overall human health, in addition to the quality of taxonomic and functional annotation. Among the most effective approaches for constructing protein databases is the utilization of metagenomic sequencing to create matched databases. However, the database, derived from isolated genomes, has yet to undergo rigorous testing for their efficacy and accuracy in protein identification and taxonomic and functional annotation. Here, we constructed a protein database DBCGR2 derived from Cultivated Genome Reference 2 (CGR2) and a complete workflow for data analysis. We compared the performances of DBCGR2 and metagenomics-derived databases. Our results indicated that DBCGR2 can be regarded as an alternative to metagenomics-derived databases, which contribute to metaproteomic data analysis.}, }
@article {pmid39900940, year = {2025}, author = {Prabhaharan, D and Go, YW and Kim, H and Kang, S and Sang, BI}, title = {Representative Metagenomes of Mesophilic Biogas Reactor Across South Korea.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {198}, pmid = {39900940}, issn = {2052-4463}, support = {MOE; 2022003480001//MOE | Korea Environmental Industry and Technology Institute (KEITI)/ ; MOE; 2022003480001//MOE | Korea Environmental Industry and Technology Institute (KEITI)/ ; MOE; 2022003480001//MOE | Korea Environmental Industry and Technology Institute (KEITI)/ ; MOE; 2022003480001//MOE | Korea Environmental Industry and Technology Institute (KEITI)/ ; }, mesh = {Republic of Korea ; *Biofuels ; *Metagenome ; *Bioreactors ; Microbiota ; Anaerobiosis ; }, abstract = {Biogas production through the anaerobic digestion (AD) of organic waste plays a crucial role in promoting sustainability and closing the carbon cycle. Over the past decade, this has driven global research on biogas-producing microbiomes, leading to significant advances in our understanding of microbial diversity and metabolic pathways within AD plants. However, substantial knowledge gaps persist, particularly in understanding the specific microbial communities involved in biogas production in countries such as South Korea. The present dataset addresses one of these gaps by providing comprehensive information on the metagenomes of five full-scale mesophilic biogas reactors in South Korea. From 110 GB of raw DNA sequences, 401 metagenome-assembled genomes (MAGs) were created, which include 42,301 annotated genes. Of these, 187 MAGs (46.7%) were classified as high-quality based on Minimum Information about Metagenome-Assembled Genome (MIMAG) standards. The data presented here contribute to a broader understanding of biogas-specific microbial communities and offers a significant resource for future studies and advancements in sustainable biogas production.}, }
@article {pmid39900569, year = {2025}, author = {Priest, T and Oldenburg, E and Popa, O and Dede, B and Metfies, K and von Appen, WJ and Torres-Valdés, S and Bienhold, C and Fuchs, BM and Amann, R and Boetius, A and Wietz, M}, title = {Seasonal recurrence and modular assembly of an Arctic pelagic marine microbiome.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {1326}, pmid = {39900569}, issn = {2041-1723}, mesh = {Arctic Regions ; *Seasons ; *Microbiota/genetics ; *Seawater/microbiology ; *Oceans and Seas ; Metagenomics/methods ; Bacteria/genetics/classification/metabolism ; RNA, Ribosomal, 16S/genetics ; Ecosystem ; DNA Barcoding, Taxonomic ; Metagenome ; Phylogeny ; }, abstract = {Deciphering how microbial communities are shaped by environmental variability is fundamental for understanding the structure and function of ocean ecosystems. While seasonal environmental gradients have been shown to structure the taxonomic dynamics of microbiomes over time, little is known about their impact on functional dynamics and the coupling between taxonomy and function. Here, we demonstrate annually recurrent, seasonal structuring of taxonomic and functional dynamics in a pelagic Arctic Ocean microbiome by combining autonomous samplers and in situ sensors with long-read metagenomics and SSU ribosomal metabarcoding. Specifically, we identified five temporal microbiome modules whose succession within each annual cycle represents a transition across different ecological states. For instance, Cand. Nitrosopumilus, Syndiniales, and the machinery to oxidise ammonia and reduce nitrite are signatures of early polar night, while late summer is characterised by Amylibacter and sulfur compound metabolism. Leveraging metatranscriptomes from Tara Oceans, we also demonstrate the consistency in functional dynamics across the wider Arctic Ocean during similar temporal periods. Furthermore, the structuring of genetic diversity within functions over time indicates that environmental selection pressure acts heterogeneously on microbiomes across seasons. By integrating taxonomic, functional and environmental information, our study provides fundamental insights into how microbiomes are structured under pronounced seasonal changes in understudied, yet rapidly changing polar marine ecosystems.}, }
@article {pmid39900484, year = {2025}, author = {Van Etten, J and Stephens, TG and Bhattacharya, D}, title = {Genetic Transfer in Action: Uncovering DNA Flow in an Extremophilic Microbial Community.}, journal = {Environmental microbiology}, volume = {27}, number = {2}, pages = {e70048}, doi = {10.1111/1462-2920.70048}, pmid = {39900484}, issn = {1462-2920}, support = {//U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231/ ; 10.46936/10.25585/60000481//Joint Genome Institute/ ; NJ01180//National Institute of Food and Agriculture/ ; 80NSSC19K1542/NASA/NASA/United States ; NASA (80NSSC19K0462)/NASA/NASA/United States ; }, mesh = {*Gene Transfer, Horizontal ; *Bacteria/genetics/classification ; Extremophiles/genetics ; Microbiota/genetics ; DNA, Bacterial/genetics ; Genome, Bacterial ; }, abstract = {Horizontal genetic transfer (HGT) is a significant driver of genomic novelty in all domains of life. HGT has been investigated in many studies however, the focus has been on conspicuous protein-coding DNA transfers that often prove to be adaptive in recipient organisms and are therefore fixed longer-term in lineages. These results comprise a subclass of HGTs and do not represent exhaustive (coding and non-coding) DNA transfer and its impact on ecology. Uncovering exhaustive HGT can provide key insights into the connectivity of genomes in communities and how these transfers may occur. In this study, we use the term frequency-inverse document frequency (TF-IDF) technique, that has been used successfully to mine DNA transfers within real and simulated high-quality prokaryote genomes, to search for exhaustive HGTs within an extremophilic microbial community. We establish a pipeline for validating transfers identified using this approach. We find that most DNA transfers are within-domain and involve non-coding DNA. A relatively high proportion of the predicted protein-coding HGTs appear to encode transposase activity, restriction-modification system components, and biofilm formation functions. Our study demonstrates the utility of the TF-IDF approach for HGT detection and provides insights into the mechanisms of recent DNA transfer.}, }
@article {pmid39897560, year = {2025}, author = {Zhang, P and Guo, R and Ma, S and Jiang, H and Yan, Q and Li, S and Wang, K and Deng, J and Zhang, Y and Zhang, Y and Wang, G and Chen, L and Li, L and Guo, X and Zhao, G and Yang, L and Wang, Y and Kang, J and Sha, S and Fan, S and Cheng, L and Meng, J and Yu, H and Chen, F and He, D and Wang, J and Liu, S and Shi, H}, title = {A metagenome-wide study of the gut virome in chronic kidney disease.}, journal = {Theranostics}, volume = {15}, number = {5}, pages = {1642-1661}, pmid = {39897560}, issn = {1838-7640}, mesh = {Humans ; *Renal Insufficiency, Chronic/virology ; *Virome/genetics ; *Gastrointestinal Microbiome/genetics ; *Metagenome/genetics ; *Feces/virology/microbiology ; Middle Aged ; Male ; Female ; Aged ; Dysbiosis/virology/microbiology ; Adult ; Viruses/genetics/classification/isolation & purification ; Bacteria/genetics/classification/isolation & purification ; }, abstract = {Rationale: Chronic kidney disease (CKD) is a progressively debilitating condition leading to kidney dysfunction and severe complications. While dysbiosis of the gut bacteriome has been linked to CKD, the alteration in the gut viral community and its role in CKD remain poorly understood. Methods: Here, we characterize the gut virome in CKD using metagenome-wide analyses of faecal samples from 425 patients and 290 healthy individuals. Results: CKD is associated with a remarkable shift in the gut viral profile that occurs regardless of host properties, disease stage, and underlying diseases. We identify 4,649 differentially abundant viral operational taxonomic units (vOTUs) and reveal that some CKD-enriched viruses are closely related to gut bacterial taxa such as Bacteroides, [Ruminococcus], Erysipelatoclostridium, and Enterocloster spp. In contrast, CKD-depleted viruses include more crAss-like viruses and often target Faecalibacterium, Ruminococcus, and Prevotella species. Functional annotation of the vOTUs reveals numerous viral functional signatures associated with CKD, notably a marked reduction in nicotinamide adenine dinucleotide (NAD[+]) synthesis capacity within the CKD-associated virome. Furthermore, most CKD viral signatures are reproducible in the gut viromes of diabetic kidney disease and several other common diseases, highlighting the considerable universality of disease-associated viromes. Conclusions: This research provides comprehensive resources and novel insights into the CKD-associated gut virome, offering valuable guidance for future mechanistic and therapeutic investigations.}, }
@article {pmid39895074, year = {2025}, author = {Lee, KA and Ul-Haq, A and Seo, H and Jo, S and Kim, S and Song, HY and Kim, HS}, title = {Characteristics of skin microbiome associated with disease severity in systemic sclerosis.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {63}, number = {1}, pages = {e.2409018}, doi = {10.71150/jm.2409018}, pmid = {39895074}, issn = {1976-3794}, support = {//Korea Health Industry Development Institute/ ; HI21C1888//Ministry of Health and Welfare/ ; //National Research Foundation of Korea/ ; RS-2023-00219563//Ministry of Science and ICT/ ; //Soonchunhyang University Research Fund/ ; }, mesh = {Humans ; *Scleroderma, Systemic/microbiology ; *Skin/microbiology/pathology ; *Microbiota ; Female ; Middle Aged ; Male ; *RNA, Ribosomal, 16S/genetics ; Adult ; *Bacteria/classification/genetics/isolation & purification ; Severity of Illness Index ; Aged ; Biomarkers ; Metagenomics ; }, abstract = {Systemic sclerosis (SSc) is a chronic autoimmune disorder characterised by skin fibrosis and internal organ involvement. Disruptions in the microbial communities on the skin may contribute to the onset of autoimmune diseases that affect the skin. However, current research on the skin microbiome in SSc is lacking. This study aimed to investigate skin microbiome associated with disease severity in SSc. Skin swabs were collected from the upper limbs of 46 healthy controls (HCs) and 36 patients with SSc. Metagenomic analysis based on the 16S rRNA gene was conducted and stratified by cutaneous subtype and modified Rodnan skin score (mRSS) severity. Significant differences in skin bacterial communities were observed between the HCs and patients with SSc, with further significant variations based on subtype and mRSS severity. The identified biomarkers were Bacteroides and Faecalibacterium for patients with diffuse cutaneous SSc with high mRSS (≥ 10) and Mycobacterium and Parabacteroides for those with low mRSS (< 10). Gardnerella, Abies, Lactobacillus, and Roseburia were the biomarkers in patients with limited cutaneous SSc (lcSS) and high mRSS, whereas Coprococcus predominated in patients with lcSS and low mRSS. Cutaneous subtype analysis identified Pediococcus as a biomarker in the HCs, whereas mRSS analysis revealed the presence of Pseudomonas in conjunction with Pediococcus. In conclusion, patients with SSc exhibit distinct skin microbiota compared with healthy controls. Bacterial composition varies by systemic sclerosis cutaneous subtype and skin thickness.}, }
@article {pmid39868213, year = {2025}, author = {Schechter, MS and Trigodet, F and Veseli, IA and Miller, SE and Klein, ML and Sever, M and Maignien, L and Delmont, TO and Light, SH and Eren, AM}, title = {Ribosomal protein phylogeography offers quantitative insights into the efficacy of genome-resolved surveys of microbial communities.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39868213}, issn = {2692-8205}, support = {T32 GM007197/GM/NIGMS NIH HHS/United States ; }, abstract = {The increasing availability of microbial genomes is essential to gain insights into microbial ecology and evolution that can propel biotechnological and biomedical advances. Recent advances in genome recovery have significantly expanded the catalogue of microbial genomes from diverse habitats. However, the ability to explain how well a set of genomes account for the diversity in a given environment remains challenging for individual studies or biome-specific databases. Here we present EcoPhylo, a computational workflow to characterize the phylogeography of any gene family through integrated analyses of genomes and metagenomes, and our application of this approach to ribosomal proteins to quantify phylogeny-aware genome recovery rates across three biomes. Our findings show that genome recovery rates vary widely across taxa and biomes, and that single amplified genomes, metagenome-assembled genomes, and isolate genomes have non-uniform yet quantifiable representation of environmental microbes. EcoPhylo reveals highly resolved, reference-free, multi-domain phylogenies in conjunction with distribution patterns of individual clades across environments, providing a means to assess genome recovery in individual studies and benchmark biome-level genome collections.}, }
@article {pmid39856391, year = {2025}, author = {Tisza, MJ and Lloyd, RE and Hoffman, K and Smith, DP and Rewers, M and Javornik Cregeen, SJ and Petrosino, JF}, title = {Longitudinal phage-bacteria dynamics in the early life gut microbiome.}, journal = {Nature microbiology}, volume = {10}, number = {2}, pages = {420-430}, pmid = {39856391}, issn = {2058-5276}, support = {U01 DK063821/DK/NIDDK NIH HHS/United States ; U01 DK63865//U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)/ ; U01 DK63829//U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)/ ; UC4 DK063821/DK/NIDDK NIH HHS/United States ; U01 DK63821//U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; *Bacteriophages/genetics/physiology/classification ; Infant ; *Bacteria/virology/genetics/classification/isolation & purification ; Child, Preschool ; Longitudinal Studies ; Metagenome ; Diabetes Mellitus, Type 1/microbiology/virology ; Feces/microbiology ; Female ; Male ; Metagenomics ; Infant, Newborn ; }, abstract = {Microbial colonization of the human gut occurs soon after birth, proceeds through well-studied phases and is affected by lifestyle and other factors. Less is known about phage community dynamics during infant gut colonization due to small study sizes, an inability to leverage large databases and a lack of appropriate bioinformatics tools. Here we reanalysed whole microbial community shotgun sequencing data of 12,262 longitudinal samples from 887 children from four countries across four years of life as part of the The Environmental Determinants of Diabetes in the Young (TEDDY) study. We developed an extensive metagenome-assembled genome catalogue using the Marker-MAGu pipeline, which comprised 49,111 phage taxa from existing human microbiome datasets. This was used to identify phage marker genes and their integration into the MetaPhlAn 4 bacterial marker gene database enabled simultaneous assessment of phage and bacterial dynamics. We found that individual children are colonized by hundreds of different phages, which are more transitory than bacteria, accumulating a more diverse phage community over time. Type 1 diabetes correlated with a decreased rate of change in bacterial and viral communities in children aged one and two. The addition of phage data improved the ability of machine learning models to discriminate samples by country. Finally, although phage populations were specific to individuals, we observed trends of phage ecological succession that correlated well with putative host bacteria. This resource improves our understanding of phage-bacteria interactions in the developing early life microbiome.}, }
@article {pmid39833544, year = {2025}, author = {Yan, X and Liu, Y and Hu, T and Huang, Z and Li, C and Guo, L and Liu, Y and Li, N and Zhang, H and Sun, Y and Yi, L and Wu, J and Feng, J and Zhang, F and Jiang, T and Tu, C and He, B}, title = {A compendium of 8,176 bat RNA viral metagenomes reveals ecological drivers and circulation dynamics.}, journal = {Nature microbiology}, volume = {10}, number = {2}, pages = {554-568}, pmid = {39833544}, issn = {2058-5276}, support = {32192423//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32022083//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32192424//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32371562//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {*Chiroptera/virology ; Animals ; China ; *Metagenome ; *Virome/genetics ; *RNA Viruses/genetics/classification/isolation & purification ; Phylogeny ; RNA, Viral/genetics ; Humans ; Genetic Variation ; Genome, Viral/genetics ; Metagenomics/methods ; }, abstract = {Bats are natural hosts for many emerging viruses for which spillover to humans is a major risk, but the diversity and ecology of bat viruses is poorly understood. Here we generated 8,176 RNA viral metagenomes by metatranscriptomic sequencing of organ and swab samples from 4,143 bats representing 40 species across 52 locations in China. The resulting database, the BtCN-Virome, expands bat RNA virus diversity by over 3.4-fold. Some viruses in the BtCN-Virome are traced to mammals, birds, arthropods, mollusks and plants. Diet, infection dynamics and environmental parameters such as humidity and forest coverage shape virus distribution. Compared with those in the wild, bats dwelling in human settlements harboured more diverse viruses that also circulated in humans and domestic animals, including Nipah and Lloviu viruses not previously reported in China. The BtCN-Virome provides important insights into the genetic diversity, ecological drivers and circulation dynamics of bat viruses, highlighting the need for surveillance of bats near human settlements.}, }
@article {pmid39777507, year = {2025}, author = {Shelton, AN and Yu, FB and Grossman, AR and Bhaya, D}, title = {Abundant and active community members respond to diel cycles in hot spring phototrophic mats.}, journal = {The ISME journal}, volume = {19}, number = {1}, pages = {}, doi = {10.1093/ismejo/wraf001}, pmid = {39777507}, issn = {1751-7370}, support = {2125965//NSF/ ; 1921429//BBSRC-NSF/BIO/ ; //Office of Science of the U.S. Department of Energy/ ; }, mesh = {*Hot Springs/microbiology ; Metagenome ; Photosynthesis ; Phototrophic Processes ; Bacteria/genetics/classification/isolation & purification/metabolism ; Metagenomics ; Microbiota ; Transcriptome ; }, abstract = {Photosynthetic microbial mats in hot springs can provide insights into the diel behaviors of communities in extreme environments. In this habitat, photosynthesis dominates during the day, leading to super-oxic conditions, with a rapid transition to fermentation and anoxia at night. Multiple samples were collected from two springs over several years to generate metagenomic and metatranscriptomic datasets. Metagenome-assembled genomes comprised 71 taxa (in 19 different phyla), of which 12 core taxa were present at high abundance in both springs. The eight most active taxa identified by metatranscriptomics were an oxygenic cyanobacterium (Synechococcus sp.), five anoxygenic phototrophs from three different phyla, and two understudied heterotrophs from phylum Armatimonadota. In all eight taxa, a significant fraction of genes exhibited a diel expression pattern, although peak timing varied considerably. The two abundant heterotrophs exhibit starkly different peak timing of expression, which we propose is shaped by their metabolic and genomic potential to use carbon sources that become differentially available during the diel cycle. Network analysis revealed pathway expression patterns that had not previously been linked to diel cycles, including ribosome biogenesis and chaperones. This provides a framework for analyzing metabolically coupled communities and the dominant role of the diel cycle.}, }
@article {pmid39761633, year = {2025}, author = {Lake, BB and McAdams, ZL and Ericsson, AC and Reinero, C and Gull, T and Lyons, BM}, title = {Feline urethral obstruction alters the urinary microbiota and comparison to oral, preputial, and rectal microbiotas.}, journal = {American journal of veterinary research}, volume = {86}, number = {2}, pages = {}, doi = {10.2460/ajvr.24.07.0213}, pmid = {39761633}, issn = {1943-5681}, mesh = {Animals ; Cats ; *Cat Diseases/microbiology/urine ; *Microbiota ; Male ; *Urethral Obstruction/veterinary/microbiology ; *Rectum/microbiology ; *RNA, Ribosomal, 16S/genetics ; Female ; Prospective Studies ; Mouth/microbiology ; Case-Control Studies ; }, abstract = {OBJECTIVE: To document differences in the microbiota of healthy cats versus cats with urethral obstruction (UO); compare the urinary microbiota with the oral, preputial, and rectal microbiota; and demonstrate that 16S rRNA gene sequencing will reveal rich and diverse urinary microbiota.
METHODS: 15 client-owned cats with UO and 15 age-matched healthy cats were included from July 2020 through April 2021. Exclusion criteria were evidence of urinary tract infection, urolithiasis, antimicrobial administration, urinary catheterization in the past 30 days, or a comorbidity. This study was a prospective, observational study. Both groups had a baseline CBC, chemistry panel, urinalysis, urine culture, and focal bladder ultrasound. Swabs of the cystocentesis site, buccal mucosa, rectum, prepuce, and urinary samples were collected, and 16S rRNA gene sequencing was used to compare the groups and sites.
RESULTS: Differences in the microbiota richness and diversity were found in the urine of cats with UO (n = 15) compared to healthy cats (15), along with differences in the preputial and oral samples, supporting the presence of a urinary dysbiosis in cats with UO.
CONCLUSIONS: Our preliminary data demonstrates a dramatic change in the urinary microbiota of cats with UO along with changes in microbiota in other sites compared to healthy cats.
CLINICAL RELEVANCE: A urinary dysbiosis in cats with UO has been minimally supported in prior studies using 16S rRNA gene sequencing. Although these are preliminary results, documenting this dysbiosis in cats with UO provides a potential avenue for novel therapeutics.}, }
@article {pmid39693209, year = {2025}, author = {Yamamoto, A and Kawashima, A and Uemura, T and Nakano, K and Matsushita, M and Ishizuya, Y and Jingushi, K and Hase, H and Katayama, K and Yamaguchi, R and Sassi, N and Motoyama, Y and Nojima, S and Mita, M and Kimura, T and Motooka, D and Horibe, Y and Okuda, Y and Oka, T and Yamamichi, G and Tomiyama, E and Koh, Y and Yamamoto, Y and Kato, T and Hatano, K and Uemura, M and Imoto, S and Wada, H and Morii, E and Tsujikawa, K and Nonomura, N}, title = {A novel mouse model of upper tract urothelial carcinoma highlights the impact of dietary intervention on gut microbiota and carcinogenesis prevention despite carcinogen exposure.}, journal = {International journal of cancer}, volume = {156}, number = {7}, pages = {1439-1456}, doi = {10.1002/ijc.35295}, pmid = {39693209}, issn = {1097-0215}, support = {19K09709//Japan Society for the Promotion of Science/ ; 21K20968//Japan Society for the Promotion of Science/ ; 22H03213//Japan Society for the Promotion of Science/ ; 22K09523//Japan Society for the Promotion of Science/ ; 22K18398//Japan Society for the Promotion of Science/ ; JP22ym0126809i0002//Japan Agency for Medical Research and Development/ ; JP23ama121054//Japan Agency for Medical Research and Development/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; Mice ; Female ; *Disease Models, Animal ; Humans ; *Carcinogens/toxicity ; Male ; *Butylhydroxybutylnitrosamine ; Carcinogenesis ; Mice, Inbred BALB C ; Urinary Bladder Neoplasms/prevention & control/chemically induced/etiology/pathology ; Urologic Neoplasms/prevention & control/diet therapy/etiology/chemically induced/pathology ; Urothelium/pathology/metabolism/microbiology ; }, abstract = {Animal models of N-butyl-N-(4-hydroxy butyl) nitrosamine (BBN)-induced urothelial carcinoma (UC), particularly bladder cancer (BC), have long been established. However, the rare incidence of BBN-induced upper urinary tract UC (UTUC), which originates from the same urothelium as BC, remains elusive. The scarcity of animal models of UTUC has made it challenging to study the biology of UTUC. To address this problem, we tried to establish a novel mouse model of UTUC by treating multiple mice strains and sexes with BBN. The molecular consistency between the UTUC mouse model and human UTUC was confirmed using multi-omics analyses, including whole-exome, whole-transcriptome, and spatial transcriptome sequencing. 16S ribosomal RNA metagenome sequencing, metabolome analysis, and dietary interventions were employed to assess changes in the gut microbiome, metabolome, and carcinogenesis of UTUC. Of all treated mice, only female BALB/c mice developed UTUC over BC. Multi-omics analyses confirmed that the UTUC model reflected the molecular characteristics and heterogeneity of human UTUC with poor prognosis. Furthermore, the model exhibited increased Tnf-related inflammatory gene expression in the upper urinary tract and a low relative abundance of Parabacteroides distasonis in the gut. Dietary intervention, mainly without alanine, led to P. distasonis upregulation and successfully prevented UTUC, as well as suppressed Tnf-related inflammatory gene expression in the upper urinary tract despite the exposure to BBN. This is the first report to demonstrate a higher incidence of UTUC than BC in a non-engineered mouse model using BBN. Overall, this model could serve as a useful tool for comprehensively investigating UTUC in future studies.}, }
@article {pmid39893166, year = {2025}, author = {Bourquin, M and Peter, H and Michoud, G and Busi, SB and Kohler, TJ and Robison, AL and Styllas, M and Ezzat, L and Geers, AU and Huss, M and Fodelianakis, S and , and Battin, TJ}, title = {Predicting climate-change impacts on the global glacier-fed stream microbiome.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {1264}, pmid = {39893166}, issn = {2041-1723}, mesh = {*Microbiota/genetics ; *Ice Cover/microbiology ; *Climate Change ; *Phylogeny ; *Bacteria/genetics/classification ; *Rivers/microbiology ; Metagenome ; Biodiversity ; Ecosystem ; }, abstract = {The shrinkage of glaciers and the vanishing of glacier-fed streams (GFSs) are emblematic of climate change. However, forecasts of how GFS microbiome structure and function will change under projected climate change scenarios are lacking. Combining 2,333 prokaryotic metagenome-assembled genomes with climatic, glaciological, and environmental data collected by the Vanishing Glaciers project from 164 GFSs draining Earth's major mountain ranges, we here predict the future of the GFS microbiome until the end of the century under various climate change scenarios. Our model framework is rooted in a space-for-time substitution design and leverages statistical learning approaches. We predict that declining environmental selection promotes primary production in GFSs, stimulating both bacterial biomass and biodiversity. Concomitantly, predictions suggest that the phylogenetic structure of the GFS microbiome will change and entire bacterial clades are at risk. Furthermore, genomic projections reveal that microbiome functions will shift, with intensified solar energy acquisition pathways, heterotrophy and algal-bacterial interactions. Altogether, we project a 'greener' future of the world's GFSs accompanied by a loss of clades that have adapted to environmental harshness, with consequences for ecosystem functioning.}, }
@article {pmid39893159, year = {2025}, author = {Sampson, TR and Wallen, ZD and Won, WJ and Standaert, DG and Payami, H and Harms, AS}, title = {Alpha synuclein overexpression can drive microbiome dysbiosis in mice.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {4014}, pmid = {39893159}, issn = {2045-2322}, support = {ASAP-020527//Aligning Science Across Parkinson's/ ; ASAP-020527//Aligning Science Across Parkinson's/ ; ASAP-020527//Aligning Science Across Parkinson's/ ; ASAP-000375//Aligning Science Across Parkinson's/ ; }, mesh = {Animals ; *alpha-Synuclein/metabolism/genetics ; *Dysbiosis/microbiology ; *Gastrointestinal Microbiome ; Mice ; *Mice, Transgenic ; *Parkinson Disease/microbiology/metabolism/genetics ; Disease Models, Animal ; Humans ; Aging ; Male ; }, abstract = {Growing evidence indicates that persons with Parkinson disease (PD), have a unique composition of indigenous gut microbes. Given the long prodromal or pre-diagnosed period, longitudinal studies of the human and rodent gut microbiome before symptomatic onset and for the duration of the disease are currently lacking. PD is partially characterized by the accumulation of the protein α-synuclein (α-syn) into insoluble aggregates, in both the central and enteric nervous systems. As such, several experimental rodent and non-human primate models of α-syn overexpression recapitulate some of the hallmark pathophysiologies of PD. These animal models provide an opportunity to assess how the gut microbiome changes with age under disease-relevant conditions. Here, we used a transgenic mouse strain, which overexpress wild-type human α-syn to test how the gut microbiome composition responds in this model of PD pathology during aging. Using shotgun metagenomics, we find significant, age and genotype-dependent bacterial taxa whose abundance becomes altered with age. We reveal that α-syn overexpression can drive alterations to the gut microbiome composition and suggest that it limits diversity through age. Taxa that were most affected by genotype-age interaction were Lactobacillus and Bifidobacteria. In a mouse model, we showed direct link between alpha synuclein geneotype (hallmark of PD), a dysbiotic and low-diversity gut microbiome, and dysbiotic levels of Bifidobacteria and Lactobacillus (most robust features of PD microbiome). Given emerging data on the potential contributions of the gut microbiome to PD pathologies, our data provide an experimental foundation to understand how the PD-associated microbiome may arise as a trigger or co-pathology to disease.}, }
@article {pmid39793775, year = {2025}, author = {Li, X and Ning, L and Zhao, H and Gu, C and Han, Y and Xu, W and Si, Y and Xu, Y and Wang, R and Ren, Q}, title = {Jiawei Ermiao Granules (JWEMGs) clear persistent HR-HPV infection though improving vaginal microecology.}, journal = {Journal of ethnopharmacology}, volume = {341}, number = {}, pages = {119342}, doi = {10.1016/j.jep.2025.119342}, pmid = {39793775}, issn = {1872-7573}, mesh = {Female ; Humans ; *Vagina/microbiology/drug effects/pathology ; *Papillomavirus Infections/drug therapy ; *Drugs, Chinese Herbal/pharmacology ; Adult ; Middle Aged ; Microbiota/drug effects ; Antiviral Agents/pharmacology ; Cytokines/metabolism ; Young Adult ; }, abstract = {Jiawei Ermiao Granules (JWEMGs), a traditional Chinese herbal formulation, has been widely used in China for the treatment of human papillomavirus (HPV) infections. However, the underlying mechanisms through which it exerts its antiviral effects remain poorly understood.
AIM OF THE STUDY: This study aimed to investigate the potential mechanisms by which JWEMGs modulate vaginal microecology and clear HPV infections, utilizing clinical trials, metagenomic sequencing, and in vitro models.
MATERIALS AND METHODS: Clinical indicators related to vaginal microecology, such as vaginal pH, cleanliness, Nugent score, Donders score, catalase, neuraminidase, and leukocyte esterase, were evaluated in 65 patients with high-risk HPV (HR-HPV) infection. The study examined the impact of two courses of oral JWEMGs on these clinical parameters. Additionally, metagenomic sequencing was performed on vaginal lavage samples from 33 patients to assess the alteration of the vaginal microbiome following JWEMGs treatment. Immunohistochemistry was used to detect ALPK1 expression in cervical exfoliated cells, and ELISA was employed to measure cytokine levels in vaginal lavage fluid. JWEMGs intervention was applied to HaCaT-HPV E6/E7 cells to evaluate its effects on restoring α-kinase 1 (ALPK1) expression and promoting the secretion of cytokines and chemokines.
RESULTS: Treatment with JWEMGs significantly improved several clinical indicators, including cleanliness, pH, Nugent score, Donders score, catalase, neuraminidase, and leukocyte esterase, in HR-HPV-infected patients. Furthermore, JWEMGs therapy led to an increased abundance of Lactobacillus species, especially Lactobacillus crispatus, and a marked reduction in Gardnerella species. JWEMGs treatment also significantly promoted ALPK1 expression in cervical exfoliated cells and augmented the secretion of key cytokines, including IL-6, IL-8, and TNF-α. In parallel, in vitro results showed that JWEMGs substantially enhanced IL-6, IL-8, TNF-α, CCL2, CCL5, and CCL7 secretion in HaCaT-HPV E6/E7 cells, which correlated with the activation of the ALPK1/NF-κB signaling pathway.
CONCLUSION: In conclusion, JWEMGs treatment effectively remodels the vaginal microbiota and bolsters mucosal immunity in the lower genital tract, thereby improving the vaginal microecology in HR-HPV-infected individuals. In vitro findings further demonstrated that JWEMGs promote cytokine and chemokine expression, activating the ALPK1/NF-κB pathway.}, }
@article {pmid39778648, year = {2025}, author = {Bellanco, A and Requena, T and Martínez-Cuesta, MC}, title = {Polysorbate 80 and carboxymethylcellulose: A different impact on epithelial integrity when interacting with the microbiome.}, journal = {Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association}, volume = {196}, number = {}, pages = {115236}, doi = {10.1016/j.fct.2025.115236}, pmid = {39778648}, issn = {1873-6351}, mesh = {*Polysorbates/pharmacology ; *Carboxymethylcellulose Sodium/chemistry ; *Gastrointestinal Microbiome/drug effects ; Humans ; Emulsifying Agents ; Bacteria/drug effects/classification/genetics/metabolism ; }, abstract = {The consumption of dietary emulsifiers, including polysorbate 80 (P80) and sodium carboxymethylcellulose (CMC), has raised safety concerns due to its interaction with the intestinal microbiome. This study demonstrated that increasing concentrations of P80 and CMC added to a dynamic four-stage gut microbiota model (BFBL gut simulator) altered the microbiome composition and impacted epithelial integrity in a dose-dependent manner. 16S rDNA amplicon-based metagenomics analysis revealed that these emulsifiers increased microbial groups with proinflammatory capacities while decreasing microbial taxa known to enhance barrier function. Increasing doses of P80 significantly decreased Bacteroides dorei and Akkermansia, taxa associated with anti-inflammatory potential, while increasing doses of CMC were linked to a higher abundance of Ruminococcus torques and Hungatella, which negatively impact barrier function. Both emulsifiers displayed a different impact on epithelial integrity when interacting with the microbiome. On one hand, supernatants from the BFBL simulator fed with P80 disrupted epithelial integrity to a lesser extent than the additive alone. On the other hand, both the microbiota and the supernatants from the BFBL simulator fed with CMC diminished the epithelial integrity, though the additive itself did not. These findings highlight the need to incorporate the gut microbiome in the risk assessment of these additives.}, }
@article {pmid39701375, year = {2025}, author = {Corbett, GA and Corcoran, S and Feehily, C and Soldati, B and Rafferty, A and MacIntyre, DA and Cotter, PD and McAuliffe, FM}, title = {Preterm-birth-prevention with Lactobacillus crispatus oral probiotics: Protocol for a double blinded randomised placebo-controlled trial (the PrePOP study).}, journal = {Contemporary clinical trials}, volume = {149}, number = {}, pages = {107776}, doi = {10.1016/j.cct.2024.107776}, pmid = {39701375}, issn = {1559-2030}, mesh = {Humans ; Female ; *Probiotics/administration & dosage/therapeutic use ; Double-Blind Method ; *Vagina/microbiology ; Pregnancy ; *Premature Birth/prevention & control/microbiology ; *Lactobacillus crispatus ; *Lactobacillus ; *Gastrointestinal Microbiome ; *Lacticaseibacillus rhamnosus ; Adult ; Administration, Oral ; Infant, Newborn ; }, abstract = {INTRODUCTION: Effective spontaneous preterm birth (sPTB) prevention is an urgent unmet clinical need. Vaginal depletion of Lactobacillus crispatus is linked to sPTB. This trial will investigate impact of an oral Lactobacillus spp. probiotic product containing an L. crispatus strain with other Lactobacilli spp., on the maternal vaginal and gut microbiome in pregnancies high-risk for sPTB.
METHODS: A double-blind, placebo-controlled, randomised trial will be performed at the National Maternity Hospital Dublin, Ireland. Inclusion criteria are women with history of sPTB or mid-trimester loss, cervical surgery (cone biopsy or two previous large-loop-excision-of-transformation-zone) or uterine anomaly. The intervention is oral supplementation for twelve weeks with probiotic or identical placebo. The probiotic will contains: ◦ 4 billion CFU Lactobacillus crispatus Lbv 88(2x10[9]CFU/Capsule) ◦ 4 billion CFU Lactobacillus rhamnosus Lbv 96(2x10[9]CFU/Capsule) ◦ 0.8 billion CFU Lactobacillus jensenii Lbv 116(0.4x10[9]CFU/Capsule) ◦ 1.2 billion CFU Lactobacillus gasseri Lbv 150(0.6x10[9]CFU/Capsule). Investigators and participants will be blinded to assignment.
RESULTS: The primary outcome is detectable L. crispatus in the vaginal microbiome after twelve weeks of treatment, measured using high-throughput DNA sequencing. A total of 126 women are required to detect a 25 % increase in detectable L. crispatus. Secondary outcomes include impact of intervention on the gut microbiome and metabolome, rate of sPTB and mid-trimester loss, neonatal outcomes and maternal morbidity.
CONCLUSIONS: This randomised trial will investigate ability of an oral probiotic containing L. crispatus to increase its abundance in the vaginal microbiome, both directly by horizontal transfer and indirectly via microbiome and metabolome of the gut.}, }
@article {pmid39891205, year = {2025}, author = {Huang, D and Liao, J and Balcazar, JL and Ye, M and Wu, R and Wang, D and Alvarez, PJJ and Yu, P}, title = {Adaptive modification of antiviral defense systems in microbial community under Cr-induced stress.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {34}, pmid = {39891205}, issn = {2049-2618}, support = {42177113//National Natural Science Foundation of China/ ; 42277418//National Natural Science Foundation of China/ ; Y2022084//the Youth Innovation Promotion Association, Chinese Academy of Sciences/ ; 2022YFC3704700//National Key Research and Development Program of China/ ; }, mesh = {*Chromium/pharmacology ; *Soil Microbiology ; *Stress, Physiological ; *Bacteria/genetics/classification/drug effects ; *Microbiota/drug effects ; Soil Pollutants ; Metagenomics/methods ; Viruses/genetics/drug effects/classification ; Soil/chemistry ; }, abstract = {BACKGROUND: The prokaryotic antiviral defense systems are crucial for mediating prokaryote-virus interactions that influence microbiome functioning and evolutionary dynamics. Despite the prevalence and significance of prokaryotic antiviral defense systems, their responses to abiotic stress and ecological consequences remain poorly understood in soil ecosystems. We established microcosm systems with varying concentrations of hexavalent chromium (Cr(VI)) to investigate the adaptive modifications of prokaryotic antiviral defense systems under abiotic stress.
RESULTS: Utilizing hybrid metagenomic assembly with long-read and short-read sequencing, we discovered that antiviral defense systems were more diverse and prevalent in heavily polluted soils, which was corroborated by meta-analyses of public datasets from various heavy metal-contaminated sites. As the Cr(VI) concentration increased, prokaryotes with defense systems favoring prokaryote-virus mutualism gradually supplanted those with defense systems incurring high adaptive costs. Additionally, as Cr(VI) concentrations increased, enriched antiviral defense systems exhibited synchronization with microbial heavy metal resistance genes. Furthermore, the proportion of antiviral defense systems carried by mobile genetic elements (MGEs), including plasmids and viruses, increased by approximately 43% and 39%, respectively, with rising Cr concentrations. This trend is conducive to strengthening the dissemination and sharing of defense resources within microbial communities.
CONCLUSIONS: Overall, our study reveals the adaptive modification of prokaryotic antiviral defense systems in soil ecosystems under abiotic stress, as well as their positive contributions to establishing prokaryote-virus mutualism and the evolution of microbial heavy metal resistance. These findings advance our understanding of microbial adaptation in stressful environments and may inspire novel approaches for microbiome manipulation and bioremediation. Video Abstract.}, }
@article {pmid39890997, year = {2025}, author = {Marter, P and Freese, HM and Ringel, V and Brinkmann, H and Pradella, S and Rohde, M and Jarek, M and Spröer, C and Wagner-Döbler, I and Overmann, J and Bunk, B and Petersen, J}, title = {Superior Resolution Profiling of the Coleofasciculus Microbiome by Amplicon Sequencing of the Complete 16S rRNA Gene and ITS Region.}, journal = {Environmental microbiology reports}, volume = {17}, number = {1}, pages = {e70066}, doi = {10.1111/1758-2229.70066}, pmid = {39890997}, issn = {1758-2229}, support = {34509606-TRR 51//Deutsche Forschungsgemeinschaft/ ; //Collaborative Research Center Roseobacter (TRR51)/ ; }, mesh = {*RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; *Cyanobacteria/genetics/classification/isolation & purification ; Sequence Analysis, DNA ; Phylogeny ; DNA, Ribosomal Spacer/genetics ; DNA, Bacterial/genetics ; Bacteria/genetics/classification/isolation & purification ; Metagenomics ; }, abstract = {The filamentous cyanobacterium Coleofasciculus chthonoplastes is the key primary producer of marine microbial mats. We elucidated the microbiomes of 32 non-axenic Coleofasciculus isolates using PacBio-based amplicon sequencing of the complete 16S rRNA gene and the internally transcribed spacer (16S-ITS). The length of authentic amplicon sequence variants (ASVs) ranged from 1827 to 3044 nucleotides (median: 2267 nt). The results, which were complemented by metagenome analyses and cultivation approaches, revealed the presence of more than 70 associated heterotrophs in the culture of Coleofasciculus sp. WW12. The great bacterial diversity in the cyanosphere is dominated by Pseudomonadota (59%) and Bacteroidota (23%). Allelic ribosomal operon variants were detected in 18 Coleofasciculus strains and our analyses proposed the presence of at least four different species. A comparative analysis of cyanobacterial microbiomes documented complementary advantages of amplicon sequencing versus metagenomics with an individual strength of the 16S-ITS approach in terms of (i) ribosomal target sequence quality, (ii) contaminant detection and (iii) identification of rare bacteria. The characterisation of the Coleofasciculus microbiome showed that long-read amplicon sequencing of the 16S-ITS region is the method of choice for rapid profiling of non-axenic cyanobacteria. Its superior resolution allows a reliable differentiation of even very closely related strains.}, }
@article {pmid39890137, year = {2025}, author = {Kennedy, EC and Ross, FC and O'Shea, CA and Lavelle, A and Ross, P and Dempsey, E and Stanton, C and Hawkes, CP}, title = {Observational study protocol: the faecal microbiome in the acute stage of new-onset paediatric type 1 diabetes in an Irish cohort.}, journal = {BMJ open}, volume = {15}, number = {1}, pages = {e089206}, doi = {10.1136/bmjopen-2024-089206}, pmid = {39890137}, issn = {2044-6055}, mesh = {Humans ; *Diabetes Mellitus, Type 1/microbiology ; *Feces/microbiology ; Child ; *Gastrointestinal Microbiome ; Male ; Female ; Prospective Studies ; Ireland ; Child, Preschool ; Adolescent ; Metabolome ; }, abstract = {INTRODUCTION: Type 1 diabetes (T1D) is an autoimmune-mediated disorder caused by the destruction of pancreatic beta cells. Although there is an underlying genetic predisposition to developing T1D, the trigger is multifactorial and likely includes environmental factors. The intestinal microbiome has been identified as one such factor. Previous studies have illustrated differences in the microbiota of people with T1D compared with healthy controls. This study aims to describe the evolution of the microbiome and metabolome during the first year of clinical T1D, or stage 3 T1D diagnosis, and investigate whether there are differences in the microbiome and metabolome of children who present with and without diabetic ketoacidosis. The study will also explore possible associations between the microbiome, metabolome, glycaemic control and beta cell reserve.
METHODS AND ANALYSIS: This prospective cohort study will include children with newly diagnosed T1D and sibling controls (n=100, males and females) and their faecal microbiome will be characterised using shotgun metagenomic sequencing at multiple time points during the first year of diagnosis. We will develop a microbial culture biobank based on culturomic studies of stool samples from the healthy controls that will support future investigation. Metabolomic analysis will aim to identify additional biomarkers which may be involved in disease presentation and progression. Through this initial exploratory study, we aim to identify specific microbial biomarkers which may be used as future interventional targets throughout the various stages of T1D progression.
ETHICS AND DISSEMINATION: This study has been approved by the Clinical Research Ethics Committee of the Cork Teaching Hospitals. Study results will be available to patients with T1D and their families, carers, support networks and microbiome societies and other researchers.
TRIAL REGISTRATION NUMBER: The clinicaltrials.gov registration number for this trial is NCT06157736.}, }
@article {pmid39793444, year = {2025}, author = {Verheijden, RJ and van Eijs, MJM and Paganelli, FL and Viveen, MC and Rogers, MRC and Top, J and May, AM and van de Wijgert, JHHM and Suijkerbuijk, KPM and , }, title = {Gut microbiome and immune checkpoint inhibitor toxicity.}, journal = {European journal of cancer (Oxford, England : 1990)}, volume = {216}, number = {}, pages = {115221}, doi = {10.1016/j.ejca.2025.115221}, pmid = {39793444}, issn = {1879-0852}, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Immune Checkpoint Inhibitors/adverse effects ; Male ; Female ; Middle Aged ; Aged ; Prospective Studies ; *Neoplasms/drug therapy/microbiology ; Dysbiosis/chemically induced/microbiology ; Adult ; Feces/microbiology ; }, abstract = {BACKGROUND: Multiple studies have suggested that gut microbiome may influence immune checkpoint inhibitor (ICI) efficacy, but its association with immune-related adverse events (irAEs) is less well studied. In this prospective cohort study, we assessed whether gut microbiome composition at start, or changes during ICI, are associated with severe irAEs.
METHODS: Stool samples of cancer patients treated with anti-PD-1 ± anti-CTLA-4 were analyzed using 16S rRNA gene sequencing and metagenomic shotgun sequencing. Differences in alpha and beta diversity between patients with and without severe irAE were assessed, as well as differential relative abundance (RA) of taxa, MetaCyc pathways, and seven prespecified literature-based bacterial groups including pathobionts and Ruminococcaceae.
FINDINGS: We analyzed 497 samples of 195 patients before and soon after starting ICI, at severe irAE onset and after starting immunosuppression. Mean RA of the pathobionts group was significantly higher in patients who developed a severe irAE (8.2 %) compared to those who did not (4.8 %; odds ratio 1.40; 95 %CI 1.07-1.87) at baseline, and also early during ICI treatment and at severe irAE onset. A significantly stronger decrease in RA of Ruminococcaceae after starting ICI was observed in patients who developed a severe irAE compared to those who did not. RAs of Ruminococcaceae, the genus Ruminococcus, and the species R. bromii and R. callidus were significantly lower at severe irAE onset compared to other time points.
INTERPRETATION: Gut microbiome dysbiosis signaled by higher RA of pathobionts and decrease in RA of Ruminococcaceae may predispose to severe irAEs.}, }
@article {pmid39628067, year = {2025}, author = {Fujimoto, S and Hatano, K and Banno, E and Motooka, D and De Velasco, MA and Kura, Y and Toyoda, S and Hashimoto, M and Adomi, S and Minami, T and Yoshimura, K and Oka, T and Hata, J and Matsushita, M and Takao, T and Takada, S and Tsujimura, A and Kojima, Y and Obara, W and Nakamura, S and Uemura, H and Nonomura, N and Fujita, K}, title = {Comparative analysis of gut microbiota in hormone-sensitive and castration-resistant prostate cancer in Japanese men.}, journal = {Cancer science}, volume = {116}, number = {2}, pages = {462-469}, doi = {10.1111/cas.16408}, pmid = {39628067}, issn = {1349-7006}, support = {//Yakult Bio-Science Foundation/ ; //The Japanese Foundation for Prostate Research (JFPR)/ ; //The Japanese Urological Association/ ; }, mesh = {Male ; *Gastrointestinal Microbiome/genetics ; Animals ; Humans ; *Prostatic Neoplasms, Castration-Resistant/microbiology/genetics/pathology ; Mice ; Aged ; Japan ; *RNA, Ribosomal, 16S/genetics ; Mice, Transgenic ; Middle Aged ; Mice, Knockout ; Disease Progression ; Lactobacillus/genetics/isolation & purification ; Aged, 80 and over ; Disease Models, Animal ; East Asian People ; }, abstract = {Gut microbiota plays a crucial role in the development and progression of prostate cancer, with previous studies indicating that certain bacterial taxa are more abundant in castration-resistant prostate cancer (CRPC) compared to hormone-sensitive prostate cancer (HSPC). Notably, the composition of gut microbiota can vary significantly by geographic region, and Japanese individuals have a distinct microbial profile. However, research exploring these differences within Japanese populations remains limited. This study investigated the gut microbiota differences between Japanese men with HSPC and CRPC and further validated these findings using a transgenic mouse model. Rectal swab samples were collected from 140 Japanese men diagnosed with HSPC (n = 84) or CRPC (n = 56) between September 2020 and July 2022. Gut microbiota composition was analyzed using 16S rRNA gene sequencing. Additionally, Pten-KO mice, which model the progression from HSPC to CRPC, underwent similar microbiota analysis. Results revealed significant differences in gut microbiota composition between HSPC and CRPC patients. Specifically, the CRPC group showed a higher abundance of Firmicutes, including Gemella and Lactobacillus, compared to the HSPC group. These differences were mirrored in the mouse model, where CRPC mice also showed an increase in these bacteria. This study identifies distinct microbial differences between HSPC and CRPC in Japanese men, suggesting that Gemella and Lactobacillus may be associated with the progression to castration resistance in prostate cancer. These findings suggest that gut microbiota differences may be associated with prostate cancer progression. Further research is needed to explore the potential of targeting the microbiota as a therapeutic strategy.}, }
@article {pmid39745433, year = {2025}, author = {Grüterich, L and Woodhouse, JN and Mueller, P and Tiemann, A and Ruscheweyh, H-J and Sunagawa, S and Grossart, H-P and Streit, WR}, title = {Assessing environmental gradients in relation to dark CO2 fixation in estuarine wetland microbiomes.}, journal = {Applied and environmental microbiology}, volume = {91}, number = {1}, pages = {e0217724}, doi = {10.1128/aem.02177-24}, pmid = {39745433}, issn = {1098-5336}, support = {407270017//Deutsche Forschungsgemeinschaft (DFG)/ ; 502681570//Deutsche Forschungsgemeinschaft (DFG)/ ; }, mesh = {*Wetlands ; *Carbon Dioxide/metabolism ; *Microbiota ; *Estuaries ; *Carbon Cycle ; *Bacteria/genetics/classification/metabolism/isolation & purification ; Soil Microbiology ; }, abstract = {UNLABELLED: The rising atmospheric concentration of CO2 is a major concern to society due to its global warming potential. In soils, CO2-fixing microorganisms are preventing some of the CO2 from entering the atmosphere. Yet, the controls of dark CO2 fixation are rarely studied in situ. Here, we examined the gene and transcript abundance of key genes involved in microbial CO2 fixation along major environmental gradients within estuarine wetlands. A combined multi-omics approach incorporating metabarcoding, deep metagenomic, and metatranscriptomic analyses confirmed that wetland microbiota harbor four out of seven known CO2 fixation pathways, namely, the Calvin cycle, reverse tricarboxylic acid cycle, Wood-Ljungdahl pathway, and reverse glycine pathway. These pathways are transcribed at high frequencies along several environmental gradients, albeit at different levels depending on the environmental niche. Notably, the transcription of the key genes for the reverse tricarboxylic acid cycle was associated with high nitrate concentration, while the transcription of key genes for the Wood-Ljungdahl pathway was favored by reducing, O2-poor conditions. The transcript abundance of the Calvin cycle was favored by niches high in organic matter. Taxonomic assignment of transcripts implied that dark CO2 fixation was mainly linked to a few bacterial phyla, namely, Desulfobacterota, Methylomirabilota, Nitrospirota, Chloroflexota, and Pseudomonadota.
IMPORTANCE: The increasing concentration of atmospheric CO2 has been identified as the primary driver of climate change and poses a major threat to human society. This work explores the mostly overlooked potential of light-independent CO2 fixation by soil microbes (a.k.a. dark CO2 fixation) in climate change mitigation efforts. Applying a combination of molecular microbial tools, our research provides new insights into the ecological niches where CO2-fixing pathways are most active. By identifying how environmental factors, like oxygen, salinity and organic matter availability, influence these pathways in an estuarine wetland environment, potential strategies for enhancing natural carbon sinks can be developed. The importance of our research is in advancing the understanding of microbial CO2 fixation and its potential role in the global climate system.}, }
@article {pmid39714193, year = {2025}, author = {Midot, F and Goh, KM and Liew, KJ and Lau, SYL and Espenberg, M and Mander, Ü and Melling, L}, title = {Temporal dynamics of soil microbial C and N cycles with GHG fluxes in the transition from tropical peatland forest to oil palm plantation.}, journal = {Applied and environmental microbiology}, volume = {91}, number = {1}, pages = {e0198624}, doi = {10.1128/aem.01986-24}, pmid = {39714193}, issn = {1098-5336}, support = {P015 790102009//The Twelfth Malaysian Plan through Ministry of Education, Innovation, and Talent Development of Sarawak/ ; FRGS/1/2023/STG02/UTM/02/1,Q.J130000.3854.22H63//Ministry of Higher Education of Malaysia through the Fundamental Research Grant Scheme and UTM Fundamental Research Grant/ ; No 101079192 (MLTOM23003R)//European Union Horizon program/ ; No 101096403 (MLTOM23415R)//EC | European Research Council (ERC)/ ; PRG-2302//Estonian Research Council/ ; }, mesh = {*Soil Microbiology ; *Greenhouse Gases/analysis ; *Forests ; Malaysia ; *Microbiota ; Methane/metabolism/analysis ; Nitrogen Cycle ; Carbon Cycle ; Soil/chemistry ; Nitrous Oxide/analysis/metabolism ; Nitrogen/analysis/metabolism ; Carbon/analysis/metabolism ; Wetlands ; Bacteria/classification/genetics/metabolism/isolation & purification ; Arecaceae ; Agriculture ; }, abstract = {Tropical peatlands significantly influence local and global carbon and nitrogen cycles, yet they face growing pressure from anthropogenic activities. Land use changes, such as peatland forests conversion to oil palm plantations, affect the soil microbiome and greenhouse gas (GHG) emissions. However, the temporal dynamics of microbial community changes and their role as GHG indicators are not well understood. This study examines the dynamics of peat chemistry, soil microbial communities, and GHG emissions from 2016 to 2020 in a logged-over secondary peat swamp forest in Sarawak, Malaysia, which transitioned to an oil palm plantation. This study focuses on changes in genetic composition governing plant litter degradation, methane (CH4), and nitrous oxide (N2O) fluxes. Soil CO2 emission increased (doubling from approximately 200 mg C m[-2] h[-1]), while CH4 emissions decreased (from 200 µg C m[-2] h[-1] to slightly negative) following land use changes. The N2O emissions in the oil palm plantation reached approximately 1,510 µg N m[-2] h[-1], significantly higher than previous land uses. The CH4 fluxes were driven by groundwater table, humification levels, and C:N ratio, with Methanomicrobia populations dominating methanogenesis and Methylocystis as the main CH4 oxidizer. The N2O fluxes correlated with groundwater table, total nitrogen, and C:N ratio with dominant nirK-type denitrifiers (13-fold nir to nosZ) and a minor role by nitrification (a threefold increase in amoA) in the plantation. Proteobacteria and Acidobacteria encoding incomplete denitrification genes potentially impact N2O emissions. These findings highlighted complex interactions between microbial communities and environmental factors influencing GHG fluxes in altered tropical peatland ecosystems.IMPORTANCETropical peatlands are carbon-rich environments that release significant amounts of greenhouse gases when drained or disturbed. This study assesses the impact of land use change on a secondary tropical peat swamp forest site converted into an oil palm plantation. The transformation lowered groundwater levels and changed soil properties. Consequently, the oil palm plantation site released higher carbon dioxide and nitrous oxide compared to previous land uses. As microbial communities play crucial roles in carbon and nitrogen cycles, this study identified environmental factors associated with microbial diversity, including genes and specific microbial groups related to nitrous oxide and methane emissions. Understanding the factors driving microbial composition shifts and greenhouse gas emissions in tropical peatlands provides baseline information to potentially mitigate environmental consequences of land use change, leading to a broader impact on climate change mitigation efforts and proper land management practices.}, }
@article {pmid39679708, year = {2025}, author = {Liu, Z and Jiang, C and Yin, Z and Ibrahim, IA and Zhang, T and Wen, J and Zhou, L and Jiang, G and Li, L and Yang, Z and Huang, Y and Yang, Z and Gu, Y and Meng, D and Yin, H}, title = {Ecological features of microbial community linked to stochastic and deterministic assembly processes in acid mine drainage.}, journal = {Applied and environmental microbiology}, volume = {91}, number = {1}, pages = {e0102824}, doi = {10.1128/aem.01028-24}, pmid = {39679708}, issn = {1098-5336}, support = {2023YFE0114500//MOST | National Key Research and Development Program of China (NKPs)/ ; 92351303//MOST | National Natural Science Foundation of China (NSFC)/ ; BX20230437//Postdoctoral Fellowship Program of CPSF/ ; }, mesh = {*Microbiota ; *Mining ; *Bacteria/genetics/classification/isolation & purification/metabolism ; Phylogeny ; Stochastic Processes ; Metagenomics ; Acids/metabolism ; Metagenome ; }, abstract = {UNLABELLED: Ecological processes greatly shape microbial community assembly, but the driving factors remain unclear. Here, we compiled a metagenomic data set of microbial communities from global acid mine drainage (AMD) and explored the ecological features of microbial community linked to stochastic and deterministic processes from the perspective of species niche position, interaction patterns, gene functions, and viral infection. Our results showed that dispersal limitation (DL) (48.5%~93.5%) dominated the assembly of phylogenetic bin in AMD microbial community, followed by homogeneous selection (HoS) (3.1%~39.2%), heterogeneous selection (HeS) (1.4%~22.2%), and drift (DR) (0.2%~2.7%). The dominant process of dispersal limitation was significantly influenced by niche position in temperature (r = -0.518, P = 0.007) and dissolved oxygen (r = 0.471, P = 0.015). Network stability had a significantly negative correlation with the relative importance of dispersal limitation, while it had a positive correlation with selection processes, implying changes in network properties could be mediated by ecological processes. Furthermore, we found that ecological processes were mostly related to the gene functions of energy production and conversion (C), and amino acid transport and metabolism (E). Meanwhile, our results showed that the number of proviruses and viral genes involved in arsenic (As) resistance is negatively associated with the relative importance of ecological drift in phylogenetic bin assembly, implying viral infection might weaken ecological drift. Taken together, these results highlight that ecological processes are associated with ecological features at multiple levels, providing a novel insight into microbial community assembly in extremely acidic environments.
IMPORTANCE: Unraveling the forces driving community assemblage is a core issue in microbial ecology, but how ecological constraints impose stochasticity and determinism remains unknown. This study presents a comprehensive investigation to uncover the association of ecological processes with species niche position, interaction patterns, microbial metabolisms, and viral infections, which provides novel insights into community assembly in extreme environments.}, }
@article {pmid39665561, year = {2025}, author = {Unzueta-Martínez, A and Girguis, PR}, title = {Taxonomic diversity and functional potential of microbial communities in oyster calcifying fluid.}, journal = {Applied and environmental microbiology}, volume = {91}, number = {1}, pages = {e0109424}, doi = {10.1128/aem.01094-24}, pmid = {39665561}, issn = {1098-5336}, support = {2109473//National Science Foundation (NSF)/ ; 9208//Gordon and Betty Moore Foundation (GBMF)/ ; }, mesh = {Animals ; *Microbiota ; *Bacteria/classification/genetics/metabolism/isolation & purification ; *Archaea/classification/genetics/metabolism ; Metagenomics ; Calcification, Physiologic ; Ostreidae/microbiology ; Biomineralization ; Viruses/classification/genetics ; Biodiversity ; }, abstract = {UNLABELLED: Creating and maintaining an appropriate chemical environment is essential for biomineralization, the process by which organisms precipitate minerals to form their shells or skeletons, yet the mechanisms involved in maintaining calcifying fluid chemistry are not fully defined. In particular, the role of microorganisms in facilitating or hindering animal biomineralization is poorly understood. Here, we investigated the taxonomic diversity and functional potential of microbial communities inhabiting oyster calcifying fluid. We used shotgun metagenomics to survey calcifying fluid microbial communities from three different oyster harvesting sites. There was a striking consistency in taxonomic composition across the three collection sites. We also observed archaea and viruses that had not been previously identified in oyster calcifying fluid. Furthermore, we identified microbial energy-conserving metabolisms that could influence the host's calcification, including genes involved in sulfate reduction and denitrification that are thought to play pivotal roles in inorganic carbon chemistry and calcification in microbial biofilms. These findings provide new insights into the taxonomy and functional capacity of oyster calcifying fluid microbiomes, highlighting their potential contributions to shell biomineralization, and contribute to a deeper understanding of the interplay between microbial ecology and biogeochemistry that could potentially bolster oyster calcification.
IMPORTANCE: Previous research has underscored the influence of microbial metabolisms in carbonate deposition throughout the geological record. Despite the ecological importance of microbes to animals and inorganic carbon transformations, there have been limited studies characterizing the potential role of microbiomes in calcification by animals such as bivalves. Here, we use metagenomics to investigate the taxonomic diversity and functional potential of microbial communities in calcifying fluids from oysters collected at three different locations. We show a diverse microbial community that includes bacteria, archaea, and viruses, and we discuss their functional potential to influence calcifying fluid chemistry via reactions like sulfate reduction and denitrification. We also report the presence of carbonic anhydrase and urease, both of which are critical in microbial biofilm calcification. Our findings have broader implications in understanding what regulates calcifying fluid chemistry and consequentially the resilience of calcifying organisms to 21st century acidifying oceans.}, }
@article {pmid39651865, year = {2025}, author = {Howland, KE and Mouradian, JJ and Uzarski, DR and Henson, MW and Uzarski, DG and Learman, DR}, title = {Nutrient amendments enrich microbial hydrocarbon degradation metagenomic potential in freshwater coastal wetland microcosm experiments.}, journal = {Applied and environmental microbiology}, volume = {91}, number = {1}, pages = {e0197224}, doi = {10.1128/aem.01972-24}, pmid = {39651865}, issn = {1098-5336}, mesh = {*Wetlands ; *Biodegradation, Environmental ; *Fresh Water/microbiology ; *Hydrocarbons/metabolism ; Bacteria/genetics/metabolism/classification ; Metagenomics ; Petroleum/metabolism ; Geologic Sediments/microbiology ; Nutrients/metabolism ; Microbiota ; Metagenome ; Benzene Derivatives/metabolism ; Volatile Organic Compounds/metabolism ; Toluene/metabolism ; Benzene/metabolism ; Water Pollutants, Chemical/metabolism ; }, abstract = {UNLABELLED: Biostimulating native microbes with fertilizers has proven to be a highly effective strategy to speed up biodegradation rates in microbial communities. This study investigates the genetic potential of microbes to degrade light synthetic crude oil in a freshwater coastal wetland. Experimental sediment microcosms were exposed to a variety of conditions (biological control, a light synthetic crude oil amendment, and light synthetic crude oil with nutrient amendment) and incubated for 30 days before volatile organic compounds (BTEX) were quantified and DNA was sequenced for metagenomic analysis. The resulting DNA sequences were binned into metagenome-assembled genomes (MAGs). Analyses of MAGs uncovered a 13-fold significant increase in the abundance of rate-limiting hydrocarbon degrading monooxygenases and dioxygenases, identified only in MAGs from the light synthetic crude oil with nutrient amendments. Further, complete degradation pathways for BTEX compounds were found only in MAGs resulting from the light synthetic crude with nutrient amendment. Moreover, volatile organic compounds (BTEX, cyclohexane, and naphthalene) analyses of microcosm sediments in the presence of nutrients documented that benzene was degraded below detection limits, toluene (98%) and ethylbenzene (67%) were predominantly reduced within 30 days. Results indicate that the genetic potential to degrade BTEX compounds in this freshwater wetland can be linked to the functional potential for bioremediation. BTEX compounds are typically more recalcitrant and tougher to degrade than alkanes. This study demonstrated that stimulating a microbial community with nutrients to enhance its ability to biodegrade hydrocarbons, even in a relatively nutrient-rich habitat like a freshwater wetland, is an effective remediation tactic.
IMPORTANCE: The impact of oil spills in a freshwater aquatic environment can pose dire social, economic, and ecological effects on the region. An oil spill in the Laurentian Great Lakes region has the potential to affect the drinking water of more than 30 million people. The light synthetic crude oil used in this experimental microcosm study is transported through an underground pipeline crossing the waterway between two Laurentian Great Lakes. This study collected metagenomic data (experiments in triplicate) and assessed the quantity of BTEX compounds, which connected microbial degradation function to gene potential. The resulting data documented the bioremediation capabilities of native microbes in a freshwater coastal wetland. This study also provided evidence for this region that bioremediation can be a viable remediation strategy instead of invasive physical methods.}, }
@article {pmid39641605, year = {2025}, author = {Bao, Z and Chen, B and Yu, K and Wei, Y and Liang, X and Yao, H and Liao, X and Xie, W and Yin, K}, title = {Microbiome dynamics and functional profiles in deep-sea wood-fall micro-ecosystem: insights into drive pattern of community assembly, biogeochemical processes, and lignocellulose degradation.}, journal = {Applied and environmental microbiology}, volume = {91}, number = {1}, pages = {e0216524}, doi = {10.1128/aem.02165-24}, pmid = {39641605}, issn = {1098-5336}, support = {42090041, 42030502//MOST | National Natural Science Foundation of China (NSFC)/ ; 42306165//MOST | National Natural Science Foundation of China (NSFC)/ ; No. 2023JJB150027//| Natural Science Foundation of Guangxi Zhuang Autonomous Region (Guangxi Natural Science Foundation)/ ; No. 311022005//Innovation Group Project of Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)/ ; SML2021SP204, SML2023SP215, SML2023SP218, SML2023SP205//Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai)/ ; }, mesh = {*Lignin/metabolism ; *Wood/microbiology/metabolism ; *Microbiota ; *Bacteria/classification/genetics/metabolism/isolation & purification ; *Fungi/genetics/classification/metabolism ; *Seawater/microbiology ; China ; Ecosystem ; Geologic Sediments/microbiology ; }, abstract = {Wood-fall micro-ecosystems contribute to biogeochemical processes in the oligotrophic deep ocean. However, the community assembly processes and biogeochemical functions of microbiomes in wood fall remain unclear. This study investigated the diversity, community structure, assembly processes, and functional profiles of bacteria and fungi in a deep-sea wood fall from the South China Sea using physicochemical indices, amplicon sequencing, and metagenomics. The results showed that distinct wood-fall contact surfaces exhibit habitat heterogeneity. The bacterial community of all contact surfaces and the fungal community of seawater contact surface (SWCS) were affected by homogeneous selection. In SWCS and transition region (TR), bacterial communities were influenced by dispersal limitation, whereas fungal communities were affected by homogenizing dispersal. The Venn diagram visualization revealed that the shared fungal community between SWCS and TR was dominated by Aspergillaceae. Additionally, the bacterial community demonstrated a higher genetic potential for sulfur, nitrogen, and methane metabolism than fungi. The sediment contact surface enriched modules were associated with dissimilatory sulfate reduction and methanogenesis, whereas the modules related to nitrate reduction exhibited enrichment characteristics in TR. Moreover, fungi showed a stronger potential for lignocellulase production compared to bacteria, with Microascaceae and Nectriaceae identified as potential contributors to lignocellulose degradation. These results indicate that environmental filtering and organism exchange levels regulated the microbial community assembly of wood fall. The biogeochemical cycling of sulfur, nitrogen, and methane was mainly driven by the bacterial community. Nevertheless, the terrestrial fungi Microascaceae and Nectriaceae might degrade lignocellulose via the combined action of multiple lignocellulases.IMPORTANCEThe presence and activity of microbial communities may play a crucial role in the biogeochemical cycle of deep-sea wood-fall micro-ecosystems. Previous studies on wood falls have focused on the microbiome diversity, community composition, and environmental impact, while few have investigated wood-fall micro-ecosystems by distinguishing among distinct contact surfaces. Our study investigated the microbiome dynamics and functional profiles of bacteria and fungi among distinct wood-fall contact surfaces. We found that the microbiome community assembly was regulated by environmental filtering and organism exchange levels. Bacteria drive the biogeochemical cycling of sulfur, nitrogen, and methane in wood fall through diverse metabolic pathways, whereas fungi are crucial for lignocellulose degradation. Ultimately, this study provides new insights into the driving pattern of community assembly, biogeochemical processes, and lignocellulose degradation in the microbiomes of deep-sea wood-fall micro-ecosystems, enhancing our comprehension of the ecological impacts of organic falls on deep-sea oligotrophic environments.}, }
@article {pmid37480259, year = {2024}, author = {Ahmad, V and Jamal, A and Khan, MI and Alzahrani, FA and Albiheyri, R and Jamal, QMS}, title = {Cefoperazone targets D-alanyl-D-alanine carboxypeptidase (DAC) to control Morganella morganii-mediated infection: a subtractive genomic and molecular dynamics approach.}, journal = {Journal of biomolecular structure & dynamics}, volume = {42}, number = {13}, pages = {6799-6812}, doi = {10.1080/07391102.2023.2238088}, pmid = {37480259}, issn = {1538-0254}, mesh = {*Morganella morganii/drug effects/enzymology ; *Enterobacteriaceae Infections/drug therapy ; *Cefoperazone/pharmacology ; Humans ; *Serine-Type D-Ala-D-Ala Carboxypeptidase/chemistry/metabolism ; *Metagenome ; Gastrointestinal Microbiome ; Escherichia coli Proteins/chemistry/metabolism ; Penicillin-Binding Proteins/chemistry/metabolism ; Escherichia coli/enzymology ; *Molecular Dynamics Simulation ; Molecular Conformation ; }, abstract = {Morganella morganii is a Gram-negative bacterial pathogen that causes bacteremia, urinary tract infections, intra-abdominal infections, chorioamnionitis, neonatal sepsis, and newborn meningitis. To control this bacterial pathogen a total of 3565 putative proteins targets in Morganella morganii were screened using comparative subtractive analysis of biochemical pathways annotated by the KEGG that did not share any similarities with human proteins. One of the targets, D-alanyl-D-alanine carboxypeptidase DacB [Morganella] was observed to be implicated in the majority of cell wall synthesis pathways, leading to its selection as a novel pharmacological target. The drug that interacted optimally with the identified target was observed to be Cefoperazone (DB01329) with the estimated free energy of binding -8.9 Kcal/mol. During molecular dynamics simulations; it was observed that DB01328-2exb and DB01329-2exb complexes showed similar values as the control FMX-2exb complex near 0.2 nm with better stability. Furthermore, MMPBSA total free energy calculation showed better binding energy than the control complex for DB01329-2exb interaction i.e. -31.50 (±0.93) kcal/mol. Our presented research suggested that D-alanyl-D-alanine carboxypeptidase DacB could be a therapeutic target and cefoperazone could be a promising ligand to inhibit the D-alanyl-D-alanine carboxypeptidase DacB protein of Morganella morganii. To identify prospective therapeutic and vaccine targets in Morganella morganii, this is the first computational and subtractive genomics investigation of various metabolic pathways exploring other therapeutic targets of Morganella morganii. In vitro/in vivo experimental validation of the identified target D-alanyl-D-alanine carboxypeptidase and the design of its inhibitors is suggested to figure out the best dose, the drug's effectiveness, and its toxicity.Communicated by Ramaswamy H. Sarma.}, }
@article {pmid39885140, year = {2025}, author = {Shao, B and Xie, YG and Zhang, L and Ruan, Y and Liang, B and Zhang, R and Xu, X and Wang, W and Lin, Z and Pei, X and Wang, X and Zhao, L and Zhou, X and Wu, X and Xing, D and Wang, A and Lee, DJ and Ren, N and Canfield, DE and Hedlund, BP and Hua, ZS and Chen, C}, title = {Versatile nitrate-respiring heterotrophs are previously concealed contributors to sulfur cycle.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {1202}, pmid = {39885140}, issn = {2041-1723}, support = {52076063//National Natural Science Foundation of China (National Science Foundation of China)/ ; 52100035//National Natural Science Foundation of China (National Science Foundation of China)/ ; 52400025//National Natural Science Foundation of China (National Science Foundation of China)/ ; 52300155//National Natural Science Foundation of China (National Science Foundation of China)/ ; 52321005//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32170014//National Natural Science Foundation of China (National Science Foundation of China)/ ; 2023DX04//State Key Laboratory of Urban Water Resource and Environment (SKLUWRE)/ ; 2024M754204//China Postdoctoral Science Foundation/ ; 2023M740917//China Postdoctoral Science Foundation/ ; }, mesh = {*Sulfur/metabolism ; *Nitrates/metabolism ; *Heterotrophic Processes ; *Denitrification ; *Oxidation-Reduction ; Bacteria/metabolism/genetics ; Geologic Sediments/microbiology ; Nitrous Oxide/metabolism ; Microbiota ; Sulfides/metabolism ; Metagenomics ; Greenhouse Gases/metabolism ; }, abstract = {Heterotrophic denitrifiers play crucial roles in global carbon and nitrogen cycling. However, their inability to oxidize sulfide renders them vulnerable to this toxic molecule, which inhibits the key enzymatic reaction responsible for reducing nitrous oxide (N2O), thereby raising greenhouse gas emissions. Here, we applied microcosm incubations, community-isotope-corrected DNA stable-isotope probing, and metagenomics to characterize a cohort of heterotrophic denitrifiers in estuarine sediments that thrive by coupling sulfur oxidation with denitrification through chemolithoheterotrophic metabolism. Remarkably, ecophysiology experiments from enrichments demonstrate that such heterotrophs expedite denitrification with sulfur acting as alternative electron sources and substantially curtail N2O emissions in both organic-rich and organic-limited environments. Their flexible, non-sulfur-dependent physiology may confer competitive advantages over conventional heterotrophic denitrifiers in detoxifying sulfide, adapting to organic matter fluctuations, and mitigating greenhouse gas emissions. Our study provides insights into the ecological role of heterotrophic denitrifiers in microbial communities with implications for sulfur cycling and climate change.}, }
@article {pmid39885121, year = {2025}, author = {Nooij, S and Plomp, N and Sanders, IMJG and Schout, L and van der Meulen, AE and Terveer, EM and Norman, JM and Karcher, N and Larralde, MF and Vossen, RHAM and Kloet, SL and Faber, KN and Harmsen, HJM and Zeller, GF and Kuijper, EJ and Smits, WK and Ducarmon, QR}, title = {Metagenomic global survey and in-depth genomic analyses of Ruminococcus gnavus reveal differences across host lifestyle and health status.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {1182}, pmid = {39885121}, issn = {2041-1723}, mesh = {Humans ; *Crohn Disease/microbiology/genetics ; *Metagenomics/methods ; *Genome, Bacterial/genetics ; *Gastrointestinal Microbiome/genetics ; Metagenome/genetics ; Health Status ; Genome-Wide Association Study ; Clostridiales/genetics/isolation & purification ; Life Style ; Phylogeny ; Infant, Newborn ; Genomics ; Female ; Male ; Adult ; Virulence Factors/genetics ; }, abstract = {Ruminococcus gnavus is a gut bacterium found in > 90% of healthy individuals, but its increased abundance is also associated with chronic inflammatory diseases, particularly Crohn's disease. Nevertheless, its global distribution and intraspecies genomic variation remain understudied. By surveying 12,791 gut metagenomes, we recapitulated known associations with metabolic diseases and inflammatory bowel disease. We uncovered a higher prevalence and abundance of R. gnavus in Westernized populations and observed bacterial relative abundances up to 83% in newborns. Next, we built a resource of R. gnavus isolates (N = 45) from healthy individuals and Crohn's disease patients and generated complete R. gnavus genomes using PacBio circular consensus sequencing. Analysis of these genomes and publicly available high-quality draft genomes (N = 333 genomes) revealed multiple clades which separated Crohn's-derived isolates from healthy-derived isolates. Presumed R. gnavus virulence factors could not explain this separation. Bacterial genome-wide association study revealed that Crohn's-derived isolates were enriched in genes related to mobile elements and mucin foraging. Together, we present a large R. gnavus resource that will be available to the scientific community and provide novel biological insights into the global distribution and genomic variation of R. gnavus.}, }
@article {pmid39881417, year = {2025}, author = {Ye, GC and Peng, H and Xiang, JC and Miao, LT and Liu, CZ and Wang, SG and Xia, QD}, title = {Comprehensive analysis of the interaction microbiome and prostate cancer: an initial exploration from multi-cohort metagenome and GWAS studies.}, journal = {Journal of translational medicine}, volume = {23}, number = {1}, pages = {130}, pmid = {39881417}, issn = {1479-5876}, mesh = {Humans ; Male ; *Prostatic Neoplasms/microbiology/genetics/pathology ; *Metagenome/genetics ; *Genome-Wide Association Study ; *Gastrointestinal Microbiome/genetics ; Cohort Studies ; Neoplasm Metastasis ; Mendelian Randomization Analysis ; }, abstract = {INTRODUCTION: Prostate cancer is one of the most common cancers in the United States with a high mortality rate. In recent years, the traditional opinion about prostate microbiome was challenged. Although there still are some arguments, an escalating number of researchers are shifting their focus toward the microbiome within the prostate tumor environment.
METHODS: We mined the data of the microbiome extracted from the metagenome, and it offers a broader taxonomic coverage and accurate functional profiling. We used Kraken2, a mapping tool, to mine the gut microbiota of prostate cancer patients. A two-sample Mendelian Randomization was conducted to reflect the association between gut microbiome and cancer.
RESULTS: In the study, we found the consistency of the special intratumor microbiome of both non-metastatic tumors and metastatic tumors. And we dig the gut microbiome in patients with different treatments. We found that some microbiotas may be associated with prostate cancer progression and a special microbiome in metastatic prostate cancer may exist. The anti-androgen therapy can significantly change both the intratumor and gut microbiome.
CONCLUSION: With the progression and metastasis of prostate cancer, some intratumor microbiome changes. And anti-androgen influences both the intratumor and gut microbiome. Our discovery may help researchers further understand the progression, metastasis, and resistance of prostate cancer from the perspective of microbiome level.}, }
@article {pmid39881387, year = {2025}, author = {Pangga, GM and Star-Shirko, B and Psifidi, A and Xia, D and Corcionivoschi, N and Kelly, C and Hughes, C and Lavery, U and Richmond, A and Ijaz, UZ and Gundogdu, O}, title = {Impact of commercial gut health interventions on caecal metagenome and broiler performance.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {30}, pmid = {39881387}, issn = {2049-2618}, support = {BB/T008709/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; EP/V030515/1//Engineering and Physical Sciences Research Council/ ; }, mesh = {Animals ; *Chickens/microbiology ; *Gastrointestinal Microbiome ; *Cecum/microbiology ; *Metagenome ; *Probiotics/administration & dosage ; Prebiotics ; Bacteria/classification/genetics/isolation & purification ; Animal Feed/microbiology ; Vaccination/veterinary ; Dietary Supplements ; }, abstract = {BACKGROUND: Maintaining gut health is a persistent and unresolved challenge in the poultry industry. Given the critical role of gut health in chicken performance and welfare, there is a pressing need to identify effective gut health intervention (GHI) strategies to ensure optimal outcomes in poultry farming. In this study, across three broiler production cycles, we compared the metagenomes and performance of broilers provided with ionophores (as the control group) against birds subjected to five different GHI combinations involving vaccination, probiotics, prebiotics, essential oils, and reduction of ionophore use.
RESULTS: Using a binning strategy, 84 (≥ 75% completeness, ≤ 5% contamination) metagenome-assembled genomes (MAGs) from 118 caecal samples were recovered and annotated for their metabolic potential. The majority of these (n = 52, 61%) had a differential response across all cohorts and are associated with the performance parameter - European poultry efficiency factor (EPEF). The control group exhibited the highest EPEF, followed closely by the cohort where probiotics are used in conjunction with vaccination. The use of probiotics B, a commercial Bacillus strain-based formulation, was determined to contribute to the superior performance of birds. GHI supplementation generally affected the abundance of microbial enzymes relating to carbohydrate and protein digestion and metabolic pathways relating to energy, nucleotide synthesis, short-chain fatty acid synthesis, and drug-transport systems. These shifts are hypothesised to differentiate performance among groups and cycles, highlighting the beneficial role of several bacteria, including Rikenella microfusus and UBA7160 species.
CONCLUSIONS: All GHIs are shown to be effective methods for gut microbial modulation, with varying influences on MAG diversity, composition, and microbial functions. These metagenomic insights greatly enhance our understanding of microbiota-related metabolic pathways, enabling us to devise strategies against enteric pathogens related to poultry products and presenting new opportunities to improve overall poultry performance and health. Video Abstract.}, }
@article {pmid39765196, year = {2025}, author = {Caballero-Gómez, J and Ávalos, G and Matas-Méndez, P and Figueiredo, AM and Castro-Scholten, S and Jiménez-Martín, D and Köster, PC and Santín, M and Bailo, B and Cano-Terriza, D and Sarmento, P and Neves, N and Carrapato, C and González-Barrio, D and Mateo, M and García-Bocanegra, I and Dashti, A and Sánchez, S and Carmena, D}, title = {Dietary profiles of wild carnivores and Blastocystis occurrence: The case of the endangered Iberian lynx (Lynx pardinus) and systematic review.}, journal = {Research in veterinary science}, volume = {184}, number = {}, pages = {105518}, doi = {10.1016/j.rvsc.2024.105518}, pmid = {39765196}, issn = {1532-2661}, mesh = {Animals ; *Lynx/parasitology ; *Blastocystis/genetics/isolation & purification ; Portugal ; Spain ; *Feces/parasitology ; *Endangered Species ; *Animals, Wild/parasitology ; Diet/veterinary ; Blastocystis Infections/veterinary/epidemiology ; }, abstract = {Recent molecular and metagenomic studies have revealed that the obligate anaerobic protist Blastocystis is found more prevalently and with higher subtype diversities in herbivore species than in carnivore species. However, information on wild carnivore species is scarce. Here, we investigated the presence of Blastocystis by molecular methods in fecal DNA samples of free-ranging and captive Iberian lynxes from Spain (n = 243) and Portugal (n = 30). In addition, a systematic review was conducted to obtain information on the Blastocystis prevalence rates and subtype diversities reported in free-living and captive wild carnivores worldwide during the period 2000-2024. Blastocystis was not detected by PCR in any of the samples investigated. Analyses of the data gathered from our systematic review revealed that Blastocystis is uncommon either in free-living (2.1 %, 29/1377) or captive (8.5 %, 100/1175) wild carnivore species. Many of these findings seem to result from accidental acquisition via prey animals, scavenging, contaminated water/feed (free-ranging wild carnivores), or cross-species transmission among animals sharing enclosures (captive wild carnivores). Comparative metagenomic studies analyzing gut microbiota profiles of carnivores are needed to fully understand how microbial communities affect Blastocystis colonization.}, }
@article {pmid38490247, year = {2025}, author = {Ahmed, S and Mahapatra, S and Mishra, R and Murmu, KC and Padhan, P and Prasad, P and Misra, R}, title = {16s RNA-based metagenomics reveal previously unreported gut microbiota associated with reactive arthritis and undifferentiated peripheral spondyloarthritis.}, journal = {Rheumatology (Oxford, England)}, volume = {64}, number = {2}, pages = {870-879}, doi = {10.1093/rheumatology/keae165}, pmid = {38490247}, issn = {1462-0332}, support = {//APLAR/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Arthritis, Reactive/microbiology ; Female ; Male ; Adult ; *RNA, Ribosomal, 16S/genetics ; *Metagenomics/methods ; *Prohibitins ; *Spondylarthritis/microbiology ; Middle Aged ; Case-Control Studies ; Feces/microbiology ; Young Adult ; }, abstract = {OBJECTIVES: Reactive arthritis (ReA) provides a unique opportunity to comprehend how a mucosal infection leads to inflammatory arthritis at a distant site without the apparent invasion of the pathogen. Unfortunately, conventional stool cultures after ReA provide limited information, and there is a dearth of metagenomic studies in ReA. The objective of this study was to identify gut microbiota associated with the development of ReA.
METHODS: Patients with ReA or undifferentiated peripheral spondyloarthritis (UpSpA) were included if they presented within 4 weeks of the onset of the current episode of arthritis. Metagenomic DNA was extracted from the stools of these patients and of 36 age- and sex-similar controls. Sequencing and analysis were done using a standard 16S ribosomal pipeline.
RESULTS: Of 55 patients, there was no difference between the gut microbiota of postdiarrheal ReA (n = 20) and of upSpA (n = 35). Comparing the gut microbiota of patients vs healthy controls, the patients had significantly higher alpha and beta diversity measures. After stringency filters, Proteobacteria had high abundance while Firmicutes had lesser as compared with the controls. Six families were overexpressed in patients, while another five were overexpressed in controls. Sixteen genera and 18 species were significantly different between patients and controls. At the species level there was strong association of Staphylococcus aureus, Clostridium septicum Klebsiella pneumoniae, Escherichia coli, Empedobacter brevis, Roseburia hominis, Bacillus velezensis and Crassaminicella with ReA.
CONCLUSION: The microbiota of classical gut-associated ReA and upSpA is similar. Patients have higher diversities in their gut microbiota compared with healthy controls. Both known and previously unreported species associated with ReA/upSpA were identified.}, }
@article {pmid39881163, year = {2025}, author = {Dash, M and Thiyageshwari, S and Selvi, D and Johnson, HKV and Ariyan, M and Rajan, K and Anandham, R}, title = {Unveiling microbial diversity in slightly and moderately magnesium deficient acidic soils.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {3696}, pmid = {39881163}, issn = {2045-2322}, mesh = {*Soil Microbiology ; *Soil/chemistry ; *Magnesium/metabolism/analysis ; *RNA, Ribosomal, 16S/genetics ; India ; Bacteria/genetics/classification/metabolism ; Metagenomics/methods ; Biodiversity ; Magnesium Deficiency/genetics ; Phosphorus/deficiency/metabolism ; Microbiota/genetics ; }, abstract = {Magnesium (Mg) an essential plant nutrient is widespread deficient in the acidic soils of Nilgiris of Tamil nadu, India. The vegetable yield and quality is especially affected due to deficiency of nutrients like Mg. This study investigates soil characteristics and bacterial diversity in the Nilgiris district of Tamil Nadu, India, with respect to Mg deficiency. The soil samples were collected from different vegetable growing regions of the Nilgiris to assess soil physiocochemical parameters, soil enzymes and soil Mg status. 16S rRNA gene-based metagenomic analysis used to investigate the functional potential and structural diversity of the bacterial communities in high Mg and low Mg deficiency soil. Results indicated mildly acidic soils with a sandy loam texture and high organic carbon content. While nitrogen (N), phosphorus (P), and potassium (K) levels were adequate, Mg deficiency was consistent. Soil enzymes such as dehydrogenase, acid phosphatase, urease and aryl sulfatase, varied across the soil samples. Additionally, 16S rRNA gene-based metagenomics analysis revealed the bacterial diversity and functional pathways in soils with high and low Mg deficiency. Low Mg levels were associated with increased bacterial richness, dominated by Proteobacteria, Gemmatimonadetes, Actinobacteria, Bacteroidetes, and Acidobacteria. Functional pathways related to carbon metabolism, amino acid biosynthesis, and various metabolic processes were more abundant in low Mg deficient soils. This research highlights the significant influence of Mg levels on bacterial diversity and functional potentials in acidic soils, providing insights into soil management strategies in Mg-deficient regions.}, }
@article {pmid39876003, year = {2025}, author = {Li, Q and Huo, J and Ni, G and Zhang, F and Zhang, S and Zhang, X and Wang, R and Jiao, J and Yu, Z and Pu, X and Yue, Y and Ungerfeld, EM and Zhang, X and Wu, J and Tan, Z and Greening, C and Wang, M}, title = {Reductive acetogenesis is a dominant process in the ruminant hindgut.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {28}, pmid = {39876003}, issn = {2049-2618}, mesh = {Animals ; *Rumen/microbiology ; *Goats/microbiology ; *Cecum/microbiology ; *Hydrogen/metabolism ; *Bacteria/classification/metabolism/genetics/isolation & purification ; *Gastrointestinal Microbiome ; *Fermentation ; *Acetates/metabolism ; *Fatty Acids, Volatile/metabolism ; Archaea/classification/metabolism/genetics ; Ruminants/microbiology ; Methane/metabolism ; }, abstract = {BACKGROUND: The microbes residing in ruminant gastrointestinal tracts play a crucial role in converting plant biomass to volatile fatty acids, which serve as the primary energy source for ruminants. This gastrointestinal tract comprises a foregut (rumen) and hindgut (cecum and colon), which differ in structures and functions, particularly with respect to feed digestion and fermentation. While the rumen microbiome has been extensively studied, the cecal microbiome remains much less investigated and understood, especially concerning the assembling microbial communities and overriding pathways of hydrogen metabolism.
RESULTS: To address this gap, we comparatively investigated the composition, capabilities, and activities of the rumen and the cecum microbiome using goats as an experimental ruminant model. In situ measurements showed significantly higher levels of dissolved hydrogen and acetate in the cecum than in the rumen. Increased dissolved hydrogen indicated distinct processes and reduced coupling between fermentative H2 production and utilization, whereas higher levels of acetate could be caused by slower VFA absorption through cecal papillae than through the rumen papillae. Microbial profiling indicated that the cecum harbors a greater abundance of mucin-degrading microbes and fermentative hydrogen producers, whereas the rumen contains a higher abundance of fibrolytic fermentative bacteria, hydrogenotrophic respiratory bacteria, and methanogenic archaea. Most strikingly, reductive acetogenic bacteria were 12-fold more abundant in the cecum. Genome-resolved metagenomic analysis unveiled that the cecum acetogens are both phylogenetically and functionally distinct from those found in the rumen. Further supporting these findings, two in vitro experiments demonstrated a marked difference in hydrogen metabolism pathways between the cecum and the rumen, with increased acetate production and reduced methanogenesis in the cecum. Moreover, comparative analysis across multiple ruminant species confirmed a strong enrichment of reductive acetogens in the hindguts, suggesting a conserved functional role.
CONCLUSIONS: These findings highlight an enrichment of acetogenesis in a key region of the gastrointestinal tract and reshape our understanding of ruminant hydrogen metabolism and how the H2 can be managed in accord to livestock methane mitigation efforts. Video Abstract.}, }
@article {pmid39742975, year = {2025}, author = {Dougherty, PE and Pedersen, MS and Forero-Junco, LM and Carstens, AB and Raaijmakers, JM and Riber, L and Hansen, LH}, title = {Novel bacteriophages targeting wheat phyllosphere bacteria carry DNA modifications and single-strand breaks.}, journal = {Virus research}, volume = {352}, number = {}, pages = {199524}, doi = {10.1016/j.virusres.2024.199524}, pmid = {39742975}, issn = {1872-7492}, mesh = {*Triticum/microbiology/virology ; *Bacteriophages/genetics/classification/isolation & purification/physiology ; *Phylogeny ; *Genome, Viral ; DNA, Viral/genetics ; DNA Breaks, Single-Stranded ; Erwinia/virology/genetics ; Pseudomonas/virology/genetics ; Metagenome ; Microbiota ; Pseudomonas Phages/genetics/classification/isolation & purification ; Bacteria/virology/genetics/classification ; }, abstract = {The phyllosphere microbiome can positively or negatively impact plant health and growth, but we currently lack the tools to control microbiome composition. Contributing to a growing collection of bacteriophages (phages) targeting bacteria living in the wheat phyllosphere, we here isolate and sequence eight novel phages targeting common phyllosphere Erwinia and Pseudomonas strains, including two jumbo phages. We characterize genomic, phylogenetic, and morphological traits from these phages and argue for establishing four novel viral genera. We also search the genomes for anti-defense systems and investigate DNA modifications using Nanopore sequencing. In Pseudomonas phage Rembedalsseter we find evidence of 13 motif-associated single-stranded DNA breaks. A bioinformatics search revealed that 60 related Pseudomonas phages are enriched in the same motif, suggesting these single-stranded nicks may be widely distributed in this family of phages. Finally, we also search the Sequence Read Archive for similar phages in public metagenomes. We find close hits to the Erwinia jumbo-phage Kaldavass in a wide variety of plant, food, and wastewater metagenomes including a near-perfect hit from a Spanish spinach sample, illustrating how interconnected geographically distant phages can be.}, }
@article {pmid39875829, year = {2025}, author = {Zhang, Z and Zong, X and Liu, Z and Dong, X and Bai, H and Fan, L and Li, T}, title = {Comprehensive analysis of vaginal microbiota in Chinese women with genital tuberculosis: implications for diagnosis and treatment.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {52}, pmid = {39875829}, issn = {1471-2180}, support = {2024-4-2119//Capital's Funds for Health Improvement and Research/ ; FCYY201916//Special Training Program for Young and Middle-aged Subject Backbone of Beijing Obstetrics and Gynecology Hospital, Capital Medical University/ ; YQRC201906//"Excellent young Talents" project of Beijing Obstetrics and Gynecology Hospital, Capital Medical University/ ; }, mesh = {Humans ; Female ; *Vagina/microbiology ; Adult ; *Tuberculosis, Female Genital/microbiology/diagnosis ; *Microbiota ; China ; Middle Aged ; Young Adult ; Antitubercular Agents/therapeutic use ; Lactobacillus/isolation & purification/genetics ; Bacteria/classification/genetics/isolation & purification ; Metagenomics/methods ; East Asian People ; }, abstract = {BACKGROUND: Tuberculosis remains an infectious disease of global concern, with potential impacts on respiratory and intestinal microbiota owing to prolonged broad-spectrum antibiotic therapy. Despite its potential to cause infertility, the vaginal microbiota of women with genital tuberculosis remains poorly understood. We comprehensively analyzed the vaginal microbiota in Chinese women with genital tuberculosis.
RESULTS: We recruited women with pelvic (n = 28), endometrial (n = 16), and pulmonary (n = 12) tuberculosis as the research group, and healthy women (n = 11) as the control group. Vaginal discharges were collected for metagenomic analysis of its microbiota. The alpha diversity of the vaginal microbiota in women with genital tuberculosis was slightly higher than that in healthy women, though the difference was not statistically significant (P = 0.23). Similarly, no significant differences in alpha diversity were observed between women with genital and pulmonary tuberculosis (P = 0.82) or between those with pelvic and endometrial tuberculosis (P = 0.82). Notably, the lowest alpha diversity was recorded six months to one year after initiating anti-tuberculosis treatment, with this decline being statistically significant (P = 0.023). The dominance of Lactobacillus iners in the vaginal microbiota was more common in women with genital tuberculosis than that of Lactobacillus crispatus. Furthermore, the abundance of short-chain fatty acid -producing anaerobes, such as Actinomycetes, Streptococcus, and Finegoldia, were significantly increased. Short-chain fatty acid precursor pathways, including the ko03010 ribosome pathway, ko00970 aminoacyl-tRNA synthesis, ko00230 purine metabolism, ko00240 pyrimidine metabolism, and ko00010 glycolysis gluconeogenesis pathway, were significantly upregulated in women with endometrial tuberculosis.
CONCLUSIONS: Extrapulmonary tuberculosis, particularly genital tuberculosis and its associated vaginal dysbiosis impacts female fecundity. Vaginal dysbiosis is more pronounced when M. tuberculosis invades the endometrium. Given the effect of antibiotics on vaginal flora, probiotic combined interventions could be used as a future research direction.
CLINICAL TRIAL NUMBER: Not applicable.}, }
@article {pmid39875095, year = {2025}, author = {Moeller, AH}, title = {Partner fidelity, not geography, drives co-diversification of gut microbiota with hominids.}, journal = {Biology letters}, volume = {21}, number = {1}, pages = {20240454}, doi = {10.1098/rsbl.2024.0454}, pmid = {39875095}, issn = {1744-957X}, support = {/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; *Phylogeny ; Hominidae/microbiology ; Bacteria/classification/genetics/isolation & purification ; Genome, Bacterial ; Geography ; }, abstract = {Bacterial strains that inhabit the gastrointestinal tracts of hominids have diversified in parallel (co-diversified) with their host species. The extent to which co-diversification has been mediated by partner fidelity between strains and hosts or by geographical distance between hosts is not clear due to a lack of strain-level data from clades of hosts with unconfounded phylogenetic relationships and geographical distributions. Here, I tested these competing hypotheses through meta-analyses of 7121 gut bacterial genomes assembled from wild-living ape species and subspecies sampled throughout their ranges in equatorial Africa. Across the gut bacterial phylogeny, strain diversification was more strongly associated with host phylogeny than with geography. In total, approximately 14% of the branch length of the gut bacterial phylogeny showed significant evidence of co-diversification independent of geography, whereas only approximately 4% showed significant evidence of diversification associated with geography independent of host phylogeny. Geographically co-occurring heterospecific hosts (Pan and Gorilla) universally maintained distinct co-diversified bacterial strains. Strains whose diversification was associated with geography independent of host phylogeny included clades of Proteobacteria known to adopt free-living lifestyles (e.g. Escherichia). These results show that co-diversification of gut bacterial strains with hominids has been driven primarily by fidelity of strains to host lineages rather than geography.}, }
@article {pmid39874239, year = {2025}, author = {Zhou, H and Balint, D and Shi, Q and Vartanian, T and Kriegel, MA and Brito, I}, title = {Lupus and inflammatory bowel disease share a common set of microbiome features distinct from other autoimmune disorders.}, journal = {Annals of the rheumatic diseases}, volume = {84}, number = {1}, pages = {93-105}, doi = {10.1136/ard-2024-225829}, pmid = {39874239}, issn = {1468-2060}, mesh = {Humans ; *Inflammatory Bowel Diseases/microbiology/immunology ; *Lupus Erythematosus, Systemic/microbiology/immunology ; *Gastrointestinal Microbiome/genetics ; *Autoimmune Diseases/microbiology/immunology ; Biomarkers ; Female ; Metagenomics/methods ; Metagenome ; Male ; Receptors, Glucocorticoid/genetics ; }, abstract = {OBJECTIVES: This study aims to elucidate the microbial signatures associated with autoimmune diseases, particularly systemic lupus erythematosus (SLE) and inflammatory bowel disease (IBD), compared with colorectal cancer (CRC), to identify unique biomarkers and shared microbial mechanisms that could inform specific treatment protocols.
METHODS: We analysed metagenomic datasets from patient cohorts with six autoimmune conditions-SLE, IBD, multiple sclerosis, myasthenia gravis, Graves' disease and ankylosing spondylitis-contrasting these with CRC metagenomes to delineate disease-specific microbial profiles. The study focused on identifying predictive biomarkers from species profiles and functional genes, integrating protein-protein interaction analyses to explore effector-like proteins and their targets in key signalling pathways.
RESULTS: Distinct microbial signatures were identified across autoimmune disorders, with notable overlaps between SLE and IBD, suggesting shared microbial underpinnings. Significant predictive biomarkers highlighted the diverse microbial influences across these conditions. Protein-protein interaction analyses revealed interactions targeting glucocorticoid signalling, antigen presentation and interleukin-12 signalling pathways, offering insights into possible common disease mechanisms. Experimental validation confirmed interactions between the host protein glucocorticoid receptor (NR3C1) and specific gut bacteria-derived proteins, which may have therapeutic implications for inflammatory disorders like SLE and IBD.
CONCLUSIONS: Our findings underscore the gut microbiome's critical role in autoimmune diseases, offering insights into shared and distinct microbial signatures. The study highlights the potential importance of microbial biomarkers in understanding disease mechanisms and guiding treatment strategies, paving the way for novel therapeutic approaches based on microbial profiles.
TRIAL REGISTRATION NUMBER: NCT02394964.}, }
@article {pmid39871406, year = {2025}, author = {Noell, SE and Abbaszadeh, J and Richards, H and Labat Saint Vincent, M and Lee, CK and Herbold, CW and Stott, MB and Cary, SC and McDonald, IR}, title = {Antarctic Geothermal Soils Exhibit an Absence of Regional Habitat Generalist Microorganisms.}, journal = {Environmental microbiology}, volume = {27}, number = {1}, pages = {e70032}, doi = {10.1111/1462-2920.70032}, pmid = {39871406}, issn = {1462-2920}, support = {18-UOW-028//Marsden Fund/ ; }, mesh = {Antarctic Regions ; *Soil Microbiology ; *Archaea/classification/genetics ; *Bacteria/classification/isolation & purification/genetics ; *Ecosystem ; Microbiota ; Phylogeny ; Hot Springs/microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Active geothermal systems are relatively rare in Antarctica and represent metaphorical islands ideal to study microbial dispersal. In this study, we tested the macro-ecological concept that high dispersal rates result in communities being dominated by either habitat generalists or specialists by investigating the microbial communities on four geographically separated geothermal sites on three Antarctic volcanoes (Mts. Erebus, Melbourne, and Rittman). We found that the microbial communities at higher temperature (max 65°C) sites (Tramway Ridge on Erebus and Rittmann) were unique from each other and were dominated by a variety of novel Archaea from class Nitrososphaeria, while lower temperature (max 50°C) sites (Western Crater on Erebus and Melbourne) had characteristically mesophilic communities (Planctomycetes, Acidobacteriota, etc.) that were highly similar. We found that 97% of the detected microbial taxa were regional habitat specialists, with no generalists, with community assembly driven by high dispersal rates and drift (25% and 30% of community assembly, respectively), not environmental selection. Our results indicate that for microbial communities experiencing high dispersal rates between isolated communities, habitat specialists may tend to out-compete habitat generalists.}, }
@article {pmid39765072, year = {2025}, author = {Khan, M and Nizamani, MM and Asif, M and Kamran, A and He, G and Li, X and Yang, S and Xie, X}, title = {Comprehensive approaches to heavy metal bioremediation: Integrating microbial insights and genetic innovations.}, journal = {Journal of environmental management}, volume = {374}, number = {}, pages = {123969}, doi = {10.1016/j.jenvman.2024.123969}, pmid = {39765072}, issn = {1095-8630}, mesh = {*Biodegradation, Environmental ; *Metals, Heavy/metabolism ; Microbiota ; Ecosystem ; Humans ; }, abstract = {The increasing contamination of ecosystems with heavy metals (HMs) due to industrial activities raises significant jeopardies to environmental health and human well-being. Addressing this issue, recent advances in the field of bioremediation have highlighted the potential of plant-associated microbiomes and genetically engineered organisms (GEOs) to mitigate HMs pollution. This review explores recent advancements in bioremediation strategies for HMs detoxification, with particular attention to omics technologies such as metagenomics, metabolomics, and metaproteomics in deepening the understanding of microbial interactions and their potential for neutralizing HMs. Additionally, Emerging strategies and technologies in GEOs and microorganism-aided nanotechnology have proven to be effective bioremediation tools, particularly for alleviating HM contamination. Despite the promising strategies developed in laboratory settings, several challenges impede their practical application, including ecological risks, regulatory limitations, and public concerns regarding the practice of genetically modified organisms. A comprehensive approach that involves interdisciplinary research is essential to enhance the efficacy and safety of bioremediation technologies. This approach should be coupled with robust regulatory frameworks and active public engagement to ensure environmental integrity and societal acceptance. This review underscores the importance of developing sustainable bioremediation strategies that align with ecological conservation goals and public health priorities.}, }
@article {pmid39723822, year = {2025}, author = {Beauchemin, ET and Hunter, C and Maurice, CF}, title = {Dextran sodium sulfate-induced colitis alters the proportion and composition of replicating gut bacteria.}, journal = {mSphere}, volume = {10}, number = {1}, pages = {e0082524}, doi = {10.1128/msphere.00825-24}, pmid = {39723822}, issn = {2379-5042}, support = {Frederick Banting and Charles Best Canada Graduate Scholarship-Master's//Canadian Government | Canadian Institutes of Health Research (CIHR)/ ; Ferrings Pharmaceuticals Fellowship//Faculty of Medicine, McGill University (McGill Faculty of Medicine)/ ; Doctoral Research grant//FRQ | Fonds de recherche du Québec - Nature et technologies (FRQNT)/ ; 950-230748 X-242502//Canada Research Chairs (Chaires de recherche du Canada)/ ; PJT-149098//Canadian Government | Canadian Institutes of Health Research (CIHR)/ ; Innovators award//Kenneth Rainin Foundation (KRF)/ ; Owens Catchpaugh IBD Graduate Research Award//McGill University Health Centre (MUHC)/ ; }, mesh = {Animals ; *Dextran Sulfate ; *Gastrointestinal Microbiome ; *Colitis/microbiology/chemically induced ; Mice ; *Disease Models, Animal ; *Bacteria/classification/isolation & purification/genetics/metabolism ; *Mice, Inbred C57BL ; Metagenomics ; Female ; Male ; Single-Cell Analysis ; }, abstract = {The bacteria living in the human gut are essential for host health. Though the composition and metabolism of these bacteria are well described in both healthy hosts and those with intestinal disease, less is known about the metabolic activity of the gut bacteria prior to, and during, disease development-especially regarding gut bacterial replication. Here, we use a recently developed single-cell technique alongside existing metagenomics-based tools to identify, track, and quantify replicating gut bacteria both ex vivo and in situ in the dextran sodium sulfate (DSS) mouse model of colitis. We show that the proportion of replicating gut bacteria decreases when mice have the highest levels of inflammation and returns to baseline levels as mice begin recovering. In addition, we report significant alterations in the composition of the replicating gut bacterial community ex vivo during colitis development. On the taxa level, we observe significant changes in the abundance of taxa such as the mucus-degrading Akkermansia and the poorly described Erysipelatoclostridium genus. We further demonstrate that many taxa exhibit variable replication rates in situ during colitis, including Akkermansia muciniphila. Lastly, we show that colitis development is positively correlated with increases in the presence and abundance of bacteria in situ which are predicted to be fast replicators. This could suggest that taxa with the potential to replicate quickly may have an advantage during intestinal inflammation. These data support the need for additional research using activity-based approaches to further characterize the gut bacterial response to intestinal inflammation and its consequences for both the host and the gut microbial community.IMPORTANCEIt is well known that the bacteria living inside the gut are important for human health. Indeed, the type of bacteria that are present and their metabolism are different in healthy people versus those with intestinal disease. However, less is known about how these gut bacteria are replicating, especially as someone begins to develop intestinal disease. This is particularly important as it is thought that metabolically active gut bacteria may be more relevant to health. Here, we begin to address this gap using several complementary approaches to characterize the replicating gut bacteria in a mouse model of intestinal inflammation. We reveal which gut bacteria are replicating, and how quickly, as mice develop and recover from inflammation. This work can serve as a model for future research to identify how actively growing gut bacteria may be impacting health, or why these particular bacteria tend to thrive during intestinal inflammation.}, }
@article {pmid39699190, year = {2025}, author = {Prattico, C and Gonzalez, E and Dridi, L and Jazestani, S and Low, KE and Abbott, DW and Maurice, CF and Castagner, B}, title = {Identification of novel fructo-oligosaccharide bacterial consumers by pulse metatranscriptomics in a human stool sample.}, journal = {mSphere}, volume = {10}, number = {1}, pages = {e0066824}, doi = {10.1128/msphere.00668-24}, pmid = {39699190}, issn = {2379-5042}, support = {DO-16//UofA | Canadian Glycomics Network (GlycoNet)/ ; PJT-437944//Canadian Government | Canadian Institutes of Health Research (CIHR)/ ; }, mesh = {Humans ; *Feces/microbiology ; *Gastrointestinal Microbiome ; *Oligosaccharides/metabolism ; *Bacteria/genetics/classification/metabolism/isolation & purification ; *Prebiotics ; Gene Expression Profiling ; Metagenomics/methods ; Fermentation ; RNA, Ribosomal, 16S/genetics ; Transcriptome ; Dietary Fiber/metabolism ; }, abstract = {UNLABELLED: Dietary fibers influence the composition of the human gut microbiota and directly contribute to its downstream effects on host health. As more research supports the use of glycans as prebiotics for therapeutic applications, the need to identify the gut bacteria that metabolize glycans of interest increases. Fructo-oligosaccharide (FOS) is a common diet-derived glycan that is fermented by the gut microbiota and has been used as a prebiotic. Despite being well studied, we do not yet have a complete picture of all FOS-consuming gut bacterial taxa. To identify new bacterial consumers, we used a short exposure of microbial communities in a stool sample to FOS or galactomannan as the sole carbon source to induce glycan metabolism genes. We then performed metatranscriptomics, paired with whole metagenomic sequencing, and 16S amplicon sequencing. The short incubation was sufficient to cause induction of genes involved in carbohydrate metabolism, like carbohydrate-active enzymes (CAZymes), including glycoside hydrolase family 32 genes, which hydrolyze fructan polysaccharides like FOS and inulin. Interestingly, FOS metabolism transcripts were notably overexpressed in Blautia species not previously reported to be fructan consumers. We therefore validated the ability of different Blautia species to ferment fructans by monitoring their growth and fermentation in defined media. This pulse metatranscriptomics approach is a useful method to find novel consumers of prebiotics and increase our understanding of prebiotic metabolism by CAZymes in the gut microbiota.
IMPORTANCE: Complex carbohydrates are key contributors to the composition of the human gut microbiota and play an essential role in the microbiota's effects on host health. Understanding which bacteria consume complex carbohydrates, or glycans, provides a mechanistic link between dietary prebiotics and their beneficial health effects, an essential step for their therapeutic application. Here, we used a pulse metatranscriptomics pipeline to identify bacterial consumers based on glycan metabolism induction in a human stool sample. We identified novel consumers of fructo-oligosaccharide among Blautia species, expanding our understanding of this well-known glycan. Our approach can be applied to identify consumers of understudied glycans and expand our prebiotic repertoire. It can also be used to study prebiotic glycans directly in stool samples in distinct patient populations to help delineate the prebiotic mechanism.}, }
@article {pmid39653637, year = {2025}, author = {Lepcha, A and Kumar, R and Dindhoria, K and Bhargava, B and Pati, AM and Kumar, R}, title = {Metagenomic insights into the functional potential of non-sanitary landfill microbiomes in the Indian Himalayan region, highlighting key plastic degrading genes.}, journal = {Journal of hazardous materials}, volume = {484}, number = {}, pages = {136642}, doi = {10.1016/j.jhazmat.2024.136642}, pmid = {39653637}, issn = {1873-3336}, mesh = {India ; *Waste Disposal Facilities ; *Microbiota/genetics ; *Plastics ; *Metagenomics ; Biodegradation, Environmental ; Bacteria/genetics/metabolism/classification ; Metals, Heavy ; Soil Microbiology ; Soil Pollutants/metabolism ; Refuse Disposal ; }, abstract = {Solid waste management in the Indian Himalayan Region (IHR) is a growing challenge, intensified by increasing population and tourism, which strain non-sanitary landfills. This study investigates microbial diversity and functional capabilities within these landfills using a high-throughput shotgun metagenomic approach. Physicochemical analysis revealed that the Manali and Mandi landfill sites were under heavy metal contamination and thermal stress. Taxonomic annotation identified a dominance of bacterial phyla, including Proteobacteria, Actinobacteria, Bacteroidetes, and Firmicutes, with genera like Pseudomonas and Bacillus prevalent. Squeezemeta analysis generated 9,216,983 open reading frames (ORFs) across the sampling sites, highlighting diverse metabolic potentials for heavy metal resistance and degrading organic, xenobiotics and plastic wastes. Hierarchical clustering and principal component analysis (PCA) identified distinct gene clusters in Manali and Mandi landfill sites, reflecting differences in pollution profiles. Functional redundancy of landfill microbiome was observed with notable xenobiotic and plastic degradation pathways. This is the first comprehensive metagenomic assessment of non-sanitary landfills in the IHR, providing valuable insights into the microbial roles in degrading persistent pollutants, plastic waste, and other contaminants in these stressed environments.}, }
@article {pmid39642737, year = {2025}, author = {Medriano, CA and Kim, S and Kim, LH and Bae, S}, title = {Chronic Exposure of Adult Zebrafish to Polyethylene and Polyester-based Microplastics: Metabolomic and Gut Microbiome Alterations Reflecting Dysbiosis and Resilience.}, journal = {Journal of hazardous materials}, volume = {484}, number = {}, pages = {136691}, doi = {10.1016/j.jhazmat.2024.136691}, pmid = {39642737}, issn = {1873-3336}, mesh = {Animals ; *Zebrafish ; *Gastrointestinal Microbiome/drug effects ; *Dysbiosis/chemically induced ; *Microplastics/toxicity ; *Water Pollutants, Chemical/toxicity ; *Metabolomics ; *Polyesters ; *Polyethylene/toxicity ; }, abstract = {The study explored the ecotoxicological effects of chronic exposure to microplastic (MP) on adult zebrafish, focusing on environmentally relevant concentrations of polyethylene (PE) beads and polyester (PES). High-throughput untargeted metabolomics via UPLC-QToF-MS and 16S metagenomics for gut microbiota analysis were used to assess ecotoxicity in zebrafish exposed to varying concentrations of PE and PES. The VIP (Variable Importance in Projection) scores indicated PE exposure primarily impacted phospholipids, ceramides, and nucleotide-related compounds, while PES exposure led to alterations in lipid-related compounds, chitin, and amino acid derivatives. From MSEA (Metabolite Set Enrichment Analysis) and Mummichog analyses, PE and PES significantly disrupted key metabolomic pathways associated with inflammation, immune responses, and apoptosis, including leukotriene and arachidonic acid metabolism and the formation of putative anti-inflammatory metabolites from EPA. PE caused physical disruption and inflammation of the epithelial barrier, whereas PES affected gut microbiota interactions, impairing digestion and metabolism. Although alpha diversity within the gut microbiome remained stable, beta diversity analysis revealed significant shifts in microbial composition and structure, suggesting a disruption of functional balance and an increased susceptibility to pathogens. Chronic PE and PES exposures induced shifts in the gut microbial community and interaction network with potential increases in pathogenic bacteria and alteration in commensal bacteria, demonstrating the microbiome's resilience and adaptability to stressors of MPs exposure. High-throughput metabolomics and 16S metagenomics revealed potential chronic diseases associated with inflammation, immune system disorders, metabolic dysfunction, and gut dysbiosis, highlighting the complex relationship between gut microbiome resilience and metabolic disruption under MP-induced stress, with significant ecological implications.}, }
@article {pmid39571716, year = {2025}, author = {González-Parra, JA and Barrera-Conde, M and Kossatz, E and Veza, E and de la Torre, R and Busquets-Garcia, A and Robledo, P and Pizarro, N}, title = {Microbiota and social behavior alterations in a mouse model of down syndrome: Modulation by a synbiotic treatment.}, journal = {Progress in neuro-psychopharmacology & biological psychiatry}, volume = {136}, number = {}, pages = {111200}, doi = {10.1016/j.pnpbp.2024.111200}, pmid = {39571716}, issn = {1878-4216}, mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; Male ; Female ; *Down Syndrome/genetics ; Mice ; *Synbiotics ; *Disease Models, Animal ; *Social Behavior ; Mice, Inbred C57BL ; Behavior, Animal/physiology ; Sex Characteristics ; }, abstract = {Sex differences in the composition and functionality of gut microbiota are an emerging field of interest in neurodevelopmental disorders, as they may help in understanding the phenotypic disparities between males and females. This study aimed to characterize sex-related specific alterations in gut microbiota composition in a mouse model of Down syndrome (Ts65Dn mice, TS mice) through the sequencing of the PCR-amplified 16S ribosomal DNA fraction. Moreover, it intended to examine whether the modulation of gut microbiota by the administration of a synbiotic (SYN) treatment would be beneficial for the behavioral alterations observed in male and female TS mice. Our results show that male, but not female, TS mice exhibit alterations in beta diversity compared to their wild-type (WT) littermates. Sex-dependent differences are also observed in the relative abundance of the classes Bacilli and Clostridia. Administering the SYN effectively counteracts hypersociability in females, and normalizes the overall abundance of Bacilli, specifically by increasing Lactobacillaceae. On the contrary, it rescues emotional recognition deficits in male TS mice and increases the relative abundance of the families Lactobacillaceae, Streptococcaceae and Atopobiaceae. In addition, a metagenome KEGG analysis of differentially enriched pathways shows relevant changes in the cofactor biosynthesis and the amino acid synthesis categories. Finally, following SYN treatment, both male and female TS mice exhibit a robust increase in propionic acid levels compared to WT littermates. These findings suggest sex-specific mechanisms that could link gut microbiota composition with behavior in TS mice, and underscore the potential of targeted gut microbiota interventions to modulate social abnormalities in neurodevelopmental disorders.}, }
@article {pmid38760649, year = {2025}, author = {Kumar, A and Sharma, S and Dindhoria, K and Thakur, A and Kumar, R}, title = {Insight into physico-chemical properties and microbial community structure of biogas slurry from household biogas plants of sub-Himalaya for its implications in improved biogas production.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {28}, number = {1}, pages = {187-200}, pmid = {38760649}, issn = {1618-1905}, mesh = {*Biofuels ; *Bacteria/classification/genetics/isolation & purification/metabolism ; *RNA, Ribosomal, 16S/genetics ; *Bioreactors/microbiology ; *Microbiota ; Phylogeny ; Anaerobiosis ; Manure/microbiology/analysis ; Carbon/analysis/metabolism ; Nitrogen/analysis ; Metagenomics ; Biodiversity ; }, abstract = {Numerous metagenomics studies, conducted in both full-scale anaerobic digesters and household biogas plants, have shed light on the composition and activity of microbial flora essential for optimizing the performance of biogas reactors, underscoring the significance of microbial community composition in biogas plant efficiency. Although the efficiency of household biogas plants in the sub-Himalayan region has been reported, there is no literature evidence on the microbial community structure of such household biogas plants in the sub-Himalayan region. The current study evaluated the physico-chemical properties and bacterial community structure from the slurry samples of household biogas plants prevalent in the sub-Himalayan region. The slurry samples were observed to be rich in nutrients; however, their carbon and nitrogen contents were higher than the recommended standard values of liquid-fermented organic manure. The species richness and diversity indices (Chao1, Shannon, and Simpson) of household biogas plants were quite similar to the advanced biogas reactors operating at mesophilic conditions. 16S rRNA gene amplicon sequencing reveals microbial diversity, showing a higher abundance of Firmicutes (70.9%) and Euryarchaeota (9.52%) in advanced biogas reactors compared to household biogas plants. Microbial analysis shows a lack of beneficial microbes for anaerobic digestion, which might be the reason for inefficient biogas production in household biogas plants of the sub-Himalayan region. The lack of efficient bacterial biomass may also be attributed to the digester design, feedstock, and ambient temperatures. This study emphasized the establishment of efficient microbial consortia for enhanced degradation rates that may increase the methane yield in biogas plants.}, }
@article {pmid38758414, year = {2025}, author = {Xiao, Z and Zhang, Y and Zhang, W and Zhang, A and Wang, G and Chen, C and Ullah, H and Ayaz, T and Li, S and Zhaxi, D and Yan, Q and Kang, J and Xu, X}, title = {Characterizations of gut bacteriome, mycobiome, and virome of healthy individuals living in sea-level and high-altitude areas.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {28}, number = {1}, pages = {173-186}, pmid = {38758414}, issn = {1618-1905}, support = {82370563//National Natural Science Foundation of China/ ; 31700697//National Natural Science Foundation of China/ ; QYXTZX-NQ2022-03//Characteristic Technology of Polysaccharides Research Programme of Naqu, Tibet/ ; }, mesh = {Humans ; *Altitude ; *Gastrointestinal Microbiome ; *Virome ; *Mycobiome ; *Bacteria/classification/genetics/isolation & purification ; *Fungi/classification/isolation & purification/genetics ; Adult ; Male ; Viruses/classification/isolation & purification/genetics ; Healthy Volunteers ; Female ; Feces/microbiology/virology ; Middle Aged ; Metagenome ; }, abstract = {BACKGROUND: The contribution of gut microbiota to human high-altitude adaptation remains inadequately understood.
METHODS: Here a comparative analysis of gut microbiota was conducted between healthy individuals living at sea level and high altitude using deep whole-metagenome shotgun sequencing, to investigate the adaptive mechanisms of gut microbiota in plateau inhabitants.
RESULTS: The results showed the gut bacteriomes in high-altitude individuals exhibited greater within-sample diversity and significant alterations in both bacterial compositional and functional profiles when compared to those of sea-level individuals, indicating the potential selection of unique bacteria associated with high-altitude environments. The strain-level investigation revealed enrichment of Collinsella aerofaciens and Akkermansia muciniphila in high-altitude populations. The characteristics of gut virome and gut mycobiome were also investigated. Compared to sea-level subjects, high-altitude subjects exhibited a greater diversity in their gut virome, with an increased number of viral operational taxonomic units (vOTUs) and unique annotated genes. Finally, correlation analyses revealed 819 significant correlations between 42 bacterial species and 375 vOTUs, while no significant correlations were observed between bacteria and fungi or between fungi and viruses.
CONCLUSION: The findings have significantly contributed to an enhanced comprehension of the mechanisms underlying the high-altitude geographic adaptation of the human gut microbiota.}, }
@article {pmid39867343, year = {2024}, author = {Guimarães, LO and Ribeiro, GO and da Couto, R and Ramos, EDSF and Morais, VDS and Telles-de-Deus, J and Helfstein, VC and Dos Santos, JM and Deng, X and Delwart, E and Pandey, RP and de Camargo-Neves, VLF and da Costa, AC and Kirchgatter, K and Leal, É}, title = {Exploring mosquito virome dynamics within São Paulo Zoo: insights into mosquito-virus-environment interactions.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1496126}, pmid = {39867343}, issn = {2235-2988}, mesh = {Animals ; Brazil ; *Virome ; *Mosquito Vectors/virology ; *Metagenomics ; Animals, Zoo/virology ; Arboviruses/genetics/classification/isolation & purification ; Culicidae/virology ; Aedes/virology ; Anopheles/virology ; Culex/virology ; Ecosystem ; }, abstract = {BACKGROUND: Mosquito-borne diseases have a significant public health threat worldwide, with arboviruses accounting for a high proportion of infectious diseases and mortality annually. Brazil, in particular, has been suffering outbreaks of diseases transmitted by mosquito viruses, notably those of the Aedes genus, such as dengue, Zika, and chikungunya. Against this background, the São Paulo Zoo is an intriguing ecological niche to explore the virome of mosquitoes, potentially shedding light on the dynamics of arbovirus transmission within a confined setting.
METHODS: In this study, we conducted a comprehensive metagenomic analysis of mosquitoes collected from diverse habitats within the zoo, focusing on the Aedes, Anopheles, and Culex genera. From 1,039 contigs of viral origin, we identified 229 viral species infecting mosquitoes, with the orders Picornavirales, Nodamuvirales and Sobelivirales being the most prevalent and abundant. The difference in virome composition was primarily driven by mosquito host species rather than specific collection sites or trap height.
RESULTS: Despite environmental disparities, the virome remained remarkably uniform across different areas of the zoo, emphasizing the strong association between mosquito species and their viral communities. Furthermore, we identified a core virome shared among mosquito species, highlighting potential cross-species transmission events and underscoring the need for targeted surveillance and control measures.
CONCLUSION: These results contribute to our understanding of the interplay between mosquitoes, the environment, and viruses, providing valuable insights for disease intervention strategies in mosquito-borne diseases.}, }
@article {pmid39866568, year = {2025}, author = {Pucci, N and Ujčič-Voortman, J and Verhoeff, AP and Mende, DR}, title = {Priority effects, nutrition and milk glycan-metabolic potential drive Bifidobacterium longum subspecies dynamics in the infant gut microbiome.}, journal = {PeerJ}, volume = {13}, number = {}, pages = {e18602}, pmid = {39866568}, issn = {2167-8359}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Milk, Human/microbiology/chemistry/metabolism ; Infant ; *Bifidobacterium/metabolism/genetics ; *Bifidobacterium longum/metabolism ; Female ; *Polysaccharides/metabolism ; Infant, Newborn ; Feces/microbiology ; Metagenome ; Breast Feeding ; Male ; }, abstract = {BACKGROUND: The initial colonization of the infant gut is a complex process that defines the foundation for a healthy microbiome development. Bifidobacterium longum is one of the first colonizers of newborns' gut, playing a crucial role in the healthy development of both the host and its microbiome. However, B. longum exhibits significant genomic diversity, with subspecies (e.g., Bifidobacterium longum subsp. infantis and subsp. longum) displaying distinct ecological and metabolic strategies including differential capabilities to break down human milk glycans (HMGs). To promote healthy infant microbiome development, a good understanding of the factors governing infant microbiome dynamics is required.
METHODOLOGY: We analyzed newly sequenced gut microbiome samples of mother-infant pairs from the Amsterdam Infant Microbiome Study (AIMS) and four publicly available datasets to identify important environmental and bifidobacterial features associated with the colonization success and succession outcomes of B. longum subspecies. Metagenome-assembled genomes (MAGs) were generated and assessed to identify characteristics of B. longum subspecies in relation to early-life gut colonization. We further implemented machine learning tools to identify significant features associated with B. longum subspecies abundance.
RESULTS: B. longum subsp. longum was the most abundant and prevalent gut Bifidobacterium at one month, being replaced by B. longum subsp. infantis at six months of age. By utilizing metagenome-assembled genomes (MAGs), we reveal significant differences between and within B. longum subspecies in their potential to break down HMGs. We further combined strain-tracking, meta-pangenomics and machine learning to understand these abundance dynamics and found an interplay of priority effects, milk-feeding type and HMG-utilization potential to govern them across the first six months of life. We find higher abundances of B. longum subsp. longum in the maternal gut microbiome, vertical transmission, breast milk and a broader range of HMG-utilizing genes to promote its abundance at one month of age. Eventually, we find B. longum subsp. longum to be replaced by B. longum subsp. infantis at six months of age due to a combination of nutritional intake, HMG-utilization potential and a diminishment of priority effects.
DISCUSSION: Our results establish a strain-level ecological framework explaining early-life abundance dynamics of B. longum subspecies. We highlight the role of priority effects, nutrition and significant variability in HMG-utilization potential in determining the predictable colonization and succession trajectories of B. longum subspecies, with potential implications for promoting infant health and well-being.}, }
@article {pmid39814067, year = {2024}, 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 = {41}, number = {1}, pages = {}, doi = {10.1093/bioinformatics/btaf020}, pmid = {39814067}, issn = {1367-4811}, support = {//National Research Foundation of Korea/ ; 2022R1A2C1007345//Korea government/ ; }, mesh = {*Metagenome ; *Metagenomics/methods ; Humans ; Metabolomics/methods ; Metabolic Networks and Pathways ; Microbiota/genetics ; Inflammatory Bowel Diseases/microbiology/metabolism/genetics ; Metabolome ; Stomach Neoplasms/metabolism/microbiology/genetics ; }, 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 Predicting Changes in Microbial metaBolites (PredCMB), 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 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.
Freely available to non-commercial users at https://www.sysbiolab.org/predcmb.}, }
@article {pmid39556491, year = {2025}, author = {Shete, O and Ghosh, TS}, title = {Normal Gut Microbiomes in Diverse Populations: Clinical Implications.}, journal = {Annual review of medicine}, volume = {76}, number = {1}, pages = {95-114}, doi = {10.1146/annurev-med-051223-031809}, pmid = {39556491}, issn = {1545-326X}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; }, abstract = {The human microbiome is a sensor and modulator of physiology and homeostasis. Remarkable tractability underpins the promise of therapeutic manipulation of the microbiome. However, the definition of a normal or healthy microbiome has been elusive. This is in part due to the underrepresentation of minority groups and major global regions in microbiome studies to date. We review studies of the microbiome in different populations and highlight a commonality among health-associated microbiome signatures along with major drivers of variation. We also provide an overview of microbiome-associated therapeutic interventions for some widespread, widely studied diseases. We discuss sources of bias and the challenges associated with defining population-specific microbiome reference bases. We propose a roadmap for defining normal microbiome references that can be used for population-customized microbiome therapeutics and diagnostics.}, }
@article {pmid39865153, year = {2025}, author = {Wu, Z and Jiang, M and Jia, M and Sang, J and Wang, Q and Xu, Y and Qi, L and Yang, W and Feng, L}, title = {The difference of oropharyngeal microbiome during acute respiratory viral infections in infants and children.}, journal = {Communications biology}, volume = {8}, number = {1}, pages = {127}, pmid = {39865153}, issn = {2399-3642}, support = {2022-I2M-CoV19-006//Chinese Academy of Medical Sciences (CAMS)/ ; }, mesh = {Humans ; *Respiratory Tract Infections/microbiology/virology ; Infant ; *Oropharynx/microbiology/virology ; *Microbiota ; Child, Preschool ; Male ; Female ; Child ; Acute Disease ; Virus Diseases/virology/microbiology/epidemiology ; }, abstract = {Acute respiratory infections (ARI) with multiple types of viruses are common in infants and children. This study was conducted to assess the difference of oropharyngeal microbiome during acute respiratory viral infection using whole-genome shotgun metagenomic sequencing. The overall taxonomic alpha diversity did not differ by the types of infected virus. The beta diversity differed by disease severity, disease-related symptoms, and types of infected virus. Nine species had significantly higher abundance in outpatients than in inpatients, with five of them in the genus Achromobacter. Three microbial community types were identified. The prevalence of community type (CT) 1 was higher among patients with influenza virus, enterovirus, and human adenvirus; CT2 was higher among patients with human metapneumovirus; and CT3 was higher among patients with respiratory syncytial virus and human adenvirus infections. Our results suggest that the oropharyngeal microbiome is associated with ARI disease severity, disease-related symptoms, and the types of infected virus.}, }
@article {pmid38385313, year = {2025}, author = {Iqbal, S and Begum, F and Ullah, I and Jalal, N and Shaw, P}, title = {Peeling off the layers from microbial dark matter (MDM): recent advances, future challenges, and opportunities.}, journal = {Critical reviews in microbiology}, volume = {51}, number = {1}, pages = {1-21}, doi = {10.1080/1040841X.2024.2319669}, pmid = {38385313}, issn = {1549-7828}, mesh = {*Metagenomics ; *Bacteria/genetics/classification/metabolism ; Genomics ; Microbiota ; Metagenome ; }, abstract = {Microbes represent the most common organisms on Earth; however, less than 2% of microbial species in the environment can undergo cultivation for study under laboratory conditions, and the rest of the enigmatic, microbial world remains mysterious, constituting a kind of "microbial dark matter" (MDM). In the last two decades, remarkable progress has been made in culture-dependent and culture-independent techniques. More recently, studies of MDM have relied on culture-independent techniques to recover genetic material through either unicellular genomics or shotgun metagenomics to construct single-amplified genomes (SAGs) and metagenome-assembled genomes (MAGs), respectively, which provide information about evolution and metabolism. Despite the remarkable progress made in the past decades, the functional diversity of MDM still remains uncharacterized. This review comprehensively summarizes the recently developed culture-dependent and culture-independent techniques for characterizing MDM, discussing major challenges, opportunities, and potential applications. These activities contribute to expanding our knowledge of the microbial world and have implications for various fields including Biotechnology, Bioprospecting, Functional genomics, Medicine, Evolutionary and Planetary biology. Overall, this review aims to peel off the layers from MDM, shed light on recent advancements, identify future challenges, and illuminate the exciting opportunities that lie ahead in unraveling the secrets of this intriguing microbial realm.}, }
@article {pmid39861468, year = {2025}, author = {Fricker, AD and Sejane, K and Desai, M and Snyder, MW and Duran, L and Mackelprang, R and Bode, L and Ross, MG and Flores, GE}, title = {A Pilot Study Exploring the Relationship Between Milk Composition and Microbial Capacity in Breastfed Infants.}, journal = {Nutrients}, volume = {17}, number = {2}, pages = {}, doi = {10.3390/nu17020338}, pmid = {39861468}, issn = {2072-6643}, support = {SC1GM136546/GM/NIGMS NIH HHS/United States ; R21HD104028/HD/NICHD NIH HHS/United States ; R01HD099813/HD/NICHD NIH HHS/United States ; }, mesh = {Humans ; *Milk, Human/chemistry/microbiology ; Pilot Projects ; Female ; *Gastrointestinal Microbiome ; Infant ; *Breast Feeding ; *Oligosaccharides/analysis ; Adult ; *Feces/microbiology/chemistry ; Cross-Sectional Studies ; Male ; Body Mass Index ; RNA, Ribosomal, 16S/genetics ; Bacteria/classification/genetics/isolation & purification ; Overweight/microbiology ; Infant, Newborn ; Obesity/microbiology ; }, abstract = {BACKGROUND: Maternal obesity may contribute to childhood obesity in a myriad of ways, including through alterations of the infant gut microbiome. For example, maternal obesity may contribute both directly by introducing a dysbiotic microbiome to the infant and indirectly through the altered composition of human milk that fuels the infant gut microbiome. In particular, indigestible human milk oligosaccharides (HMOs) are known to shape the composition of the infant gut microbiome. The goal of this study was to characterize the HMO profiles of normal-weight and overweight mothers and to quantitatively link HMO concentrations to the taxonomic composition and functional potential of the infant gut microbiome.
METHODS: Normal-weight (BMI = 18.5-24.9; n = 9) and overweight/obese (OW/OB; BMI > 25; n = 11) breastfeeding mothers and their infants were enrolled in this single-center, cross-sectional pilot study. Human milk from the mothers and rectal stool swabs from the infants were collected 7-9 weeks postpartum. The HMO composition, microbiome composition, and microbial functions were assessed using HPLC, 16S rRNA gene sequencing, and metagenomic sequencing, respectively.
RESULTS: Neither the HMO profiles nor the infant microbiome composition varied according to maternal BMI status. Taxonomically, the gut microbiota of infants were dominated by typical gut lineages including Bifidobacterium. Significant correlations between individual HMOs and bacterial genera were identified, including for Prevotella, a genus of the Bacteroidota phylum that was positively correlated with the concentrations of lacto-N-neotetraose (LNnT) and lacto-N-hexaose (LNH). Using metagenomic assembled genomes, we were also able to identify the broad HMO-degradative capacity across the Bifidobacterium and Prevotella genera.
CONCLUSIONS: These results suggest that the maternal BMI status does not impact the HMO profiles of human milk. However, select HMOs were correlated with specific bacterial taxa, suggesting that the milk composition influences both the taxonomic composition and the functional capacity of the infant gut microbiome.}, }
@article {pmid39860966, year = {2024}, author = {Laryushina, Y and Samoilova-Bedych, N and Turgunova, L and Marchenko, A and Turgunov, Y and Kozhakhmetov, S and Suieubayev, M and Mukhanbetzhanov, N and Kabdulina, N}, title = {Interrelationships of the Intestinal Microbiome, Trimethylamine N-Oxide and Lipopolysaccharide-Binding Protein with Crohn's Disease Activity.}, journal = {Pathogens (Basel, Switzerland)}, volume = {14}, number = {1}, pages = {}, doi = {10.3390/pathogens14010005}, pmid = {39860966}, issn = {2076-0817}, support = {AP14871959//Science Committee of the Ministry of Science and Higher Education of the Republic of Kazakhstan/ ; }, mesh = {Humans ; *Methylamines/metabolism ; *Gastrointestinal Microbiome/physiology ; *Crohn Disease/microbiology/metabolism ; Female ; Male ; Adult ; *Acute-Phase Proteins/metabolism/analysis ; *Feces/microbiology/chemistry ; Middle Aged ; *Membrane Glycoproteins/metabolism ; Carrier Proteins/metabolism ; Young Adult ; Lipopolysaccharides/metabolism ; }, abstract = {UNLABELLED: Crohn's disease (CD) is a multifactorial inflammatory bowel disease whose pathogenetic mechanisms are a field of ongoing study. Changes in the intestinal microbiome in CD may influence metabolite production and reflect the disease's severity. We investigate the relationship between trimethylamine N-oxide (TMAO) and lipopolysaccharide-binding protein (LPS) levels and changes in the gut microbiome in patients with CD of various degrees of activity.
METHODS: In total, 29 CD patients and 15 healthy individuals were investigated for their levels of TMAO by HPLC-MS, and LPS protein by ELISA and metagenomic 16 s-sequencing of feces was performed.
RESULTS: We found significant differences in TMAO levels in patients in the remission/mild and moderate/severe groups compared to the control group (p = 0.02 and p = 0.014), changes in alpha diversity with the Shannon index (p = 0. 0151 and p = 0.0018) and in beta diversity (ANOSIM p = 0.009 and PERMANOVA p = 0.005) in both groups compared to controls. Strongly positive correlations in TMAO levels and mixed correlations of LPS with alpha diversity metrics were found, as well as significant correlations with microbiota species.
CONCLUSIONS: Changes in the level of metabolites may reflect specific disturbances in the composition of the intestinal microbiome at different degrees of severity of CD.}, }
@article {pmid39859429, year = {2025}, author = {Vicente-Valor, J and Tesolato, S and Paz-Cabezas, M and Gómez-Garre, D and Ortega-Hernández, A and de la Serna, S and Domínguez-Serrano, I and Dziakova, J and Rivera, D and Jarabo, JR and Gómez-Martínez, AM and Hernando, F and Torres, A and Iniesta, P}, title = {Fecal Microbiota Strongly Correlates with Tissue Microbiota Composition in Colorectal Cancer but Not in Non-Small Cell Lung Cancer.}, journal = {International journal of molecular sciences}, volume = {26}, number = {2}, pages = {}, doi = {10.3390/ijms26020717}, pmid = {39859429}, issn = {1422-0067}, support = {PI19/00073//Carlos III Health Institute (Ministerio de Economía y Competitividad), Spain and co-funded by the European Union through the European Regional Development Fund (ERDF) 'A way to make Europe'/ ; }, mesh = {Humans ; *Carcinoma, Non-Small-Cell Lung/microbiology ; *Feces/microbiology ; *Colorectal Neoplasms/microbiology ; *Lung Neoplasms/microbiology ; Female ; Male ; Middle Aged ; Aged ; RNA, Ribosomal, 16S/genetics ; Microbiota/genetics ; Gastrointestinal Microbiome/genetics ; Metagenomics/methods ; Adult ; }, abstract = {Microbiota could be of interest in the diagnosis of colorectal and non-small cell lung cancer (CRC and NSCLC). However, how the microbial components of tissues and feces reflect each other remains unknown. In this work, our main objective is to discover the degree of correlation between the composition of the tissue microbiota and that of the feces of patients affected by CRC and NSCLC. Specifically, we investigated tumor and non-tumor tissues from 38 recruited patients with CRC and 19 with NSCLC. DNA from samples was submitted for 16S rDNA metagenomic sequencing, followed by data analysis through the QIIME2 pipeline and further statistical processing with STATA IC16. Tumor and non-tumor tissue selected genera were highly correlated in both CRC and NSCLC (100% and 81.25%). Following this, we established tissue-feces correlations, using selected genera from a LEfSe analysis previously published. In CRC, we found a strong correlation between the taxa detected in feces and those from colorectal tissues. However, our data do not demonstrate this correlation in NSCLC. In conclusion, our findings strongly reinforce the utility of fecal microbiota as a non-invasive biomarker for CRC diagnosis, while highlighting critical distinctions for NSCLC. Furthermore, our data demonstrate that the microbiota components of tumor and non-tumor tissues are similar, with only minor differences being detected.}, }
@article {pmid39856742, year = {2025}, author = {Benitez, AJ and Tanes, C and Friedman, ES and Zackular, JP and Ford, E and Gerber, JS and DeRusso, PA and Kelly, A and Li, H and Elovitz, MA and Wu, GD and Zemel, B and Bittinger, K}, title = {Antibiotic exposure is associated with minimal gut microbiome perturbations in healthy term infants.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {21}, pmid = {39856742}, issn = {2049-2618}, support = {KL2TR001879/TR/NCATS NIH HHS/United States ; R01DK107565/DK/NIDDK NIH HHS/United States ; R01DK107565/DK/NIDDK NIH HHS/United States ; R01DK107565/DK/NIDDK NIH HHS/United States ; R01DK107565/DK/NIDDK NIH HHS/United States ; R01DK107565/DK/NIDDK NIH HHS/United States ; R01DK107565/DK/NIDDK NIH HHS/United States ; R01DK107565/DK/NIDDK NIH HHS/United States ; R01DK107565/DK/NIDDK NIH HHS/United States ; R01DK107565/DK/NIDDK NIH HHS/United States ; R01DK107565/DK/NIDDK NIH HHS/United States ; R01DK107565/DK/NIDDK NIH HHS/United States ; R35GM138369/GM/NIGMS NIH HHS/United States ; UL1TR001878//NIH National Center for Research Resources Clinical and Translational Science Program/ ; unrestricted donation//American Beverage Foundation for a Healthy America/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Anti-Bacterial Agents/adverse effects/pharmacology ; Infant ; *Feces/microbiology/chemistry ; Female ; *Bile Acids and Salts/metabolism ; Male ; Prospective Studies ; *Breast Feeding ; Longitudinal Studies ; Infant, Newborn ; Metagenomics ; Bacteria/classification/genetics/drug effects/isolation & purification ; Child, Preschool ; Black or African American ; Amoxicillin ; Bifidobacterium/drug effects/isolation & purification/genetics ; White ; }, abstract = {BACKGROUND: The evolving infant gut microbiome influences host immune development and later health outcomes. Early antibiotic exposure could impact microbiome development and contribute to poor outcomes. Here, we use a prospective longitudinal birth cohort of n = 323 healthy term African American children to determine the association between antibiotic exposure and the gut microbiome through shotgun metagenomics sequencing as well as bile acid profiles through liquid chromatography-mass spectrometry.
RESULTS: Stool samples were collected at ages 4, 12, and 24 months for antibiotic-exposed (n = 170) and unexposed (n = 153) participants. A short-term substudy (n = 39) collected stool samples at first exposure, and over 3 weeks following antibiotics initiation. Antibiotic exposure (predominantly amoxicillin) was associated with minimal microbiome differences, whereas all tested taxa were modified by breastfeeding. In the short-term substudy, we observed microbiome differences only in the first 2 weeks following antibiotics initiation, mainly a decrease in Bifidobacterium bifidum. The differences did not persist a month after antibiotic exposure. Four species were associated with infant age. Antibiotic exposure was not associated with an increase in antibiotic resistance gene abundance or with differences in microbiome-derived fecal bile acid composition.
CONCLUSIONS: Short-term and long-term gut microbiome perturbations by antibiotic exposure were detectable but substantially smaller than those associated with breastfeeding and infant age.}, }
@article {pmid39856709, year = {2025}, author = {Li, D and Chen, W and Luo, W and Zhang, H and Liu, Y and Shu, D and Wei, G}, title = {Seed microbiomes promote Astragalus mongholicus seed germination through pathogen suppression and cellulose degradation.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {23}, pmid = {39856709}, issn = {2049-2618}, support = {42177106//National Natural Science Foundation of China/ ; 42177106//National Natural Science Foundation of China/ ; 42177106//National Natural Science Foundation of China/ ; 42177106//National Natural Science Foundation of China/ ; 42177106//National Natural Science Foundation of China/ ; 42177106//National Natural Science Foundation of China/ ; 42177106//National Natural Science Foundation of China/ ; }, mesh = {*Seeds/microbiology ; *Germination ; *Microbiota ; *Bacteria/classification/genetics/isolation & purification ; *Cellulose/metabolism ; Astragalus Plant/microbiology ; Soil Microbiology ; Metagenome ; }, abstract = {BACKGROUND: Seed-associated microorganisms play crucial roles in maintaining plant health by providing nutrients and resistance to biotic and abiotic stresses. However, their functions in seed germination and disease resistance remain poorly understood. In this study, we investigated the microbial community assembly features and functional profiles of the spermosphere and endosphere microbiomes related to germinated and ungerminated seeds of Astragalus mongholicus by using amplicon and shotgun metagenome sequencing techniques. Additionally, we aimed to elucidate the relationship between beneficial microorganisms and seed germination through both in vitro and in vivo pot experiments.
RESULTS: Our findings revealed that germination significantly enhances the diversity of microbial communities associated with seeds. This increase in diversity is driven through environmental ecological niche differentiation, leading to the enrichment of potentially beneficial probiotic bacteria such as Pseudomonas and Pantoea. Conversely, Fusarium was consistently enriched in ungerminated seeds. The co-occurrence network patterns revealed that the microbial communities within germinated and ungerminated seeds presented distinct structures. Notably, germinated seeds exhibit more complex and interconnected networks, particularly for bacterial communities and their interactions with fungi. Metagenome analysis showed that germinated seed spermosphere soil had more functions related to pathogen inhibition and cellulose degradation. Through a combination of culture-dependent and germination experiments, we identified Fusarium solani as the pathogen. Consistent with the metagenome analysis, germination experiments further demonstrated that bacteria associated with pathogen inhibition and cellulose degradation could promote seed germination and vigor. Specifically, Paenibacillus sp. significantly enhanced A. mongholicus seed germination and plant growth.
CONCLUSIONS: Our study revealed the dynamics of seed-associated microorganisms during seed germination and confirmed their ecological role in promoting A. mongholicus seed germination by suppressing pathogens and degrading cellulose. This study offers a mechanistic understanding of how seed microorganisms facilitate successful seed germination, highlighting the potential for leveraging these microbial communities to increase plant health. Video Abstract.}, }
@article {pmid39856104, year = {2025}, author = {Özcan, E and Yu, KB and Dinh, L and Lum, GR and Lau, K and Hsu, J and Arino, M and Paramo, J and Lopez-Romero, A and Hsiao, EY}, title = {Dietary fiber content in clinical ketogenic diets modifies the gut microbiome and seizure resistance in mice.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {987}, pmid = {39856104}, issn = {2041-1723}, support = {R01NS115537//U.S. Department of Health & Human Services | NIH | National Institute of Neurological Disorders and Stroke (NINDS)/ ; }, mesh = {*Diet, Ketogenic ; Animals ; *Gastrointestinal Microbiome ; *Dietary Fiber/administration & dosage ; *Seizures/diet therapy/metabolism ; Mice ; Male ; Humans ; Mice, Inbred C57BL ; Disease Models, Animal ; Infant Formula ; Female ; }, abstract = {The gut microbiome modulates the anti-seizure effects of the ketogenic diet, but how specific dietary formulations differentially modify the gut microbiome in ways that impact seizure outcome is poorly understood. We find that medical ketogenic infant formulas vary in macronutrient ratio, fat source, and fiber content and differentially promote resistance to 6-Hz seizures in mice. Dietary fiber, rather than fat ratio or source, drives substantial metagenomic shifts in a model human infant microbial community. Addition of fiber to a fiber-deficient ketogenic formula restores seizure resistance, and supplementing protective formulas with excess fiber potentiates seizure resistance. By screening 13 fiber sources and types, we identify metagenomic responses in the model community that correspond with increased seizure resistance. Supplementing with seizure-protective fibers enriches microbial genes related to queuosine biosynthesis and preQ0 biosynthesis and decreases genes related to sucrose degradation and TCA cycle, which are also seen in seizure-protected mice that are fed fiber-containing ketogenic formulas. This study reveals that different formulations of ketogenic diets, and dietary fiber content in particular, differentially impact seizure outcome in mice, likely by modifying the gut microbiome. Understanding interactions between diet, microbiome, and host susceptibility to seizures could inform novel microbiome-guided approaches to treat refractory epilepsy.}, }
@article {pmid39856097, year = {2025}, author = {Pidgeon, R and Mitchell, S and Shamash, M and Suleiman, L and Dridi, L and Maurice, CF and Castagner, B}, title = {Diet-derived urolithin A is produced by a dehydroxylase encoded by human gut Enterocloster species.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {999}, pmid = {39856097}, issn = {2041-1723}, support = {PJT-437944//Gouvernement du Canada | Canadian Institutes of Health Research (Instituts de Recherche en Santé du Canada)/ ; }, mesh = {Humans ; *Coumarins/metabolism ; *Gastrointestinal Microbiome ; *Operon/genetics ; Feces/microbiology ; Diet ; Bacterial Proteins/metabolism/genetics ; Proteomics ; }, abstract = {Urolithin A (uroA) is a polyphenol derived from the multi-step metabolism of dietary ellagitannins by the human gut microbiota. Once absorbed, uroA can trigger mitophagy and aryl hydrocarbon receptor signaling pathways, altering host immune function, mitochondrial health, and intestinal barrier integrity. Most individuals harbor a microbiota capable of uroA production; however, the mechanisms underlying the dehydroxylation of its catechol-containing precursor (uroC) are unknown. Here, we use a combination of untargeted bacterial transcriptomics, proteomics, and comparative genomics to uncover an inducible uroC dehydroxylase (ucd) operon in Enterocloster species. We show that the ucd operon encodes a predicted molybdopterin-dependent enzyme complex that dehydroxylates urolithins at a specific position (9-OH). By interrogating publicly available metagenomics datasets, we observed that uroC-metabolizing Enterocloster species and ucd operon genes are prevalent in human feces. In ex vivo experiments with human fecal samples, only samples actively transcribing ucd could produce uroA, possibly explaining differences in urolithin metabolism between individuals. Collectively, this work identifies Enterocloster species and the ucd operon as important contributors to uroA production and establishes a multi-omics framework to further our mechanistic understanding of polyphenol metabolism by the human gut microbiota.}, }
@article {pmid39856057, year = {2025}, author = {Hu, H and Huang, Y and Yang, F and Ma, L and Zhang, J and Deng, X and Ma, N and Wang, K and Tao, Y and Lin, Q and Li, Y and Bai, X and Pan, H}, title = {Metagenome-assembled microbial genomes (n = 3,448) of the oral microbiomes of Tibetan and Duroc pigs.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {141}, pmid = {39856057}, issn = {2052-4463}, mesh = {Animals ; *Metagenome ; Swine/microbiology ; *Mouth/microbiology ; *Microbiota ; Genome, Microbial ; Metagenomics ; Tibet ; }, abstract = {Compared with leaner breeds, local Chinese pig breeds have distinct intestinal microbial, as determined by metagenomic techniques, and the interactions between oral microorganisms and their hosts are also gradually being clarified. However, the high host genome content means that few metagenome-based oral microbiomes have been reported. Here, we combined dilution-based metagenomic sequencing and binning approaches to extract the microbial genomes from the oral microbiomes of Tibetan and Duroc pigs. The host contamination rates were reduced to 13.64%, a quarter of the normal metagenomic level (65.25% on average). Medium-high-quality metagenome-assembled genomes (MAGs; n = 3,448) spanning nine phyla were retrieved and 70.79% were novel species. Of the nonredundant MAGs, only 13.37% were shared, revealing the strong disparities between Tibetan and Duroc pigs. The oral microbial diversity of the Duroc pig was greater than that of the Tibetan pig. We present the first large-scale dilute-based metagenomic data on the pig oral microbiome, which should facilitate further investigation of the functions of oral microorganisms in pigs.}, }
@article {pmid39536492, year = {2025}, author = {Chu, J and Ye, Y and Wu, YH}, title = {A glimpse of microbial potential in metal metabolism in the Clarion-Clipperton Fracture Zone in the eastern Pacific Ocean based on metagenomic analysis.}, journal = {Marine genomics}, volume = {79}, number = {}, pages = {101159}, doi = {10.1016/j.margen.2024.101159}, pmid = {39536492}, issn = {1876-7478}, mesh = {Pacific Ocean ; *Metagenome ; *Bacteria/genetics/metabolism/classification ; *Archaea/genetics/metabolism ; *Metagenomics ; Metals/metabolism ; Geologic Sediments/microbiology ; Microbiota ; }, abstract = {The polymetallic nodules distributed in the abyssal ocean floor are full of economic value, rich in manganese, iron, copper and rare-earth elements. Little is currently known about the diversity and the metabolic potential of microorganisms inhabiting the Clarion-Clipperton Fracture Zone (CCFZ) in eastern Pacific Ocean. In this study, the surface sediments (0-8 cm), which were divided into eight parts at 1 cm intervals were collected from the CCFZ. The microbial diversity and the metabolic potential of metal were examined by metagenomic sequencing and binning. The metal redox genes and metal transporter genes also showed a certain trend at different depths, the highest in the surface layer, about the same at 0-6 cm, and greater changes after >6 cm. 58 high- and medium metagenome-assembled genomes (MAGs) were recovered and assigned to 14 bacterial phyla and 1 archaeal phylum after dereplication. Alphaproteobacteria mainly carried out the oxidation of Fe/Mn and the reduction of Hg, Gammaproteobacteria mainly for the oxidation of Mn/Cu and the reduction of Cr/Hg and Methylomirabilota mainly for the oxidation of Mn and the reduction of As/Cr/Hg. Among the five Thermoproteota MAGs identified, only one had genes annotated for Mn oxidation, suggesting a limited but potentially significant role in this process at the bottom layer. By identifying the microbial diversity and the metabolic potential of metal in different depth, our study strengthens the understanding of metal metabolism in CCFZ and provides the foundation for further analyses of metal metabolism in such ecosystems.}, }
@article {pmid39853798, year = {2025}, author = {Lutz, KC and Neugent, ML and Bedi, T and De Nisco, NJ and Li, Q}, title = {A Generalized Bayesian Stochastic Block Model for Microbiome Community Detection.}, journal = {Statistics in medicine}, volume = {44}, number = {3-4}, pages = {e10291}, doi = {10.1002/sim.10291}, pmid = {39853798}, issn = {1097-0258}, support = {2113674//National Science Foundation/ ; 2210912//National Science Foundation/ ; AT-2030-20200401//Welch Foundation/ ; 1F32DK128975-01A1/NH/NIH HHS/United States ; 1R01DK131267-01/NH/NIH HHS/United States ; 1R01GM141519/NH/NIH HHS/United States ; }, mesh = {*Bayes Theorem ; Humans ; *Microbiota/genetics ; *Markov Chains ; Computer Simulation ; Female ; Monte Carlo Method ; Stochastic Processes ; Models, Statistical ; Metagenomics/methods ; High-Throughput Nucleotide Sequencing/methods ; Metagenome ; }, abstract = {Advances in next-generation sequencing technology have enabled the high-throughput profiling of metagenomes and accelerated microbiome studies. Recently, there has been a rise in quantitative studies that aim to decipher the microbiome co-occurrence network and its underlying community structure based on metagenomic sequence data. Uncovering the complex microbiome community structure is essential to understanding the role of the microbiome in disease progression and susceptibility. Taxonomic abundance data generated from metagenomic sequencing technologies are high-dimensional and compositional, suffering from uneven sampling depth, over-dispersion, and zero-inflation. These characteristics often challenge the reliability of the current methods for microbiome community detection. To study the microbiome co-occurrence network and perform community detection, we propose a generalized Bayesian stochastic block model that is tailored for microbiome data analysis where the data are transformed using the recently developed modified centered-log ratio transformation. Our model also allows us to leverage taxonomic tree information using a Markov random field prior. The model parameters are jointly inferred by using Markov chain Monte Carlo sampling techniques. Our simulation study showed that the proposed approach performs better than competing methods even when taxonomic tree information is non-informative. We applied our approach to a real urinary microbiome dataset from postmenopausal women. To the best of our knowledge, this is the first time the urinary microbiome co-occurrence network structure in postmenopausal women has been studied. In summary, this statistical methodology provides a new tool for facilitating advanced microbiome studies.}, }
@article {pmid39853685, year = {2025}, author = {Sun, Y and Gan, Z and Liu, S and Zhang, S and Zhong, W and Liu, J and Huang, X and He, W and Zhong, H and Cao, Q}, title = {Metagenomic and Transcriptomic Analysis Reveals Crosstalk Between Intratumor Mycobiome and Hosts in Early-Stage Nonsmoking Lung Adenocarcinoma Patients.}, journal = {Thoracic cancer}, volume = {16}, number = {2}, pages = {e15527}, doi = {10.1111/1759-7714.15527}, pmid = {39853685}, issn = {1759-7714}, support = {220904094208//Fifth Affiliated Hospital of Sun Yat-sen University Qingdong Cao's talent-attracting fund/ ; 3320104100430//Exploration and Practice of a Tri-Party Personalized Oncology Strategy Based on Precision Medicine in Patient-Doctor-Research Collaboration/ ; }, mesh = {Humans ; *Lung Neoplasms/microbiology/genetics/pathology ; *Adenocarcinoma of Lung/microbiology/genetics/pathology ; *Mycobiome ; Female ; *Metagenomics/methods ; Male ; Middle Aged ; Gene Expression Profiling ; Aged ; Transcriptome ; Prognosis ; Tumor Microenvironment ; Case-Control Studies ; }, abstract = {BACKGROUND: The mycobiome in the tumor microenvironment of non-smokers with early-stage lung adenocarcinoma (ES-LUAD) has been minimally investigated.
METHODS: In this study, we conducted ultra-deep metagenomic and transcriptomic sequencing on 128 samples collected from 46 nonsmoking ES-LUAD patients and 41 healthy controls (HC), aiming to characterize the tumor-resident mycobiome and its interactions with the host.
RESULTS: The results revealed that ES-LUAD patients exhibited fungal dysbiosis characterized by reduced species diversity and significant imbalances in specific fungal abundances. Concurrently, microbial functional analysis revealed significant alterations associated with genes such as ribosomal proteins and histones. We observed correlations between Yarrowia lipolytica, Saccharomyces paradoxus, and tumor-infiltrating immune cells (TIICs), and identified a strong association (|rho| > 0.7) between S. paradoxus and 14 transcription factors. A signature of three prognostic genes (GRIA1, CDO1, FHL1) closely associated with S. paradoxus was identified and they suggest that the interaction between the mycobiome and the host may contribute to prolonged overall survival (OS). Finally, a predictive model based on six fungi demonstrated decent classification performance in distinguishing ES-LUAD cases from HCs (AUC = 0.724).
CONCLUSIONS: Our study demonstrates that the interactions between the mycobiome and transcriptome within tumors may help elucidate the pathogenic mechanisms of ES-LUAD. Fungi, as a potential predictive tool, can be used as an additional resource for accurately detecting and discriminating individuals with ES-LUAD.}, }
@article {pmid39850835, year = {2025}, author = {Zhang, Q and Zhen, M and Wang, X and Zhao, F and Dong, Y and Wang, X and Gao, S and Wang, J and Shi, W and Zhang, Y}, title = {Antibiotic exposure enriches streptococci carrying resistance genes in periodontitis plaque biofilms.}, journal = {PeerJ}, volume = {13}, number = {}, pages = {e18835}, pmid = {39850835}, issn = {2167-8359}, mesh = {Humans ; *Biofilms/drug effects/growth & development ; *Periodontitis/microbiology/drug therapy ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; *Streptococcus/drug effects/genetics ; Female ; Male ; Adult ; *Dental Plaque/microbiology ; *Amoxicillin/pharmacology/therapeutic use ; RNA, Ribosomal, 16S/genetics ; Middle Aged ; Drug Resistance, Bacterial/genetics ; Microbiota/drug effects/genetics ; Tetracycline/pharmacology/therapeutic use ; Metronidazole/pharmacology/therapeutic use ; Clindamycin/pharmacology/therapeutic use ; }, abstract = {BACKGROUND: Periodontitis is not always satisfactorily treated with conventional scaling and root planing, and adjunctive use of antibiotics is required in clinical practice. Therefore, it is important for clinicians to understand the diversity and the antibiotic resistance of subgingival microbiota when exposed to different antibiotics.
MATERIALS AND METHODS: In this study, subgingival plaques were collected from 10 periodontitis patients and 11 periodontally healthy volunteers, and their microbiota response to selective pressure of four antibiotics (amoxicillin, metronidazole, clindamycin, and tetracycline) were evaluated through 16S rRNA gene amplicon and metagenomic sequencing analysis. Additionally, sensitive and resistant strains were isolated and cultured in vitro for resistance evaluation.
RESULTS: Cultivation of subgingival microbiota revealed the oral microbiota from periodontitis patients were more resistant to antibiotics than that of healthy. Significant differences were also observed for the microbial community between with and without antibiotics (especially amoxicillin and tetracycline) treated in periodontitis group.
CONCLUSION: Overall, after the two antibiotics (amoxicillin and tetracycline) exposed, the oral subgingival microbiota in periodontitis patients exhibited different diversity and composition. Streptococcus may account for oral biofilm-specific antibiotic resistance in periodontitis. This provides information for personalized treatment of periodontitis.}, }
@article {pmid39849759, year = {2025}, author = {Peng, Q and Huang, J and Li, S and Chen, Z and Zhu, Q and Yuan, H and Li, J and Massou, BB and Xie, G}, title = {Dynamics of microbial communities and metabolites during the fermentation of Ningxia goji berry wine: An integrated metagenomics and metabolomics approach.}, journal = {Food research international (Ottawa, Ont.)}, volume = {201}, number = {}, pages = {115609}, doi = {10.1016/j.foodres.2024.115609}, pmid = {39849759}, issn = {1873-7145}, mesh = {*Fermentation ; *Wine/analysis/microbiology ; *Metabolomics ; *Metagenomics ; *Microbiota ; Volatile Organic Compounds/analysis/metabolism ; Bacteria/metabolism/genetics/classification ; Fruit ; Taste ; Food Microbiology ; }, abstract = {Ningxia Goji Berry Wine (NGBW), a traditional Chinese fermented beverage, exhibits complex flavor quality changes during fermentation, the mechanisms of which remain insufficiently elucidated. This study aimed to elucidate the dynamic shifts in physicochemical properties, metabolites, and microbial communities throughout the controlled fermentation process of NGBW. Metabolomic analysis identified 8 key differential volatile metabolites (VOCs) and 406 differential non-volatile metabolites. The enrichment analysis of KEGG metabolic pathways revealed that, during the fermentation of NGBW, ten critical metabolic pathways-Purine metabolism, Glycine, Serine, and Threonine metabolism, Galactose metabolism, and the Citric Acid (TCA) Cycle-play essential roles. Amplicon sequencing indicated that 25 bacterial genera dominated the microbial ecosystem (relative abundance ≥ 0.1 %). Spearman correlation analysis revealed significant associations between 5 core microorganism and flavor compounds, and 25 core microbes with non-volatile metabolites, suggesting their pivotal roles in flavor formation. This study provides a theoretical basis for optimizing the fermentation process and enhancing the flavor quality of NGBW.}, }
@article {pmid39849445, year = {2025}, author = {Xie, H and Chen, Z and Wu, G and Wei, P and Gong, T and Chen, S and Xu, Z}, title = {Application of metagenomic next-generation sequencing (mNGS) to describe the microbial characteristics of diabetic foot ulcers at a tertiary medical center in South China.}, journal = {BMC endocrine disorders}, volume = {25}, number = {1}, pages = {18}, pmid = {39849445}, issn = {1472-6823}, support = {[2021]76//the High-level Hospital and Clinical Specialty Discipline Construction Programme for Fujian Medical Development, China/ ; 2023J01692//Fujian Provincial Natural Science Foundation of China/ ; 2022J01243//Fujian Provincial Natural Science Foundation of China/ ; 2020Y9094//the Joint Funds for the innovation of science and Technology,Fujian province, China/ ; 2023Y9213//the Joint Funds for the innovation of science and Technology,Fujian province, China/ ; 2021Y9068//the Joint Funds for the innovation of science and Technology,Fujian province, China/ ; 82002034//National Natural Science Foundation of China/ ; }, mesh = {Humans ; *Diabetic Foot/microbiology/diagnosis ; China/epidemiology ; *High-Throughput Nucleotide Sequencing/methods ; *Tertiary Care Centers ; Male ; Female ; *Metagenomics/methods ; Middle Aged ; Aged ; Microbiota/genetics ; Adult ; }, abstract = {BACKGROUND: Diabetic foot ulcers (DFUs) are characterized by dynamic wound microbiome, the timely and accurate identification of pathogens in the clinic is required to initiate precise and individualized treatment. Metagenomic next-generation sequencing (mNGS) has been a useful supplement to routine culture method for the etiological diagnosis of DFUs. In this study, we utilized a routine culture method and mNGS to analyze the same DFU wound samples and the results were compared.
METHODS: Forty samples from patients with DFUs at a tertiary medical center in South China were collected, the microorganisms were identified with mNGS and routine culture method simultaneously.
RESULTS: The results showed that the positive detection rate of microorganisms in DFUs with mNGS was much higher (95% vs. 60%). Thirteen strains of microorganisms were detected with routine culture method, and seventy-seven strains were detected with mNGS. Staphylococcus aureus was the most common microorganism detected with culture method, while Enterococcus faecalis was the most common microorganism detected with mNGS. The false negative rate of the culture method was 35%, that was, 14 samples with negative results with culture method were found to be positive with mNGS.
CONCLUSION: The mNGS method had a higher positive detection rate and identified a broader spectrum of microorganisms in DFUs, thus, mNGS provided a more comprehensive understanding of the microbiome of DFUs to facilitate the development of timely and optimal treatment.
TRIAL REGISTRATION: The study was conducted in accordance with the Declaration of Helsinki and approved by the Ethical Review Committee of the Fujian Medical University Union Hospital (approval number 2021KY054).}, }
@article {pmid39693966, year = {2025}, author = {Li, T and Wang, P and Zhi, Z and Guo, T and Zhou, J and Zhang, H and Cao, C and Cai, Y and Li, Y and Zhang, J}, title = {Free-caged rearing modes regulate chicken intestinal metabolism by influencing gut microbial homeostasis.}, journal = {Poultry science}, volume = {104}, number = {1}, pages = {104381}, pmid = {39693966}, issn = {1525-3171}, mesh = {Animals ; *Chickens ; *Gastrointestinal Microbiome/physiology ; *Homeostasis ; *Animal Husbandry/methods ; Cecum/microbiology/metabolism ; Housing, Animal ; Bacteria/classification/metabolism/genetics ; Male ; }, abstract = {Free-caged rearing modes, which prioritize animal welfare, are believed to enhance the quality of animal products. The impact of rearing modes on meat quality may play a key role in the superior quality of local chicken breeds. This study analyzed the cecal contents of free-range and caged black-bone chickens at different ages using metagenomic and metabolomic sequencing. We identified 32 metabolites and 367 microbial species significantly affected by the rearing mode. Linear discriminant analysis Effect Size (LefSe) highlighted five key microorganisms, Gemmiger formicilis, Bacteria unclassified, Bacteroides sp. ET225, Massilistercora timonensis, and Bacteroidales unclassified, that showed distinct abundance patterns across all age points. Among them, Bacteroides sp. ET225 and Massilistercora timonensis were positively associated with certain phospholipids and plant-derived metabolites, while negatively correlated with others like demissidine and acylcarnitine. Functional analysis revealed that rearing modes impact gut metabolites involved in gut metabolism as well as broader processes such as signal transduction, protein digestion, and autophagy. This study offers new insights into how rearing modes influence gut microbiota and metabolites, shedding light on the study of rearing mode-mediated muscle development and fat deposition.}, }
@article {pmid39849165, year = {2025}, author = {Sandhu, S and Kumar, S and Singh, P and Singh, BP and Jurel, SK and Lal, N and Mohit, and Sharma, V and Rai, N and Chand, P}, title = {Metagenomic profiling of plaque microbiota in Indian subjects: identified hidden ecological tapestry.}, journal = {Current genetics}, volume = {71}, number = {1}, pages = {3}, pmid = {39849165}, issn = {1432-0983}, mesh = {Humans ; *Dental Plaque/microbiology ; *Metagenomics/methods ; Male ; *Microbiota/genetics ; Female ; India/epidemiology ; Adult ; *Metagenome ; *RNA, Ribosomal, 16S/genetics ; Middle Aged ; Young Adult ; Adolescent ; Bacteria/genetics/classification/isolation & purification ; Streptococcus/genetics/isolation & purification/classification ; }, abstract = {Dental plaque biofilms are the primary etiologic factor for various chronic oral infectious diseases. In recent years, dental plaque shows enormous potential to know about an individual microbiota. Various microbiome studies of oral cavity from different geographical locations reveals abundance of microbial species. Although, the representation of Indian population in this respect is limited, which make us curious to undergo this study. This study investigates the dental plaque microbiota of North Indian individuals based on their age, gender, and dietary patterns; specifically, food preference and availability of water source using 16 S rRNA metagenomics analysis. The findings from this study revealed that Streptococcus levels are high across genders, age groups, and water source, highlighting its role as a predominant dental caries associated species like Streptococcus mutans, Streptococcus pyogenes, Streptococcus sobrinus and Streptococcus oralis in the studied population groups. Additionally, the abundance of Actinomyces is observed higher in young individuals and females whereas Fusobacterium and Leptotrichia were high in elderly individuals. Moreover, non-vegetarians have higher abundance of Streptococcus and Fusobacterium, whereas vegetarians show higher abundance of Prevotella and Leptotrichia. The study also highlights the influence of water type on bacterial composition of dental plaque in the studied population i.e., individuals consuming underground water has high abundance of Streptococcus, whereas individuals consuming RO water exhibit elevated Prevotella and Leptotrichia. Insights emerged from the analysis illuminates the complex dynamics of microbiota in dental plaque among North Indians. This study also highlight that this variation of microbiome is influenced by age, gender, and dietary habits (vegetarian or non-vegetarian lifestyle). These results will fill a significant knowledge gap regarding the Indian dental plaque microbiome but also offer a foundation to conduct metagenome studies and potential therapeutic implications for future personalized oral health interventions.}, }
@article {pmid39844180, year = {2025}, author = {Chen, J and Pan, Q and Lu, L and Huang, X and Wang, S and Liu, X and Lun, J and Xu, X and Su, H and Guo, F and Yang, L and You, L and Xiao, H and Luo, W and Liu, HF and Pan, Q}, title = {Atg5 deficiency in basophils improves metabolism in lupus mice by regulating gut microbiota dysbiosis.}, journal = {Cell communication and signaling : CCS}, volume = {23}, number = {1}, pages = {40}, pmid = {39844180}, issn = {1478-811X}, support = {No. 82070757, 82270770//National Natural Science Foundation of China/ ; No. 82070757, 82270770//National Natural Science Foundation of China/ ; 2022B1212030003//Guangdong Provincial Key Laboratory of Autophagy and Major Chronic Noncommunicable Diseases/ ; 2022B1212030003//Guangdong Provincial Key Laboratory of Autophagy and Major Chronic Noncommunicable Diseases/ ; 2022B1212030003//Guangdong Provincial Key Laboratory of Autophagy and Major Chronic Noncommunicable Diseases/ ; 2021A05067//Science and Technology Planning Project of Zhanjiang City/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; *Lupus Erythematosus, Systemic/metabolism ; *Basophils/metabolism ; *Dysbiosis ; Mice ; *Autophagy-Related Protein 5/genetics/metabolism ; Mice, Inbred MRL lpr ; Mice, Knockout ; Female ; Autophagy ; Mice, Inbred C57BL ; }, abstract = {Autophagic activation in immune cells, gut microbiota dysbiosis, and metabolic abnormalities have been reported separately as characteristics of systemic lupus erythematosus (SLE). Elucidating the crosstalk among the immune system, commensal microbiota, and metabolites is crucial to understanding the pathogenesis of autoimmune diseases. Emerging evidence shows that basophil activation plays a critical role in the pathogenesis of SLE; however, the underlying mechanisms remain largely unknown. Here, we investigated the effects of autophagic inhibition on the pathogenesis of basophils in SLE using Autophagy-related gene 5 (Atg5) knockout (Atg5[-/-]) as an autophagic inhibitor. Specifically, we knocked out basophilic Atg5 in vivo to investigate its impact on lupus metabolism. Furthermore, Atg5[-/-] basophils were transferred to basophil-depleted MRL/MpJ-Fas[lpr] (MRL/lpr) mice to study their effect on disease metabolism. Metagenomic and targeted metabolomic sequencing results indicated considerable reduction in the levels of plasma autoantibodies and inflammatory cytokines in the Atg5[-/-] basophil transfer group compared with that in the control group. Transplanting Atg5[-/-] basophils improved the gut microbiota balance in MRL/lpr mice, increasing the abundance of beneficial bacteria, such as Ligilactobacillus murinus and Faecalitalea rodentium, and reducing that of potentially pathogenic bacteria such as Phocaeicola salanitronis. The transplantation of Atg5-deficient basophils improved lupus symptoms by modulating lipid and amino acid metabolism. This improvement was linked to changes in the gut microbiota, particularly an increase in Ligilactobacillus murinus and Faecalitalea rodentium populations. These microbial shifts are believed to promote the production of beneficial metabolites, such as γ-linolenic acid and oleoyl-1-palmitoyl-sn-glycero-3-phosphocholine, while reducing the levels of harmful metabolites such as arginine. These alterations in the metabolic profile contribute to the alleviation of lupus symptoms. Collectively, these findings reveal a novel role of basophil autophagy in SLE, highlighting its potential as a therapeutic target.}, }
@article {pmid39843539, year = {2025}, author = {Laczkó, L and Nagy, NA and Nagy, Á and Maroda, Á and Sály, P}, title = {An updated reference genome of Barbatula barbatula (Linnaeus, 1758).}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {137}, pmid = {39843539}, issn = {2052-4463}, support = {OTKA PD142602//Nemzeti Kutatási, Fejlesztési és Innovációs Hivatal (NKFI Office)/ ; }, mesh = {Animals ; *Genome ; *Microsatellite Repeats ; Cypriniformes/genetics ; }, abstract = {The stone loach Barbatula barbatula is a benthic fish species widely distributed throughout Europe, primarily inhabiting stony upper sections of stream networks. This study presents an updated genome assembly of B. barbatula, contributing to the species' available genomic resources for downstream applications such as conservation genetics. The draft assembly was 550 Mbp in size, with an N50 of 11.21 Mbp. We used the species' available chromosome scaffolds to finish the genome. The final assembly had a BUSCO score of 96.7%. We identified 23270 protein-coding genes, and the proteome exhibited high completeness with BUSCO (93.1%) and OMArk (90.81%). Despite using multiple approaches to reduce duplicate contigs, we observed a relatively high duplicate ratio of 6.1% (BUSCO) and 8.52% (OMArk) in the annotations. We aimed to find microsatellite loci present in both the species' publicly available genome and the new assembly to aid marker development for downstream analyses. This dataset serves as a reference for genomic analysis and is useful for developing markers to study the species' biodiversity and support conservation efforts.}, }
@article {pmid39843522, year = {2025}, author = {Bray, AS and Broberg, CA and Hudson, AW and Wu, W and Nagpal, RK and Islam, M and Valencia-Bacca, JD and Shahid, F and Hernandez, GE and Nutter, NA and Walker, KA and Bennett, EF and Young, TM and Barnes, AJ and Ornelles, DA and Miller, VL and Zafar, MA}, title = {Klebsiella pneumoniae employs a type VI secretion system to overcome microbiota-mediated colonization resistance.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {940}, pmid = {39843522}, issn = {2041-1723}, support = {AI178595//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; AI166642//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; AI173244//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; }, mesh = {*Klebsiella pneumoniae/genetics/metabolism ; *Type VI Secretion Systems/genetics/metabolism ; Animals ; *Gastrointestinal Microbiome/genetics ; Mice ; *Klebsiella Infections/microbiology ; Gene Expression Regulation, Bacterial ; Gastrointestinal Tract/microbiology ; Bacterial Proteins/metabolism/genetics ; DNA Transposable Elements/genetics ; Female ; Mice, Inbred C57BL ; }, abstract = {Microbial species must compete for space and nutrients to persist in the gastrointestinal (GI) tract, and our understanding of the complex pathobiont-microbiota interactions is far from complete. Klebsiella pneumoniae, a problematic, often drug-resistant nosocomial pathogen, can colonize the GI tract asymptomatically, serving as an infection reservoir. To provide insight on how K. pneumoniae interacts with the resident gut microbiome, we conduct a transposon mutagenesis screen using a murine model of GI colonization with an intact microbiota. Among the genes identified were those encoding a type VI secretion system (T6SS), which mediates contact-dependent killing of gram-negative bacteria. From several approaches, we demonstrate that the T6SS is critical for K. pneumoniae gut colonization. Metagenomics and in vitro killing assays reveal that K. pneumoniae reduces Betaproteobacteria species in a T6SS-dependent manner, thus identifying specific species targeted by K. pneumoniae. We further show that T6SS gene expression is controlled by several transcriptional regulators and that expression only occurs in vitro under conditions that mimic the gut environment. By enabling K. pneumoniae to thrive in the gut, the T6SS indirectly contributes to the pathogenic potential of this organism. These observations advance our molecular understanding of how K. pneumoniae successfully colonizes the GI tract.}, }
@article {pmid39843444, year = {2025}, author = {Bechtold, EK and Ellenbogen, JB and Villa, JA and de Melo Ferreira, DK and Oliverio, AM and Kostka, JE and Rich, VI and Varner, RK and Bansal, S and Ward, EJ and Bohrer, G and Borton, MA and Wrighton, KC and Wilkins, MJ}, title = {Metabolic interactions underpinning high methane fluxes across terrestrial freshwater wetlands.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {944}, pmid = {39843444}, issn = {2041-1723}, support = {EAR-2029686//National Science Foundation (NSF)/ ; PRFB-2109592//National Science Foundation (NSF)/ ; DEB-1754756//National Science Foundation (NSF)/ ; DE-SC0023084//U.S. Department of Energy (DOE)/ ; DE-SC0021067//U.S. Department of Energy (DOE)/ ; DE-SC000054//U.S. Department of Energy (DOE)/ ; DE-SC0007144//U.S. Department of Energy (DOE)/ ; DE-SC0012088//U.S. Department of Energy (DOE)/ ; DESC0023297//U.S. Department of Energy (DOE)/ ; DE-SC0023456//U.S. Department of Energy (DOE)/ ; DE-SC0023456//U.S. Department of Energy (DOE)/ ; DE-SC0023084//U.S. Department of Energy (DOE)/ ; DE-SC0023084//U.S. Department of Energy (DOE)/ ; DE-SC000054//U.S. Department of Energy (DOE)/ ; DE-SC0021067//U.S. Department of Energy (DOE)/ ; DE-SC0023084//U.S. Department of Energy (DOE)/ ; DE-SC000054//U.S. Department of Energy (DOE)/ ; DE-SC0021067//U.S. Department of Energy (DOE)/ ; DE-SC0022191//U.S. Department of Energy (DOE)/ ; DE-SC0023084//U.S. Department of Energy (DOE)/ ; DE-SC0021350//U.S. Department of Energy (DOE)/ ; DE-SC0023084//U.S. Department of Energy (DOE)/ ; DE-SC0021350//U.S. Department of Energy (DOE)/ ; DESC000054//U.S. Department of Energy (DOE)/ ; DE-SC0021067//U.S. Department of Energy (DOE)/ ; }, mesh = {*Methane/metabolism ; *Wetlands ; *RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; *Fresh Water/microbiology ; Metagenome ; Bacteria/metabolism/genetics/classification ; Climate Change ; }, abstract = {Current estimates of wetland contributions to the global methane budget carry high uncertainty, particularly in accurately predicting emissions from high methane-emitting wetlands. Microorganisms drive methane cycling, but little is known about their conservation across wetlands. To address this, we integrate 16S rRNA amplicon datasets, metagenomes, metatranscriptomes, and annual methane flux data across 9 wetlands, creating the Multi-Omics for Understanding Climate Change (MUCC) v2.0.0 database. This resource is used to link microbiome composition to function and methane emissions, focusing on methane-cycling microbes and the networks driving carbon decomposition. We identify eight methane-cycling genera shared across wetlands and show wetland-specific metabolic interactions in marshes, revealing low connections between methanogens and methanotrophs in high-emitting wetlands. Methanoregula emerged as a hub methanogen across networks and is a strong predictor of methane flux. In these wetlands it also displays the functional potential for methylotrophic methanogenesis, highlighting the importance of this pathway in these ecosystems. Collectively, our findings illuminate trends between microbial decomposition networks and methane flux while providing an extensive publicly available database to advance future wetland research.}, }
@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 = {6}, number = {1}, pages = {101919}, doi = {10.1016/j.xcrm.2024.101919}, pmid = {39809266}, issn = {2666-3791}, mesh = {*Gastrointestinal Microbiome/genetics ; *Autism Spectrum Disorder/metabolism/microbiology/genetics ; *gamma-Aminobutyric Acid/metabolism ; Humans ; Animals ; Female ; Male ; Mice ; Child ; Child, Preschool ; Metabolomics/methods ; RNA, Ribosomal, 16S/genetics ; Escherichia/metabolism/genetics ; Feces/microbiology ; Glutamic Acid/metabolism ; Mice, Inbred C57BL ; Escherichia coli/genetics/metabolism ; Metabolome ; }, 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 {pmid39739308, year = {2024}, author = {Chaabane, F and Pillonel, T and Bertelli, C}, title = {MeSS and assembly_finder: a toolkit for in silico metagenomic sample generation.}, journal = {Bioinformatics (Oxford, England)}, volume = {41}, number = {1}, pages = {}, doi = {10.1093/bioinformatics/btae760}, pmid = {39739308}, issn = {1367-4811}, mesh = {*Metagenomics/methods ; *Software ; Microbiota/genetics ; Computational Biology/methods ; Humans ; Computer Simulation ; Metagenome ; Sequence Analysis, DNA/methods ; }, abstract = {SUMMARY: The intrinsic complexity of the microbiota combined with technical variability render shotgun metagenomics challenging to analyze for routine clinical or research applications. In silico data generation offers a controlled environment allowing for example to benchmark bioinformatics tools, to optimize study design, statistical power, or to validate targeted applications. Here, we propose assembly_finder and the Metagenomic Sequence Simulator (MeSS), two easy-to-use Bioconda packages, as part of a benchmarking toolkit to download genomes and simulate shotgun metagenomics samples, respectively. Outperforming existing tools in speed while requiring less memory, MeSS reproducibly generates accurate complex communities based on a list of taxonomic ranks and their abundance.
All code is released under MIT License and is available on https://github.com/metagenlab/MeSS and https://github.com/metagenlab/assembly_finder.}, }
@article {pmid39523638, year = {2024}, author = {Munjita, SM and Mubemba, B and Tembo, J and Bates, M and Munsaka, S}, title = {Rhipicephalus simus ticks: new hosts for phleboviruses.}, journal = {Parasitology}, volume = {151}, number = {9}, pages = {962-970}, doi = {10.1017/S0031182024001033}, pmid = {39523638}, issn = {1469-8161}, support = {RIA2016E-1609//European and Developing Countries Clinical Trials Partnership/ ; }, mesh = {*Rhipicephalus/microbiology/virology ; *Phlebovirus/classification/genetics ; Metagenome/genetics ; Genome, Viral/genetics ; Zambia ; Phylogeny ; Biodiversity ; Animals ; Disease Vectors ; }, abstract = {Ticks are widespread arthropods that transmit microorganisms of veterinary and medical significance to vertebrates, including humans. Rhipicephalus simus, an ixodid tick frequently infesting and feeding on humans, may play a crucial role in transmitting infectious agents across species. Despite the known association of many Rhipicephalus ticks with phleboviruses, information on R. simus is lacking. During a study in a riverine area in Lusaka Zambia, ten R. simus ticks were incidentally collected from the grass and bushes and subjected to metagenomic next generation sequencing (mNGS) in 2 pools of 5. Analysis detected a diverse microbial profile, including bacteria 82% (32/39), fungi 15.4% (6/39), and viruses 2.6% (1/39). Notably, viral sequence LSK-ZM-102022 exhibited similarity to tick phleboviruses, sharing 74.92% nucleotide identity in the RdRp gene and 72% in the NP gene with tick-borne phlebovirus (TBPV) from Greece and Romania, respectively. Its RNA-dependent RNA polymerase (RdRp) encoding region carried conserved RdRp and endonuclease domains characteristic of phenuiviridae viruses. Phylogenetic analysis positioned LSK-ZM-102022 in a distinct but lone lineage within tick phleboviruses basal to known species like brown dog tick phlebovirus and phlebovirus Antigone. Pair-wise genetic distance analysis revealed similar findings. This study emphasizes the urgency of further research on the ecology, transmission dynamics, and pathogenic potential of LSK-ZM-102022 and related TBPVs, crucial for local and global preparedness against emerging tick-borne diseases.}, }
@article {pmid38709227, year = {2025}, author = {Unzueta-Medina, JA and González-Chávez, SA and Salas-Leiva, JS and Silva-Sánchez, SE and Pacheco-Tena, C}, title = {Differential Composition and Structure of the Microbiota from Active and Inactive Stages of HLA-B27-associated Uveitis by Paired Fecal Metagenomes.}, journal = {Ocular immunology and inflammation}, volume = {33}, number = {1}, pages = {56-64}, doi = {10.1080/09273948.2024.2346818}, pmid = {38709227}, issn = {1744-5078}, mesh = {Humans ; *HLA-B27 Antigen/genetics/immunology ; Male ; *Feces/microbiology ; Prospective Studies ; Adult ; Female ; *RNA, Ribosomal, 16S/genetics ; Middle Aged ; *Uveitis, Anterior/microbiology/immunology ; Metagenome ; Bacteria/genetics/isolation & purification ; DNA, Bacterial/genetics ; Microbiota ; Acute Disease ; }, abstract = {PURPOSE: To compare the diversities and abundances of bacterial taxa in the microbiome of patients with HLA B27-positive acute anterior uveitis (AAU) in the active and inactive phases.
METHODS: An observational descriptive prospective and comparative study was conducted in ten HLA-B27-positive AAU patients (44.6 ± 13.4 years). The microbiome of the stool samples obtained in the active and inactive stages was analyzed by sequencing the V3 region of the 16S rRNA gene.
RESULTS: The differences in the bacteria profile between active and inactive stages in each individual were confirmed (p < 0.0001). Ten OTUs were found exclusively in the active phase of 90% of the individuals, suggesting a proinflammatory association. Blautia OUT_4 and Faecalibacterium OUT_2 abundances showed a direct relationship between abundance and severity of ocular inflammation. Two OTUs were exclusive of the inactive stage, suggesting an anti-inflammatory role.
CONCLUSION: The metagenomic profile of the fecal microbiota differs in the acute phase of the AAU compared to when the inflammation subsides, despite being the same individual and a short time-lapse. AAU is a fertile field for studying the connection between subtle rapid changes in microbiota and their systemic consequences.}, }
@article {pmid39841201, year = {2025}, author = {Geng, P and Zhao, N and Zhou, Y and Harris, RS and Ge, Y}, title = {Faecalibacterium prausnitzii regulates carbohydrate metabolic functions of the gut microbiome in C57BL/6 mice.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2455503}, doi = {10.1080/19490976.2025.2455503}, pmid = {39841201}, issn = {1949-0984}, mesh = {Animals ; *Gastrointestinal Microbiome ; *Mice, Inbred C57BL ; Mice ; *Carbohydrate Metabolism ; *Faecalibacterium prausnitzii/metabolism/genetics ; *Phylogeny ; *Feces/microbiology ; RNA, Ribosomal, 16S/genetics ; Probiotics/administration & dosage ; Male ; Metagenome ; }, abstract = {The probiotic impact of microbes on host metabolism and health depends on both host genetics and bacterial genomic variation. Faecalibacterium prausnitzii is the predominant human gut commensal emerging as a next-generation probiotic. Although this bacterium exhibits substantial intraspecies diversity, it is unclear whether genetically distinct F. prausnitzii strains might lead to functional differences in the gut microbiome. Here, we isolated and characterized a novel F. prausnitzii strain (UT1) that belongs to the most prevalent but underappreciated phylogenetic clade in the global human population. Genome analysis showed that this butyrate-producing isolate carries multiple putative mobile genetic elements, a clade-specific defense system, and a range of carbohydrate catabolic enzymes. Multiomic approaches were used to profile the impact of UT1 on the gut microbiome and associated metabolic activity of C57BL/6 mice at homeostasis. Both 16S rRNA and metagenomic sequencing demonstrated that oral administration of UT1 resulted in profound microbial compositional changes including a significant enrichment of Lactobacillus, Bifidobacterium, and Turicibacter. Functional profiling of the fecal metagenomes revealed a markedly higher abundance of carbohydrate-active enzymes (CAZymes) in UT1-gavaged mice. Accordingly, UT1-conditioned microbiota possessed the elevated capability of utilizing starch in vitro and exhibited a lower availability of microbiota-accessible carbohydrates in the gut. Further analysis uncovered a functional network wherein UT1 reduced the abundance of mucin-degrading CAZymes and microbes, which correlated with a concomitant reduction of fecal mucin glycans. Collectively, our results reveal a crucial role of UT1 in facilitating the carbohydrate metabolism of the gut microbiome and expand our understanding of the genetic and phenotypic diversity of F. prausnitzii.}, }
@article {pmid39838431, year = {2025}, author = {Sun, Q and Li, BR and Li, DH and Wang, XY and Wang, QY and Jiang, ZM and Ning, SB and Sun, T}, title = {WKB ameliorates DSS-induced colitis through inhibiting enteric glial cells activation and altering the intestinal microbiota.}, journal = {Journal of translational medicine}, volume = {23}, number = {1}, pages = {93}, pmid = {39838431}, issn = {1479-5876}, support = {No. 22YXQN034//Air Force Medical Center Youth Talent Program Project/ ; No. 2020-4-5123//Capital's Funds for Health Improvement and Research/ ; }, mesh = {Animals ; *Dextran Sulfate ; *Gastrointestinal Microbiome ; *Colitis/pathology/microbiology/chemically induced/complications ; *Mice, Inbred C57BL ; Male ; *Neuroglia/metabolism/pathology ; Cytokines/metabolism ; Colon/pathology/microbiology ; Permeability ; Body Weight ; Inflammation/pathology ; Intestinal Mucosa/pathology/microbiology/metabolism ; Mice ; }, abstract = {BACKGROUND: Inflammatory bowel disease (IBD) is a chronic condition influenced by diet, which affects gut microbiota and immune functions. The rising prevalence of IBD, linked to Western diets in developing countries, highlights the need for dietary interventions. This study aimed to assess the impact of white kidney beans (WKB) on gut inflammation and microbiota changes, focusing on their effects on enteric glial cells (EGCs) and immune activity in colitis.
METHODS: Male C57BL/6 mice were divided into four groups: normal diet (ND), ND with 2.5% dextran sulfate sodium (DSS) for colitis induction, ND with 20% WKB, and WKB with 2.5% DSS. The dietary intervention lasted 17 weeks, with DSS given in the final week. Colonic inflammation was assessed by body weight, disease activity index, and histopathology. Epithelial barrier integrity was evaluated using immunofluorescence, transmission electron microscopy, and permeability assays. EGCs activity was analyzed via immunofluorescence and quantitative real-time PCR. Immune responses were measured using flow cytometry and cytokine profiling, while gut microbiota changes were examined through metagenomic sequencing.
RESULTS: WKB supplementation significantly alleviated DSS-induced colitis in mice, evidenced by reduced weight loss, disease activity, and improved colonic histology. This effect was linked to enhanced mucosal barrier integrity, seen through increased tight junction protein and Muc2 expression, accompanied by favorable ultrastructural changes. WKB modulated EGCs activity via TNF-like cytokine 1 A inhibition, resulting in reduced glial fibrillary acidic protein expression. Immunologically, it downregulated Th1 and Th17 pro-inflammatory cells, increased Treg cells, and altered cytokine profiles (reduced TNF-α, IFN-γ, IL-17; increased IL-10). Metagenomic analysis showed that WKB restored gut microbiota balance, particularly enhancing beneficial bacteria like Akkermansia. KEGG pathway analysis further indicated that WKB supplementation improved key metabolic pathways, notably those related to phenylalanine, tyrosine, and tryptophan biosynthesis, thereby countering DSS-induced metabolic disruptions.
CONCLUSIONS: WKB shows promise for treating IBD by enhancing mucosal barriers, inhibiting EGCs activity, balancing Th1/Th17/Treg cells, and restoring gut microbiota and metabolic homeostasis, thereby alleviating colitis symptoms.}, }
@article {pmid39838419, year = {2025}, author = {Liu, X and Ding, H and Zhang, X and Ta, N and Zhao, J and Zhang, Q and Liu, H and Sun, M and Zhang, X}, title = {Dynamic changes in the gastrointestinal microbial communities of Gangba sheep and analysis of their functions in plant biomass degradation at high altitude.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {17}, pmid = {39838419}, issn = {2049-2618}, mesh = {Animals ; Sheep/microbiology ; *Gastrointestinal Microbiome ; *Bacteria/classification/genetics/isolation & purification/metabolism ; *Altitude ; *Biomass ; Metagenome ; Animal Feed/microbiology ; Archaea/genetics/classification ; Gastrointestinal Tract/microbiology ; Plants/microbiology ; }, abstract = {BACKGROUND: While Gangba sheep being well known for their unique flavour and nutritional value, harsh environmental factors negatively affect their growth and development, leading to poor productivity. The gastrointestinal tract microbiota plays an important role in host nutrient absorption and metabolism. The identification of dynamic changes in the gastrointestinal microbial communities and their functions is an important step towards improving animal production performance and health.
RESULTS: A comprehensive multi-omics survey of the microbial communities of the Gangba sheep gastrointestinal tract was performed under three distinct feeding strategies: natural grazing, semi-grazing with supplementation, and barn feeding. The dynamic changes, cross-kingdom partnerships and functional potential profiles were analysed and the results revealed that the feeding strategies had a greater impact on the microbial communities than the site of the gastrointestinal tract. The different microbial associations among the groups were revealed by co-occurrence networks based on the amplicon sequence variants (ASVs). Moreover, a Gangba sheep gastrointestinal microbial genomic catalogue was constructed for the first time, including 1146 metagenome-assembled genomes (MAGs) with completeness > 50% and contamination < 10%, among which, 504 bacterial and 15 archaeal MAGs were of high quality with completeness > 80% and contamination < 10%. About 40% of the high-quality MAGs displaying enzyme activity were related to the microbial species that contribute to plant biomass degradation. Most of these enzymes were expressed in rumen metatranscriptome datasets, especially in Prevotella spp. and Ruminococcus spp., suggesting that gastrointestinal microbial communities in ruminants play major roles in the digestion of plant biomass to provide nutrition and energy for the host.
CONCLUSIONS: These findings suggest that feeding strategies are the primary cause of changes in the gastrointestinal microbiome. Diversification of livestock feed might be an effective strategy to maintain the diversity and ecological multifunctionality of microbial communities in the gastrointestinal tract. Additionally, the catalogue of microbial genomes and the encoded biomass-degrading enzymes identified here provide insights into the potential microbial functions of the gastrointestinal tract of Gangba sheep at high altitudes. This paves the way for microbial interventions to improve the growth performance, productivity and product quality of ruminant livestock. Video Abstract.}, }
@article {pmid39838369, year = {2025}, author = {Fan, J and Zeng, F and Zhong, H and Cai, J and Shen, W and Cheng, C and He, C and Liu, Y and Zhou, Y and Chen, S and Zhu, Y and Liu, T and Zheng, JS and Wang, L and Chen, YM and Ma, W and Zhou, D}, title = {Potential roles of cigarette smoking on gut microbiota profile among Chinese men.}, journal = {BMC medicine}, volume = {23}, number = {1}, pages = {25}, pmid = {39838369}, issn = {1741-7015}, mesh = {Humans ; Male ; *Gastrointestinal Microbiome ; *Cigarette Smoking/adverse effects ; Middle Aged ; Adult ; China ; RNA, Ribosomal, 16S/genetics ; Asian People ; Actinomyces ; Aged ; East Asian People ; }, abstract = {BACKGROUND: Cigarette smoking is posited as a potential factor in disrupting the balance of the human gut microbiota. However, existing studies with limited sample size have yielded inconclusive results.
METHODS: Here, we assessed the association between cigarette smoking and gut microbial profile among Chinese males from four independent studies (N total = 3308). Both 16S rRNA and shotgun metagenomic sequencing methods were employed, covering 206 genera and 237 species. Microbial diversity and abundance were compared among non-smokers, current smokers, and former smokers.
RESULTS: Actinomyces[g], Atopobium[g], Haemophilus[g], Turicibacter[g], and Lachnospira[g] were found to be associated with smoking status (current smokers vs. non-smokers). Metagenomic data provided a higher resolution at the species level, particularly for the Actinomyces[g] branch. Additionally, serum γ-glutamylcysteine (γ-Glu-Cys) was found to have a potential role in connecting smoking and Actinomyces[g]. Furthermore, we revealed putative mediation roles of the gut microbiome in the associations between smoking and common diseases including cholecystitis and type 2 diabetes.
CONCLUSIONS: We characterized the gut microbiota profile in male smokers and further revealed their potential involvement in mediating the impact of smoking on health outcomes. These findings advance our understanding of the intricate association between cigarette smoking and the gut microbiome.}, }
@article {pmid39838275, year = {2025}, author = {Nabisubi, P and Kanyerezi, S and Kebirungi, G and Sserwadda, I and Nsubuga, M and Kisitu, G and Nahirya, PN and Mulindwa, B and Akabwai, GP and Nantongo, S and Kekitiinwa, A and Kigozi, E and Luutu, NM and Katabazi, FA and Kalema, L and Katabalwa, A and Jjingo, D and Mboowa, G}, title = {Beyond the fever: shotgun metagenomic sequencing of stool unveils pathogenic players in HIV-infected children with non-malarial febrile illness.}, journal = {BMC infectious diseases}, volume = {25}, number = {1}, pages = {96}, pmid = {39838275}, issn = {1471-2334}, support = {TMA2020CDF-3159//European and Developing Countries Clinical Trials Partnership/ ; TMA2020CDF-3159//European and Developing Countries Clinical Trials Partnership/ ; TMA2020CDF-3159//European and Developing Countries Clinical Trials Partnership/ ; TMA2020CDF-3159//European and Developing Countries Clinical Trials Partnership/ ; TMA2020CDF-3159//European and Developing Countries Clinical Trials Partnership/ ; }, mesh = {Humans ; *Feces/microbiology/virology ; *Metagenomics ; Female ; *HIV Infections/complications/microbiology/virology ; Male ; Child, Preschool ; Child ; Fever/microbiology ; Uganda/epidemiology ; Infant ; Candida albicans/genetics/isolation & purification/classification/pathogenicity ; Giardia/genetics/isolation & purification/classification ; Bacteroides/genetics/isolation & purification/classification ; Gastrointestinal Microbiome/genetics ; }, abstract = {BACKGROUND: Non-malarial febrile illnesses (NMFI) pose significant challenges in HIV-infected children, often leading to severe complications and increased morbidity. While traditional diagnostic approaches focus on specific pathogens, shotgun metagenomic sequencing offers a comprehensive tool to explore the microbial landscape underlying NMFI in this vulnerable population ensuring effective management.
METHODS: In this study, we employed shotgun metagenomics to analyse stool samples from HIV-infected children at the Baylor Children's Clinic Uganda presenting with non-malarial febrile illness. Samples were collected and subjected to DNA extraction at the Molecular and Genomics Laboratory, Makerere University followed by shotgun metagenomics sequencing at the Chan Zuckerberg Biohub San Francisco. Bioinformatics analysis was conducted to identify and characterise the microbial composition and potential pathogenic taxa associated with NMFI using the CZID pipeline.
RESULTS: Our findings reveal a diverse array of microbial taxa in the stool samples of HIV-infected children with NMFI. Importantly, shotgun metagenomics revealed potentially pathogenic players including Trichomonas vaginalis, Candida albicans, Giardia, and Bacteroides in stool from this patient population. This sheds light on the complexities of microbial interactions that potentially underpin non-malarial febrile illness in this group. Taxonomic profiling identified recognised pathogens and comorbidities and revealed possible new correlations with NMFI, shedding light on the pathophysiology of fever in HIV-infected children.
CONCLUSION: Shotgun metagenomics is a valuable method for understanding the gut microbial landscape of NMFI in HIV-infected children, providing a comprehensive approach to pathogen identification and characterisation. By revealing potential pathogenic actors beyond the fever, this work demonstrates how metagenomic sequencing may improve our knowledge of infectious illnesses in vulnerable groups and inspire targeted therapies for better clinical care and outcomes.}, }
@article {pmid39838107, year = {2025}, author = {Teso-Pérez, C and López-Gazcón, A and Peralta-Sánchez, JM and Martínez-Bueno, M and Valdivia, E and Fárez-Vidal, ME and Martín-Platero, AM}, title = {Bacteriocin-Producing Enterococci Modulate Cheese Microbial Diversity.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {175}, pmid = {39838107}, issn = {1432-184X}, support = {PEJ2018-003019-A//Plan Estatal de Garantía Juvenil (Fondo Social Europeo, Gobierno de España/ ; Group BIO 309//PAIDI Program/ ; A-BIO-083-UGR18//Programa Operativo FEDER Andalucía 2014-2020/ ; }, mesh = {*Cheese/microbiology ; *Bacteriocins/metabolism/biosynthesis ; *Enterococcus/metabolism/genetics ; *Microbiota ; Biodiversity ; Food Microbiology ; RNA, Ribosomal, 16S/genetics ; Milk/microbiology ; Animals ; }, abstract = {Cheese production involves various lactic acid bacteria (LAB) that break down lactose, milk proteins, and fats, producing key nutrients and influencing the cheese's flavor. They form communities that play a crucial role in determining the cheese's organoleptic properties. The composition of cheeses' microbial communities is shaped by physicochemical factors (e.g., temperature, pH, and salinity) and biological factors (i.e. microbial interactions). While starter cultures are introduced to control these communities, non-starter LAB represent a significant portion of the final microbial assemblage, but their interactions remain unclear. LAB often produce bacteriocins, antimicrobial peptides that antagonize other bacteria, but their role within LAB communities is not fully understood. This study aimed to assess the impact of bacteriocin production on LAB diversity in cheese, using Enterococcus as a model organism, a common bacteriocin producer. We analyzed enterocin production of enterococcal isolates by antimicrobial assays and microbial diversity differences in raw milk cheeses by two approaches: 16S RNA gene amplicon metagenomic sequencing for the whole microbial community and multi-locus sequence analysis (MLSA) for the enterococcal diversity. Our results revealed that LAB communities were dominated by lactococci, lactobacilli, and streptococci, with enterococci present in lower numbers. However, cheeses containing bacteriocin-producing enterococci exhibited higher microbial diversity. Interestingly, the highest diversity occurred at low levels of bacteriocin producers, but this effect was not observed within enterococcal populations. These findings suggest that bacteriocin production plays a key role in shaping LAB communities during cheese ripening, although further research is needed to understand its broader implications in other microbial ecosystems.}, }
@article {pmid39772525, year = {2025}, author = {Yum, SJ and Yu, SY and Kim, SM and Jeong, HG}, title = {Antibiotic Resistance Genes and Microbiota in Brassica oleracea var. acephala Cultivated in South Korea: Potential for Resistance Transmission.}, journal = {Journal of agricultural and food chemistry}, volume = {73}, number = {3}, pages = {2156-2166}, doi = {10.1021/acs.jafc.4c11161}, pmid = {39772525}, issn = {1520-5118}, mesh = {*Brassica/microbiology ; Republic of Korea ; *Microbiota/drug effects ; *Bacteria/genetics/classification/drug effects/isolation & purification ; *Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Antimicrobial resistance (AMR) poses a critical global public health challenge. This study investigates the microbiome of Brassica oleracea var. acephala (kale) to evaluate the role of food production systems, particularly plant-derived foods, in AMR dissemination. Using 16S rRNA gene sequencing and metagenomic shotgun sequencing, we analyzed microbial diversity and antimicrobial resistance genes (ARGs) in kale samples. Results showed significant regional differences in microbiota composition and ARG distribution, with traditional fertilizer use linked to higher ARG prevalence in coliform bacteria compared to farms using other fertilization methods. Additionally, we confirmed ARG transfer potential by Klebsiella pneumoniae within coliform populations. Storage conditions notably affected microbial dynamics, with higher temperatures promoting K. pneumoniae growth in washed samples. These findings revealed the importance of AMR research in plant-derived foods and highlight the need for improved agricultural practices to mitigate the risks associated with high ARG abundance in coliform bacteria.}, }
@article {pmid39722326, year = {2025}, author = {Liu, X and Chen, Y and Liu, Y and Hu, Y and Wang, K and Huang, L and Ke, X and Peng, L and Guo, Z}, title = {Protective effects and mechanisms of extracts of Gleditsia sinensis Lam. Thorn on DSS-induced colitis in mice.}, journal = {Journal of ethnopharmacology}, volume = {340}, number = {}, pages = {119244}, doi = {10.1016/j.jep.2024.119244}, pmid = {39722326}, issn = {1872-7573}, mesh = {Animals ; *Dextran Sulfate ; *Plant Extracts/pharmacology ; Mice ; Male ; *Gastrointestinal Microbiome/drug effects ; *Cytokines/metabolism ; *Mice, Inbred C57BL ; Colitis/chemically induced/drug therapy/pathology ; Disease Models, Animal ; Colon/drug effects/pathology/metabolism ; Anti-Inflammatory Agents/pharmacology ; Colitis, Ulcerative/chemically induced/drug therapy/pathology ; }, abstract = {Inflammatory Bowel Disease (IBD), encompassing Ulcerative Colitis (UC) and Crohn's Disease (CD), stems from a multifaceted interaction of hereditary, immunological, ecological, and microbial elements. Current treatments have limitations, necessitating new therapeutic approaches.
AIM OF THE STUDY: This study investigates the safeguarding impacts and fundamental processes of extracts of Gleditsia sinensis Lam. thorn (EGST) in a dextran sulfate sodium (DSS)-induced colitis model in mice.
MATERIALS AND METHODS: A total of 180g of dried EGST were prepared, and untargeted metabolomic profiling using high-resolution liquid chromatography electrospray ionization orbitrap mass spectrometry (HR-LC-ESI-Orbitrap-MS) identified 930 compounds. UC model mice were administered 3% DSS for 7 d, followed by EGST treatment. The analysis encompassed physiological and pathological evaluations, serum cytokine ELISA, gut microbiota (GM) metagenomic sequencing, GC-MS metabolomics, mRNA sequencing, and Western Blot.
RESULTS: EGST markedly mitigated colitis symptoms, evidenced by reduced weight loss, lower DAI scores, and less colon shortening. It also decreased levels of pro-inflammatory cytokines (TNF-α, IL-6, IL-1β) while boosting IL-10. Histological examination revealed diminished tissue damage, restoration of crypts, and reduced inflammation, with barrier integrity maintained via upregulation of occludin and ZO-1. Metagenomic sequencing demonstrated that EGST modulated the GM, enhancing the levels of Firmicutes and Bacteroidetes while reducing the levels of Proteobacteria and Verrucomicrobia. Metabolomic analysis indicated that EGST influenced critical pathways, including those involving D-amino acids, glutathione, cysteine, and methionine metabolism. Furthermore, mRNA sequencing identified 2625 differentially expressed genes (DEGs), comprising 1729 with increased and 896 with decreased expression, and highlighted EGST's impact on the PPARγ/AMPK/NF-κB pathway.
CONCLUSION: Overall, EGST mitigates DSS-induced colitis through modulation of GM, metabolic profiles, and gene expression, suggesting its promise as a naturally derived treatment for colitis.}, }
@article {pmid39675450, year = {2025}, author = {Ye, X and Niu, X and Li, L and Lv, M and Zhang, D and Chen, D and Line, Y and Yang, Z}, title = {Insights into the impact of 6PPD-Q and 6PPD on nitrogen metabolism and microbial community in the anammox system.}, journal = {Environmental research}, volume = {266}, number = {}, pages = {120485}, doi = {10.1016/j.envres.2024.120485}, pmid = {39675450}, issn = {1096-0953}, mesh = {*Nitrogen/metabolism ; Water Pollutants, Chemical/metabolism ; Microbiota/drug effects ; Bacteria/metabolism/genetics ; Waste Disposal, Fluid/methods ; Wastewater/microbiology ; Bioreactors/microbiology ; Oxidation-Reduction ; Anaerobiosis ; }, abstract = {N-(1,3-Dimethylbutyl)-N'-phenyl-p-phenylenediamine (6PPD) is an antioxidant commonly used in tire manufacturing, and its release into the environment has significantly increased due to rapid urbanization. When subjected to ozonation, 6PPD converts into the harmful pollutant 6PPD quinone (6PPDQ). These substances enter wastewater treatment plants (WWTPs) via stormwater runoff and pipelines, posing significant risks to the functional microorganisms. Anammox, a strictly controlled and sensitive microbial nitrogen removal process, is especially susceptible to the effects of the pollutants. This study investigates the comprehensive impact of 6PPD-Q and 6PPD on anammox communities based on characterization analysis and metagenomics. At environmental concentrations, 6PPD-Q at 200 ng/L-1000 ng/L led to the disintegration of anammox granules. Extended exposure to both 6PPD-Q and 6PPD significantly reduces the population of anammox bacteria (AnAOB). By utilizing organic matter from dead cells and incoming carbonate as a carbon source, the system evolved into a nitrogen metabolism network primarily focused on denitrification and dissimilatory nitrate reduction to ammonium (DNRA). This transformation was accompanied by a reshuffling of the microbial community and associated genes, resulting in an accumulation of NH4[+]-N. These findings underscore the toxicity of 6PPD-Q and 6PPD to anammox and stress the importance of incorporating 6PPD into regulatory and preventive strategies.}, }
@article {pmid39672497, year = {2025}, author = {Zhou, L and Zhang, L and Dang, R and Han, G and Liu, J and Zhou, M and Xiao, L}, title = {Microbiota-induced asymmetry in coastal methane emission potential under experimental precipitation gradients.}, journal = {Environmental research}, volume = {266}, number = {}, pages = {120601}, doi = {10.1016/j.envres.2024.120601}, pmid = {39672497}, issn = {1096-0953}, mesh = {*Methane/metabolism ; *Microbiota ; China ; *Rain ; Wetlands ; Soil Microbiology ; Air Pollutants/analysis/toxicity ; }, abstract = {Climate models predict that the frequency and intensity of extreme precipitation events will increase globally. Despite carbon budget in coastal wetlands is known to be sensitive to precipitation variability, in where CH4 productions and potential mechanisms remain poorly understood. We investigated CH4 emission potential and its drivers after 7-year of field experiments with five precipitation gradients (-60%, -40%, ambient condition, +40%, +60%) in Yellow River Delta, China. The response of CH4 emission potential to precipitation gradients exhibited significant asymmetry, with the highest emission potential occurring under +40% precipitation. [13]C-isotope tracing experiment discovered the primary contribution of acetoclastic methanogenic pathway. +40% precipitation significantly improved the accumulation of aboveground biomass, soil organic carbon and total nitrogen. Microbial community abundance, but not composition, referring to metagenome-assembled genomes also actively responded to precipitation changes. For example, +40% precipitation increased the relative abundance of Methanosarcinia and Methanobacteria. Furthermore, CH4 emission potential was also promoted by higher microbial enzyme activity. Collectively, CH4 emission potential in response to 7-year experimental precipitations was regulated by microbiota-driven, showing obvious asymmetry.}, }
@article {pmid39363100, year = {2025}, author = {Chu, VT and Glascock, A and Donnell, D and Grabow, C and Brown, CE and Ward, R and Love, C and Kalantar, KL and Cohen, SE and Cannon, C and Woodworth, MH and Kelley, CF and Celum, C and Luetkemeyer, AF and Langelier, CR}, title = {Impact of doxycycline post-exposure prophylaxis for sexually transmitted infections on the gut microbiome and antimicrobial resistome.}, journal = {Nature medicine}, volume = {31}, number = {1}, pages = {207-217}, pmid = {39363100}, issn = {1546-170X}, support = {K23 AI144036/AI/NIAID NIH HHS/United States ; R01 AI143439/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects/genetics ; *Doxycycline/pharmacology ; Male ; Female ; Adult ; *Anti-Bacterial Agents/pharmacology/administration & dosage ; Post-Exposure Prophylaxis ; Sexually Transmitted Diseases/microbiology/prevention & control ; Drug Resistance, Bacterial/genetics ; Homosexuality, Male ; Transgender Persons ; Middle Aged ; }, abstract = {Doxycycline post-exposure prophylaxis (doxy-PEP) reduces bacterial sexually transmitted infections among men who have sex with men and transgender women. Although poised for widespread clinical implementation, the impact of doxy-PEP on antimicrobial resistance remains a primary concern as its effects on the gut microbiome and resistome, or the antimicrobial resistance genes (ARGs) present in the gut microbiome, are unknown. To investigate these effects, we studied participants from the DoxyPEP trial, a randomized clinical trial comparing doxy-PEP use, a one-time doxycycline 200-mg dose taken after condomless sex (DP arm, n = 100), to standard of care (SOC arm, n = 50) among men who have sex with men and transgender women. From self-collected rectal swabs at enrollment (day-0) and after 6 months (month-6), we performed metagenomic DNA sequencing (DNA-seq) or metatranscriptomic RNA sequencing (RNA-seq). DNA-seq data were analyzable from 127 samples derived from 89 participants, and RNA-seq data were analyzable from 86 samples derived from 70 participants. We compared the bacterial microbiome and resistome between the two study arms and over time. The median number of doxycycline doses taken since enrollment by participants with DNA-seq data was zero (interquartile range (IQR): 0-7 doses) for the SOC arm and 42 (IQR: 27-64 doses) for the DP arm. Tetracycline ARGs were detected in all day-0 DNA-seq samples and in 85% of day-0 RNA-seq samples. The proportional mass of tetracycline ARGs in the resistome increased between day-0 and month-6 in DP participants from 46% to 51% in the metagenome (P = 2.3 × 10[-2]) and from 4% to 15% in the metatranscriptome (P = 4.5 × 10[-6]), but no statistically significant increases in other ARG classes were observed. Exposure to a higher number of doxycycline doses correlated with proportional enrichment of tetracycline ARGs in the metagenome (Spearman's ρ = 0.23, P = 9.0 × 10[-3]) and metatranscriptome (Spearman's ρ = 0.55, P = 3.7 × 10[-8]). Bacterial microbiome alpha diversity, beta diversity and total bacterial mass did not differ between day-0 and month-6 samples from DP participants when assessed by either DNA-seq or RNA-seq. In an abundance-based correlation analysis, we observed an increase over time in the strength of the correlation between tetracycline ARGs and specific bacterial taxa, including some common human pathogens. In sum, doxy-PEP use over a 6-month period was associated with an increase in the proportion of tetracycline ARGs comprising the gut resistome and an increase in the expression of tetracycline ARGs. At 6 months of doxy-PEP use, no residual differences were observed in alpha and beta diversity or taxonomic composition of the gut microbiome. As doxy-PEP is implemented as a public health strategy, further studies and population-level surveillance of doxycycline-resistant pathogens are needed to understand the implications of these findings. ClinicalTrials.gov registration number: NCT03980223 .}, }
@article {pmid39078977, year = {2025}, author = {Ismail, HM and Perera, D and Mandal, R and DiMeglio, LA and Evans-Molina, C and Hannon, T and Petrosino, J and Javornik Cregeen, S and Schmidt, NW}, title = {Gut Microbial Changes Associated With Obesity in Youth With Type 1 Diabetes.}, journal = {The Journal of clinical endocrinology and metabolism}, volume = {110}, number = {2}, pages = {364-373}, pmid = {39078977}, issn = {1945-7197}, support = {K23 DK129799/DK/NIDDK NIH HHS/United States ; /NH/NIH HHS/United States ; //(NIH)/ ; /TR/NCATS NIH HHS/United States ; KL2TR002530//Clinical and Translational Sciences Award/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Diabetes Mellitus, Type 1/microbiology/metabolism/complications ; Female ; Male ; Adolescent ; Pilot Projects ; *Feces/microbiology ; Fatty Acids, Volatile/metabolism/analysis ; Body Mass Index ; Obesity/microbiology/metabolism ; Pediatric Obesity/microbiology/metabolism ; Child ; Young Adult ; }, abstract = {CONTEXT: Obesity is prevalent in type 1 diabetes (T1D) and is problematic with higher risk for diabetes complications. It is unknown to what extent gut microbiome changes are associated with obesity and T1D.
OBJECTIVE: This work aimed to describe the gut microbiome and microbial metabolite changes associated with obesity in T1D. We hypothesized statistically significant gut microbial and metabolite differences in lean T1D youth (body mass index [BMI]: 5%-<85%) vs those with obesity (BMI: ≥95%).
METHODS: We analyzed stool samples for gut microbial (using metagenomic shotgun sequencing) and short-chain fatty acid (SCFA) differences in lean (n = 27) and obese (n = 21) T1D youth in a pilot study. The mean ± SD age was 15.3 ± 2.2 years, glycated hemoglobin A1c 7.8 ± 1.3%, diabetes duration 5.1 ± 4.4 years, 42.0% female, and 94.0% were White.
RESULTS: Bacterial community composition showed between sample diversity differences (β-diversity) by BMI group (P = .013). There was a higher ratio of Prevotella to Bacteroides in the obese group (P = .0058). There was a differential distribution of significantly abundant taxa in either the lean or obese groups, including increased relative abundance of Prevotella copri, among other taxa in the obese group. Functional profiling showed an upregulation of branched-chain amino acid (BCAA) biosynthesis in the obese group and upregulation of BCAA degradation, tyrosine metabolism, and secondary bile acid biosynthesis in the lean group. Stool SCFAs were higher in the obese vs the lean group (P < .05 for all).
CONCLUSION: Our findings identify a gut microbiome and microbial metabolite signature associated with obesity in T1D. These findings could help identify gut microbiome-targeted therapies to manage obesity in T1D.}, }
@article {pmid39835966, year = {2025}, author = {Levine, BH and Hoffman, JM}, title = {Microbiome transplants may not improve health and longevity in Drosophila melanogaster.}, journal = {Biology open}, volume = {14}, number = {1}, pages = {}, doi = {10.1242/bio.061745}, pmid = {39835966}, issn = {2046-6390}, support = {R00AG059920/NH/NIH HHS/United States ; //Augusta University; University of South Carolina/ ; }, mesh = {Animals ; *Drosophila melanogaster/microbiology/physiology ; *Longevity ; *Gastrointestinal Microbiome ; Female ; Male ; Microbiota ; }, abstract = {The gut microbiome, which is composed of bacteria, viruses, and fungi, and is involved in multiple essential physiological processes, changes measurably as a person ages, and can be associated with negative health outcomes. Microbiome transplants have been proposed as a method to improve gut function and reduce or reverse multiple disorders, including age-related diseases. Here, we take advantage of the laboratory model organism, Drosophila melanogaster, to test the effects of transplanting the microbiome of a young fly into middle-aged flies, across multiple genetic backgrounds and both sexes, to test whether age-related lifespan could be increased, and late-life physical health declines mitigated. Our results suggest that, overall, microbiome transplants do not improve longevity and may even be detrimental in flies, and the health effects of microbiome transplants were minor, but sex- and genotype-dependent. This discovery supports previous evidence that axenic flies, those with no gut microbiome, live healthier and longer lives than their non-axenic counterparts. The results of this study suggest that, at least for fruit flies, microbiome transplants may not be a viable intervention to improve health and longevity, though more research is still warranted.}, }
@article {pmid39833973, year = {2025}, author = {Rampanelli, E and Romp, N and Troise, AD and Ananthasabesan, J and Wu, H and Gül, IS and De Pascale, S and Scaloni, A and Bäckhed, F and Fogliano, V and Nieuwdorp, M and Bui, TPN}, title = {Gut bacterium Intestinimonas butyriciproducens improves host metabolic health: evidence from cohort and animal intervention studies.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {15}, pmid = {39833973}, issn = {2049-2618}, mesh = {Animals ; *Gastrointestinal Microbiome ; Humans ; Mice ; Feces/microbiology ; Male ; Lysine/metabolism ; Female ; Fermentation ; Butyrates/metabolism ; Cohort Studies ; Clostridiales/metabolism/classification ; Fructose/metabolism ; Mice, Inbred C57BL ; Middle Aged ; Obesity/microbiology/metabolism ; Probiotics/administration & dosage/metabolism ; Disease Models, Animal ; }, abstract = {BACKGROUND: The human gut microbiome strongly influences host metabolism by fermenting dietary components into metabolites that signal to the host. Our previous work has shown that Intestinimonas butyriciproducens is a prevalent commensal bacterium with the unique ability to convert dietary fructoselysine to butyrate, a well-known signaling molecule with proven health benefits. Dietary fructoselysine is an abundant Amadori product formed in foods during thermal treatment and is part of foods rich in dietary advanced glycation end products which have been associated with cardiometabolic disease. It is therefore of interest to investigate the causal role of this bacterium and fructoselysine metabolism in metabolic disorders.
RESULTS: We assessed associations of I. butyriciproducens with metabolic risk biomarkers at both strain and functional levels using a human cohort characterized by fecal metagenomic analysis. We observed that the level of the bacterial strain as well as fructoselysine fermentation genes were negatively associated with BMI, triglycerides, HbA1c, and fasting insulin levels. We also investigated the fructoselysine degradation capacity within the Intestinimonas genus using a culture-dependent approach and found that I. butyriciproducens is a key player in the butyrogenic fructoselysine metabolism in the gut. To investigate the function of I. butyriciproducens in host metabolism, we used the diet-induced obesity mouse model to mimic the human metabolic syndrome. Oral supplementation with I. butyriciproducens counteracted body weight gain, hyperglycemia, and adiposity. In addition, within the inguinal white adipose tissue, bacterial administration reduced inflammation and promoted pathways involved in browning and insulin signaling. The observed effects may be partly attributable to the formation of the short-chain fatty acids butyrate from dietary fructoselysine, as butyrate plasma and cecal levels were significantly increased by the bacterial strain, thereby contributing to the systemic effects of the bacterial treatment.
CONCLUSIONS: I. butyriciproducens ameliorates host metabolism in the context of obesity and may therefore be a good candidate for new microbiota-therapeutic approaches to prevent or treat metabolic diseases. Video Abstract.}, }
@article {pmid39833341, year = {2025}, author = {Zhang, C and Yu, Y and Yue, L and Chen, Y and Chen, Y and Liu, Y and Guo, C and Su, Q and Xiang, Z}, title = {Gut microbiota profiles of sympatric snub-nosed monkeys and macaques in Qinghai-Tibetan Plateau show influence of phylogeny over diet.}, journal = {Communications biology}, volume = {8}, number = {1}, pages = {95}, pmid = {39833341}, issn = {2399-3642}, support = {32171487//National Natural Science Foundation of China (National Science Foundation of China)/ ; 31870509//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32400413//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; *Phylogeny ; *Diet ; Tibet ; RNA, Ribosomal, 16S/genetics ; Colobinae/microbiology ; Macaca mulatta ; Macaca/microbiology ; Bacteria/classification/genetics/isolation & purification ; }, abstract = {The unique environment of the Qinghai-Tibetan Plateau provides a great opportunity to study how primate intestinal microorganisms adapt to ecosystems. The 16S rRNA gene amplicon and metagenome analysis were conducted to investigate the correlation between gut microbiota in primates and other sympatric animal species living between 3600 and 4500 m asl. Results showed that within the same geographical environment, Macaca mulatta and Rhinopithecus bieti exhibited a gut microbiome composition similar to that of Tibetan people, influenced by genetic evolution of host, while significantly differing from other distantly related animals. The gut microbiota of plateau species has developed similar strategies to facilitate their hosts' adaptation to specific environments, including broadening its dietary niche and enhancing energy absorption. These findings will enhance our comprehension of the significance of primate gut microbiota in adapting to specific habitats.}, }
@article {pmid39756329, year = {2025}, author = {Dai, J and Li, M and He, J and Duan, L and Zhu, X and Liu, L and Meng, M and Shao, X and Zhu, G}, title = {Gut microbiota changes are associated with abnormal metabolism activity in children and adolescents with obsessive-compulsive disorder.}, journal = {Journal of psychiatric research}, volume = {181}, number = {}, pages = {728-737}, doi = {10.1016/j.jpsychires.2024.12.041}, pmid = {39756329}, issn = {1879-1379}, mesh = {Humans ; *Obsessive-Compulsive Disorder/metabolism/microbiology ; Adolescent ; *Gastrointestinal Microbiome/physiology ; Male ; Child ; Female ; *Feces/microbiology ; *RNA, Ribosomal, 16S ; Metabolomics ; Metagenomics ; }, abstract = {Obsessive-compulsive disorder (OCD) is a chronic and disabling psychiatric disorder characterized by recurrent intrusive thoughts or repetitive behaviors. We sought to better understand the structure of gut microbiota in first visit registration, treatment-naive children and adolescents with OCD, and the relationship between gut microbiota and fecal metabolites. Thus we studied the gut microbial population using 16 S rRNA sequencing in 49 children (8-17 years of age) with OCD, 42 healthy controls (HCs). We found a significant decrease in α-diversity in the OCD group, and the OCD and HC groups had distinctive intestinal flora. To further investigate the potential interaction effects between OCD and functional pathways of the intestinal flora, the 19 OCD patients and 18 aged-matched HCs were selected to undergo metagenomics analysis. We showed that several functional pathways of gut microbiota in patients with OCD were disrupted, such as glucolipid metabolism, amino acid metabolism, steroid biosynthesis, and the second messenger system. Changes in the clinical characteristics of OCD patients were associated with specific bacteria. Metabolomics analysis was also performed on stool samples from 91 subjects. Intestinal microflora metabolite expression in OCD patients was disturbed, and the related metabolic pathway functions were abnormal. Abnormal metabolites of gut microbiota in OCD patients are mainly involved in folate biosynthesis, the prion disease pathway, and the amino acid metabolic network. This study detailed the intestinal microbiota of children and adolescents with OCD. Our study suggests possible modalities for early OCD intervention by targeting the specific bacteria associated with neurotransmitter metabolism.}, }
@article {pmid39714212, year = {2025}, author = {Fang, Y and Meng, L and Xia, J and Gotoh, Y and Hayashi, T and Nagasaki, K and Endo, H and Okazaki, Y and Ogata, H}, title = {Genome-resolved year-round dynamics reveal a broad range of giant virus microdiversity.}, journal = {mSystems}, volume = {10}, number = {1}, pages = {e0116824}, doi = {10.1128/msystems.01168-24}, pmid = {39714212}, issn = {2379-5077}, support = {21H05057//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; Nos. 2018-31//Kyoto University | Institute for Chemical Research, Kyoto University (ICR)/ ; Nos. 2017-25//Kyoto University | Institute for Chemical Research, Kyoto University (ICR)/ ; 22H00384//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; 22H00385//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; 16H06279//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; 16H06429//Ministry of Education, Culture, Sports, Science and Technology (MEXT)/ ; 16K21723//Ministry of Education, Culture, Sports, Science and Technology (MEXT)/ ; 16H06437//Ministry of Education, Culture, Sports, Science and Technology (MEXT)/ ; Nos. 2021-33//Kyoto University | Institute for Chemical Research, Kyoto University (ICR)/ ; Nos. 2019-33//Kyoto University | Institute for Chemical Research, Kyoto University (ICR)/ ; }, mesh = {*Genome, Viral ; *Seawater/virology ; *Giant Viruses/genetics ; Metagenome ; Metagenomics ; Phylogeny ; Genetic Variation/genetics ; Seasons ; Biodiversity ; }, abstract = {Giant viruses are crucial for marine ecosystem dynamics because they regulate microeukaryotic community structure, accelerate carbon and nutrient cycles, and drive the evolution of their hosts through co-evolutionary processes. Previously reported long-term observations revealed that these viruses display seasonal fluctuations in abundance. However, the underlying genetic mechanisms driving such dynamics of these viruses remain largely unknown. In this study, we investigated the dynamics of giant viruses using time-series metagenomes from eutrophic coastal seawater samples collected over 20 months. A newly developed computational pipeline generated 1,065 high-quality genomes covering six major giant virus lineages. These genomic data revealed year-round recovery of the viral community structure at the study site and distinct dynamics of viral populations that were classified as persistent (n = 9), seasonal (n = 389), sporadic (n = 318), or others. By profiling the intra-species nucleotide-resolved microdiversity through read mapping, we also identified year-round recovery dynamics at subpopulation level for viruses classified as persistent or seasonal. Our results further indicated that giant viruses with broader niche breadth tended to exhibit higher levels of microdiversity. We argue that greater microdiversity of viruses likely enhances adaptability and thus survival under the virus-host arms race during prolonged interactions with their hosts.IMPORTANCERecent genome-resolved metagenomic surveys have uncovered the vast genomic diversity of giant viruses, which play significant roles in aquatic ecosystems by acting as bloom terminators and influencing biogeochemical cycles. However, the relationship between the ecological dynamics of giant viruses and underlying genetic structures of viral populations remains unresolved. In this study, we performed deep metagenomic sequencing of seawater samples collected across a time-series from a coastal area in Japan. The results revealed a significant positive correlation between microdiversity and temporal persistence of giant virus populations, suggesting that population structure is a crucial factor for adaptation and survival in the interactions with their hosts.}, }
@article {pmid39714168, year = {2025}, author = {Bhosle, A and Jackson, MI and Walsh, AM and Franzosa, EA and Badri, DV and Huttenhower, C}, title = {Response of the gut microbiome and metabolome to dietary fiber in healthy dogs.}, journal = {mSystems}, volume = {10}, number = {1}, pages = {e0045224}, doi = {10.1128/msystems.00452-24}, pmid = {39714168}, issn = {2379-5077}, support = {A-2019-687-HL//Hill's Pet Nutrition (Hill's)/ ; }, mesh = {Animals ; *Dietary Fiber/metabolism ; Dogs/microbiology ; *Gastrointestinal Microbiome/physiology ; *Metabolome/physiology ; *Feces/microbiology ; Male ; Female ; }, abstract = {UNLABELLED: Dietary fiber confers multiple health benefits originating from the expansion of beneficial gut microbial activity. However, very few studies have established the metabolic consequences of interactions among specific fibers, microbiome composition, and function in either human or representative animal models. In a study design reflective of realistic population dietary variation, fecal metagenomic and metabolomic profiles were analyzed from healthy dogs fed 12 test foods containing different fiber sources and quantities (5-13% as-fed basis). Taxa and functions were identified whose abundances were associated either with overall fiber intake or with specific fiber compositions. Fourteen microbial species were significantly enriched in response to ≥1 specific fiber source; enrichment of fiber-derived metabolites was more pronounced in response to these fiber sources. Positively associated fecal metabolites, including short-chain fatty acids, acylglycerols, fiber bound sugars, and polyphenols, co-occurred with microbes enriched in specific food groups. Critically, the specific metabolite pools responsive to differential fiber intake were dependent on differences both in individual microbial community membership and in overall ecological configuration. This helps to explain, for the first time, differences in microbiome-diet associations observed in companion animal epidemiology. Thus, our study corroborates findings in human cohorts and reinforces the role of personalized microbiomes even in seemingly phenotypically homogeneous subjects.
IMPORTANCE: Consumption of dietary fiber changes the composition of the gut microbiome and, to a larger extent, the associated metabolites. Production of health-relevant metabolites such as short-chain fatty acids from fiber depends both on the consumption of a specific fiber and on the enrichment of beneficial metabolite-producing species in response to it. Even in a seemingly homogeneous population, the benefit received from fiber consumption is personalized and emphasizes specific fiber-microbe-host interactions. These observations are relevant for both population-wide and personalized nutrition applications.}, }
@article {pmid39714161, year = {2025}, author = {Neumann, CJ and Mohammadzadeh, R and Woh, PY and Kobal, T and Pausan, M-R and Shinde, T and Haid, V and Mertelj, P and Weiss, E-C and Kolovetsiou-Kreiner, V and Mahnert, A and Kumpitsch, C and Jantscher-Krenn, E and Moissl-Eichinger, C}, title = {First-year dynamics of the anaerobic microbiome and archaeome in infants' oral and gastrointestinal systems.}, journal = {mSystems}, volume = {10}, number = {1}, pages = {e0107124}, doi = {10.1128/msystems.01071-24}, pmid = {39714161}, issn = {2379-5077}, support = {10.55776/KLI784 and 10.55776/DOC31//Austrian Science Fund (FWF)/ ; }, mesh = {Humans ; Infant ; *Mouth/microbiology ; *Gastrointestinal Microbiome/physiology ; *Breast Feeding ; Female ; Male ; Archaea/classification ; Gastrointestinal Tract/microbiology ; Anaerobiosis/physiology ; Microbiota/physiology ; Longitudinal Studies ; }, abstract = {UNLABELLED: Recent research provides new insights into the early establishment of the infant gut microbiome, emphasizing the influence of breastfeeding on the development of gastrointestinal microbiomes. In our study, we longitudinally examined the taxonomic and functional dynamics of the oral and gastrointestinal tract (GIT) microbiomes of healthy infants (n = 30) in their first year, focusing on the often-over-looked aspects, the development of archaeal and anaerobic microbiomes. Breastfed (BF) infants exhibit a more defined transitional phase in their oral microbiome compared to non-breastfed (NBF) infants, marked by a decrease in Streptococcus and the emergence of anaerobic genera such as Granulicatella. This phase, characterized by increased alpha-diversity and significant changes in beta-diversity, occurs earlier in NBF infants (months 1-3) than in BF infants (months 4-6), suggesting that breastfeeding supports later, more defined microbiome maturation. We demonstrated the presence of archaea in the infant oral cavity and GIT microbiome from early infancy, with Methanobrevibacter being the predominant genus. Still, transient patterns show that no stable archaeome is formed. The GIT microbiome exhibited gradual development, with BF infants showing increased diversity and complexity between the third and eighth months, marked by anaerobic microbial networks. NBF infants showed complex microbial co-occurrence patterns from the start. These strong differences between BF and NBF infants' GIT microbiomes are less pronounced on functional levels than on taxonomic levels. Overall, the infant microbiome differentiates and stabilizes over the first year, with breastfeeding playing a crucial role in shaping anaerobic microbial networks and overall microbiome maturation.
IMPORTANCE: The first year of life is a crucial period for establishing a healthy human microbiome. Our study analyses the role of archaea and obligate anaerobes in the development of the human oral and gut microbiome, with a specific focus on the impact of breastfeeding in this process. Our findings demonstrated that the oral and gut microbiomes of breastfed infants undergo distinct phases of increased dynamics within the first year of life. In contrast, the microbiomes of non-breastfed infants are more mature from the first month, leading to a steadier development without distinct transitional phases in the first year. Additionally, we found that archaeal signatures are present in infants under 1 year of age, but they do not form a stable archaeome. In contrast to this, we could track specific bacterial strains transitioning from oral to gut or persisting in the gut over time.}, }
@article {pmid39699181, year = {2025}, author = {Olson, N and Lamar, F and Mucache, H and Fafetine, J and Saíde, J and Milisse, A and Brito, DRA and Jesser, KJ and Levy, K and Freeman, MC and Nadimpalli, ML}, title = {Farm-to-fork changes in poultry microbiomes and resistomes in Maputo City, Mozambique.}, journal = {mSystems}, volume = {10}, number = {1}, pages = {e0103724}, doi = {10.1128/msystems.01037-24}, pmid = {39699181}, issn = {2379-5077}, support = {//Rollins School of Public Health Dean's Pilot and Innovation Award/ ; OPP 1189339//Bill and Melinda Gates Foundation (GF)/ ; 5T32ES007032-37, 5T32ES012870-15//HHS | NIH | National Institute of Environmental Health Sciences (NIEHS)/ ; T32AI138952//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; 5T32ES012870//HHS | NIH | National Institute of Environmental Health Sciences (NIEHS)/ ; }, mesh = {Animals ; Mozambique/epidemiology ; *Chickens/microbiology ; *Feces/microbiology ; Microbiota/genetics ; Farms ; Drug Resistance, Bacterial/genetics ; Humans ; Poultry/microbiology ; Gastrointestinal Microbiome/genetics ; Bacteria/genetics/drug effects/isolation & purification/classification ; Metagenomics ; }, abstract = {UNLABELLED: Increasing demand for poultry has spurred poultry production in low- and middle-income countries like Mozambique. Poultry may be an important source of foodborne, antimicrobial-resistant bacteria to consumers in settings with limited water, sanitation, and hygiene infrastructure. The Chicken Exposures and Enteric Pathogens in Children Exposed through Environmental Pathways (ChEEP ChEEP) study was conducted in Maputo City, Mozambique from 2019 to 2021 to quantify enteric pathogen exposures along the supply chain for commercial and local (i.e., scavenger) chicken breeds. Here, we performed metagenomic sequencing of total DNA from banked ChEEP ChEEP samples to characterize fecal and carcass microbiomes and resistome diversity between chicken breeds and along the supply chain. Fecal samples (n = 26) were collected from commercial and local chickens at production sites and markets and carcass (n = 49) and rinse bucket samples (n = 26) from markets. We conducted taxonomic profiling and identified antimicrobial resistance genes (ARGs) from metagenomic sequence data, focusing especially on potential human pathogens and "high-risk" ARGs. We estimated alpha diversity for each sample and compared by site and breed. We estimated Bray-Curtis dissimilarity between samples and examined clustering. We found that commercial and local chickens harbored distinct fecal potential pathogens and resistomes at production and market sites. Many potentially pathogenic bacteria and ARGs present in chicken fecal samples are also present on carcasses sold to consumers. Finally, commercial chicken carcasses contain high-risk ARGs that are not necessarily introduced from chicken feces. These results indicate markets are an important site of exposure to potentially pathogenic bacteria and high-risk ARGs.
IMPORTANCE: While chicken eggs and meat are a critical protein source in low-income settings, antibiotics are routinely fed to chickens with consequences for selection of antimicrobial resistance. Evaluating how poultry gut bacterial communities, including potential human pathogens and high-risk antimicrobial resistance genes, differ from farm to market could help identify where to target interventions to minimize transmission risks to human populations. In this study in Maputo City, Mozambique, we found compositional differences between commercial and local chicken breeds at production and market sites. We also found that while all potentially pathogenic bacteria and many high-risk antimicrobial resistance genes persisted from production and market through processing, some resistance genes were detected on carcass samples only after processing, suggesting human or environmental contamination is occurring within markets. Overall, our findings indicate that open-air markets may represent a critical juncture for human exposures to pathogens and antimicrobial resistance genes from poultry and poultry products.}, }
@article {pmid39611812, year = {2025}, author = {Shi, M and Zhao, B and Cai, W and Yuan, H and Liang, X and Li, Z and Liu, X and Jin, Y and Liu, X and Wei, C}, title = {Multi-omics mechanical analysis of gut microbiota, carboxylic acids, and cardiac gene expression interaction triggering diabetic cardiomyopathy.}, journal = {mSystems}, volume = {10}, number = {1}, pages = {e0145024}, doi = {10.1128/msystems.01450-24}, pmid = {39611812}, issn = {2379-5077}, support = {82170268,82200482//MOST | National Natural Science Foundation of China (NSFC)/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; *Diabetic Cardiomyopathies/genetics/microbiology/metabolism ; Mice ; Male ; Carboxylic Acids/metabolism ; Metabolomics ; Diabetes Mellitus, Type 2/microbiology/genetics/metabolism ; Metagenomics ; Receptors, Leptin/genetics/metabolism ; Myocardium/metabolism ; Mice, Inbred C57BL ; Diabetes Mellitus, Experimental/microbiology/genetics/metabolism ; Multiomics ; }, abstract = {UNLABELLED: It is well known that gut microbial imbalance is a potential factor for the occurrence and development of diabetes mellitus (DM) and its complications. Moreover, the heart and gut microbiota can regulate each other through the gut-metabolite-heart axis. In this study, metagenomics, metabolomics, and transcriptomics were chosen to sequence the changes in gut microbiota, serum metabolite levels, and differentially expressed genes (DEGs) in leptin receptor-deficient db/db mice and analyze the correlation between serum metabolites and gut microbiota or DEGs. According to the results, there were significant differences in the 1,029 cardiac genes and 353 serum metabolites in diabetic mice of the db/db group, including DEGs enriched in the PPAR signaling pathway and increased short-chain carboxylic acids (CAs), when compared with the normal db/m group. According to metagenomics, the gut microbiota of mice in the db/db group were disrupted, and particularly Lachnospiraceae bacteria and Oscillospiraceae bacteria significantly decreased. Also, according to the Pearson correlation analysis, a significant positive correlation was found between CAs and PPAR signaling pathway-related DEGs, and a negative correlation was found between CAs and the abundance of the above-mentioned species. To sum up, type 2 diabetes mellitus (T2DM) can upregulate the expression of partial cardiac genes through the levels of serum short-chain CAs affected by gut microbiota, thus playing a role in the occurrence and development of diabetic cardiomyopathy (DCM).
IMPORTANCE: Our research results clearly link the changes in heart genes of T2DM and normal mice with changes in serum metabolites and gut microbiota, indicating that some genes in biological processes are closely related to the reduction of protective microbiota in the gut microbiota. This study provides a theoretical basis for investigating the mechanism of DCM and may provide preliminary evidence for the future use of gut microbiota therapy for DCM.}, }
@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.}, }
@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.}, }
@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.}, }
@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.}, }
@article {pmid39763865, year = {2024}, author = {Gonzalez, FL and Ranaivoson, HC and Andrianiaina, A and Andry, S and Raharinosy, V and Randriambolamanantsoa, TH and Lacoste, V and Dussart, P and Héraud, JM and Brook, CE}, title = {Genomic characterization of novel bat kobuviruses in Madagascar: implications for viral evolution and zoonotic risk.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39763865}, issn = {2692-8205}, support = {DP2 AI171120/AI/NIAID NIH HHS/United States ; R01 AI129822/AI/NIAID NIH HHS/United States ; R25 GM066522/GM/NIGMS NIH HHS/United States ; }, abstract = {Kobuviruses (family Picornaviridae, genus Kobuvirus) are enteric viruses that infect a wide range of both human and animal hosts. Much of the evolutionary history of kobuviruses remains elusive, largely due to limited screening in wildlife. Bats have been implicated as major sources of virulent zoonoses, including coronaviruses, henipaviruses, and filoviruses, though much of the bat virome still remains uncharacterized. While most bat virus research has historically focused on immediately recognizable zoonotic clades (e.g. SARS-related coronaviruses), a handful of prior reports catalog kobuvirus infection in bats and posit the role of bats as potential progenitors of downstream kobuvirus evolution. As part of a multi-year study, we carried out metagenomic Next Generation Sequencing (mNGS) on fecal samples obtained from endemic, wild-caught Madagascar fruit bats to characterize potentially zoonotic viruses circulating within these populations. The wild bats of Madagascar represent diverse Asian and African phylogeographic histories, presenting a unique opportunity for viruses from disparate origins to mix, posing significant public health threats. Here, we report detection of kobuvirus RNA in Malagasy fruit bat (Eidolon dupreanum) feces and undertake phylogenetic characterization of one full genome kobuvirus sequence, which nests within the Aichivirus A clade - a kobuvirus clade known to infect a wide range of hosts including humans, rodents, canids, felids, birds, and bats. Given the propensity of kobuviruses for recombination and cross-species infection, further characterization of this clade is critical to accurate evaluation of future zoonotic threats.}, }
@article {pmid39742897, year = {2025}, author = {Jumaylawee, HRH and Komijani, M and Shahrjerdi, S and Sargolzaei, J}, title = {The interplay of gut microbiota and heavy metals in multiple sclerosis patients.}, journal = {Microbial pathogenesis}, volume = {199}, number = {}, pages = {107269}, doi = {10.1016/j.micpath.2024.107269}, pmid = {39742897}, issn = {1096-1208}, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Metals, Heavy/blood ; *Multiple Sclerosis/microbiology ; *Feces/microbiology/chemistry ; *RNA, Ribosomal, 16S/genetics ; Male ; Adult ; Female ; Arsenic/analysis ; Interleukin-10/blood/metabolism ; Middle Aged ; Bacteria/classification/isolation & purification/genetics ; Metagenomics ; Mass Spectrometry ; Young Adult ; Nickel ; }, abstract = {Multiple Sclerosis (MS) is a chronic inflammatory disease characterized by central nervous system (CNS). In this study, the concentration of heavy metals was measured in stool samples of MS patients by Inductively Coupled Plasma-Mass Spectroscopy (ICP-MS) method and compared with healthy people. Also, another goal of this study is to investigate the alteration of the gut microbiome of MS patients by metagenomics technique based on the 16S rRNA gene sequencing. The IL-10 ELISA assay showed no significant differences between the serum level of the IL-10 in the patients and the control group (p = 0.510). Heavy metal measurement by ICP-MS showed significantly higher levels of arsenic (As, Mean = 32.77 μg/kg), nickel (Ni, Mean = 7.154 μg/kg), manganese (Mn, Mean = 3723 μg/kg), and zinc (Zn, Mean = 5508 μg/kg) in the stool samples of the MS group compared to the control group, while concentrations of iron (Fe, Mean = 9585 μg/kg), lead (Pb, Mean = 18.54 μg/kg), titanium (Ti, Mean = 69.69 μg/kg), and tin (Sn, Mean = 13.92 μg/kg) were significantly lower. The result of gut microbiome analysis showed an increase in the abundance of the Verrumicrobiaceae, Lachnospiraceae and Ruminococcaceae families was considerably increased in MS patients compared to the control group (p < 0.05). This study reports that high levels of heavy metals such as Ars, Ni, Mn, and Zn, deficiency of Fe, Pb, Ti, and Sn, and alteration of the gut microbiome are involved in the pathogenesis of MS. The novelty of this study lies in its multi-faceted approach to understanding MS by integrating the measurement of heavy metals in stool samples with the analysis of gut microbiome alterations, thereby providing comprehensive insights into heavy metals, the gut microbiome, and potential therapeutic avenues. This study suggests several potential applications and practical implications based on its findings regarding heavy metals, gut microbiome alterations, and IL-10 levels in MS. First, the identification of elevated levels of specific heavy metals and deficiencies in others may lead to targeted screening and monitoring, informing preventive strategies for MS patients. Additionally, the observed gut microbiome changes could facilitate the development of microbiome-based therapies, such as probiotics or dietary interventions, aimed at restoring microbial balance. Finally, exploring the interplay between heavy metals, gut microbiome, and immune response may guide the creation of novel therapeutic interventions, ultimately enhancing treatment efficacy and providing new avenues for managing MS, thereby alleviating the burden of this chronic condition.}, }
@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.}, }
@article {pmid39675442, year = {2025}, author = {Tian, C and Yang, Q and Lv, H and Yue, F}, title = {Integrative analysis of gut microbiota and fecal metabolites in cynomolgus monkeys with spontaneous type 2 diabetes mellitus.}, journal = {Microbial pathogenesis}, volume = {199}, number = {}, pages = {107228}, doi = {10.1016/j.micpath.2024.107228}, pmid = {39675442}, issn = {1096-1208}, mesh = {Animals ; *Gastrointestinal Microbiome ; *Feces/microbiology/chemistry ; *Macaca fascicularis ; *Diabetes Mellitus, Type 2/microbiology/metabolism ; *Fatty Acids, Volatile/metabolism/analysis ; *Metabolomics ; *Dysbiosis/microbiology ; *Bacteria/classification/metabolism/genetics/isolation & purification ; Biomarkers ; Disease Models, Animal ; Metagenomics ; Male ; Metabolome ; }, abstract = {BACKGROUND: Accumulating evidence suggests that gut microbiota (GM) is clearly associated with the pathogenesis of type 2 diabetes mellitus (T2DM). However, the underlying mechanism of GM dysbiosis participates the onset of T2DM is not fully understood. The spontaneous T2DM cynomolgus monkeys are a powerful model for understanding the pathological mechanism of T2DM.
METHODS: Fecal samples were collected from 7 spontaneous T2DM cynomolgus monkeys and 7 healthy controls matched with similar age for multi-omics analysis, including shotgun metagenomic sequencing, untargeted metabolomics profiling, and targeted metabolomics focusing on short chain fatty acids (SCFAs). Lastly, the correlation network between differential gut microbial species and fecal metabolites was performed to explore the potential biomarkers of T2DM.
RESULTS: We found that 17 low-abundance species showed significant differences between the two groups. Analysis of gut microbial functions revealed that 16 KEGG pathways and 51 KEGG modules were significantly different in the two groups. Meanwhile, 276 fecal DEMs were identified, and these DEMs were enriched in the KEGG pathways, including Nucleotide metabolism, ABC transporters, Purine metabolism and so on. Lastly, Spearman correlation network analysis showed that the species of Anaerostipes_hadrus and Lachnoanaerobaculum_umeaense, and the metabolites including Glycerophospho-N-palmitoyl ethanolamine and 2-Hydroxycinnamic acid might serve as potential biomarkers of T2DM.
CONCLUSIONS: Our study provides novel insights into specific alterations in the GM composition, gene functions, and fecal metabolic profiles in spontaneous T2DM cynomolgus monkeys.}, }
@article {pmid39468772, year = {2025}, author = {Chero-Sandoval, L and Higuera-Gómez, A and Martínez-Urbistondo, M and Castejón, R and Mellor-Pita, S and Moreno-Torres, V and de Luis, D and Cuevas-Sierra, A and Martínez, JA}, title = {Comparative assessment of phenotypic markers in patients with chronic inflammation: Differences on Bifidobacterium concerning liver status.}, journal = {European journal of clinical investigation}, volume = {55}, number = {2}, pages = {e14339}, doi = {10.1111/eci.14339}, pmid = {39468772}, issn = {1365-2362}, support = {CD22/00011//Instituto de Salud Carlos III/ ; Y2020/6600//Consejería de Educación, Juventud y Deporte, Comunidad de Madrid/ ; }, mesh = {Humans ; Female ; *Gastrointestinal Microbiome/genetics ; Male ; Adult ; Middle Aged ; *Bifidobacterium ; *Biomarkers/metabolism ; *Inflammation ; *Lupus Erythematosus, Systemic/microbiology/immunology ; Phenotype ; Feces/microbiology ; Liver ; Fatty Liver/microbiology ; }, abstract = {BACKGROUND: The relationship between systemic lupus erythematosus (SLE) and low-grade metabolic inflammation (MI) with the microbiota is crucial for understanding the pathogenesis of these diseases and developing effective therapeutic interventions. In this context, it has been observed that the gut microbiota plays a key role in the immune regulation and inflammation contributing to the exacerbation through inflammatory mediators. This research aimed to describe similarities/differences in anthropometric, biochemical, inflammatory, and hepatic markers as well as to examine the putative role of gut microbiota concerning two inflammatory conditions: SLE and MI.
METHODS: Data were obtained from a cohort comprising adults with SLE and MI. Faecal samples were determined by 16S technique. Statistical analyses compared anthropometric and clinical variables, and LEfSe and MetagenomeSeq were used for metagenomic data. An interaction analysis was fitted to investigate associations of microbiota with fatty liver index (FLI) depending on the inflammatory condition.
RESULTS: Participants with low-grade MI showed worse values in anthropometry and biochemicals compared with patients with SLE. The liver profile of patients with MI was unhealthier, while no relevant differences were found in most of the inflammatory markers between groups. LEfSe analysis revealed an overrepresentation of Bifidobacteriaceae family in SLE group. An interactive association between gut Bifidobacterium abundance and type of disease was identified for FLI values, suggesting an effect modification of the gut microbiota concerning liver markers depending on the inflammatory condition.
CONCLUSION: This study found phenotypical and microbial similarities and disparities between these two inflammatory conditions, evidenced in clinical and hepatic markers, and showed the interactive interplay between gut Bifidobacterium and liver health (measured by FLI) that occur in a different manner depending on the type of inflammatory disease. These results underscore the importance of personalized approaches and individual microbiota in the screening of different inflammatory situations, considering unique hepatic and microbiota profiles.}, }
@article {pmid39363651, year = {2025}, author = {Vazquez Bucheli, JE and Lee, Y and Kim, B and Azevedo, NF and Azevedo, AS and Todorov, SD and Ji, Y and Kang, H and Holzapfel, WH}, title = {Use of FISH-FLOW as a Method for the Identification and Quantification of Bacterial Populations.}, journal = {Molecular nutrition & food research}, volume = {69}, number = {2}, pages = {e2400494}, doi = {10.1002/mnfr.202400494}, pmid = {39363651}, issn = {1613-4133}, support = {NRF-2018M3A9F3021964//NRF Korea/ ; RS-2023-00222687//NRF Korea/ ; 739489//Consejo Nacional de Humanidades, Ciencias y Tecnologías/ ; 2023/05394-9//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; LA/P/0045/2020UIDP/00511/2020,POCI-01-0145-FEDER-030431//FCT Portugal/ ; }, mesh = {*In Situ Hybridization, Fluorescence/methods ; *RNA, Ribosomal, 16S/genetics ; *Feces/microbiology ; Humans ; *Gastrointestinal Microbiome ; *Flow Cytometry/methods ; *Bacteria/isolation & purification/genetics/classification ; Proteobacteria/isolation & purification/genetics ; Gastrointestinal Tract/microbiology ; Bacteroidetes/isolation & purification/genetics ; Actinobacteria/isolation & purification/genetics ; Firmicutes/isolation & purification/genetics ; Female ; Male ; }, abstract = {The gastrointestinal tract (GIT) harbors the largest group of microbiotas among the microbial communities of the human host. The resident organisms typical of a healthy gut are well adapted to the gastrointestinal environment while alteration of these populations can trigger disorders that may affect the health and well-being of the host. Various investigations have applied different tools to study bacterial communities in the gut and their correlation with gastrointestinal disorders such as inflammatory bowel disease (IBD), obesity, and diabetes. This study proposes fluorescent in situ hybridization, combined with flow cytometry (FISH-FLOW), as an alternative approach for phylum level identification of Firmicutes, Bacteroidetes, Actinobacteria, and Proteobacteria and quantification of target bacteria from the GIT based on analysis of fecal samples, where results are validated by quantitative polymerase chain reaction (qPCR) and 16S ribosomal ribonucleic acid (16s rRNA) sequencing. The results obtained via FISH-FLOW experimental approach show high specificity for the developed probes for hybridization with the target bacteria. The study, therefore, suggests the FISH-FLOW as a reliable method for studying bacterial communities in the gut with results correlating well with those of metagenomic investigations of the same fecal samples.}, }
@article {pmid38458256, year = {2025}, author = {Mishra, S and Tejesvi, MV and Hekkala, J and Turunen, J and Kandikanti, N and Kaisanlahti, A and Suokas, M and Leppä, S and Vihinen, P and Kuitunen, H and Sunela, K and Koivunen, J and Jukkola, A and Kalashnikov, I and Auvinen, P and Kääriäinen, OS and Peñate Medina, T and Peñate Medina, O and Saarnio, J and Meriläinen, S and Rautio, T and Aro, R and Häivälä, R and Suojanen, J and Laine, M and Erawijattari, PP and Lahti, L and Karihtala, P and Ruuska, TS and Reunanen, J}, title = {Gut microbiome-derived bacterial extracellular vesicles in patients with solid tumours.}, journal = {Journal of advanced research}, volume = {68}, number = {}, pages = {375-386}, doi = {10.1016/j.jare.2024.03.003}, pmid = {38458256}, issn = {2090-1224}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Extracellular Vesicles/metabolism ; *Neoplasms/microbiology/metabolism ; *Feces/microbiology ; *Bacteria/metabolism/classification/genetics ; Female ; Male ; RNA, Ribosomal, 16S/genetics ; Middle Aged ; Proteomics/methods ; High-Throughput Nucleotide Sequencing/methods ; Adult ; Proteome/metabolism/analysis ; Aged ; }, abstract = {INTRODUCTION: Gut microbiome-derived nanoparticles, known as bacterial extracellular vesicles (bEVs), have garnered interest as promising tools for studying the link between the gut microbiome and human health. The diverse composition of bEVs, including their proteins, mRNAs, metabolites, and lipids, makes them useful for investigating diseases such as cancer. However, conventional approaches for studying gut microbiome composition alone may not be accurate in deciphering host-gut microbiome communication. In clinical microbiome research, there is a gap in the knowledge on the role of bEVs in solid tumor patients.
OBJECTIVES: Analyzing the functionality of bEVs using (meta)genomics and proteomics could highlight the unique aspects of host-gut microbiome interactions in solid tumor patients. Therefore, we performed a comparative analysis of the proteome and microbiota composition of gut microbiome-derived bEVs isolated from patients with solid tumors and healthy controls.
METHODS: After isolating bEVs from the feces of solid tumor patients and healthy controls, we performed spectrometry analysis of their proteomes and next-generation sequencing (NGS) of the 16S gene. We also investigated the gut microbiomes of feces from patients and controls using 16S sequencing and used machine learning to classify the samples into patients and controls based on their bEVs and fecal microbiomes.
RESULTS: Solid tumor patients showed decreased microbiota richness and diversity in both the bEVs and feces. However, the bEV proteomes were more diverse in patients than in the controls and were enriched with proteins associated with the metabolism of amino acids and carbohydrates, nucleotide binding, and oxidoreductase activity. Metadata classification of samples was more accurate using fecal bEVs (100%) compared with fecal samples (93%).
CONCLUSION: Our findings suggest that bEVs are unique functional entities. There is a need to explore bEVs together with conventional gut microbiome analysis in functional cancer research to decipher the potential of bEVs as cancer diagnostic or therapeutic biomarkers.}, }
@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.}, }
@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.}, }
@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.}, }
@article {pmid39793467, year = {2025}, author = {Cardacino, A and Turco, S and Balestra, GM}, title = {Seasonal dynamics of kiwifruit microbiome: A case study in a KVDS-affected orchard.}, journal = {Microbiological research}, volume = {292}, number = {}, pages = {128044}, doi = {10.1016/j.micres.2024.128044}, pmid = {39793467}, issn = {1618-0623}, mesh = {*Soil Microbiology ; *Plant Diseases/microbiology ; *Microbiota ; *Seasons ; *Actinidia/microbiology ; *Bacteria/classification/genetics/isolation & purification ; *Fungi/classification/genetics/isolation & purification ; *Plant Roots/microbiology ; Italy ; Metagenomics ; Temperature ; }, abstract = {Over the past decade, Italian kiwifruit orchards and overall production have faced a significant threat from Kiwifruit Vine Decline Syndrome (KVDS). Despite the insights gained from metagenomics studies into the microbial communities associated with the disease, unanswered questions still remain. In this study, the evolution of bacterial, fungal, and oomycetes communities in soil and root endosphere at three different time points during the vegetative season was investigated for the first time in a KVDS-affected orchard in the Lazio Region. The fungal and oomycetes genera previously associated with the syndrome, including Fusarium, Ilyonectria, Thelonectria, Phytophthora, Pythium and Globisporangium, were identified in both groups. In contrast, the characterization of bacterial communities revealed the first instance of the presence of the genus Ralstonia in soil and root samples. The microbiome composition shifts between KVDS-affected and asymptomatic plants were significant as evidenced by the results, particularly after a temperature increase. This temperature change coincided with the onset of severe disease symptoms and may indicate a key role in the progression of KVDS.}, }
@article {pmid39761739, year = {2025}, author = {Yavorov-Dayliev, D and Milagro, FI and Ayo, J and Oneca, M and Goyache, I and López-Yoldi, M and FitzGerald, JA and Crispie, F and Cotter, PD and Aranaz, P}, title = {Pediococcus acidilactici CECT 9879 (pA1c®) and heat inactivated pA1c® (pA1c® HI) ameliorate gestational diabetes mellitus in mice.}, journal = {Life sciences}, volume = {362}, number = {}, pages = {123359}, doi = {10.1016/j.lfs.2024.123359}, pmid = {39761739}, issn = {1879-0631}, mesh = {Animals ; Female ; Pregnancy ; Mice ; *Diabetes, Gestational/metabolism/microbiology ; *Mice, Inbred C57BL ; *Probiotics/therapeutic use/administration & dosage ; *Gastrointestinal Microbiome ; *Pediococcus acidilactici/metabolism ; Insulin Resistance ; Blood Glucose/metabolism ; Hot Temperature ; }, abstract = {AIMS: Gestational diabetes mellitus (GDM) is the most common complication of pregnancy and is known to be associated with an increased risk of postpartum metabolic disease. Based on the important role that the intestinal microbiota plays in blood glucose regulation and insulin sensitivity, supplementation of probiotic and postbiotic strains could improve glucose metabolism and tolerance in GDM.
MAIN METHODS: 56 4-week-old female C57BL/6J-mice were divided into 4 groups (n = 14 animals/group): control (CNT), high-fat/high-sucrose (HFS), pA1c® alive (pA1c®) and heat-inactivated pA1c® (pA1c®HI). Serum biochemical parameters were analyzed, gene expression analyses were conducted, and fecal microbiota composition was evaluated by shot-gun sequencing.
KEY FINDINGS: pA1c®- and pA1c® HI-supplemented groups presented reduced fasting blood glucose levels and reduced insulin resistance during gestation and exhibited lower visceral adiposity and increased muscle tissue, together with an improvement in intrahepatic TGs content and ALT levels. Liver gene expression analyses demonstrated that pA1c® and pA1c® HI activities were mediated by modulation of the insulin receptor, but also by an overexpression of beta-oxidation genes, and downregulation of fatty acid biosynthesis genes. Shot-gun metagenomics demonstrated that Pediococcus acidilactici was detected in the feces of all the pA1c® and pA1c® HI-group after the supplementation period (75 % of the microbial profile was Pediococcus acidilactici) in only nine weeks of supplementation, and modulated gut microbiota composition.
SIGNIFICANCE: These results may be considered as future perspectives for the development of preventive, even therapeutic options for GDM based on hyperglycemia reduction, blood glucose regulation, hepatic steatosis attenuation and insulin resistance alleviation.}, }
@article {pmid39427267, year = {2025}, author = {Singh, AB and Paul, T and Shukla, SP and Kumar, S and Kumar, S and Kumar, G and Kumar, K}, title = {Gut microbiome as biomarker for triclosan toxicity in Labeo rohita: bioconcentration, immunotoxicity and metagenomic profiling.}, journal = {Ecotoxicology (London, England)}, volume = {34}, number = {1}, pages = {102-111}, pmid = {39427267}, issn = {1573-3017}, support = {DST/TMD-EWO-WTI/2K19/EWFH/2019/214//Department of Science and Technology, Ministry of Science and Technology, India/ ; }, mesh = {Animals ; *Triclosan/toxicity ; *Gastrointestinal Microbiome/drug effects ; *Water Pollutants, Chemical/toxicity ; *Cyprinidae ; *Biomarkers ; Metagenomics ; }, abstract = {Triclosan (TCS) is a lipophilic, broad spectrum antimicrobial agent commonly used in personal care products with a projected continuous escalation in aquatic environments in the post COVID 19 era. There is rich documentation in the literature on the alteration of physiological responses in fish due to TCS exposure; however, studies on gut associated bacteria of fish are still scarce. This is the first attempt to determine changes in bacterial community structure due to exposure of TCS on Labeo rohita, a commercially essential freshwater species, using 16S V3-V4 region ribosomal RNA (rRNA) next-generation sequencing (NGS). Chronic exposure of TCS at environmentally realistic concentrations viz. 1/5th (T1: 0.129 mg/L) and 1/10th (T2: 0.065 mg/L) of LC50 for 28 days resulted in the dose dependent bioconcentration of TCS in the fish gut. Prolonged exposure to TCS leads to disruption of gut bacteria evidenced by down regulation of the host immune system. Additionally, high-throughput sequencing analysis showed alternation in the abundance and diversity of microbial communities in the gut, signifying Proteobacteria and Verrucomicrobia as dominant phyla. Significant changes were also observed in the relative abundance of Chloroflexi and Gammatimonadetes phyla in TCS exposed groups. The study revealed that gut microbiome can be used as a biomarker in assessing the degree of TCS toxicity in commercially important fish species.}, }
@article {pmid39181210, year = {2025}, author = {Zhang, YH and Xie, R and Dai, CS and Gao, HW and Zhou, G and Qi, TT and Wang, WY and Wang, H and Cui, YM}, title = {Thyroid hormone receptor-beta agonist HSK31679 alleviates MASLD by modulating gut microbial sphingolipids.}, journal = {Journal of hepatology}, volume = {82}, number = {2}, pages = {189-202}, doi = {10.1016/j.jhep.2024.08.008}, pmid = {39181210}, issn = {1600-0641}, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Sphingolipids/metabolism ; *Thyroid Hormone Receptors beta/agonists/metabolism ; Male ; Humans ; Spiro Compounds/pharmacology/administration & dosage/therapeutic use ; Double-Blind Method ; Disease Models, Animal ; Liver/metabolism/drug effects ; Mice, Inbred C57BL ; Pyridazines ; Uracil/analogs & derivatives ; }, abstract = {BACKGROUND & AIMS: As the first approved medication for metabolic dysfunction-associated steatohepatitis (MASH), the thyroid hormone receptor-β (THR-β) agonist MGL-3196 (resmetirom) has garnered much attention as a liver-directed, bioactive oral drug. However, studies on MGL-3196 have also identified remarkable heterogeneity of individual clinical efficacy and its interference with gut microbiota in host hepatoenteral circulation remains to be elucidated.
METHODS: We compared MASH attenuation by MGL-3196 and its derivative drug HSK31679 between germ-free (GF) and specific-pathogen free (SPF) mice to evaluate the role of gut microbiota. Then cross-omics analyses of microbial metagenome, metabolome and single-cell RNA-sequencing were applied to a randomized, double-blind, placebo-controlled multiple ascending dose cohort receiving HSK31679 treatment (n = 32) or placebo (n = 8), to comprehensively investigate the altered gut microbiota metabolism and circulating immune signatures.
RESULTS: HSK31679 outperformed MGL-3196 in ameliorating MASH diet-induced steatohepatitis of SPF mice but not GF mice. In the multiple ascending dose cohort of HSK31679, the relative abundance of B. thetaiotaomicron was significantly enriched, impairing glucosylceramide synthase (GCS)-catalyzed monoglucosylation of microbial Cer(d18:1/16:0) and Cer(d18:1/24:1). In contrast to the non-inferior effect of MGL-3196 and HSK31679 on MASH resolution in GF[BTΔGCS] mice, HSK31679 led to superior benefit on steatohepatitis in GF[BTWT] mice, due to its steric hindrance of R123 and Y401 of gut microbial GCS. For participants with high fecal GCS activity, the administration of 160 mg HSK31679 induced a shift in peripheral compartments towards an immunosuppressive niche, characterized by decreased CD8α[+] dendritic cells and MINCLE[+] macrophages.
CONCLUSIONS: This study provided novel insights into the gut microbiota that are key to the efficacy of HSK31679 treatment, revealing microbial GCS as a potential predictive biomarker in MASH, as well as a new target for further microbiota-based treatment strategies for MASH.
IMPACT AND IMPLICATIONS: Remarkable heterogeneity in individual clinical efficacy of thyroid hormone receptor-β agonists and their interferences with the microbiome in host hepatoenteral circulation are poorly understood. In our current germ-free mouse models and a randomized, double-blind, multiple-dose cohort study, we identified microbial glucosylceramide synthase as a key mechanistic node in the resolution of metabolic dysfunction-associated steatohepatitis. Microbial glucosylceramide synthase activity could be a predictive biomarker of response to HSK31679 treatment or a new target for microbiota-based therapeutics in metabolic dysfunction-associated steatohepatitis.}, }
@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.}, }
@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.}, }
@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.}, }
@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.}, }
@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.}, }
@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.}, }
@article {pmid39680298, year = {2025}, author = {Han, L and Lin, C and Lan, Y and Hua, Y and Wu, J and Fan, Z and Li, Y}, title = {Metagenomic Analysis of Gut Microbiome of Persistent Pulmonary Hypertension of the Newborn.}, journal = {Cardiovascular toxicology}, volume = {25}, number = {1}, pages = {135-147}, pmid = {39680298}, issn = {1559-0259}, support = {2021YFQ0061//Technology Project of Sichuan Province of China/ ; 82270249//National Natural Science Foundation of China/ ; }, mesh = {Humans ; Infant, Newborn ; *Gastrointestinal Microbiome ; *Metagenomics ; *Feces/microbiology ; Case-Control Studies ; Male ; *Bacteria/genetics/isolation & purification/classification/metabolism/growth & development ; Female ; Persistent Fetal Circulation Syndrome/microbiology/genetics ; Dysbiosis ; Host-Pathogen Interactions ; Intestines/microbiology ; }, abstract = {Persistent pulmonary hypertension of the newborn (PPHN) is one of the most common diseases in the neonatal intensive care unit which severely affects neonatal survival. Gut microbes play an increasingly important role in human health, but there are rarely reported how gut microbiota contribute to PPHN. In our study, the metagenomic sequencing of feces from 12 PPHN's neonates and 8 controls were performed to expose the relation between neonatal gut microbes and PPHN disease. Firstly, we found that the abundance of Actinobacteria, Proteobacteria, Bacteroidetes were significantly increased in PPHN compared with controls, but the Firmicutes components was reduced. And some pathogenic strains (like Vibrio metschnikovii) were significantly enriched in the PPHN compared with controls. Secondly, functional annotation of genes found that PPHN up-regulated transmembrane transport, but down-regulated ribosome and ATP binding. Lastly, microbial metabolic pathway enrichment analysis indicated that some metabolic pathway in PPHN were conflicting and contradictory, showed that an abnormally increased metabolism, disturbed protein synthesis and genomic instability in the PPHN neonate. Our results contribute to understanding the changes in the species and function of gut microbiota in PPHN, thus providing a theoretical basis for the explanation and treatment of PPHN.}, }
@article {pmid39520618, year = {2025}, author = {Men, Z and Chen, Z and Gu, X and Wang, Y and Zhang, X and Fang, F and Shen, M and Huang, S and Wu, S and Zhou, L and Bai, Z}, title = {Clinical relevance of lung microbiota composition in critically ill children with acute lower respiratory tract infections: insights from a retrospective analysis of metagenomic sequencing.}, journal = {European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology}, volume = {44}, number = {1}, pages = {83-98}, pmid = {39520618}, issn = {1435-4373}, support = {H2023106//Medical Research Project of Jiangsu Provincial Commission of Health/ ; SKY2022178//Science and Technology Development Project of Suzhou/ ; SKJY2021108//Science and Technology Development Project of Suzhou/ ; BK20211077//Natural Science Foundation of Jiangsu Province/ ; BE2023714//Science and Technology Support Program of Jiangsu Province/ ; GSWS2019015//Gusu Health Talent Program/ ; ML13100423//Suzhou Medical College Clinician Scientist Program/ ; }, mesh = {Humans ; Retrospective Studies ; Male ; Female ; Child, Preschool ; *Metagenomics/methods ; Child ; *Lung/microbiology ; Infant ; *Microbiota/genetics ; *Respiratory Tract Infections/microbiology ; *Critical Illness ; *Bronchoalveolar Lavage Fluid/microbiology ; High-Throughput Nucleotide Sequencing ; Bacteria/classification/genetics/isolation & purification ; Prognosis ; Metagenome ; Severity of Illness Index ; Clinical Relevance ; }, abstract = {PURPOSE: Acute lower respiratory tract infections (ALRIs) is a leading cause of child mortality worldwide. Metagenomic next-generation sequencing (mNGS) identifies ALRIs pathogens and explores the lung microbiota's role in disease severity and clinical outcomes. This study examines the association between lung microbiota and ALRIs outcomes in children, exploring its potential as a prognostic biomarker.
METHODS: We retrospectively analyzed mNGS data from the bronchoalveolar lavage fluid (BALF) of 83 pediatric ALRIs patients from 2019 to 2023. Microbial diversity and relative abundances of specific taxa were compared between survivor and non-survivor groups, as well as between varying severity levels. LEfSe was employed to identify key biomarkers related to survival and disease severity.
RESULTS: Among the 83 patients, 68 survived and 15 died. Patients were also divided into a low severity group (n = 38) and a moderate-to-very-high severity group (n = 45) according to mPIRO score at admission. Significant differences in beta diversity were observed between the survival groups and across different severity levels. Prevotella, Haemophilus and Veillonella exhibited higher abundances in both the survivor and low severity groups, suggesting their potential as predictors of better outcomes. Conversely, Enterococcus and Acinetobacter baumannii were more prevalent in the non-survivor and moderate-to-very-high severity groups. Additionally, Streptococcus pneumoniae and Streptococcus mitis showed increased abundances in survivors. LEfSe further revealed that these microorganisms may predict outcomes and severity in ALRIs.
CONCLUSION: Our findings underscore the complex relationship between lung microbiota and ALRIs, with specific microbial profiles associated with disease severity and clinical outcomes. This underscores the need for further research to explore and validate its prognostic predictive capacity.
CLINICAL TRIAL NUMBER: Not applicable.}, }
@article {pmid39096471, year = {2025}, author = {Maharana, B and Mahalle, S and Bhende, R and Dafale, NA}, title = {Repercussions of Prolonged Pesticide Use on Natural Soil Microbiome Dynamics Using Metagenomics Approach.}, journal = {Applied biochemistry and biotechnology}, volume = {197}, number = {1}, pages = {73-93}, pmid = {39096471}, issn = {1559-0291}, mesh = {*Soil Microbiology ; *Microbiota/drug effects ; *Pesticides ; *Metagenomics ; Soil/chemistry ; Bacteria/genetics/drug effects/isolation & purification/classification ; }, abstract = {The residual pesticides in soil can affect the natural microbiome composition and genetic profile that drive nutrient cycling and soil fertility. In the present study, metagenomic approach was leveraged to determine modulations in nutrient cycling and microbial composition along with connected nexus of pesticide, antibiotic, and heavy metal resistance in selected crop and fallow soils having history of consistent pesticide applications. GC-MS analysis estimated residuals of chlorpyrifos, hexachlorbenzene, and dieldrin showing persistent nature of pesticides that pose selective pressure for microbial adaptation. Taxonomic profiling showed increased abundance of pesticide degrading Streptomyces, Xanthomonas, Cupriavidus, and Pseudomonas across the selected soils. Genes encoding for pesticide degrading cytochrome p450, organophosphorus hydrolase, aldehyde dehydrogenase, and oxidase were predominant and positively correlated with Bacillus, Sphingobium, and Burkholderia. Nitrogen-fixing genes (nifH, narB, and nir) were relatively less abundant in crop soils, correlating to the decrease in nitrogen-fixing bacteria (Anabaena, Pantoea, and Azotobacter). Microbial enzymes involved in carbon (pfkA, gap, pgi, and tpiA) and phosphorus cycle (gmbh and phnJ) were significantly higher in crop soils indicating extensive utilization of pesticide residuals as a nutrient source by the indigenous soil microbiota. Additionally, presence of antibiotic and heavy metal resistance genes suggested potential cross-resistance under pressure from pesticide residues. The results implied selective increase in pesticide degrading microbes with decrease in beneficial bacteria that resulted in reduced soil health and fertility. The assessment of agricultural soil microbial profile will provide a framework to develop sustainable agriculture practices to conserve soil health and fertility.}, }
@article {pmid39724786, year = {2025}, author = {Ma, X and Zhang, J and Jiang, Q and Li, YX and Yang, G}, title = {Human microbiome-derived peptide affects the development of experimental autoimmune encephalomyelitis via molecular mimicry.}, journal = {EBioMedicine}, volume = {111}, number = {}, pages = {105516}, pmid = {39724786}, issn = {2352-3964}, mesh = {*Encephalomyelitis, Autoimmune, Experimental/immunology/etiology/microbiology/metabolism ; Animals ; Humans ; *Molecular Mimicry ; Mice ; *Myelin-Oligodendrocyte Glycoprotein/immunology ; *Gastrointestinal Microbiome ; Multiple Sclerosis/etiology/immunology/microbiology/metabolism ; Peptides/immunology/chemistry ; Disease Models, Animal ; Protein Binding ; CD4-Positive T-Lymphocytes/immunology/metabolism ; Receptors, Antigen, T-Cell/metabolism ; Microbiota ; Peptide Fragments/immunology/metabolism ; Histocompatibility Antigens Class II/metabolism/immunology ; Female ; Computational Biology/methods ; }, abstract = {BACKGROUND: Gut commensal microbiota has been identified as a potential environmental risk factor for multiple sclerosis (MS), and numerous studies have linked the commensal microorganism with the onset of MS. However, little is known about the mechanisms underlying the gut microbiome and host-immune system interaction.
METHODS: We employed bioinformatics methodologies to identify human microbial-derived peptides by analyzing their similarity to the MHC II-TCR binding patterns of self-antigens. Subsequently, we conducted a range of in vitro and in vivo assays to assess the encephalitogenic potential of these microbial-derived peptides.
FINDINGS: We analyzed 304,246 human microbiome genomes and 103 metagenomes collected from the MS cohort and identified 731 nonredundant analogs of myelin oligodendrocyte glycoprotein peptide 35-55 (MOG35-55). Of note, half of these analogs could bind to MHC II and interact with TCR through structural modeling of the interaction using fine-tuned AlphaFold. Among the 8 selected peptides, the peptide (P3) shows the ability to activate MOG35-55-specific CD4[+] T cells in vitro. Furthermore, P3 shows encephalitogenic capacity and has the potential to induce EAE in some animals. Notably, mice immunized with a combination of P3 and MOG35-55 develop severe EAE. Additionally, dendritic cells could process and present P3 to MOG35-55-specific CD4[+] T cells and activate these cells.
INTERPRETATION: Our data suggests the potential involvement of a MOG35-55-mimic peptide derived from the gut microbiota as a molecular trigger of EAE pathogenesis. Our findings offer direct evidence of how microbes can initiate the development of EAE, suggesting a potential explanation for the correlation between certain gut microorganisms and MS prevalence.
FUNDING: National Natural Science Foundation of China (82371350 to GY).}, }
@article {pmid39647263, year = {2025}, author = {Fu, Y and Gou, W and Zhong, H and Tian, Y and Zhao, H and Liang, X and Shuai, M and Zhuo, LB and Jiang, Z and Tang, J and Ordovas, JM and Chen, YM and Zheng, JS}, title = {Diet-gut microbiome interaction and its impact on host blood glucose homeostasis: a series of nutritional n-of-1 trials.}, journal = {EBioMedicine}, volume = {111}, number = {}, pages = {105483}, pmid = {39647263}, issn = {2352-3964}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Blood Glucose/metabolism ; *Homeostasis ; Female ; Male ; Adult ; Metagenomics/methods ; Diet ; Middle Aged ; Metagenome ; Dietary Carbohydrates/metabolism ; }, abstract = {BACKGROUND: The interplay between diet and gut microbiome substantially influences host metabolism, but uncertainties remain regarding their relationships tailored for each subject given the huge inter-individual variability. Here we aim to investigate diet-gut microbiome interaction at single-subject resolution and explore its effects on blood glucose homeostasis.
METHODS: We conducted a series of nutritional n-of-1 trials (NCT04125602), in which 30 participants were assigned high-carbohydrate (HC) and low-carbohydrate (LC) diets in a randomized sequence across 3 pair of cross-over periods lasting 72 days. We used shotgun metagenomic sequencing and continuous glucose monitoring systems to profile the gut microbiome and blood glucose, respectively. An independent cohort of 1219 participants with available metagenomics data are included as a validation cohort.
FINDINGS: We demonstrated that the gut microbiome exhibited both intra-individually dynamic and inter-individually personalized signatures during the interventions. At the single-subject resolution, we observed person-specific response patterns of gut microbiota to interventional diets. Furthermore, we discovered a personal gut microbial signature represented by a carb-sensitivity score, which was closely correlated with glycemic phenotypes during the HC intervention, but not LC intervention. We validate the role of this score in the validation cohort and find that it reflects host glycemic sensitivity to the personal gut microbiota profile when sensing the dietary carbohydrate inputs.
INTERPRETATION: Our finding suggests that the HC diet modulates gut microbiota in a person-specific manner and facilitates the connection between gut microbiota and glycemic sensitivity. This study represents a new paradigm for investigating the diet-microbiome interaction in the context of precision nutrition.
FUNDING: This work was supported by the National Key R&D Program of China, National Natural Science Foundation of China and Zhejiang Provincial Natural Science Foundation of China.}, }
@article {pmid39644773, year = {2025}, author = {Hu, Y and Hu, X and Jiang, L and Luo, J and Huang, J and Sun, Y and Qiao, Y and Wu, H and Zhou, S and Li, H and Li, J and Zhou, L and Zheng, S}, title = {Microbiome and metabolomics reveal the effect of gut microbiota on liver regeneration of fatty liver disease.}, journal = {EBioMedicine}, volume = {111}, number = {}, pages = {105482}, pmid = {39644773}, issn = {2352-3964}, mesh = {Animals ; *Gastrointestinal Microbiome ; *Liver Regeneration ; Mice ; *Metabolomics/methods ; *Fatty Liver/metabolism/etiology/microbiology ; Male ; Diet, High-Fat/adverse effects ; Disease Models, Animal ; Metabolome ; Hepatectomy ; Mice, Inbred C57BL ; Metagenomics/methods ; Liver/metabolism ; RNA, Ribosomal, 16S/genetics ; Akkermansia ; }, abstract = {BACKGROUND: Metabolic dysfunction-associated fatty liver disease (MAFLD) is associated with impaired regenerative capacity and poor postoperative prognosis following hepatectomy. Previous research has highlighted the importance of the gut-liver axis in the physiological and pathological processes of the liver. However, the contribution of gut bacteria to the regeneration of livers with MAFLD and its metabolic regulatory mechanisms remain elusive.
METHODS: Partial hepatectomy (PHx) was performed on C57Bl/6J mice fed with high-fat diet (HFD) for 12 weeks. Pathological examination, immunohistochemistry, and qRT-PCR analysis were performed to assess the severity of steatosis and proliferative potential. The gut microbiome was examined by 16S rRNA gene sequencing and shotgun metagenomics, whereas liver metabolomics was analysed via untargeted and targeted metabolomics using liquid chromatography-tandem mass spectrometry (LC-MS).
FINDINGS: HFD-induced hepatic steatosis in mice led to impaired liver regeneration following PHx. The gut microbiota and liver metabolites were altered along with the liver regeneration process. Longitudinal time-series analysis revealed dynamic alterations in these data, whereas correlation analysis screened out bacterial candidates that potentially influence liver regeneration in MAFLD by modulating metabolic pathways. Among these bacteria, the dominant bacterium Akkermansia was selected for subsequent investigation. MAFLD mice gavaged with Akkermansia muciniphila (A. muciniphila) exhibited reduced liver lipid accumulation and accelerated liver regeneration, possibly through the regulation of the tricarboxylic acid (TCA) cycle.
INTERPRETATION: These data demonstrated the interplay between the gut microbiome, liver metabolomics, and liver regeneration in mice with MAFLD. A. muciniphila has the potential to serve as a clinical intervention agent to accelerate postoperative recovery in MAFLD.
FUNDING: This work was supported by the Research Project of Jinan Microecological Biomedicine Shandong Laboratory [JNL-2022008B]; the Zhejiang Provincial Natural Science Foundation of China [LZ21H180001]; the Fundamental Research Funds for the Central Universities [No. 2022ZFJH003].}, }
@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.}, }
@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.}, }
@article {pmid39709798, year = {2025}, author = {Wang, RX and Zhou, HB and Gao, JX and Bai, WF and Wang, J and Bai, YC and Jiang, SY and Chang, H and Shi, SL}, title = {Metagenomics and metabolomics to investigate the effect of Amygdalus mongolica oil on intestinal microbiota and serum metabolites in rats.}, journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology}, volume = {136}, number = {}, pages = {156335}, doi = {10.1016/j.phymed.2024.156335}, pmid = {39709798}, issn = {1618-095X}, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; Male ; *Metabolomics ; *Rats, Sprague-Dawley ; Rats ; Metagenomics ; Plant Oils/pharmacology ; Fibrosis ; Kidney/drug effects ; Renal Insufficiency, Chronic/blood/drug therapy/microbiology ; }, abstract = {BACKGROUND: Renal fibrosis (RF) is an inevitable consequence of multiple manifestations of progressive chronic kidney diseases (CKDs). Mechanism of Amygdalus mongolica (Maxim.) in the treatment of RF needs further investigation.
PURPOSE: The study further investigated the potential mechanism of A. mongolica in the treatment of RF.
METHODS: A rat model of RF was induced by unilateral ureteral obstruction (UUO), followed by treatment with varying dosages of A. mongolica oil for 4 weeks. Body weight was measured weekly. We detected serum levels of interleukin (IL)-6, IL-1β, type Ⅲ procollagen (Col-Ⅲ), type IV collagen (Col-Ⅳ), laminin (LN), hyaluronidase (HA), and tissue levels of albumin (ALB), blood urea nitrogen (BUN), creatinine (Cre), superoxide dismutase (SOD), malondialdehyde (MDA), and hydroxyproline (HYP). Shotgun metagenomics analyzed the composition of the intestinal microbiota. High-performance liquid chromatography coupled with a quadrupole-exactive mass spectrometer (HPLC-Q-Exactive-MS) monitored changes in metabolite levels in serum and gut. Multiple reaction monitoring-mass spectrometry (MRM-MS) determined the levels of amino acids in serum.
RESULTS: A. mongolica oil significantly alleviated indicators related to RF (p < 0.05). A. mongolica oil reduced the ratio of Firmicutes to Bacteroidetes and restored the balance of intestinal microbiota in rats with RF. A. mongolica oil modulated levels of metabolites in gut content and serum. It regulated 11 metabolic pathways including arachidonic acid metabolism. Targeted metabolomics of amino acids showed that 17 amino acids were significantly changed by A. mongolica oil, including L-glycine, L-serine and L-glutamine.
CONCLUSION: A. mongolica oil regulates intestinal microbiota and metabolites, restoring amino acid metabolism to treat RF.}, }
@article {pmid39591767, year = {2025}, author = {Geng, Q and Wang, Z and Shi, T and Wen, C and Xu, J and Jiao, Y and Diao, W and Gu, J and Wang, Z and Zhao, L and Deng, T and Xiao, C}, title = {Cannabidiol regulates L-carnitine and butyric acid metabolism by modulating the gut microbiota to ameliorate collagen-induced arthritis.}, journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology}, volume = {136}, number = {}, pages = {156270}, doi = {10.1016/j.phymed.2024.156270}, pmid = {39591767}, issn = {1618-095X}, mesh = {Animals ; *Cannabidiol/pharmacology ; *Gastrointestinal Microbiome/drug effects ; *Arthritis, Experimental/drug therapy/metabolism ; *Carnitine/pharmacology ; *Butyric Acid/pharmacology ; Rats ; *Dysbiosis/drug therapy ; Male ; *Arthritis, Rheumatoid/drug therapy ; }, abstract = {BACKGROUND: Rheumatoid arthritis (RA) is one of the most common autoimmune diseases, affecting multiple systems in the body. Cannabidiol (CBD) is one of the most medically valuable active ingredients in cannabis. At present, CBD has been shown to alleviate the progression of RA; however, owing to its multiple targets, the mechanism of CBD is not clear.
METHODS: On the basis of the gut microbiota, we explored the mechanism by which CBD inhibits RA progression. Metagenomic and nontargeted metabolomic analyses were used to determine the changes in the intestinal ecology and plasma metabolites of collagen-induced arthritis (CIA) rats after CBD treatment.
RESULTS: CBD reversed gut dysbiosis in CIA rats, notably altering the abundances of Allobaculum_unclassified, Allobaculum_fili, and Prevotella_unclassified. In addition, metabolomic analysis confirmed that CBD increased the contents of butyric acid and L-carnitine. Allobaculum could produce butyric acid and Prevotella could accelerate the metabolism of L-carnitine. In addition, in vitro experiments demonstrated that L-carnitine participated in the regulation of neutrophils, macrophages and RA-fibroblast-like synoviocytes (RA-FLSs), which was consistent with the synovial changes in CIA rats caused by CBD.
CONCLUSION: In summary, CBD increased the plasma contents of butyric acid and L-carnitine by altering the abundances of gut microbiota, thereby inhibiting inflammation in neutrophils, macrophages and RA-FLSs. Our study is the first to explain the mechanism by which CBD alleviates progression in CIA rats from the perspective of gut microbes and metabolites, providing new views into CBD mechanisms, which warrants clinical attention.}, }
@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.}, }
@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.}, }
@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.}, }
@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/ ; }, mesh = {Humans ; Child ; *Virome ; Male ; Female ; *Mycoplasma pneumoniae/genetics/isolation & purification/classification ; *Pneumonia, Mycoplasma/epidemiology/microbiology/virology ; Viruses/classification/isolation & purification/genetics ; Metagenomics ; Bronchoalveolar Lavage Fluid/virology/microbiology ; Respiratory System/virology/microbiology ; COVID-19/virology/epidemiology ; Respiratory Tract Infections/virology/microbiology/epidemiology ; Adolescent ; }, 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/ ; }, mesh = {*Soil Microbiology ; *Bacteria/genetics/classification/isolation & purification/drug effects ; *Anti-Bacterial Agents/pharmacology ; *Microbiota/genetics ; Metagenomics ; Genes, Bacterial/genetics ; Drug Resistance, Microbial/genetics ; Oxytetracycline/pharmacology ; Soil/chemistry ; Drug Resistance, Bacterial/genetics ; }, 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/ ; }, mesh = {Animals ; *Lithocholic Acid/metabolism ; *Gastrointestinal Microbiome/drug effects ; *Colitis/microbiology/pathology/chemically induced/metabolism ; Humans ; *Dextran Sulfate ; *Mice, Inbred C57BL ; Male ; Inflammation/pathology ; Feces/microbiology ; Female ; Colon/pathology/microbiology/metabolism ; Bile Acids and Salts/metabolism ; Inflammatory Bowel Diseases/microbiology/pathology/metabolism ; Mice ; Signal Transduction ; Middle Aged ; }, 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 {pmid39740461, year = {2025}, author = {Rana, S and Pandey, H and Shridhar, V and Tiwary, P and Kukreti, S and Arunachalam, K and Singh, V}, title = {Structural and functional analysis of rhizospheric bacterial diversity in the Pranmati basin, Himalayan critical zone observatory.}, journal = {Journal of environmental management}, volume = {373}, number = {}, pages = {123872}, doi = {10.1016/j.jenvman.2024.123872}, pmid = {39740461}, issn = {1095-8630}, mesh = {*Soil Microbiology ; *Rhizosphere ; Bacteria ; Soil/chemistry ; Microbiota ; Ecosystem ; Biodiversity ; Forests ; }, abstract = {The study explores the structural and functional dynamics of rhizospheric bacterial diversity in the Pranmati basin, focusing on their ecological significance, diversity, and functional roles across dominant vegetation types; Rhododendron arboreum, Myrica esculenta, and Quercus leucotrichophora. The research provides critical insights into soil health and ecosystem functioning by analysing rhizospheric soil properties among the selected vegetations. The research findings reveal that Myrica esculenta exhibits the highest root colonization (95.8%) and moisture content (92.6%), while Quercus leucotrichophora shows the lowest (76.2% and 83.2%), respectively. The microbial community is predominantly composed of Proteobacteria, with 62-65% abundance across different vegetation types. Key genera such as Bacillus, Acinetobacter, and Paenibacillus are notably enriched, highlighting their significant role in phosphate solubilization and nutrient cycling. Venn diagram analysis identified 136 common bacterial species among vegetation types reflecting ecological significance in forest ecosystem. The functional metabolism, diversity indices, and core microbiome analysis underscore the distinct microbial profiles associated with different vegetation types, which are crucial for overall forest soil health. The importance of this research lies in its contribution to environmental management by providing a comprehensive understanding of how microbial communities interact with various vegetation types and influence soil health in the Pranmati basin. These insights are essential for developing targeted strategies to enhance soil fertility and manage forest ecosystems in terms of conservation and restoration efforts in sensitive ecological regions. This study is pioneer as it establishes a functional analysis of rhizospheric bacterial diversity in the Pranmati basin, offering a baseline data for future research on bacterial community structure and their functional role in Himalayan Critical Zone Observatory to the best of our knowledge.}, }
@article {pmid39733577, year = {2025}, author = {Heisi, HD and Nkuna, R and Matambo, T}, title = {Rhizosphere microbial community structure and PICRUSt2 predicted metagenomes function in heavy metal contaminated sites: A case study of the Blesbokspruit wetland.}, journal = {The Science of the total environment}, volume = {959}, number = {}, pages = {178147}, doi = {10.1016/j.scitotenv.2024.178147}, pmid = {39733577}, issn = {1879-1026}, mesh = {*Wetlands ; *Metals, Heavy/analysis ; *Biodegradation, Environmental ; *Microbiota ; *Rhizosphere ; South Africa ; *Soil Microbiology ; Soil Pollutants/analysis ; Metagenome ; Bacteria/classification/genetics ; Eichhornia/microbiology ; Fungi ; Poaceae/microbiology ; Typhaceae ; }, abstract = {This study investigated the microbial diversity inhabiting the roots (rhizosphere) of macrophytes thriving along the Blesbokspruit wetland, South Africa's least conserved Ramsar site. The wetland suffers from decades of pollution from mining wastewater, agriculture, and sewage. The current study focused on three macrophytes: Phragmites australis (common reed), Typha capensis (bulrush), and Eichhornia crassipes (water hyacinth). The results revealed a greater abundance and diversity of microbes (Bacteria and Fungi) associated with the free-floating E. crassipes compared to P. australis and T. capensis. Furthermore, the correlation between microbial abundance and metals, showed a strong correlation between fungal communities and metals such as nickel (Ni) and arsenic (As), while bacterial communities correlated more with lead (Pb) and chromium (Cr). The functional analysis predicted by PICRUSt2 identified genes related to xenobiotic degradation, suggesting the potential of these microbes to break down pollutants. Moreover, specific bacterial groups - Proteobacteria, Verrucomicrobia, Cyanobacteria, and Bacteroidetes - were linked to this degradation pathway. These findings suggest a promising avenue for microbe-assisted phytoremediation, a technique that utilizes plants and their associated microbes to decontaminate polluted environments.}, }
@article {pmid39729842, year = {2025}, author = {Wang, M and Zhao, J and Gu, Y and Wu, Y and Liu, Y and Tang, Z and Xu, Y and Mao, X and Zhang, J and Tian, W}, title = {Deciphering the mechanism of rhizosphere microecosystem in modulating rice cadmium accumulation via integrating metabolomics and metagenomics.}, journal = {The Science of the total environment}, volume = {959}, number = {}, pages = {178181}, doi = {10.1016/j.scitotenv.2024.178181}, pmid = {39729842}, issn = {1879-1026}, mesh = {*Cadmium/metabolism/analysis ; *Oryza/microbiology/metabolism ; *Rhizosphere ; *Soil Pollutants/metabolism/analysis ; Metabolomics ; Metagenomics ; Soil Microbiology ; Microbiota ; }, abstract = {Cadmium (Cd) accumulation in rice poses significant risks to human health. The Cd accumulation levels vary widely among cultivars and are strongly associated with the rhizosphere microecosystem. However, the underlying mechanisms remain poorly understood. Here, we conducted a field experiment in Cd-contaminated areas with 24 popular regional cultivars. These cultivars were categorized into high Cd accumulation (HA) and low Cd accumulation (LA) groups based on their grain Cd content. Rhizosphere soil physicochemical properties were monitored, and key metabolites, microbiomes, and their interaction contributing to Cd accumulation were analyzed using omics-sequencing technologies and bioinformatics analysis. Metabolomic analysis identified distinct rhizosphere metabolite profiles between the HA and LA groups, with key metabolites showing strong correlations with Cd accumulation. Key metabolites in the LA group were linked to reduced Cd uptake and enhanced antioxidant defense mechanisms, while those in the HA group were associated with increased Cd mobility and uptake. Metagenomic analysis of the rhizosphere soil showed that the LA group harbored a more diverse and interconnected microbial community, with tax such as Syntrophaceae, Anaerolineae, Thermoflexales, and Syntrophales, along with metabolite such as disopyramide, playing central roles in Cd immobilization and detoxification. Additionally, the enhanced carbon, nitrogen, and phosphorus cycling in the LA group suggests a more robust nutrient assimilation process that supports plant growth and reduces Cd uptake. This study highlights the critical role of the rhizosphere microecosystem in regulating Cd accumulation and underscores the potential of selecting rice cultivars with favorable rhizosphere traits as a strategy for reducing Cd uptake.}, }
@article {pmid39721532, year = {2025}, author = {Chauhan, A and Jain, A and Kolton, M and Pathak, A}, title = {Impacts of long-term irrigation of municipally-treated wastewater to the soil microbial and nutrient properties.}, journal = {The Science of the total environment}, volume = {959}, number = {}, pages = {178143}, doi = {10.1016/j.scitotenv.2024.178143}, pmid = {39721532}, issn = {1879-1026}, mesh = {*Wastewater ; *Soil Microbiology ; *Agricultural Irrigation/methods ; *Soil/chemistry ; *Waste Disposal, Fluid/methods ; Microbiota ; Nitrogen/analysis ; }, abstract = {Reusing treated wastewater (TWW) for crop irrigation has shown to provide environmental and economic benefits as well as drawbacks. This study was conducted using soils collected from a wastewater reuse facility in Tallahassee, FL, mainly to elucidate the long-term impact(s) of TWW irrigation on soil microbiome and nutrient status. Approximately 890 ha of land have been spray-irrigated with TWW since the 1980's to grow fodder crops. Soil cores were collected from six irrigated and six control sites at depths of 0-15, 15-30, and 30-60 cm during summer and winter, followed by nutrient analysis and assessment of bacterial, fungal, and denitrifier communities using SSU rRNA, ITS, nirK, nirS, and nosZ phylogenetic markers. TWW irrigation significantly increased soil pH, soluble salts, nitrate, phosphate, calcium, magnesium, and organic matter, alongside shifts in the prokaryotic and fungal community structures, particularly in summer. Beta-diversity analyses indicated that wastewater quality and season collectively explained 23 % of prokaryotic community similarity and 9.8 % of fungal community dissimilarity. Indicator species analysis, supported by random forest machine learning, identified 37 prokaryotic and 11 fungal bioindicators whose occurrences varied significantly with wastewater quality and season. Key nitrogen-cycling microbes included ammonia-oxidizing families of Nitrosomonadaceae, Nitrosopumilaceae, Nitrososphaeraceae, Nitrosotaleaceae, and comammox-performing Nitrospiraceae. The fungal community was predominated by Ascomycota (78.6 % ± 4.2 %). FUNGuild analysis showed dominant trophic levels of symbiotrophs, saprotrophs, and pathotrophs, averaging 42 % ± 7.1 %. Overall, this study points to the long-term impacts of TWW irrigation on the studied soil properties and microbial communities.}, }
@article {pmid39700995, year = {2025}, author = {Xu, X and Hao, Y and Cai, Z and Cao, Y and Jia, W and Zhao, J and White, JC and Ma, C}, title = {Nanoscale‑boron nitride positively alters rhizosphere microbial communities and subsequent cucumber (Cucumis sativa) growth: A metagenomic analysis.}, journal = {The Science of the total environment}, volume = {958}, number = {}, pages = {178115}, doi = {10.1016/j.scitotenv.2024.178115}, pmid = {39700995}, issn = {1879-1026}, mesh = {*Rhizosphere ; *Soil Microbiology ; *Cucumis sativus/microbiology ; *Microbiota/drug effects ; Metagenomics ; Boron Compounds ; Plant Growth Regulators ; Soil/chemistry ; }, abstract = {Boron (B) deficiency affects over 132 crop species globally, making effective B supplement crucial for enhancing agricultural yield and health. This study explores an innovative application of nanoscale boron nitride (nano-BN) as a sustainable solution for addressing B deficiency in crops. Cucumber seedlings were treated with different contents of nano-BN under greenhouse conditions and both B and N ionic treatments were set as comparisons. Results show that soil application of 10 mg/kg nano-BN achieved a remarkable 15.8 % increase in fresh weight compared to the control. Notably, nano-BN exhibited superior efficiency in providing essential micronutrients without inducing toxicity as compared to traditional ionic B sources. Phytohormone correlation analysis reveals that nano-BN application significantly enhances levels of indole-3-acetic acid (IAA) and cytokinins while reducing abscisic acid (ABA), fostering optimal plant growth conditions. Furthermore, increases in dissolved organic matter (DOM) and dissolved organic carbon (DOC) levels in the rhizosphere improve nutrient availability and promote beneficial microbial activity in the soil as affected by nano-BN. Metagenomics techniques were used to investigate the impact of nano-BN on soil carbon and nitrogen cycling, alongside its effects on the soil microbiome. The upregulation of genes associated with fermentation pathways as affected by nano-BN suggests the enhanced carbon cycling. Additionally, nano-BN upregulated a number of functional genes involved in nitrogen-based processes, leading to a significant increase in microorganisms harboring nitrogen-fixing genes, including Phenylobacterium, Novosphingobium, and Reyranella. Overall, these findings provide valuable insight into the application of nano-BN in agriculture to sustainably increase crop productivity and enhance the efficiency of carbon and nitrogen cycling.}, }
@article {pmid39700989, year = {2025}, author = {Liu, F and Zeng, J and Ding, J and Wang, C and He, Z and Liu, Z and Shu, L}, title = {Microbially-driven phosphorus cycling and its coupling mechanisms with nitrogen cycling in mangrove sediments.}, journal = {The Science of the total environment}, volume = {958}, number = {}, pages = {178118}, doi = {10.1016/j.scitotenv.2024.178118}, pmid = {39700989}, issn = {1879-1026}, mesh = {*Phosphorus/metabolism ; *Geologic Sediments/microbiology ; *Nitrogen/metabolism ; *Nitrogen Cycle ; Microbiota ; Wetlands ; Bacteria/metabolism ; }, abstract = {The phosphorus (P) cycle plays a crucial role in the biogeochemical cycling of mangrove sediments. However, the diversity of microbially-driven P-cycling and its coupling with nitrogen (N)-cycling remain poorly understood. In this study, we used metagenomic approaches to investigate microbial P-cycling and its potential interactions with N-cycling in mangrove sediments. Our results revealed that pH, total carbon, and total nitrogen were key environmental factors influencing the diversity of P-cycling microbial communities. Phosphorus metabolic pathways differed among mangrove sediment depths. In surface sediments (0-5 cm), microbial communities primarily acquired readily available inorganic phosphorus, whereas, in deeper sediments (>60 cm), they hydrolyzed more persistent triphosphates, reabsorbed nucleotides, and sourced free phosphate, reflecting a shift in phosphorus transport modes. We also identified glutamate metabolism as a potential pathway linking P-cycling with N-cycling, with these functions co-occurring in both contigs and genomes. Additionally, the diversity of microbial communities associated with the P-cycling increased with sediment depth, suggesting that microbially-driven P-cycling diversifies as depth increases. This study provides new insights into P-cycling and its potential coupling with N-cycling through glutamate metabolism, its coupling with N-cycling through glutamate metabolism.}, }
@article {pmid39674156, year = {2025}, author = {Erkorkmaz, BA and Zeevi, D and Rudich, Y}, title = {Dust storm-driven dispersal of potential pathogens and antibiotic resistance genes in the Eastern Mediterranean.}, journal = {The Science of the total environment}, volume = {958}, number = {}, pages = {178021}, doi = {10.1016/j.scitotenv.2024.178021}, pmid = {39674156}, issn = {1879-1026}, mesh = {*Dust/analysis ; *Drug Resistance, Microbial/genetics ; *Air Microbiology ; Environmental Monitoring ; Iran ; Saudi Arabia ; Iraq ; Microbiota/drug effects ; Air Pollutants/analysis ; }, abstract = {The atmosphere hosts a microbiome that connects distant ecosystems yet remains relatively unexplored. In this study, we tested the hypothesis that dust storms enhance the spread of pathogenic microorganisms and whether these microorganisms carry antibiotic resistance and virulence-related genes in the Eastern Mediterranean. We collected air samples during a seasonal transition period, capturing data from 13 dusty days originating from Middle Eastern sources, including the Saharan Desert, Iraq, Iran, and Saudi Arabia, and 32 clear days, with temperatures ranging from 16.5 to 27.1 °C. Using metagenomic analysis, we identified several facultative pathogens like Klebsiella pneumoniae, Stenotrophomonas maltophilia, and Aspergillus fumigatus, which are linked to human respiratory diseases, and others like Zymoseptoria tritici, Fusarium poae, and Puccinia striiformis, which are harmful to wheat. The abundance of these pathogens increased during dust storms and with rising temperatures. Although we did not find strong evidence that these species harbored antibiotic resistance or virulence-related genes, which could be linked to their pathogenic potential, dust storms transported up to 125 times more total antibiotic resistance genes, as measured by RPKM abundance, compared to clear conditions. These levels during dust storms far exceeded those found in other ecosystems. While further research is needed to determine whether dust storms and temperature variations pose an immediate threat to public health and the environment, our findings underscore the importance of continuous monitoring of atmospheric microbiomes. This surveillance is crucial for assessing potential risks to human health and ecosystem stability, particularly in the face of accelerating global climate change.}, }
@article {pmid39671945, year = {2025}, author = {Justine, EE and Lee, HJ and Jung, KH and Lee, YS and Kim, YJ}, title = {Methane emission mitigation of Paenibacillus yonginensis DCY84[T] incorporated with silicate on paddy rice (Oryzae sativa L.) plantation revealed in soil microbiome profiling.}, journal = {The Science of the total environment}, volume = {958}, number = {}, pages = {177996}, doi = {10.1016/j.scitotenv.2024.177996}, pmid = {39671945}, issn = {1879-1026}, mesh = {*Oryza/microbiology ; *Soil Microbiology ; *Silicates ; *Methane/metabolism ; *Paenibacillus/physiology/metabolism ; *Microbiota ; Biodegradation, Environmental ; Agriculture/methods ; }, abstract = {Anthropogenic methane emissions from paddy cultivation contribute to greenhouse gas levels owing to the anaerobic conditions in flooded rice fields, which promotes the activity of methanogenic bacteria. This study explored bioremediation strategies to mitigate methane release through the application of plant growth-promoting rhizobacteria combined with silicate in rice cultivation. Rice seeds were coated with Paenibacillus yonginensis DCY84[T], with and without the addition of silicate, prior to sowing. Results revealed notable reduction in methane flux during the peak growth stage of rice in seeds treated with DCY84[T] (27.215 ± 1.975 mg m[-2] h[-1]), with a further reduction observed when silicate was also applied (23.592 ± 3.112 mg m[-2] h[-1]), compared to untreated seeds (37.305 ± 2.990 mg m[-2] h[-1]). Additionally, treatment with DCY84[T] (28.24 ± 0.55 g) resulted in an increase in rice yield (p < 0.05), as evidenced by a greater 1000-grain weight compared to both the control group (26.91 ± 0.09 g) and the application of silicate (27.37 ± 0.57 g). The beta diversity of the soil microbial community highlighted distinct differences between the treated and control groups, indicating DCY84[T] inoculation with or without silicate altered the soil microbial structure. Particularly, the treated groups showed dominance of the phylum Proteobacteria, especially the classes Alphaproteobacteria and Deltaproteobacteria. Furthermore, the addition of silicate to DCY84[T]-coated rice seeds resulted in a higher abundance of bacterial families, such as Anaerolinaceae, Clostridiceae, and Nitrospirae which compete with methanogens for organic substrates, thereby reducing their methane production. Notably, the DCY84[T]-silicate treatment group showed higher levels of methane metabolism biomarkers such as formate dehydrogenase within the soil microbiome, which correlated with the observed reduction in methane emissions. These findings suggest that coating rice seeds with DCY84[T] and silicate prior to sowing effectively mediates methane production and release during rice cultivation by promoting beneficial soil bacterial communities.}, }
@article {pmid39667337, year = {2025}, author = {Chen, YT and Reid, T and Weisener, C}, title = {Microbial community and functional shifts across agricultural and urban landscapes within a Lake Erie watershed.}, journal = {Journal of environmental management}, volume = {373}, number = {}, pages = {123683}, doi = {10.1016/j.jenvman.2024.123683}, pmid = {39667337}, issn = {1095-8630}, mesh = {*Lakes/microbiology ; *Agriculture ; *Nitrogen/metabolism/analysis ; *Microbiota ; Ontario ; Ecosystem ; }, abstract = {The role of sediment microbial communities in regulating the loss and retention of nutrients in aquatic ecosystems has been increasingly recognised. However, in the Great Lakes, where nutrient mitigation focuses on harmful algal blooms, there are limited studies examining the fundamental role of water/sediment microbes in nutrient biogeochemical cycling. Little is understood in this regard considering the increase in anthropogenic pressure on in-stream biological processes impacting nutrient flux to lakes. In this study, metagenomic and metatranscriptomic approaches were used to investigate the microbial community and gene regulation. The study focused on nitrogen (N) metabolism in a nutrient-polluted watershed of Lake Erie in southwestern Ontario, Canada. Nutrients and microbial analyses of water and sediments were collected in 2020 and 2021 from Sturgeon Creek headwaters to the nearshore of Lake Erie. Results showed no significant shifts in community structure with nutrient concentrations or land use. Metabolically, active genes involved in denitrification (consisting of 32-53% of N metabolic transcripts) showed the highest expression within agricultural and wetland dominant locations. Based on active gene expression patterns, the urbanised location coinciding with peak nitrate (NO3[-]) concentrations showed the greatest potential for nitrous oxide (N2O) emission and nitrogen loss along this transect. In contrast to denitrification, direct nitrification (5-21% of N metabolic transcripts) increased two-fold approaching downstream and nearshore lake locations. Across this river-lake corridor, expression of key functional genes associated with N transformation showed strong correlation with the change in concentrations of aqueous NO3[-] and nitrite (NO2[-]) and the ratio of NO2[-]/NO3[-]. Our findings demonstrated a clear link between sediment microbial metabolism and overlying water chemistry in this lotic system. We suggest that future studies assessing nutrient mitigation consider sediment biogeochemical processes and N-metabolising bacteria, and their fundamental role and cooperative relationship with nutrient and hydrological dynamics of overlying waters.}, }
@article {pmid39662407, year = {2025}, author = {Wang, Y and Yi, H and Li, G and Li, A and Wang, H and Ding, D}, title = {Influence of enriched nitrate reducing bacteria communities on bacterial community structure and groundwater condition during in situ bioremediation of nitrate in acidic uranium-contaminated groundwater.}, journal = {The Science of the total environment}, volume = {958}, number = {}, pages = {177896}, doi = {10.1016/j.scitotenv.2024.177896}, pmid = {39662407}, issn = {1879-1026}, mesh = {*Groundwater/microbiology/chemistry ; *Nitrates/metabolism ; *Biodegradation, Environmental ; *Uranium/metabolism ; *Bacteria/metabolism ; China ; *Water Pollutants, Radioactive/metabolism ; Microbiota ; Water Pollutants, Chemical/metabolism/analysis ; }, abstract = {In-situ leaching (ISL) is the predominant technology used in uranium mining currently, although it leads to significant environmental challenges. Nitrates, a key component in leaching agents, not only pose a threat to human health but also impede the bioreduction of U(VI) in uranium-contaminated water. In this study, the nitrate reducing bacterial (NRB) communities adapted to acidic uranium-contaminated groundwater from a site in Northwest China were gained by an enrichment micro-model. The effects of the NRB communities on the groundwater parameters and microbial diversity were evaluated using the groundwater-core column leaching system during the in-situ bioremediation of nitrate. The enrichment experiments revealed that NRB communities adapted to acidic uranium-contaminated groundwater were successfully enriched, of which Tumebacillus was the main functional bacterium. The column leaching experiment results showed that adding NRB communities successfully reduced nitrate levels from 100.91 mg/L to 0.7 mg/L in just 8 days, improved groundwater acidity and redox conditions. Additionally, the metagenomic analysis showed that introducing NRB communities increased biomass and indigenous NRB, but decreased microbial diversity. The KEGG enrichment analysis suggested that butanoate metabolism and valine, leucine and isoleucine degradation were promoted by adding enriched NRB communities. This research lays the groundwork for nitrate removal from contaminated groundwater in areas affected by ISL in uranium mines, setting the stage for future in situ bioremediation of U(VI).}, }
@article {pmid39647796, year = {2025}, author = {Zhu, Y and Zhao, S and Qi, S and Zhang, H and Zhang, X and Li, S and Wang, X and Gu, J and Zhang, T and Xi, H and Liu, X}, title = {Effects of energetic compounds on soil microbial communities and functional genes at a typical ammunition demolition site.}, journal = {Chemosphere}, volume = {370}, number = {}, pages = {143913}, doi = {10.1016/j.chemosphere.2024.143913}, pmid = {39647796}, issn = {1879-1298}, mesh = {*Soil Microbiology ; *Trinitrotoluene/toxicity ; *Soil Pollutants/toxicity ; *Triazines ; *Microbiota/drug effects ; *Azocines ; Explosive Agents/toxicity ; Soil/chemistry ; Proteobacteria/genetics/drug effects ; Metagenomics ; }, abstract = {High concentrations of energetic compounds such as 2,4,6-trinitrotoluene (TNT), hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX), and octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) in military-contaminated sites pose a serious threat to human health and ecosystems. Better understanding about their effects on microbial diversity and functional genes in soil of ammunition demolition sites is required. In this study, the information of soil microbial community composition was obtained by metagenomic sequencing, and the impacts of energetic compounds on microbial community structure at the level of functional genes and enzymes based on Nr (Non-Redundant Protein Sequence Database), KEGG (Kyoto Encyclopedia of Genes and Genomes), CAZy (Carbohydrate-Active enZymes Database) and other databases were discussed. The results showed that soil microbial diversity and functional gene abundance decreased significantly with the increase of the concentrations of energetic compounds. Conversely, the relative abundance of Proteobacteria increased significantly, reaching over 80% in the heavily TNT-contaminated area near explosive-wastewater pool. Furthermore, functional gene analysis indicated that Proteobacteria had an advantage in degrading energetic compounds, and thus had the potential to improve the soil quality at ammunition demolition sites. This study provides a scientific basis for the future remediation and management of contaminated soils at ammunition demolition sites, as well as for the selection of efficient degraders of energetic compounds.}, }
@article {pmid39642837, year = {2025}, author = {Li, Y and Liu, K and Qiu, H and Chen, F and Zhang, J and Zheng, Z}, title = {Dynamics of antibiotic resistance genes and bacterial community structure within substrate biofilms.}, journal = {Journal of environmental management}, volume = {373}, number = {}, pages = {123512}, doi = {10.1016/j.jenvman.2024.123512}, pmid = {39642837}, issn = {1095-8630}, mesh = {*Biofilms/drug effects ; Drug Resistance, Microbial/genetics ; Wastewater/microbiology ; Anti-Bacterial Agents/pharmacology ; Bacteria/genetics/drug effects ; Genes, Bacterial ; Microbiota ; }, abstract = {Biofilms that develop on the surface of substrates are critical for treating wastewater. The accumulation of antibiotic resistance genes (ARGs) within these biofilms is particularly noteworthy. Despite their importance, studies that focus on biofilms attached to substrate surfaces remain scarce. This investigation explored the prevalence and succession of ARGs and microbial dynamics in biofilms on different substrates (ceramic, biomass filter, and steel slag) versus water biofilms over a year. Results showed distinct differences in ARG profiles between water and substrate biofilms. Multidrug ARGs constituted 39.14-46.73% of all ARGs in the substrate biofilms, with macrolide ARGs making up 11.98-14.52%. Seasonal variations influenced the diversity of the ARGs, notably increasing during the spring. The neutral community model suggested that the ARG assembly was dominantly driven by stochastic process. Proteobacteria, Actinobacteria and Campylobacter emerged as the predominant phyla within these biofilms. The microbial community distribution was predominantly influenced by ammonium nitrogen (NH4[+]-N) (R[2] = 0.4113), temperature and total nitrogen (TN). Notably, temperature exerted a critical impact on the microbial community distribution (P = 0.001), identifying it as the principal factor for spatial arrangement. Furthermore, the structural variations of ARGs were primarily driven by total organic carbon (TOC) (R[2] = 0.3988), temperature, oxidation-reduction potential (ORP) and NH4[+]-N. Our findings provided new insights into the optimization of substrate selection and ecological management to manage ARG enrichment, offering a promising strategy for aquatic ecological restoration and pollution control.}, }
@article {pmid39639495, year = {2024}, author = {Alanzi, AR}, title = {Exploring Microbial Dark Matter for the Discovery of Novel Natural Products: Characteristics, Abundance Challenges and Methods.}, journal = {Journal of microbiology and biotechnology}, volume = {35}, number = {}, pages = {e2407064}, doi = {10.4014/jmb.2407.07064}, pmid = {39639495}, issn = {1738-8872}, mesh = {*Biological Products/metabolism ; *Metagenomics/methods ; *Bacteria/genetics/classification/isolation & purification/metabolism ; *Phylogeny ; Microbiota ; }, abstract = {The objective of this review is to investigate microbial dark matter (MDM) with a focus on its potential for discovering novel natural products (NPs). This first part will examine the characteristics and abundance of these previously unexplored microbial communities, as well as the challenges faced in identifying and harnessing their unique biochemical properties and novel methods in this field. MDMs are thought to hold great potential for the discovery of novel NPs, which could have significant applications in medicine, agriculture, and industry. In recent years, there has been a growing interest in exploring MDM to unlock its potential. In fact, developments in genome-sequencing technologies and sophisticated phylogenetic procedures and metagenomic techniques have contributed to drastically make important changes in our sights on the diversity of microbial life, including the very outline of the tree of life. This has led to the development of novel technologies and methodologies for studying these elusive microorganisms, such as single-cell genomics, metagenomics, and culturomics. These approaches enable researchers to isolate and analyze individual microbial cells, as well as entire communities, providing insights into their genetic and metabolic potential. By delving into the MDM, scientists hope to uncover new compounds and biotechnological advancements that could have far-reaching impacts on various fields.}, }
@article {pmid39626398, year = {2025}, author = {Song, A and Si, Z and Xu, D and Wei, B and Wang, E and Chong, F and Fan, F}, title = {Lanthanum and cerium added to soil influence microbial carbon and nitrogen cycling genes.}, journal = {Journal of environmental management}, volume = {373}, number = {}, pages = {123509}, doi = {10.1016/j.jenvman.2024.123509}, pmid = {39626398}, issn = {1095-8630}, mesh = {*Soil Microbiology ; *Soil/chemistry ; *Carbon/metabolism ; *Cerium ; *Nitrogen/metabolism ; *Lanthanum ; *Nitrogen Cycle ; Microbiota ; }, abstract = {The soil microbiome plays an important role in carbon (C) and nitrogen (N) processing and storage and is influenced by rare earth elements (REEs), which can have both direct and indirect effects on plant metabolic processes. Using conventional physicochemical methods and metagenomic-based analyses, we investigated REEs effects on soil respiration, soil mineral N, soil microbial community structure and functional genes related to C and N metabolism. High doses of cerium (0.16 and 0.32 mmol kg[-1] soil) increased CO2 net production rate by 59 and 42%, and N2O net production rate by 255 and 609%, respectively, compared to no REEs. Similarly, high doses of lanthanum (0.16 and 0.32 mmol kg[-1] soil) increased CO2 net production rate by 47 and 39%, and N2O net production rate by 105 and 187%, respectively. Increased soil respiration from altered relative abundances of key soil microorganisms associated with soil N cycling and organic matter degradation and functional genes encoding enzymes involved in C and N metabolism, accelerated N mineralization. Elevated REEs levels substantially increased the relative abundances of functional genes related to cellulose, chitin, glucans, hemicellulose, lignin, and peptidoglycan degradation. REEs also influenced multiple functional genes associated with the N cycle. The abundance of genes responsible for organic N degradation and synthesis, such as asnB, gdh_K15371, glsA, and gs, increased with elevated cerium and lanthanum concentrations. Similarly, the abundances of denitrification genes, including narl, narJ, narZ, and nosZ, also rose with increasing amounts of cerium and lanthanum. However, the decrease in narB and nirB gene abundance with increasing REE concentrations was attributed to the reduction of nitrate to amino groups. Our findings highlight the influence of REEs on key soil microorganisms associated with soil N cycling and organic matter degradation and key functional genes in soil C and N metabolism, with implications for agriculture, environmental protection, and human health.}, }
@article {pmid39615467, year = {2025}, author = {Khandeparker, L and Kale, D and Hede, N and Anil, AC}, title = {Application of functional metagenomics in the evaluation of microbial community dynamics in the Arabian Sea: Implications of environmental settings.}, journal = {Journal of environmental management}, volume = {373}, number = {}, pages = {123449}, doi = {10.1016/j.jenvman.2024.123449}, pmid = {39615467}, issn = {1095-8630}, mesh = {*Metagenomics ; Cyanobacteria/genetics/metabolism ; Microbiota ; Seawater/microbiology ; Chlorophyll A/metabolism ; Climate Change ; }, abstract = {Ocean microbial communities form the base of marine food webs, facilitating energy transfer and nutrient cycling, thereby supporting higher trophic levels. We investigated their composition and functional profiles across depths (surface waters 0, 29, and 63 m and bottom waters 100, 150, and 200 m) in the central-eastern Arabian Sea (CEAS) using next-generation sequencing. It was hypothesized that the composition and functional diversity of these communities would be influenced by depth and environmental parameters. Our research showed that microbial communities vary with depth and are shaped by environmental factors like irradiance, temperature, dissolved oxygen, suspended particulate matter, chlorophyll a, and ammonia concentrations. Cyanobacteria (Prochlorococcus sp) and Mamiellaceae, belonging to picoeukaryotes, exhibited distinct depth-specific distributions up to subsurface chlorophyll maxima (SCM) at 63 m. On the other hand, a community shift in the microbial communities comprising Firmicutes, Bacteroidetes, and Actinobacteria phyla was observed at the deeper water depths. The profiling of functional genes pointed out the expression of carbon fixation by photosynthetic organisms at the surface (0, 29, and 63 m), which shifted to prokaryotic carbon fixation in deeper waters (0, 150, and 200 m). Microcosm experiments (mixing of surface water with water from the SCM) carried out simulating disturbances such as climate change forced mixing (cyclones), revealed shifts in microbial structure and function. It was observed that within 48 h, the carbon fixation activity changed from photosynthetic organisms to prokaryotes and indicated an increase in stress-related biosynthetic pathways such as expression of quorum sensing, biosynthesis of antibiotics, lipopolysaccharides, and secondary metabolites. These findings have implications for predictive modelling of food web dynamics and fisheries management in the context of climate change.}, }
@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.}, }
@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).}, }
@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.}, }
@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.}, }
@article {pmid39760260, year = {2025}, author = {You, H and Yang, B and Liu, H and Wu, W and Yu, F and Lin, N and Yang, W and Hu, B and Liu, Y and Zou, H and Hao, S and Xiao, Y and Xu, T and Jiang, Y}, title = {Unravelling distinct patterns of metagenomic surveillance and respiratory microbiota between two P1 genotypes of Mycoplasma pneumoniae.}, journal = {Emerging microbes & infections}, volume = {14}, number = {1}, pages = {2449087}, doi = {10.1080/22221751.2024.2449087}, pmid = {39760260}, issn = {2222-1751}, mesh = {Humans ; *Mycoplasma pneumoniae/genetics/isolation & purification ; *Pneumonia, Mycoplasma/epidemiology/microbiology ; Retrospective Studies ; Child ; Female ; Male ; Child, Preschool ; *Microbiota ; Adolescent ; *Metagenomics ; *Genotype ; Middle Aged ; Adult ; COVID-19/epidemiology/microbiology ; Young Adult ; Infant ; Aged ; Bronchoalveolar Lavage Fluid/microbiology ; }, abstract = {To unravel distinct patterns of metagenomic surveillance and respiratory microbiota between Mycoplasma pneumoniae (M. pneumoniae) P1-1 and P1-2 and to explore the impact of the COVID-19 pandemic on epidemiological features, we conducted a multicentre retrospective study which spanned 90,886 pneumonia patients, among which 3164 cases M. pneumoniae were identified. Our findings revealed a concurrent outbreak of M. pneumoniae, with the positivity rate rising sharply to 9.62% from July 2023, compared to the 0.16% to 4.06% positivity rate observed during the 2020-2022 COVID-19 pandemic. P1-1 had a higher odds ratio of co-detecting opportunistic pathogens. However, no significant differences were observed in the co-detection odds ratio between children and other age groups in P1-2. This study is the first to demonstrate differences in relative abundance, diversity of respiratory microbiota and co-detection rate of opportunistic pathogen between M. pneumoniae P1-1 and P1-2. Through bronchoalveolar lavage (BAL) metagenomic and host transcriptomic analyses, we identified variations in co-detection rates of M. pneumoniae P1-1 genotype with opportunistic pathogens like S. pneumoniae, alterations in respiratory microbiota composition, lung inflammation, and disruption of ciliary function. Consistent with the results of host transcriptome, we found that P1-1 infections were associated with significantly higher rates of requiring respiratory support and mechanical ventilation compared to P1-2 infections (Fisher's exact test, p-value = 0.035/0.004). Our study provides preliminary evidence of clinical severity between M. pneumoniae strains, underscoring the need for ongoing research and development of targeted therapeutic strategies.}, }
@article {pmid39126385, year = {2025}, author = {Jangi, S and Zhao, N and Hsia, K and Park, YS and Michaud, DS and Yoon, H}, title = {Specific Bacterial Co-abundance Groups Are Associated With Inflammatory Status in Patients With Ulcerative Colitis.}, journal = {Journal of Crohn's & colitis}, volume = {19}, number = {1}, pages = {}, doi = {10.1093/ecco-jcc/jjae125}, pmid = {39126385}, issn = {1876-4479}, support = {/TR/NCATS NIH HHS/United States ; /NH/NIH HHS/United States ; //National Research Foundation/ ; }, mesh = {Humans ; *Colitis, Ulcerative/microbiology ; *Gastrointestinal Microbiome ; Male ; Adult ; Female ; Prospective Studies ; Middle Aged ; Clostridiales/isolation & purification ; Candida/isolation & purification ; Republic of Korea ; Feces/microbiology ; }, abstract = {BACKGROUND AND AIMS: While there is increasing interest in microbiome-directed therapies for patients with ulcerative colitis (UC), the identification of microbial targets remains elusive, underlining the need for novel approaches.
METHODS: Utilizing metagenomic data from the Study of a Prospective Adult Research Cohort with Inflammatory Bowel Disease (SPARC IBD), available via the IBD Plexus Program of the Crohn's & Colitis Foundation, we used a tree-based dichotomous approach to assemble distinct clusters of species-level bacterial co-abundance groups (CAGs). We evaluated the abundance of bacterial CAGs and fungal taxa during remission (n = 166) and activity (n = 46). We examined if the bacterial CAGs identified in our cohorts were conserved in 2 healthy cohorts and a Korean UC cohort.
RESULTS: CAG3 and CAG8, dominated by bacteria from the family Lachnospiraceae, were associated with remission. Low abundance of CAG8 and elevated abundance of Candida genus were predictive of active UC. Constituents from CAG8 were influential hub species of the remission-associated microbial UC network, including Ruminococcus gnavus, Erysipelatoclostridium ramosum, Blautia, and Dorea species. These hub species interactions were preserved in 2 healthy cohorts and were partially recapitulated in a Korean UC cohort. CAG8 abundance correlated with the secondary bile acid production pathway. Bacterial CAGs did not correlate with Candida; however, Bifidobacterium adolescentis and Alistipes putredinis were negatively associated with Candida.
CONCLUSIONS: Lachnospiraceae-dominated bacterial CAGs were associated with remission in UC, with key bacterial interactions within the CAG also observed in 2 healthy cohorts and a Korean UC cohort. Bacterial CAG-based analyses may aid in designing candidate consortia for microbiome-based therapeutics.}, }
@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.}, }
@article {pmid39700725, year = {2025}, author = {Petersen, JF and Valk, LC and Verhoeven, MD and Nierychlo, MA and Singleton, CM and Dueholm, MKD and Nielsen, PH}, title = {Diversity and physiology of abundant Rhodoferax species in global wastewater treatment systems.}, journal = {Systematic and applied microbiology}, volume = {48}, number = {1}, pages = {126574}, doi = {10.1016/j.syapm.2024.126574}, pmid = {39700725}, issn = {1618-0984}, mesh = {*Wastewater/microbiology/chemistry ; *Phylogeny ; *RNA, Ribosomal, 16S/genetics ; DNA, Bacterial/genetics ; Metagenome ; Water Purification ; Sequence Analysis, DNA ; Denmark ; Biodiversity ; Oxidation-Reduction ; Genome, Bacterial/genetics ; }, abstract = {Wastewater treatment plants rely on complex microbial communities for bioconversion and removal of pollutants, but many process-critical species are still poorly investigated. One of these genera is Rhodoferax, an abundant core genus in wastewater treatment plants across the world. The genus has been associated with many metabolic traits such as iron reduction and oxidation and denitrification. We used 16S rRNA gene amplicon data to uncover the diversity and abundance of Rhodoferax species in Danish and global treatment plants. Publicly available metagenome-assembled genomes were analyzed based on phylogenomics to delineate species and assign taxonomies based on the SeqCode. The phylogenetic analysis of "Rhodoferax" revealed that species previously assigned to Rhodoferax in wastewater treatment plants should be considered as at least eight different genera, with five representing previously undescribed genera. Genome annotation showed potential for several key-bioconversions in wastewater treatment, such as nitrate reduction, carbohydrate degradation, and accumulations of various storage compounds. Iron oxidation and reduction capabilities were not predicted for abundant species. Species-resolved FISH-Raman was performed to gain an overview of the morphology and ecophysiology of selected taxa to clarify their potential role in global wastewater treatment systems. Our study provides a first insight into the functional and ecological characteristics of several novel genera abundant in global wastewater treatment plants, previously assigned to the Rhodoferax genus.}, }
@article {pmid39528052, year = {2025}, author = {Jiang, Q and Zhu, X and Sun, L and Xie, C and Wang, X and Ma, L and Yan, X}, title = {Akkermansia muciniphila Promotes SIgA Production and Alters the Reactivity Toward Commensal Bacteria in Early-Weaned Piglets.}, journal = {The Journal of nutrition}, volume = {155}, number = {1}, pages = {52-65}, doi = {10.1016/j.tjnut.2024.11.002}, pmid = {39528052}, issn = {1541-6100}, mesh = {Animals ; Swine ; *Immunoglobulin A, Secretory/metabolism ; *Weaning ; *Akkermansia ; *Gastrointestinal Microbiome ; *Feces/microbiology ; Male ; Mice ; Mice, Inbred C57BL ; Verrucomicrobia ; Bacteria/classification ; Intestines/microbiology/immunology ; }, abstract = {BACKGROUND: Secretory IgA (SIgA) is the first line of defense in protecting the intestinal epithelium against pathogenic bacteria, regulating gut microbiota composition, and maintaining intestinal homeostasis. Early weaning strategies may disrupt SIgA levels in piglet intestines, causing a decline in immune response and early weaning stress. However, the specific microbial mechanisms modulating SIgA in early-weaned piglets are not well understood.
OBJECTIVES: We hypothesized that Akkermansia muciniphila increases intestinal SIgA production in the early-weaned piglets.
METHODS: Fecal SIgA levels, SIgA-coated bacteria abundance, and fecal metagenomes were compared between 6 Huanjiang miniature (HM) and 6 Duroc×Landrace×Yorkshire (DLY) early-weaned piglets to identify bacterial species involved in SIgA modulation. Four bacterial species were investigated using 5 groups (Control, A. muciniphila, L. amylovorus, L. crispatus, and L. acidophilus) of male specific pathogen-free C57BL/6J mice, weaned 3 wk postbirth (n = 8/group). Subsequently, 10-d-old Landrace×Yorkshire (LY) piglets were randomly assigned to 3 groups (Control, 10[9]A. muciniphila, and 10[8]A. muciniphila) (n = 10/group) to evaluate the effect of orally administered A. muciniphila on intestinal SIgA production and microbial composition.
RESULTS: HM early-weaned piglets showed significantly higher SIgA levels [7.59 μg/mg, 95% confidence interval (CI): 3.2, 12, P = 0.002] and SIgA-coated bacteria abundance (8.64%, 95% CI: 3.2, 14, P = 0.014) than DLY piglets. In the mouse model, the administration of A. muciniphila significantly increased SIgA levels (3.50 μg/mg, 95% CI: 0.59, 6.4, P = 0.018), SIgA-coated bacteria abundance (9.06%, 95% CI: 4, 14, P = 0.018), and IgA[+] plasma cell counts (6.1%, 95% CI: 4.3, 8, P = 0.005). In the pig experiments, the oral administration of A. muciniphila to LY piglets significantly enhanced intestinal SIgA concentrations (4.22 μg/mg, 95% CI: 0.37, 8.5, P = 0.034) and altered the SIgA-coated bacterial landscape.
CONCLUSIONS: Early intervention with A. muciniphila in nursing piglets can increases intestinal SIgA production and alter the reactivity toward commensal bacteria upon early weaning.}, }
@article {pmid39305900, year = {2025}, author = {Liu, Q and Huang, B and Zhou, Y and Wei, Y and Li, Y and Li, B and Li, Y and Zhang, J and Qian, Q and Chen, R and Lyu, Z and Wang, R and Cao, Q and Xu, Q and Wang, Q and Miao, Q and You, Z and Lian, M and Gershwin, ME and Jin, Q and Xiao, X and Ma, X and Tang, R}, title = {Gut microbiome pattern impacts treatment response in primary biliary cholangitis.}, journal = {Med (New York, N.Y.)}, volume = {6}, number = {1}, pages = {100504}, doi = {10.1016/j.medj.2024.08.003}, pmid = {39305900}, issn = {2666-6340}, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Liver Cirrhosis, Biliary/drug therapy/microbiology ; *Ursodeoxycholic Acid/therapeutic use ; Female ; Male ; Middle Aged ; Prospective Studies ; Dysbiosis/microbiology ; Feces/microbiology ; Aged ; Cholagogues and Choleretics/therapeutic use ; Clostridium/isolation & purification/drug effects/genetics ; Adult ; Metagenomics/methods ; Metagenome/drug effects ; Metabolomics ; }, abstract = {BACKGROUND: Primary biliary cholangitis (PBC) is a progressive autoimmune liver disease. An inadequate response to ursodeoxycholic acid (UDCA) poses a high risk of progression toward end-stage liver disease. Gut dysbiosis has been implicated in PBC. Here, we aimed to investigate microbial signatures that permit risk stratification and provide mechanistic insights into novel therapies for PBC.
METHODS: We prospectively recruited UDCA treatment-naive patients with PBC and performed metagenomic sequencing and metabolomic profiling using stool and serum samples obtained before (n = 132) and after (n = 59) treatment. PBC microbiome subtypes were identified using unsupervised machine learning methods and validated in two independent cohorts.
FINDINGS: PBC baseline metagenomes clustered into two community subtypes characterized by varying abundances of Clostridia taxa. Compared with Clostridia[low] microbiomes, Clostridia[high] microbiomes were more similar to healthy controls. Notably, patients in the Clostridia[low] subtype exhibited a 2-fold higher UDCA non-response rate compared to those in the Clostridia[high] subtype (41% vs. 20%, p = 0.015). Integrative analysis of metagenomic and metabolomic data revealed divergent functional modules and metabolic activities between the two metacommunities. In particular, anaerobic fermentation and the production of bioactive metabolites, including tryptophan derivatives and secondary bile acids, crucial for immune regulation and gut barrier maintenance, were markedly diminished in the Clostridia[low] subtype. Moreover, UDCA administration reconfigured the fecal microbial and metabolic profiles only in the Clostridia[high] group. Importantly, the microbiome subtypes and their associations with UDCA response were reproducible in two independent treatment-naive PBC cohorts.
CONCLUSIONS: Characterizing baseline microbiota patterns may enable the prediction of treatment outcomes in PBC and facilitate personalized treatment strategies.
FUNDING: This research was mainly supported by the National Natural Science Foundation of China.}, }
@article {pmid39797569, year = {2025}, author = {Rogers, AB and Kale, V and Baldi, G and Alberdi, A and Gilbert, MTP and Gupta, D and Limborg, MT and Li, S and Payne, T and Petersen, B and Rasmussen, JA and Richardson, L and Finn, RD}, title = {HoloFood Data Portal: holo-omic datasets for analysing host-microbiota interactions in animal production.}, journal = {Database : the journal of biological databases and curation}, volume = {2025}, number = {}, pages = {}, doi = {10.1093/database/baae112}, pmid = {39797569}, issn = {1758-0463}, mesh = {Animals ; *Chickens/microbiology ; Host Microbial Interactions/genetics ; Salmon/microbiology ; Microbiota ; Databases, Genetic ; Gastrointestinal Microbiome ; }, abstract = {The HoloFood project used a hologenomic approach to understand the impact of host-microbiota interactions on salmon and chicken production by analysing multiomic data, phenotypic characteristics, and associated metadata in response to novel feeds. The project's raw data, derived analyses, and metadata are deposited in public, open archives (BioSamples, European Nucleotide Archive, MetaboLights, and MGnify), so making use of these diverse data types may require access to multiple resources. This is especially complex where analysis pipelines produce derived outputs such as functional profiles or genome catalogues. The HoloFood Data Portal is a web resource that simplifies access to the project datasets. For example, users can conveniently access multiomic datasets derived from the same individual or retrieve host phenotypic data with a linked gut microbiome sample. Project-specific metagenome-assembled genome and viral catalogues are also provided, linking to broader datasets in MGnify. The portal stores only data necessary to provide these relationships, with possible linking to the underlying repositories. The portal showcases a model approach for how future multiomics datasets can be made available. Database URL: https://www.holofooddata.org.}, }
@article {pmid39797470, year = {2025}, author = {Záhonová, K and Kaur, H and Furgason, CC and Smirnova, AV and Dunfield, PF and Dacks, JB}, title = {Comparative Analysis of Protist Communities in Oilsands Tailings Using Amplicon Sequencing and Metagenomics.}, journal = {Environmental microbiology}, volume = {27}, number = {1}, pages = {e70029}, doi = {10.1111/1462-2920.70029}, pmid = {39797470}, issn = {1462-2920}, support = {e-INFRA CZ (90254)//the Ministry of Education, Youth and Sports of the Czech Republic/ ; CRDPJ 542973-19//Natural Sciences and Engineering Research Council of Canada/ ; RES0021028//Natural Sciences and Engineering Research Council of Canada/ ; }, mesh = {Alberta ; *Metagenomics/methods ; *Oil and Gas Fields ; *Eukaryota/genetics/classification ; RNA, Ribosomal, 18S/genetics ; Biodiversity ; Phylogeny ; }, abstract = {The Canadian province of Alberta contains substantial oilsands reservoirs, consisting of bitumen, clay and sand. Extracting oil involves separating bitumen from inorganic particles using hot water and chemical diluents, resulting in liquid tailings waste with ecotoxicologically significant compounds. Ongoing efforts aim to reclaim tailings-affected areas, with protist colonisation serving as one assessment method of reclamation progress. Oilsands-associated protist communities have mainly been evaluated using amplicon sequencing of the 18S rRNA V4 region; however, this barcode may overlook important protist groups. This study examined how community assessment methods between the V4 and V9 regions differ in representing protist diversity across four oilsands-associated environments. The V9 barcode identified more operational taxonomical units (OTUs) for Discoba, Metamonada and Amoebozoa compared with the V4. A comparative shotgun metagenomics approach revealed few eukaryotic contigs but did recover a complete Paramicrosporidia mitochondrial genome, only the second publicly available from microsporidians. Both V4 and V9 markers were informative for assessing community diversity in oilsands-associated environments and are most effective when combined for a comprehensive taxonomic estimate, particularly in anoxic environments.}, }
@article {pmid39796619, year = {2025}, author = {Johnson, AJ and Alvear, A and Knights, D and Chow, LS and Bantle, AE}, title = {A Randomized Pilot Study of Time-Restricted Eating Shows Minimal Microbiome Changes.}, journal = {Nutrients}, volume = {17}, number = {1}, pages = {}, doi = {10.3390/nu17010185}, pmid = {39796619}, issn = {2072-6643}, support = {KL2TR002492//National Institutes of Health, National Center of Advancing Translational Sciences/ ; UL1TR002494//National Institutes of Health, National Center for Advancing Translational Sciences/ ; K23DK115906/DK/NIDDK NIH HHS/United States ; 17SFR-2YR50LC//Healthy Foods, Healthy Lives Institute at the University of Minnesota/ ; }, mesh = {Humans ; Pilot Projects ; *Gastrointestinal Microbiome ; Male ; *Feces/microbiology ; Female ; Adult ; Obesity/microbiology ; Middle Aged ; Body Composition ; Fasting ; Time Factors ; }, abstract = {OBJECTIVE: TRE is an emerging approach in obesity treatment, yet there is limited data on how it influences gut microbiome composition in humans. Our objective was to characterize the gut microbiome of human participants before and after a TRE intervention. This is a secondary analysis of a previously published clinical trial examining the effects of time-restricted eating (TRE).
METHODS: In a previously published, 12-week randomized controlled trial, Chow et al. evaluated the effects of an 8-h TRE intervention on body composition in human participants. Chow et al. demonstrated significant reductions in weight, lean mass, and visceral fat in the TRE group compared to those following time-unrestricted eating (non-TRE). Stool samples were collected by a subset of those participants using home kits at both baseline and post-intervention for shotgun metagenomic sequencing for this secondary analysis. Microbiome community composition was compared before and after intervention as alpha and beta diversity.
RESULTS: Sixteen participants provided stool samples (eight in the TRE group and eight in the non-TRE group). Stool samples were collected from all participants at at least one time point, but both pre- and post-treatment samples were available from only five participants who completed both baseline and post-treatment collections. In alignment with the findings of Chow et al., the participants in the TRE group of the secondary analysis who collected microbiome sample(s) successfully reduced their eating window from an average of 15.3 ± 0.8 h at baseline to 9.3 ± 1.7 h during the intervention (mean ± SD, p < 0.001) and the non-TRE group's eating window remained unchanged. While the TRE group lost weight and visceral fat mass, no effect of the TRE intervention was observed on alpha diversity (Shannon index, Simpson index, and number of taxa, linear mixed models), beta diversity (Bray-Curtis, PERMANOVA), even after controlling for weight and visceral fat changes.
CONCLUSIONS: Our analysis did not detect any significant differences in gut microbiome composition or diversity indices between participants undergoing a TRE intervention and those in the control group. The study's findings are limited by a small sample size, short duration, and the collection of stool samples at only two time points. Future studies with larger sample sizes, longer durations, and more frequent sampling, and collection of detailed dietary data are needed to better understand the relationship between TRE and gut microbiome dynamics.}, }
@article {pmid39796584, year = {2024}, author = {Firrman, J and Deyaert, S and Mahalak, KK and Liu, L and Baudot, A and Joossens, M and Poppe, J and Cameron, SJS and Van den Abbeele, P}, title = {The Bifidogenic Effect of 2'Fucosyllactose Is Driven by Age-Specific Bifidobacterium Species, Demonstrating Age as an Important Factor for Gut Microbiome Targeted Precision Medicine.}, journal = {Nutrients}, volume = {17}, number = {1}, pages = {}, doi = {10.3390/nu17010151}, pmid = {39796584}, issn = {2072-6643}, support = {8072-41000-102-00D//United States Department of Agriculture/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Trisaccharides/pharmacology ; *Bifidobacterium/drug effects ; Infant ; *Feces/microbiology ; Aged ; Adult ; Child, Preschool ; *Precision Medicine ; Middle Aged ; Child ; Female ; Male ; Age Factors ; Young Adult ; Adolescent ; Milk, Human/chemistry ; Oligosaccharides/pharmacology ; Lactose ; }, abstract = {BACKGROUND: The human gut microbiota develops in concordance with its host over a lifetime, resulting in age-related shifts in community structure and metabolic function. Little is known about whether these changes impact the community's response to microbiome-targeted therapeutics. Providing critical information on this subject, faecal microbiomes of subjects from six age groups, spanning from infancy to 70-year-old adults (n = six per age group) were harvested. The responses of these divergent communities to treatment with the human milk oligosaccharide 2'-fucosyllactose (2'FL), fructo-oligosaccharides (FOS), and lactose was investigated using the Ex vivo SIFR[®] technology that employs bioreactor fermentation and is validated to be predictive of clinical findings. Additionally, it was evaluated whether combining faecal microbiomes of a given age group into a single pooled microbiome produced similar results as the individual microbiomes.
RESULTS: First, marked age-dependent changes in community structure were identified. Bifidobacterium levels strongly declined as age increased, and Bifidobacterium species composition was age-dependent: B. longum, B. catenulatum/pseudocatenulatum, and B. adolescentis were most prevalent for breastfed infants, toddlers/children, and adults, respectively. Metabolomic analyses (LA-REIMS) demonstrated that these age-dependent differences particularly impacted treatment effects of 2'FL (more than FOS/lactose). Further analysis revealed that while 2'FL enhanced production of short-chain fatty acids (SCFAs) and exerted potent bifidogenic effects, regardless of age, the specific Bifidobacterium species enhanced by 2'FL, as well as subsequent cross-feeding interactions, were highly age-dependent. Furthermore, single-pooled microbiomes produced results that were indicative of the average treatment response for each age group. Nevertheless, pooled microbiomes had an artificially high diversity, thus overestimating treatment responses (especially for infants), did not recapitulate interindividual variation, and disallowed for the correlative analysis required to unravel mechanistic actions.
CONCLUSIONS: Age is an important factor in shaping the gut microbiome, with the dominant taxa and their metabolites changing over a lifetime. This divergence affects the response of the microbiota to therapeutics, demonstrated in this study using 2'FL. These results evidence the importance of screening across multiple age groups separately to provide granularity of how therapeutics impact the microbiome and, consequently, human health.}, }
@article {pmid39796532, year = {2024}, author = {Paterson, S and Majchrzak, M and Gómez-Garre, D and Ortega-Hernández, A and Sánchez-González, S and de la Fuente, MÁ and Gómez-Cortés, P and Hernández-Ledesma, B}, title = {Role of Simulated Nannochloropsis gaditana Digests in Shaping Gut Microbiota and Short-Chain Fatty Acid Levels.}, journal = {Nutrients}, volume = {17}, number = {1}, pages = {}, doi = {10.3390/nu17010099}, pmid = {39796532}, issn = {2072-6643}, support = {PID2021-122989OB-I00//Ministerio de Ciencia, Innovación y Universidades/ ; PIPF-2022/BIO-24996//Comunidad Autónoma de Madrid/ ; }, mesh = {*Gastrointestinal Microbiome/physiology/drug effects ; Humans ; *Fatty Acids, Volatile/metabolism ; *Microalgae ; *Fermentation ; Stramenopiles/metabolism ; RNA, Ribosomal, 16S ; Bacteria/metabolism/classification/genetics ; Colon/microbiology/metabolism ; }, abstract = {The connection between gut microbiota and factors like diet is crucial for maintaining intestinal balance, which in turn impacts the host's overall health. Nannochloropsis gaditana microalgae is a sustainable source of bioactive compounds, mainly known for its used in aquaculture and extraction of bioactive lipids, with potential health benefits whose effects on human gut microbiota are still unknown. Therefore, the goal of this work was to assess the impact of N. gaditana on human gut microbiota composition and derived metabolites by combining the INFOGEST protocol and in vitro colonic fermentation process to evaluate potential effects on human gut microbiota conformation through 16S rRNA gene sequencing and its metabolic functionality. The results have demonstrated the ability of the digests from N. gaditana to significantly modify gut microbiota composition, promoting an increase in beneficial bacterial genera such as Akkermansia, Butyricicoccus, Eisenbergiella, Lachnoclostridium, and Marvinbryantia, in contrast to inulin, after 48 h of colonic fermentation. Additionally, the digests increased the levels of both major and minor short-chain fatty acids (SCFAs), particularly butyric and valeric acids, considered as intestinal biomarkers, and increased ammonium production. This research has demonstrated, for the first time, the potential of N. gaditana microalgae as a sustainable agent for influencing the composition and functionality of human gut microbiota.}, }
@article {pmid39796518, year = {2024}, author = {Vega-Rojas, A and Haro, C and Molina-Abril, H and Guil-Luna, S and Santos-Marcos, JA and Gutierrez-Mariscal, FM and Garcia-Fernandez, H and Caballero-Villarraso, J and Rodriguez-Ariza, A and Lopez-Miranda, J and Perez-Martinez, P and Hervas, A and Camargo, A}, title = {Gut Microbiota Interacts with Dietary Habits in Screenings for Early Detection of Colorectal Cancer.}, journal = {Nutrients}, volume = {17}, number = {1}, pages = {}, doi = {10.3390/nu17010084}, pmid = {39796518}, issn = {2072-6643}, support = {PI-0055-2021//Consejería de Salud y Consumo/ ; PI-0156-2016//Consejería de Salud y Consumo/ ; AGL2015-67896-P//Ministerio de Ciencia, Innovación y Universidades/ ; n.a.//European Union/ ; CP14/00114//Instituto de Salud Carlos III/ ; PI19/00299//Instituto de Salud Carlos III/ ; DTS19/00007//Instituto de Salud Carlos III/ ; PI22/00925//Instituto de Salud Carlos III/ ; C1-0001-2022//Andalusian Health Service/ ; }, mesh = {Humans ; *Colorectal Neoplasms/microbiology/diagnosis ; *Gastrointestinal Microbiome ; *Early Detection of Cancer/methods ; Male ; Female ; Middle Aged ; *Feeding Behavior ; *Colonoscopy ; Aged ; Adenocarcinoma/microbiology ; Occult Blood ; Diet ; Colonic Polyps/microbiology/diagnosis ; Feces/microbiology ; }, abstract = {BACKGROUND/OBJECTIVES: Gut microbiota interacts with nutrients, which may be relevant to assigning a microbial signature to colorectal cancer (CRC). We aim to evaluate the potential of gut microbiota combined with dietary habits in the early detection of pathological findings related to CRC in the course of a screening program.
METHODOLOGY: The colonoscopy performed on 152 subjects positive for fecal occult blood test showed that 6 subjects had adenocarcinoma, 123 had polyps, and 23 subjects had no pathological findings. Gut microbiota was analyzed by 16S metagenomic. Caret package was used to build the classification models in R.
RESULTS: Random forest (RF) classifier models were used to test the potential of gut microbiota alone or combined with dietary habits as a biomarker to discern between individuals with CRC-related lesions (polyps or adenocarcinoma) versus individuals without pathological findings. RF classifier models yielded an area under the curve of 0.790 using gut microbiota data, 0.710 using dietary habits data, and 0.804 in the combined model including gut microbiota and dietary habits data. The abundance of Suterella, Oscillospirales, Proteobacteria, and Burkholderiales was highly discriminant between groups, together with the consumption of fruit and vegetables and the consumption of carbonated and/or sweetened beverages.
CONCLUSIONS: Our results suggest that the interaction between gut microbiota and dietary habits is relevant when a microbial signature is used as a marker in CRC. Moreover, gut microbiota signature and information about the dietary habits of the individuals seem to be important for improving screening programs for the early detection of CRC.}, }
@article {pmid39796082, year = {2024}, author = {Kim, DG and Lee, CM and Lee, YS and Yoon, SH and Kim, SY}, title = {Isolation of a Novel Low-Temperature-Active and Organic-Solvent-Stable Mannanase from the Intestinal Metagenome of Hermetia illucens.}, journal = {International journal of molecular sciences}, volume = {26}, number = {1}, pages = {}, doi = {10.3390/ijms26010216}, pmid = {39796082}, issn = {1422-0067}, support = {Project No. PJ008604//Rural Development Administration/ ; }, mesh = {*Mannans/metabolism ; Animals ; Phylogeny ; Metagenome ; Diptera/microbiology ; Mannosidases/metabolism/genetics/chemistry ; Gastrointestinal Microbiome ; Substrate Specificity ; Amino Acid Sequence ; Galactans/metabolism ; Enzyme Stability ; Cold Temperature ; Plant Gums/chemistry/metabolism ; Hydrogen-Ion Concentration ; Intestines/microbiology ; Solvents/chemistry ; Recombinant Proteins/metabolism/genetics/chemistry ; Galactose/analogs & derivatives ; }, abstract = {The black soldier fly, Hermetia illucens, is a voracious scavenger of various organic materials; therefore, it could be exploited as a biological system for processing daily food waste. In order to survey novel hydrolytic enzymes, we constructed a fosmid metagenome library using unculturable intestinal microorganisms from H. illucens. Through functional screening of the library on carboxymethyl cellulose plates, we identified a fosmid clone, the product of which displayed hydrolytic activity. Sequence analysis of the fosmid revealed a novel mannan-degrading gene, ManEM6, composed of 1185 base pairs encoding 394 amino acids, with a deduced 20-amino-acid N-terminal signal peptide sequence. The conceptual translation of ManEM6 exhibited the highest identity (78%) to endo-1,4-β-mannosidase from Dysgonomonas mossii. Phylogenetic and domain analyses indicated that ManEM6 encodes a novel mannanase with a glycoside hydrolase family 26 domain. The recombinant protein rManEM6 showed its highest activity at 40 °C and pH 7.0, and it remained stable in the range of pH 5-10.0. rManEM6 hydrolyzed substrates with β-1,4-glycosidic mannoses, showing maximum enzymatic activity toward locust bean gum galactomannan, while it did not hydrolyze p-nitrophenyl-β-pyranosides, demonstrating endo-form mannosidase activity. rManEM6 was highly stable under stringent conditions, including those of polar organic solvents, as well as reducing and denaturing reagents. Therefore, ManEM6 may be an attractive candidate for the degradation of mannan under high-organic-solvent and protein-denaturing processes in the food and feed industries.}, }
@article {pmid39794871, year = {2025}, author = {Samodova, D and Stankevic, E and Søndergaard, MS and Hu, N and Ahluwalia, TS and Witte, DR and Belstrøm, D and Lubberding, AF and Jagtap, PD and Hansen, T and Deshmukh, AS}, title = {Salivary proteomics and metaproteomics identifies distinct molecular and taxonomic signatures of type-2 diabetes.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {5}, pmid = {39794871}, issn = {2049-2618}, support = {74550801//European Foundation for the Study of Diabetes/ ; NNF18CC0034900; NNF23SA0084103//Novo Nordisk Fonden/ ; NNF18CC0034900; NNF23SA0084103//Novo Nordisk Fonden/ ; }, mesh = {Humans ; *Diabetes Mellitus, Type 2/microbiology/metabolism ; *Saliva/microbiology ; *Proteomics/methods ; Male ; Middle Aged ; Female ; *Microbiota ; Biomarkers/metabolism ; Bacterial Proteins/genetics ; Adult ; Bacteria/classification/metabolism/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Computational Biology/methods ; Salivary Proteins and Peptides/metabolism ; Case-Control Studies ; Aged ; }, abstract = {BACKGROUND: Saliva is a protein-rich body fluid for noninvasive discovery of biomolecules, containing both human and microbial components, associated with various chronic diseases. Type-2 diabetes (T2D) imposes a significant health and socio-economic burden. Prior research on T2D salivary microbiome utilized methods such as metagenomics, metatranscriptomics, 16S rRNA sequencing, and low-throughput proteomics.
RESULTS: We conducted ultrafast, in-depth MS-based proteomic and metaproteomic profiling of saliva from 15 newly diagnosed T2D individuals and 15 age-/BMI-matched healthy controls (HC). Using state-of-the-art proteomics, over 4500 human and bacterial proteins were identified in a single 21-min run. Bioinformatic analysis revealed host signatures of altered immune-, lipid-, and glucose-metabolism regulatory systems, increased oxidative stress, and possible precancerous changes in T2D saliva. Abundance of peptides for bacterial genera such as Neisseria and Corynebacterium were altered showing biomarker potential, offering insights into disease pathophysiology and microbial applications for T2D management.
CONCLUSIONS: This study presents a comprehensive mapping of salivary proteins and microbial communities, serving as a foundational resource for enhancing understanding of T2D pathophysiology. The identified biomarkers hold promise for advancing diagnostics and therapeutic approaches in T2D and its associated long-term complication Video Abstract.}, }
@article {pmid39794618, year = {2025}, author = {Nguyen, HP and Le, BT and Nguyen, HN and Nguyen, TT and Duong, TH and Hoang, TC and Duy, NPT and Nguyen, MV and Duong, LN and Le, LQ and Pham, TT}, title = {Demonstration of adapted packed-bed bioreactor for accurate and rapid estimation of biochemical oxygen demand: insights into the influence of microbial community structure and functions.}, journal = {World journal of microbiology & biotechnology}, volume = {41}, number = {2}, pages = {31}, pmid = {39794618}, issn = {1573-0972}, support = {NCUD.02-2019.52//Vietnam National Foundation for Science and Technology Development (NAFOSTED)/ ; NCUD.02-2019.52//Vietnam National Foundation for Science and Technology Development (NAFOSTED)/ ; NCUD.02-2019.52//Vietnam National Foundation for Science and Technology Development (NAFOSTED)/ ; NCUD.02-2019.52//Vietnam National Foundation for Science and Technology Development (NAFOSTED)/ ; NCUD.02-2019.52//Vietnam National Foundation for Science and Technology Development (NAFOSTED)/ ; NCUD.02-2019.52//Vietnam National Foundation for Science and Technology Development (NAFOSTED)/ ; NCUD.02-2019.52//Vietnam National Foundation for Science and Technology Development (NAFOSTED)/ ; NCUD.02-2019.52//Vietnam National Foundation for Science and Technology Development (NAFOSTED)/ ; NCUD.02-2019.52//Vietnam National Foundation for Science and Technology Development (NAFOSTED)/ ; }, mesh = {*Bioreactors/microbiology ; *Wastewater/microbiology/chemistry ; *Biological Oxygen Demand Analysis ; *Microbial Consortia ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Metagenomics/methods ; Biodegradation, Environmental ; Cocos/microbiology ; Glucose/metabolism ; Azo Compounds/metabolism ; Metagenome ; }, abstract = {This study demonstrated a novel approach to accurately estimate 5-day biochemical oxygen demand (BOD5) in textile wastewater using a microbial consortium from food processing wastewater fixed on coconut fibers. Although glucose-glutamic acid (GGA) has been widely known as the most preferred substrates for microbial respiration, its calibration surprisingly resulted in an overestimation of BOD5 in textile wastewater due to its lower utilization rate compared to that of textile wastewater. After being adapted with a new nutrient environment composed of GGA and textile wastewater, the adapted packed-bed bioreactors (PBBRs) was capable of accurate estimation of BOD5 in textile wastewater using GGA standard solution. Metagenomic analysis revealed the dominance of the genera Enterobacter, Acinetobacter, Chryseobacterium, and Comamonas in the adapted microbial community, which are recognized for their significant potential in azo dye degradation. The imputed metagenome showed an enhanced showed an enhanced abundance of "Amino Acid Degradation" and "Carbohydrate Degradation" functions, confirming the improved ability of adapted community to utilization of GGA in the standard solution. These findings suggest that adaptation of exogenous microbial consortium to a nutrient environment composed of GGA and target wastewater may shift the community to that dominated by strains having both utilization ability of GGA and target compounds which, in turn, enhance the accuracy of the adapted PBBRs for estimation of BOD5 in target wastewater.}, }
@article {pmid39762435, year = {2025}, author = {Fackelmann, G and Manghi, P and Carlino, N and Heidrich, V and Piccinno, G and Ricci, L and Piperni, E and Arrè, A and Bakker, E and Creedon, AC and Francis, L and Capdevila Pujol, J and Davies, R and Wolf, J and Bermingham, KM and Berry, SE and Spector, TD and Asnicar, F and Segata, N}, title = {Gut microbiome signatures of vegan, vegetarian and omnivore diets and associated health outcomes across 21,561 individuals.}, journal = {Nature microbiology}, volume = {10}, number = {1}, pages = {41-52}, pmid = {39762435}, issn = {2058-5276}, support = {microTOUCH-101045015)//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; }, mesh = {*Gastrointestinal Microbiome ; Humans ; *Diet ; *Diet, Vegetarian ; *Diet, Vegan ; *Bacteria/classification/genetics/isolation & purification ; Female ; Vegans ; Male ; Adult ; Metagenomics ; Feces/microbiology ; Middle Aged ; Diet, Western/adverse effects ; }, abstract = {As plant-based diets gain traction, interest in their impacts on the gut microbiome is growing. However, little is known about diet-pattern-specific metagenomic profiles across populations. Here we considered 21,561 individuals spanning 5 independent, multinational, human cohorts to map how differences in diet pattern (omnivore, vegetarian and vegan) are reflected in gut microbiomes. Microbial profiles distinguished these common diet patterns well (mean AUC = 0.85). Red meat was a strong driver of omnivore microbiomes, with corresponding signature microbes (for example, Ruminococcus torques, Bilophila wadsworthia and Alistipes putredinis) negatively correlated with host cardiometabolic health. Conversely, vegan signature microbes were correlated with favourable cardiometabolic markers and were enriched in omnivores consuming more plant-based foods. Diet-specific gut microbes partially overlapped with food microbiomes, especially with dairy microbes, for example, Streptococcus thermophilus, and typical soil microbes in vegans. The signatures of common western diet patterns can support future nutritional interventions and epidemiology.}, }
@article {pmid39753668, year = {2025}, author = {Rohwer, RR and Kirkpatrick, M and Garcia, SL and Kellom, M and McMahon, KD and Baker, BJ}, title = {Two decades of bacterial ecology and evolution in a freshwater lake.}, journal = {Nature microbiology}, volume = {10}, number = {1}, pages = {246-257}, pmid = {39753668}, issn = {2058-5276}, support = {DEB-0822700//National Science Foundation (NSF)/ ; DEB-1440297//National Science Foundation (NSF)/ ; MCB-9977903//National Science Foundation (NSF)/ ; DEB-1344254//National Science Foundation (NSF)/ ; WIS01789//U.S. Department of Agriculture (United States Department of Agriculture)/ ; WIS01516//U.S. Department of Agriculture (United States Department of Agriculture)/ ; R01-GM116853//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; DBI-2011002//National Science Foundation (NSF)/ ; DEB-1831730//National Science Foundation (NSF)/ ; R01 GM116853/GM/NIGMS NIH HHS/United States ; DEB-0702395//National Science Foundation (NSF)/ ; DEB-2025982//National Science Foundation (NSF)/ ; DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; DEB-9632853//National Science Foundation (NSF)/ ; DEB-0217533//National Science Foundation (NSF)/ ; }, mesh = {*Lakes/microbiology ; *Bacteria/genetics/classification/isolation & purification ; *Microbiota/genetics ; Metagenome ; Seasons ; Phylogeny ; Genome, Bacterial ; Evolution, Molecular ; Biological Evolution ; }, abstract = {Ecology and evolution are considered distinct processes that interact on contemporary time scales in microbiomes. Here, to observe these processes in a natural system, we collected a two-decade, 471-metagenome time series from Lake Mendota (Wisconsin, USA). We assembled 2,855 species-representative genomes and found that genomic change was common and frequent. By tracking strain composition via single nucleotide variants, we identified cyclical seasonal patterns in 80% and decadal shifts in 20% of species. In the dominant freshwater family Nanopelagicaceae, environmental extremes coincided with shifts in strain composition and positive selection of amino acid and nucleic acid metabolism genes. These genes identify organic nitrogen compounds as potential drivers of freshwater responses to global change. Seasonal and long-term strain dynamics could be regarded as ecological processes or, equivalently, as evolutionary change. Rather than as distinct interacting processes, we propose a conceptualization of ecology and evolution as a continuum to better describe change in microbial communities.}, }
@article {pmid39747695, year = {2025}, author = {Wang, X and Fang, Y and Liang, W and Cai, Y and Wong, CC and Wang, J and Wang, N and Lau, HC and Jiao, Y and Zhou, X and Ye, L and Mo, M and Yang, T and Fan, M and Song, L and Zhou, H and Zhao, Q and Chu, ES and Liang, M and Liu, W and Liu, X and Zhang, S and Shang, H and Wei, H and Li, X and Xu, L and Liao, B and Sung, JJY and Kuang, M and Yu, J}, title = {Gut-liver translocation of pathogen Klebsiella pneumoniae promotes hepatocellular carcinoma in mice.}, journal = {Nature microbiology}, volume = {10}, number = {1}, pages = {169-184}, pmid = {39747695}, issn = {2058-5276}, support = {82173191//National Science Foundation of China | National Natural Science Foundation of China-Yunnan Joint Fund (NSFC-Yunnan Joint Fund)/ ; }, mesh = {Animals ; *Carcinoma, Hepatocellular/microbiology/pathology ; *Klebsiella pneumoniae/pathogenicity/genetics ; Mice ; *Liver Neoplasms/microbiology/pathology/metabolism ; Humans ; *Toll-Like Receptor 4/metabolism/genetics ; *Gastrointestinal Microbiome ; *Klebsiella Infections/microbiology ; *Bacterial Translocation ; *Liver/microbiology/pathology ; Fecal Microbiota Transplantation ; Disease Models, Animal ; Mice, Inbred C57BL ; Male ; Carcinogenesis ; Cell Proliferation ; Bacterial Proteins/metabolism/genetics ; }, abstract = {Hepatocellular carcinoma (HCC) is accompanied by an altered gut microbiota but whether the latter contributes to carcinogenesis is unclear. Here we show that faecal microbiota transplantation (FMT) using stool samples from patients with HCC spontaneously initiate liver inflammation, fibrosis and dysplasia in wild-type mice, and accelerate disease progression in a mouse model of HCC. We find that HCC-FMT results in gut barrier injury and translocation of live bacteria to the liver. Metagenomic analyses and bacterial culture of liver tissues reveal enrichment of the gut pathogen Klebsiella pneumoniae in patients with HCC and mice transplanted with the HCC microbiota. Moreover, K. pneumoniae monocolonization recapitulates the effect of HCC-FMT in promoting liver inflammation and hepatocarcinogenesis. Mechanistically, K. pneumoniae surface protein PBP1B interacts with and activates TLR4 on HCC cells, leading to increased cell proliferation and activation of oncogenic signalling. Targeting gut colonization using K. oxytoca or TLR4 inhibition represses K. pneumoniae-induced HCC progression. These findings indicate a role for an altered gut microbiota in hepatocarcinogenesis.}, }
@article {pmid39747694, year = {2025}, author = {Hsu, TY and Nzabarushimana, E and Wong, D and Luo, C and Beiko, RG and Langille, M and Huttenhower, C and Nguyen, LH and Franzosa, EA}, title = {Profiling lateral gene transfer events in the human microbiome using WAAFLE.}, journal = {Nature microbiology}, volume = {10}, number = {1}, pages = {94-111}, pmid = {39747694}, issn = {2058-5276}, support = {K23DK125838//U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)/ ; R24DK110499//U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)/ ; Research Scholars Award//American Gastroenterological Association (AGA)/ ; Career Development Award//Crohn's and Colitis Foundation (Crohn's & Colitis Foundation)/ ; T32CA009001//U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI)/ ; U54DE023798//U.S. Department of Health & Human Services | NIH | National Institute of Dental and Craniofacial Research (NIDCR)/ ; }, mesh = {Humans ; *Gene Transfer, Horizontal ; *Microbiota/genetics ; *Metagenome ; *Phylogeny ; *Algorithms ; Bacteria/genetics/classification/isolation & purification ; Metagenomics/methods ; Genome, Bacterial ; Computational Biology/methods ; }, abstract = {Lateral gene transfer (LGT), also known as horizontal gene transfer, facilitates genomic diversification in microbial populations. While previous work has surveyed LGT in human-associated microbial isolate genomes, the landscape of LGT arising in personal microbiomes is not well understood, as there are no widely adopted methods to characterize LGT from complex communities. Here we developed, benchmarked and validated a computational algorithm (WAAFLE or Workflow to Annotate Assemblies and Find LGT Events) to profile LGT from assembled metagenomes. WAAFLE prioritizes specificity while maintaining high sensitivity for intergenus LGT. Applying WAAFLE to >2,000 human metagenomes from diverse body sites, we identified >100,000 high-confidence previously uncharacterized LGT (~2 per microbial genome-equivalent). These were enriched for mobile elements, as well as restriction-modification functions associated with the destruction of foreign DNA. LGT frequency was influenced by biogeography, phylogenetic similarity of involved pairs (for example, Fusobacterium periodonticum and F. nucleatum) and donor abundance. These forces manifest as networks in which hub taxa donate unequally with phylogenetic neighbours. Our findings suggest that human microbiome LGT may be more ubiquitous than previously described.}, }
@article {pmid39747693, year = {2025}, author = {Michoud, G and Peter, H and Busi, SB and Bourquin, M and Kohler, TJ and Geers, A and Ezzat, L and , and Battin, TJ}, title = {Mapping the metagenomic diversity of the multi-kingdom glacier-fed stream microbiome.}, journal = {Nature microbiology}, volume = {10}, number = {1}, pages = {217-230}, pmid = {39747693}, issn = {2058-5276}, support = {Vanishing Glaciers Project//NOMIS Stiftung (NOMIS Foundation)/ ; }, mesh = {*Microbiota/genetics ; *Rivers/microbiology ; *Metagenome ; *Bacteria/genetics/classification/isolation & purification ; *Ice Cover/microbiology ; Biofilms/growth & development ; Metagenomics ; Fungi/genetics/classification ; Geologic Sediments/microbiology ; Ecosystem ; Viruses/genetics/classification ; Biodiversity ; Phylogeny ; }, abstract = {Glacier-fed streams (GFS) feature among Earth's most extreme aquatic ecosystems marked by pronounced oligotrophy and environmental fluctuations. Microorganisms mainly organize in biofilms within them, but how they cope with such conditions is unknown. Here, leveraging 156 metagenomes from the Vanishing Glaciers project obtained from sediment samples in GFS from 9 mountains ranges, we report thousands of metagenome-assembled genomes (MAGs) encompassing prokaryotes, algae, fungi and viruses, that shed light on biotic interactions within glacier-fed stream biofilms. A total of 2,855 bacterial MAGs were characterized by diverse strategies to exploit inorganic and organic energy sources, in part via functional redundancy and mixotrophy. We show that biofilms probably become more complex and switch from chemoautotrophy to heterotrophy as algal biomass increases in GFS owing to glacier shrinkage. Our MAG compendium sheds light on the success of microbial life in GFS and provides a resource for future research on a microbiome potentially impacted by climate change.}, }
@article {pmid39747692, year = {2025}, author = {Olm, MR and Spencer, SP and Takeuchi, T and Silva, EL and Sonnenburg, JL}, title = {Metagenomic immunoglobulin sequencing reveals IgA coating of microbial strains in the healthy human gut.}, journal = {Nature microbiology}, volume = {10}, number = {1}, pages = {112-125}, pmid = {39747692}, issn = {2058-5276}, support = {T32DK007056//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; K08DK134856//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; K08 DK134856/DK/NIDDK NIH HHS/United States ; DP1AT009892//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; T32 DK007056/DK/NIDDK NIH HHS/United States ; F32DK128865//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; }, mesh = {Humans ; *Immunoglobulin A/immunology ; *Gastrointestinal Microbiome/genetics ; *Feces/microbiology ; *Metagenomics/methods ; *Bacteria/genetics/classification/immunology/metabolism ; Host Microbial Interactions/immunology ; Healthy Volunteers ; Intestinal Mucosa/microbiology/immunology/metabolism ; }, abstract = {IgA, the primary human antibody secreted from the gut mucosa, shapes the intestinal microbiota. Methodological limitations have hindered defining which microbial strains are targeted by IgA and the implications of binding. Here we develop a technique, metagenomic immunoglobulin sequencing (MIg-seq), that provides strain-level resolution of microbes coated by IgA and use it to determine IgA coating levels for 3,520 gut microbiome strains in healthy human faeces. We find that both health and disease-associated bacteria are targeted by IgA. Microbial genes are highly predictive of IgA binding levels; in particular, mucus degradation genes are correlated with high binding, and replication rates are significantly reduced for microbes bound by IgA. We demonstrate that IgA binding is more correlated with host immune status than traditional relative abundance measures of microbial community composition. This study introduces a powerful technique for assessing strain-level IgA binding in human stool, paving the way for deeper understanding of IgA-based host-microbe interactions.}, }
@article {pmid39718972, year = {2025}, author = {Pittaluga, AM and Miccoli, FE and Guerrero, LD and Relling, AE}, title = {Effect of multispecies fungal extract supplementation on growth performance, nutrient digestibility, ruminal fermentation, and the rumen microbiome composition of beef cattle fed forage-based diets.}, journal = {Journal of animal science}, volume = {103}, number = {}, pages = {}, doi = {10.1093/jas/skae387}, pmid = {39718972}, issn = {1525-3163}, support = {//Biopremix Technologies LLC/ ; OHO01461//USDA National Institute of Food and Agriculture/ ; }, mesh = {Animals ; Cattle/physiology/growth & development ; *Rumen/microbiology/metabolism ; *Animal Feed/analysis ; *Digestion/drug effects ; *Diet/veterinary ; *Fermentation ; *Dietary Supplements/analysis ; Male ; *Gastrointestinal Microbiome/drug effects ; *Animal Nutritional Physiological Phenomena ; Female ; Cross-Over Studies ; Fungi ; Random Allocation ; Nutrients/metabolism ; }, abstract = {Our objective was to evaluate the effect of a multispecies fungal extract (MFE) on growth performance, apparent total tract digestibility (ATTD), fermentation characteristics, and rumen microbiome composition of beef cattle fed forage-based diets. For experiment 1, ruminally cannulated Angus × SimAngus cows (n = 4; body weight [BW] = 569 ± 21 kg) were used in a randomized crossover design with two 21-d study periods and a 23-d washout period to evaluate the effect of dietary inclusion of an MFE on in situ digestion, ruminal fermentation, and the composition of the rumen microbiome. Treatments consisted of a forage-based diet with or without the inclusion of a MFE. Rumen samples were collected on days 5, 10, and 20. Experiment 2 evaluated different inclusion rates of the MFE in a randomized complete block design using Angus × SimAngus-crossbred steers (n = 80; BW = 370 ± 44 kg). Steers were blocked by BW and randomly assigned to one of four treatments (2 pens/treatment): diet with no MFE, 0.02%, 0.04%, and 0.08% of the MFE (dry matter [DM] basis). Steers were fed a forage-based diet for 122 d. Subsets of 10 steers/treatment were randomly selected for the determination of ATTD on d 20, 40, and 60. All data were analyzed using the MIXED procedure of SAS. In exp 1, adding the MFE to the diet tended to increase the ruminal disappearance rate of the DM on day 10 (P = 0.06). No interactions or treatment effects were observed for the short-chain fatty acid profile of the rumen fluid (P ≥ 0.13). Metagenomic analysis of the rumen microbiome showed an MFE × d interaction for the Fibrobacter genus (P = 0.01), which on day 20 was less abundant in the rumen of cows fed the MFE. In exp 2, steers supplemented with 0.04% of MFE had a lower average daily gain and were lighter at the end of the experiment (cubic, P ≤ 0.04) compared to steers supplemented with 0.02% MFE. Steers fed the diet with 0.02% of MFE had the greatest gain-to-feed ratio among the MFE-supplemented groups (cubic, P < 0.01). Dietary inclusion of the MFE increased neutral detergent fiber digestibility (linear, P = 0.05). Steers supplemented with 0.04% of MFE had the greatest acid detergent fiber digestibility among treatments (quadratic, P = 0.03). Collectively, results showed that ruminal disappearance rate and digestibility of forage-based diets increased due to MFE supplementation, but did not translate into growth performance improvements or beneficially alter rumen fermentation.}, }
@article {pmid39635985, year = {2025}, author = {Mulders, MCF and Van Koetsveld, PM and Feelders, RA and Hofland, LJ and de Herder, WW and Kraaij, R and Hofland, J}, title = {Gut microbial and functional alterations lead to metagenomic signatures for midgut neuroendocrine tumor patients and for carcinoid syndrome.}, journal = {Endocrine-related cancer}, volume = {32}, number = {2}, pages = {}, doi = {10.1530/ERC-24-0145}, pmid = {39635985}, issn = {1479-6821}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Neuroendocrine Tumors/microbiology/genetics/pathology ; Female ; Male ; Middle Aged ; Aged ; Malignant Carcinoid Syndrome/microbiology/genetics ; Adult ; Intestinal Neoplasms/microbiology/genetics/pathology ; Metagenomics/methods ; Feces/microbiology ; Metagenome ; }, abstract = {Midgut neuroendocrine tumors (NET) derive from enterochromaffin cells, which have a close interrelationship with intestinal microbiota. Recently, we have utilized 16S rRNA sequencing to uncover that midgut NET patients have a depleted gut microbiome and a specific fecal microbial signature. This study aims to validate these findings and to further characterize the role of microbes and microbial metabolic pathways in midgut NET patients with and without carcinoid syndrome (CS). Fecal samples from 60 midgut NET patients and 20 household-matched controls were subjected to whole metagenome sequencing. The gut microbial community composition of midgut NET patients differed from that of controls, with 2 genera, 17 species and 9 microbial pathways showing differential abundance (P < 0.001). No differences in the microbial composition were observed between midgut NET patients with and without CS (P > 0.05). However, we did observe changes in inter-genus correlations of Bacteroides, Odoribacter, Parasutterella, Klebsiella, Ruminococcus and Proteobacteria when comparing these two patient groups. A signature of 16 microbial species (area under the receiver operating characteristics (AUROC) curve 0.892) or 18 microbial pathways (AUROC 0.909) accurately predicted the presence of a midgut NET. Furthermore, a microbial signature consisting of 14 functional microbial pathways distinguished CS patients from non-CS patients (AUROC 0.807). Thus, this study confirms that the gut microbiome of midgut NET patients is altered at the metagenomic level, which is not related to the presence of CS. A fecal microbial signature could constitute a novel biomarker for the diagnosis of midgut NET or CS.}, }
@article {pmid39541968, year = {2025}, author = {Nishijima, S and Stankevic, E and Aasmets, O and Schmidt, TSB and Nagata, N and Keller, MI and Ferretti, P and Juel, HB and Fullam, A and Robbani, SM and Schudoma, C and Hansen, JK and Holm, LA and Israelsen, M and Schierwagen, R and Torp, N and Telzerow, A and Hercog, R and Kandels, S and Hazenbrink, DHM and Arumugam, M and Bendtsen, F and Brøns, C and Fonvig, CE and Holm, JC and Nielsen, T and Pedersen, JS and Thiele, MS and Trebicka, J and Org, E and Krag, A and Hansen, T and Kuhn, M and Bork, P and , }, title = {Fecal microbial load is a major determinant of gut microbiome variation and a confounder for disease associations.}, journal = {Cell}, volume = {188}, number = {1}, pages = {222-236.e15}, doi = {10.1016/j.cell.2024.10.022}, pmid = {39541968}, issn = {1097-4172}, mesh = {*Gastrointestinal Microbiome ; *Feces/microbiology ; Humans ; Machine Learning ; Female ; Bacteria/classification/genetics/isolation & purification ; Male ; Metagenomics/methods ; Adult ; }, abstract = {The microbiota in individual habitats differ in both relative composition and absolute abundance. While sequencing approaches determine the relative abundances of taxa and genes, they do not provide information on their absolute abundances. Here, we developed a machine-learning approach to predict fecal microbial loads (microbial cells per gram) solely from relative abundance data. Applying our prediction model to a large-scale metagenomic dataset (n = 34,539), we demonstrated that microbial load is the major determinant of gut microbiome variation and is associated with numerous host factors, including age, diet, and medication. We further found that for several diseases, changes in microbial load, rather than the disease condition itself, more strongly explained alterations in patients' gut microbiome. Adjusting for this effect substantially reduced the statistical significance of the majority of disease-associated species. Our analysis reveals that the fecal microbial load is a major confounder in microbiome studies, highlighting its importance for understanding microbiome variation in health and disease.}, }
@article {pmid39042247, year = {2024}, author = {Çalık Koç, G and Rezaei, F and Kahraman Ilıkkan, Ö and Bağdat, EŞ}, title = {Effect of seed priming with polyethylene glycol, distilled water, and sorbitol on physical, chemical quality parameters, and nodule microbiota of lentil.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {55}, number = {4}, pages = {3997-4008}, pmid = {39042247}, issn = {1678-4405}, support = {21/07//Baskent Üniversitesi/ ; }, mesh = {*Lens Plant/microbiology/chemistry ; *Seeds/microbiology/chemistry ; *Polyethylene Glycols/pharmacology/chemistry ; *Microbiota/drug effects ; *Water/chemistry ; *Sorbitol/pharmacology/metabolism ; Bacteria/classification/genetics/drug effects/isolation & purification ; Root Nodules, Plant/microbiology ; Germination/drug effects ; }, abstract = {The aim of this study was to investigate the effects of different seed priming solutions on physical and chemical quality parameters of lentils as well as nodule bacterial diversity before sowing. Therefore, lentil seeds were treated with polyethylene glycol (PEG 6000) (15%), sorbitol (6%), and distilled water, and none pretreated lentils (Lens culinaris) were used as control. The seeds were kept in these solutions for 24 h, then dried on toweling paper for 24 h, and used for the experiment. For nodule microbiota analysis, the plant root was divided into two equal parts, upper and lower, according to the root length and all nodules were collected from each region. According to the results, it was observed that emergence and flowering started late in the control compared to other seed priming treatments. Sorbitol application was found to provide advantages in terms of germination and seedling development. PEG and distilled water (DW) treatments showed an increase in total phenolic component activity; however, no significant change was observed in DPPH radical scavenging activity. Amplicon-based metagenomic analysis revealed that sorbitol and distilled water were the seed priming solutions altering the species diversity, especially Rhizobium sp. as the genus. In the comparison of samples taken from different parts of the root nodules, more Rhizobium sp. as a genus and Rhizobium leguminosarum as the species were found in the nodules collected from the top of the root. According to the overall results of lentil pod, lentil plant, and microbiota, sorbitol and DW can be considered to be a good priming solutions.}, }
@article {pmid39789436, year = {2025}, author = {Cao, T and Guo, Y and Lin, L and Wang, D and Liu, Z and Zou, X and Ke, Y and Lv, Z}, title = {Effect of folpet on hypoglycaemia, intestinal microbiota, and drug resistance genes in mice.}, journal = {BMC microbiology}, volume = {25}, number = {1}, pages = {11}, pmid = {39789436}, issn = {1471-2180}, support = {JCYJ20210324124014040//Shenzhen Science and Technology Program/ ; JCYJ20210324124201004//Shenzhen Science and Technology Program/ ; SZSM202011008//Sanming Project of Medicine in Shenzhen/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects/genetics ; Mice ; *Hypoglycemia/genetics/chemically induced ; Blood Glucose/metabolism/drug effects ; Sulfonamides/pharmacology ; Bacteria/drug effects/genetics/classification/isolation & purification ; Male ; Metagenomics ; }, abstract = {BACKGROUND: Folpet is a nonspecific sulfonamide fungicide widely used to protect crops from mildew. However, the in vivo effects of folpet on glucose metabolism homeostasis, gut microbiota, and abundance of drug resistance genes remain unknown. The purpose of this study was to assess the effects of the pesticide, folpet, on glucose metabolism homeostasis, and folpet-induced changes in the intestinal microbiota and resistance genes in mice.
METHODS: Mice were orally administered folpet at 0, 1, 10, and 100 mg/kg body weight/day for 5 weeks. Blood sugar levels in mice were measured after 5 weeks of folpet administration. Metagenomic sequencing and drug resistance gene analyses were performed to explore changes in the abundance of gut microbiota members and drug resistance genes in mice after folpet administration. Correlation analysis was performed using metabolomics to explore the relationship between intestinal microbiota, drug resistance genes, and glucose metabolism.
RESULTS: Mice in the folpet group had significantly lower blood glucose levels than those in the control group. The abundance of Atopobium, Libanicoccus, Collinsella, and Parabacteroides in the intestinal microbiota of folpet-treated mice was significantly higher than that in the control group. However, the abundance of Mailhella, Bilophila, Roseburia, and Bacteroides were reduced in folpet-treated mice. Compared with the control group, the abundance of APH6-Ic and AAC6-Ie-APH2-Ia resistance genes in mice treated with folpet significantly increased. The abundance of tetQ, ermE, and BahA resistance genes was significantly reduced after folpet treatment.
CONCLUSIONS: Folpet is associated with changes in the abundance of gut microbiota in mice and may also affect the abundance of drug-resistance genes and the regulation of blood glucose levels.}, }
@article {pmid39788986, year = {2025}, author = {Patova, A and Ribeiro, PA and Murillo, FJ and Riesgo, A and Taboada, S and Pomponi, SA and Rapp, HT and Kenchington, E and Xavier, JR}, title = {Population genomics and connectivity of Vazella pourtalesii sponge grounds of the northwest Atlantic with conservation implications of deep sea vulnerable marine ecosystems.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {1540}, pmid = {39788986}, issn = {2045-2322}, mesh = {*Metagenomics ; *Porifera/genetics/metabolism ; Atlantic Ocean ; *Ecosystem ; *Aquatic Organisms/genetics/metabolism ; *Conservation of Natural Resources ; Hunting/statistics & numerical data ; Animal Distribution ; Animals ; Polymorphism, Single Nucleotide/genetics ; Nova Scotia ; }, abstract = {Sponges are key ecosystem engineers that shape, structure and enhance the biodiversity of marine benthic communities globally. Sponge aggregations and reefs are recognized as vulnerable marine ecosystems (or VMEs) due to their susceptibility to damage from bottom-contact fishing gears. Ensuring their long-term sustainability, preservation, and ecosystem functions requires the implementation of sound scientific conservation tools. Here, the genetic diversity, structure, and connectivity of the deep-sea glass sponge, Vazella pourtalesii (Schmidt, 1870), was investigated using 1,102 neutral SNPs obtained in RADseq. This species is distributed across the northwest Atlantic from Florida, USA to Nova Scotia, Canada and we sequenced samples covering this full distribution and provided evidence of strong genetic structure with two distinct clusters: Florida together with the Carolina Shelves and the Scotian Shelf. We estimated moderate levels of diversity with low migration across large distances (> 1000 kms) and high connectivity at smaller scales (< 300 kms). Further, fishing pressure on genetic diversity was evaluated, within two Sponge Conservation Areas (SCAs) on the Scotian Shelf. Those areas have different disturbance histories, and cumulative fishing pressure. Slightly lower levels of genetic diversity were found inside the SCAs, and yet they encompassed a high proportion of the diversity observed within the Scotian Shelf. We provide baseline data for future monitoring of the SCAs, discussing our findings in the light of existing area-based management tools.}, }
@article {pmid39788961, year = {2025}, author = {Banerjee, G and Papri, SR and Huang, H and Satapathy, SK and Banerjee, P}, title = {Deep sequencing-derived Metagenome Assembled Genomes from the gut microbiome of liver transplant patients.}, journal = {Scientific data}, volume = {12}, number = {1}, pages = {39}, pmid = {39788961}, issn = {2052-4463}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Liver Transplantation ; *Metagenome ; High-Throughput Nucleotide Sequencing ; Akkermansia ; Fatty Liver/microbiology ; }, abstract = {Recurrence of metabolic dysfunction-associated steatotic liver disease (MASLD) after liver transplantation (LT) is a continuing concern. The role of gut microbiome dysbiosis in MASLD initiation and progression has been well established. However, there is a lack of comprehensive gut microbiome shotgun sequence data for patients experiencing MASLD recurrence after LT. In this data descriptor, we describe a dataset of deep metagenomic sequences of a well-defined LT recipient population. Community-based analysis revealed a high abundance of Akkermansia muciniphila, consistently observed in most patient samples with a low (0-2) MASLD Activity Score (NAS). We constructed 357 metagenome-assembled genomes (MAGs), including 220 high-quality MAGs (>90% completion). The abundance of different species of Bacteroides MAGs dominated in patient samples with NAS > 5 ("definite MASH"). In contrast, the MAGs of A. muciniphila, Akkermansia sp., and Blutia sp. dominated in samples from patients without MASH (NAS = 0-2). In addition, the phylogenetic analysis of A. muciniphila and Akkermansia sp. MAGs identified two new phylogroups of Akkermansia that are distinct from the previously reported three phylogroups.}, }
@article {pmid39788783, year = {2025}, author = {Franz, K and Markó, L and Mähler, A and Chakaroun, R and Heinitz, S and Schlögl, H and Sacher, J and Steckhan, N and Dechend, R and Adams, N and Andersen, M and Glintborg, D and Viehweger, M and Bahr, LS and Forslund-Startceva, SK}, title = {Sex hormone-dependent host-microbiome interactions and cardiovascular risk (XCVD): design of a longitudinal multi-omics cohort study.}, journal = {BMJ open}, volume = {15}, number = {1}, pages = {e087982}, doi = {10.1136/bmjopen-2024-087982}, pmid = {39788783}, issn = {2044-6055}, mesh = {Humans ; *Cardiovascular Diseases/microbiology/epidemiology ; Longitudinal Studies ; Male ; Female ; *Gonadal Steroid Hormones/metabolism/blood ; *Gastrointestinal Microbiome ; Host Microbial Interactions ; Transgender Persons ; Research Design ; Heart Disease Risk Factors ; Adult ; Sex Reassignment Procedures ; Multiomics ; }, abstract = {INTRODUCTION: Cardiovascular diseases (CVDs) present differently in women and men, influenced by host-microbiome interactions. The roles of sex hormones in CVD outcomes and gut microbiome in modifying these effects are poorly understood. The XCVD study examines gut microbiome mediation of sex hormone effects on CVD risk markers by observing transgender participants undergoing gender-affirming hormone therapy (GAHT), with findings expected to extrapolate to cisgender populations.
METHODS AND ANALYSES: This observational, longitudinal cohort study includes baseline, 1- and 2-year follow-ups with transgender participants beginning GAHT. It involves comprehensive phenotyping and microbiome genotyping, integrating computational analyses of high-dimensional data. Microbial diversity will be assessed using gut, skin, and oral samples via 16S rRNA and shotgun metagenomic sequencing of gut samples. Blood measurements will include sex hormones, CVD risk markers, cardiometabolic parameters, cytokines, and immune cell counts. Hair samples will be analysed for cortisol. Participants will complete online questionnaires on physical activity, mental health, stress, quality of life, fatigue, sleep, pain, and gender dysphoria, tracking medication use and diet to control for confounders. Statistical analyses will integrate phenomic, lifestyle, and multi-omic data to model health effects, testing gut microbiome mediation of CVD risk as the endocrine environment shifts between that typical for cisgender men to women and vice versa.
ETHICS AND DISSEMINATION: The study adheres to Good Clinical Practice and the Declaration of Helsinki. The protocol was approved by the Charité Ethical Committee (EA1/339/21). Signed informed consent will be obtained. Results will be published in peer-reviewed journals and conferences and shared as accessible summaries for participants, community groups, and the public, with participants able to view their data securely after public and patient involvement review for accessibility.
TRIAL REGISTRATION NUMBER: The XCVD study was registered on ClinicalTrials.gov (NCT05334888) as 'Sex-differential host-microbiome CVD risk - a longitudinal cohort approach (XCVD)" on 4 April 2022. Data set link can be found at https://classic.
CLINICALTRIALS: gov/ct2/show/NCT05334888.}, }
@article {pmid39786931, year = {2025}, author = {Ni, B and Xiao, L and Lin, D and Zhang, TL and Zhang, Q and Liu, Y and Chen, Q and Zhu, D and Qian, H and Rillig, MC and Zhu, YG}, title = {Increasing pesticide diversity impairs soil microbial functions.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {122}, number = {2}, pages = {e2419917122}, doi = {10.1073/pnas.2419917122}, pmid = {39786931}, issn = {1091-6490}, support = {41991332//MOST | National Natural Science Foundation of China (NSFC)/ ; 42307027//MOST | National Natural Science Foundation of China (NSFC)/ ; 42222701//MOST | National Natural Science Foundation of China (NSFC)/ ; 2022A-163-G//Ningbo Yongjiang Talent Project/ ; 2021-DST-004//Ningbo S&T project/ ; 2023321//Youth Innovation Promotion Association, Chinese Academy of Sciences/ ; }, mesh = {*Soil Microbiology ; *Pesticides ; *Bacteria/genetics/metabolism/classification/drug effects ; *Soil/chemistry ; *Fertilizers ; *Nitrogen/metabolism ; Phosphorus/metabolism ; Carbon/metabolism ; Sulfur/metabolism ; Agriculture/methods ; Metagenomics/methods ; Microbiota/drug effects ; }, abstract = {Pesticide application is essential for stabilizing agricultural production. However, the effects of increasing pesticide diversity on soil microbial functions remain unclear, particularly under varying nitrogen (N) fertilizer management practices. In this study, we investigated the stochasticity of soil microbes and multitrophic networks through amplicon sequencing, assessed soil community functions related to carbon (C), N, phosphorus (P), and sulfur (S) cycling, and characterized the dominant bacterial life history strategies via metagenomics along a gradient of increasing pesticide diversity under two N addition levels. Our findings show that higher pesticide diversity enriches the abundance of bacterial specialists and opportunists capable of degrading or resisting pesticides, reducing the proportion of bacterial generalists in the absence of N addition. These shifts can complicate multitrophic microbial networks. Under increased pesticide diversity, selective pressure may drive bacteria to streamline their average genome size to conserve energy while enhancing C, N, P, and S metabolic capacities, thus accelerating soil nutrient loss. In comparison, N addition was found to reduce bacterial niche differentiation at higher pesticide diversity, mitigating the impacts of network complexity and functional traits associated with pesticide diversity, ultimately alleviating soil nutrient loss. Our results reveal the contrasting impacts of pesticide diversity on microbial functions under different N input scenarios and emphasize that strategic N fertilizer management can mitigate the ecological effects of pesticide use in agricultural systems.}, }
@article {pmid39781512, year = {2025}, author = {Sato, N and Katayama, K and Miyaoka, D and Uematsu, M and Saito, A and Fujimoto, K and Uematsu, S and Imoto, S}, title = {stana: an R package for metagenotyping analysis and interactive application based on clinical data.}, journal = {NAR genomics and bioinformatics}, volume = {7}, number = {1}, pages = {lqae191}, pmid = {39781512}, issn = {2631-9268}, mesh = {Humans ; *Software ; *Gastrointestinal Microbiome/genetics ; Crohn Disease/genetics/microbiology ; Metagenomics/methods ; Parkinson Disease/genetics ; Kidney Failure, Chronic/genetics ; Metagenome/genetics ; }, abstract = {Metagenotyping of metagenomic data has recently attracted increasing attention as it resolves intraspecies diversity by identifying single nucleotide variants. Furthermore, gene copy number analysis within species provides a deeper understanding of metabolic functions in microbial communities. However, a platform for examining metagenotyping results based on relevant grouping data is lacking. Here, we have developed the R package, stana, for the processing and analysis of metagenotyping results. The package consists of modules for preprocessing, statistical analysis, functional analysis and visualization. An interactive analysis environment for exploring the metagenotyping results was also developed and publicly released with over 1000 publicly available metagenome samples related to human diseases. Three examples exploring the relationship between the metagenotypes of the gut microbiome and human diseases are presented-end-stage renal disease, Crohn's disease and Parkinson's disease. The results suggest that stana facilitated the confirmation of the original study's findings and the generation of a new hypothesis. The GitHub repository for the package is available at https://github.com/noriakis/stana.}, }
@article {pmid39779932, year = {2025}, author = {Wei, Y and Zhu, Y and Yang, L and Chen, C and Yue, M and Mao, Z and Wang, Y and Li, Q and Li, Y and Lv, J and Xue, W}, title = {Effects of oil pollution on the growth and rhizosphere microbial community of Calamagrostis epigejos.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {1278}, pmid = {39779932}, issn = {2045-2322}, support = {22NYYF029//Xi'an Agricultural Technology R&D Projects/ ; S2024-JC-YB-2574//Natural Science Foundation of Science and Technology Department of Shaanxi Province/ ; 2020ZDLSF06-01//Natural Science Foundation of Science and Technology Department of Shaanxi Province/ ; 2021K-25//Strategic Reserve Talent Training Program of Shaanxi Academy of Sciences/ ; 2023JH-NJGG-0167//Xi'an Science Technology Bureau Fund/ ; KRDL K6-2207039//the Project of the First Investigation of Wild Plants Resources in Xi'an/ ; }, mesh = {*Soil Microbiology ; *Rhizosphere ; *Fungi/genetics ; *Bacteria/genetics/classification ; *Archaea/genetics/growth & development/metabolism ; Petroleum Pollution/adverse effects ; Petroleum ; Microbiota/drug effects ; Soil Pollutants ; }, abstract = {Bacteria, fungi, archaea, and viruses are reflective organisms that indicate soil health. Investigating the impact of crude oil pollution on the community structure and interactions among bacteria, fungi, archaea, and viruses in Calamagrostis epigejos soil can provide theoretical support for remediating crude oil pollution in Calamagrostis epigejos ecosystems. In this study, Calamagrostis epigejos was selected as the research subject and subjected to different levels of crude oil addition (0 kg/hm[2], 10 kg/hm[2], 40 kg/hm[2]). Metagenomic sequencing technology was employed to analyze the community structure and diversity of soil bacteria, fungi, archaea, and viruses. Additionally, molecular ecological network analysis was integrated to explore species interactions and ecosystem stability within these microbial communities. The functional profiles of soil microorganisms were elucidated based on data from the KEGG database. Results demonstrated a significant increase in petroleum hydrocarbon content, polyphenol oxidase activity, hydrogen peroxide enzyme activity, and acid phosphatase activity upon crude oil addition, while β-glucosidase content, fiber disaccharide hydrolase content, and tiller number decreased (P < 0.05). Proteobacteria and Actinobacteria were identified as dominant bacterial phyla; Ascomycota, Basidiomycota, and Mucoromycota were found to be dominant fungal phyla; Thaumarchaeota emerged as a dominant archaeal phylum; and Uroviricota represented a dominant viral phylum. The diversity of soil bacterial, fungal, archaeal, and viral communities increased with higher amounts of added crude oil. Ecological network analysis revealed a robust collaborative relationship among bacterial, fungal, archaeal, and viral community species in the control treatment (CK), while strong competitive relationships were observed among these species in the treatments with 10% (F10) and 40% (F40) crude oil concentrations. Structural equation modeling analysis indicated significant positive correlations between fungal community, viral community, enzyme activity, and plant growth; conversely, bacterial and archaeal communities showed significant negative correlations with plant growth (P < 0.05). Correlation analysis identified acid phosphatase as the primary environmental factor influencing soil microbial function. Acid phosphatase levels along with tiller number, aboveground biomass, and petroleum hydrocarbons significantly influenced the fungal community (P < 0.05), while underground biomass had a significant impact on the archaeal community (P < 0.05). Acid phosphatase levels along with cellulose-hydrolyzing enzymes, tiller number, and petroleum hydrocarbons exhibited significant effects on the viral community (P < 0.05). This study investigated variations in bacterial, fungal, archaeal, and viral communities under different crude oil concentrations as well as their driving factors, providing a theoretical foundation for evaluating Calamagrostis epigejos' potential to remediate crude oil pollution.}, }
@article {pmid39779716, year = {2025}, author = {Gałęcka, I and Rychlik, A and Całka, J}, title = {Influence of selected dosages of plastic microparticles on the porcine fecal microbiome.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {1269}, pmid = {39779716}, issn = {2045-2322}, support = {2020/37/N/NZ7/01383//Narodowe Centrum Nauki/ ; The Regional Initiative of Excellence Program//Minister of Science Poland/ ; }, mesh = {Animals ; Swine ; *Feces/microbiology ; *Gastrointestinal Microbiome/drug effects ; *Microplastics/toxicity ; Female ; Plastics ; Bacteria/classification/genetics/isolation & purification ; }, abstract = {Studies conducted so far have shown that nano- and microplastic may disturb the intestinal microenvironment by interacting with the intestinal epithelium and the gut microbiota. Depending on the research model used, the effect on the microbiome is different-an increase or decrease in selected taxa resulting in the development of dysbiosis. Dysbiosis may be associated with intestinal inflammation, development of mental disorders or diabetes. The aim of the study was to analyze the intestinal microbiome in 15 gilts divided into 3 research groups (n = 5; control group, receiving micropartices at a dose 0.1 g/day (LD) and 1 g/day (HD)). Feaces were collected before and after 28 days of exposure to PET microplastics. The analysis of the intestinal microbiome was performed using next-generation sequencing. Alpha and beta diversity indices were compared, showing, that repetition affected only the abundance indices in the control and LD groups, but not in the HD group. The relationships between the number of reads at the phylum, genus and species level and the microplastic dose were calculated using statistical methods (r-Pearson correlation, generalized regression model, analysis of variance). The statistical analysis revealed, that populations of Family XIII AD3011 group, Coprococcus, V9D2013 group, UCG-010 and Sphaerochaeta increased with increasing MP-PET dose. The above-mentioned taxa are mainly responsible for the production of short-chain fatty acids (SCFA). It may be assumed, that SCFA are one of the mechanisms involved in the response to oral exposure to MP-PET.}, }
@article {pmid39779118, year = {2025}, author = {Wang, C and Bin, Z and Wang, L and Zhu, G and Tang, S and Chen, Y and Xiao, D and Guo, X}, title = {Metagenomic and metabolomic profiling analyses to unravel the formation mechanism of n-propanol during the first and second round of Jiangxiangxing Baijiu fermentation.}, journal = {Food research international (Ottawa, Ont.)}, volume = {200}, number = {}, pages = {115459}, doi = {10.1016/j.foodres.2024.115459}, pmid = {39779118}, issn = {1873-7145}, mesh = {*Fermentation ; *Metabolomics/methods ; *1-Propanol/metabolism ; *Metagenomics/methods ; Lactobacillus/metabolism/genetics ; Alcoholic Beverages/microbiology ; Pichia/metabolism/genetics ; Saccharomyces cerevisiae/metabolism/genetics ; Food Microbiology ; Microbiota ; }, abstract = {N-propanol is one of the higher alcohols, a moderate amount of n-propanol is beneficial for the harmony of the liquor body, whereas excessive or repeated intake will lead to discomfort and pose significant harm to human health. In actual production process of Jiangxiangxing Baijiu, the n-propanol content of the base baijiu in first round (FR) is far higher than that of second round (SR). Nevertheless, the formation mechanism and the key n-propanol producing microbials remain unclear and this limits the quality control of baijiu fermentation. Here, we combined metagenomics and metabolomics to verify the biosynthesis pathway of n-propanol and to identify characteristic microorganisms in FR and SR. The results showed that the preliminary period of pit fermentation was critical for the accumulation of n-propanol. FR was enriched in Lactobacillus plantarum, Lactobacillus ponits, Lactobacillus brevis and Lactobacillus panis, while it was harbored greater abundances of Pichia kudriazevii, Saccharomyces cerevisiae and Lactobacillus acetotolerans in SR. Function analysis combined with KEGG providing comprehensive evidence for the main synthetic pathways of n-propanol in Jiangxiangxing baijiu, and L. panis was key microbial. In addition, the experiments of inoculating L. panis and L. acetotolerans in situ indicated L. panis was mainly responsible for n-propanol production while L. acetotolerans not conducive to the production of n-propanol. Besides, the bioturbation effect on microbiota and flavor compounds were also analyzed. These results are useful for elucidating the mechanism of flavor formation in baijiu fermentation and promoting the further application of bioturbation technology in the traditional fermentation industry.}, }
@article {pmid39778056, year = {2025}, author = {Silva, JK and Hervé, V and Mies, US and Platt, K and Brune, A}, title = {A Novel Lineage of Endosymbiotic Actinomycetales: Genome Reduction and Acquisition of New Functions in Bifidobacteriaceae Associated With Termite Gut Flagellates.}, journal = {Environmental microbiology}, volume = {27}, number = {1}, pages = {e70010}, pmid = {39778056}, issn = {1462-2920}, support = {//Max-Planck-Gesellschaft/ ; }, mesh = {*Symbiosis ; Animals ; *Isoptera/microbiology ; *Genome, Bacterial ; *RNA, Ribosomal, 16S/genetics ; *Phylogeny ; *Actinomycetales/genetics/metabolism ; Gene Transfer, Horizontal ; Gastrointestinal Microbiome ; Gastrointestinal Tract/microbiology/parasitology ; Metagenome ; }, abstract = {Cellulolytic flagellates are essential for the symbiotic digestion of lignocellulose in the gut of lower termites. Most species are associated with host-specific consortia of bacterial symbionts from various phyla. 16S rRNA-based diversity studies and taxon-specific fluorescence in situ hybridization revealed a termite-specific clade of Actinomycetales that colonise the cytoplasm of Trichonympha spp. and other gut flagellates, representing the only known case of intracellular Actinomycetota in protists. Comparative analysis of eleven metagenome-assembled genomes from lower termites allowed us to describe them as new genera of Bifidobacteriaceae. Like the previously investigated Candidatus Ancillula trichonymphae, they ferment sugars via the bifidobacterium shunt but, unlike their free-living relatives, experienced significant genome erosion. Additionally, they acquired new functions by horizontal gene transfer from other gut bacteria, including the capacity to produce hydrogen. Members of the genus Ancillula (average genome size 1.56 ± 0.2 Mbp) retained most pathways for the synthesis of amino acids, including a threonine/serine exporter, providing concrete evidence for the basis of the mutualistic relationship with their host. By contrast, Opitulatrix species (1.23 ± 0.1 Mbp) lost most of their biosynthetic capacities, indicating that an originally mutualistic symbiosis is on the decline.}, }
@article {pmid39777846, year = {2025}, author = {Liu, R and He, X and Ren, G and Li, DW and Zhao, M and Lehtovirta-Morley, L and Todd, JD and Zhang, XH and Liu, J}, title = {Niche Partitioning and Intraspecific Variation of Thaumarchaeota in Deep Ocean Sediments.}, journal = {Environmental microbiology}, volume = {27}, number = {1}, pages = {e70018}, doi = {10.1111/1462-2920.70018}, pmid = {39777846}, issn = {1462-2920}, support = {41976101//National Natural Science Foundation of China/ ; 92051115//National Natural Science Foundation of China/ ; 92251303//National Natural Science Foundation of China/ ; 202141009//Fundamental Research Funds for the Central Universities/ ; 202172002//Fundamental Research Funds for the Central Universities/ ; 2022QNLM030004-3//Laoshan Laboratory/ ; LSKJ202203206//Laoshan Laboratory/ ; ZR2022YQ38//Natural Science Foundation of Shandong Province/ ; ZR2024JQ006//Natural Science Foundation of Shandong Province/ ; }, mesh = {*Geologic Sediments/microbiology ; *Archaea/genetics/classification ; *Phylogeny ; Oceans and Seas ; Metagenome ; Ecosystem ; Seawater/microbiology ; Metagenomics ; Ammonia/metabolism ; Genome, Archaeal ; }, abstract = {Deep-sea sediments contain a large number of Thaumarchaeota that are phylogenetically distinct from their pelagic counterparts. However, their ecology and evolutionary adaptations are not well understood. Metagenomic analyses were conducted on samples from various depths of a 750-cm sediment core collected from the Mariana Trench Challenger Deep. The abundance of Thaumarchaeota and archaeal amoA generally decreased with depth, except for an unexpected peak midway through the core. The thaumarchaeotal metagenome-assembled genomes were classified into diverse phylogenetic clusters associated with amoA-NP-γ, amoA-NP-θ, and amoA-NP-δ of ammonia-oxidising Thaumarchaeota and non-ammonia-oxidising lineages. The most abundant group was within amoA-NP-γ, which is usually found in coastal and shallow habitats, indicating potential niche expansion from marine shallow to hadal environments. This benthic group showed within-species genomic variations compared to the previously identified Hadal water group, suggesting microdiversification of hadal Thaumarchaeota along with niche separation between benthic and pelagic environments. Evolutionary adaptations associated with the benthic-to-pelagic transition included reduced genome size, loss of motility/cell adhesion, altered energy metabolism, and different mechanisms for substrate acquisition and regulation (e.g., ammonium). These findings offer new insights into the evolution of hadal Thaumarchaeota and demonstrate, for the first time, intraspecies-level genomic variation in Thaumarchaeota related to the benthic-versus-pelagic niche partitioning in the deep ocean.}, }
@article {pmid39777550, year = {2025}, author = {Byers, AK and Wakelin, SA and Condron, L and Black, A}, title = {Land Use Change Disrupts the Network Complexity and Stability of Soil Microbial Carbon Cycling Genes Across an Agricultural Mosaic Landscape.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {167}, pmid = {39777550}, issn = {1432-184X}, mesh = {*Soil Microbiology ; *Carbon Cycle ; New Zealand ; *Agriculture ; *Soil/chemistry ; *Microbiota ; *Bacteria/genetics/classification/metabolism ; Carbon/metabolism ; Gene Regulatory Networks ; Forests ; Ecosystem ; }, abstract = {To understand the effects of agricultural land use change and management on soil carbon (C) cycling, it is crucial to examine how these changes can influence microbial soil C cycling. Network analysis can offer insights into the structure, complexity, and stability of the soil microbiome in response to environmental disturbances, including land use change. Using SparCC-based co-occurrence networks, we studied how land use change impacts the connectivity, complexity, and stability of microbial C-cycling gene networks across an agricultural mosaic landscape in Canterbury, New Zealand. The most densely connected networks were found in land uses that were under the most intensive agricultural management, or under naturally regenerating vegetation. The microbial C-cycling gene networks from both land uses presented high network connectivity, low modularity, and a low proportion of negative gene interactions. In contrast, microbial C-cycling genes from native forests, which had the most stable and undisturbed plant cover, had the lowest network connectivity, highest modularity, and a greater proportion of negative gene interactions. Although the differences in total soil C content between land uses were small, the large effects of land use on the network structure of microbial C-cycling genes may have important implications for long-term microbial soil C cycling. Furthermore, this research highlights the value of using microbial network analysis to study the metabolic gene interactions shaping the functional structure of soil microbial communities in a manner not typically captured by more traditional forms of microbial diversity analysis.}, }
@article {pmid39774426, year = {2024}, author = {Segura, D and Sharma, D and Espin-Garcia, O}, title = {Comparing subsampling strategies for metagenomic analysis in microbial studies using amplicon sequence variants versus operational taxonomic units.}, journal = {PloS one}, volume = {19}, number = {12}, pages = {e0315720}, pmid = {39774426}, issn = {1932-6203}, mesh = {Humans ; *Metagenomics/methods ; *RNA, Ribosomal, 16S/genetics ; Gastrointestinal Microbiome/genetics ; Microbiota/genetics ; Infant ; Sequence Analysis, DNA/methods ; Bacteria/genetics/classification ; Metagenome/genetics ; }, abstract = {The microbiome is increasingly regarded as a key component of human health, and analysis of microbiome data can aid in the development of precision medicine. Due to the high cost of shotgun metagenomic sequencing (SM-seq), microbiome analyses can be done cost-effectively in two phases: Phase 1-sequencing of 16S ribosomal RNA, and Phase 2-SM-seq of an informative subsample. Existing research suggests strategies to select the subsample based on biological diversity and dissimilarity metrics calculated using operational taxonomic units (OTUs). However, the microbiome field has progressed towards amplicon sequencing variants (ASVs), as they provide more precise microbe identification and sample diversity information. The aim of this work is to compare the subsampling strategies for two-phase metagenomic studies when using ASVs instead of OTUs, and to propose data driven strategies for subsample selection through dimension reduction techniques. We used 199 samples of infant-gut microbiome data from the DIABIMMUNE project to generate ASVs and OTUs, then generated subsamples based on five existing biologically driven subsampling methods and two data driven methods. Linear discriminant analysis Effect Size (LEfSe) was used to assess differential representation of taxa between the subsamples and the overall sample. The use of ASVs showed a 50-93% agreement in the subsample selection with the use of OTUs for the subsampling methods evaluated, and showed a similar bacterial representation across all methods. Although sampling using ASVs and OTUs typically lead to similar results for each subsample, ASVs had more clades that differed in expression levels between allergic and non-allergic individuals across all sample sizes compared to OTUs, and led to more biomarkers discovered at Phase 2-SM-seq level.}, }
@article {pmid39770890, year = {2024}, author = {Wells, RK and Torres, A and Mau, MK and Maunakea, AK}, title = {Racial-Ethnic Disparities of Obesity Require Community Context-Specific Biomedical Research for Native Hawaiians and Other Pacific Islanders.}, journal = {Nutrients}, volume = {16}, number = {24}, pages = {}, pmid = {39770890}, issn = {2072-6643}, support = {P20GM139753//NIH-NIGMS/ ; R01MD016593//NIH-NIMHD/ ; R56MD014630//NIH-NIMHD/ ; UG03HL169657//NIH-NHLBI/ ; }, mesh = {Humans ; *Native Hawaiian or Other Pacific Islander ; *Obesity/ethnology ; Hawaii/epidemiology ; *Biomedical Research ; Health Status Disparities ; Gastrointestinal Microbiome ; Pacific Island People ; }, abstract = {Compared to the general population of Hawai'i, Native Hawaiians and Other Pacific Islanders (NHPI) shoulder a disproportionately high risk for obesity-related cardiometabolic disorders, such as type 2 diabetes and cardiovascular disease. The gut microbiome is an area of rapid research interest for its role in regulating adjacent metabolic pathways, offering novel opportunities to better understand the etiology of these health disparities. Obesity and the gut microbiome are influenced by regional, racial-ethnic, and community-specific factors, limiting the generalizability of current literature for understudied populations. Additionally, anthropometric and directly measured obesity indices are variably predictive of adiposity and metabolic health risk in this diverse population. Thus, further NHPI-inclusive research is required to adequately characterize community-specific factors in the context of obesity-related disease etiology. Culturally responsible research ethics and scientific communication are crucial to conducting such research, especially among indigenous and understudied populations. In this review, we explore these limitations in current literature, emphasizing the urgent need for NHPI-inclusive research to assess community-specific factors accurately. Such accuracy in Indigenous health research may ensure that findings relevant to individual or public health recommendations and/or policies are meaningful to the communities such research aims to serve.}, }
@article {pmid39770772, year = {2024}, author = {Long, Y and Zhang, X and Peng, X and Yang, H and Ni, H and Zou, L and Long, Z}, title = {Metagenomic Analysis Revealing the Impact of Water Contents on the Composition of Soil Microbial Communities and the Distribution of Major Ecological Functional Genes in Poyang Lake Wetland Soil.}, journal = {Microorganisms}, volume = {12}, number = {12}, pages = {}, pmid = {39770772}, issn = {2076-2607}, support = {31960015//The National Natural Science Foundation of China/ ; 20192BAB204001//Natural Science Foundation of Jiangxi Province, China/ ; }, abstract = {Poyang Lake is the largest freshwater lake in China, which boasts unique hydrological conditions and rich biodiversity. In this study, metagenomics technology was used to sequence the microbial genome of soil samples S1 (sedimentary), S2 (semi-submerged), and S3 (arid) with different water content from the Poyang Lake wetland; the results indicate that the three samples have different physicochemical characteristics and their microbial community structure and functional gene distribution are also different, resulting in separate ecological functions. The abundance of typical ANME archaea Candidatus Menthanoperedens and the high abundance of mcrA in S1 mutually demonstrate prominent roles in the methane anaerobic oxidation pathway during the methane cycle. In S2, the advantageous bacterial genus Nitrospira with ammonia oxidation function is validated by a large number of nitrification functional genes (amoA, hao, nxrA), manifesting in that it plays a monumental role in nitrification in the nitrogen cycle. In S3, the dominant bacterial genus Nocardioides confirms a multitude of antibiotic resistance genes, indicating their crucial role in resistance and their emphatic research value for microbial resistance issues. The results above have preliminarily proved the role of soil microbial communities as indicators predicting wetland ecological functions, which will help to better develop plans for restoring ecological balance and addressing climate change.}, }
@article {pmid39770743, year = {2024}, author = {Peng, X and Li, S and Dou, W and Li, M and Gontcharov, AA and Peng, Z and Qi, B and Wang, Q and Li, Y}, title = {Metagenomic Insight into the Associated Microbiome in Plasmodia of Myxomycetes.}, journal = {Microorganisms}, volume = {12}, number = {12}, pages = {}, pmid = {39770743}, issn = {2076-2607}, support = {31770011//National Natural Science Foundation of China/ ; }, abstract = {During the trophic period of myxomycetes, the plasmodia of myxomycetes can perform crawling feeding and phagocytosis of bacteria, fungi, and organic matter. Culture-based studies have suggested that plasmodia are associated with one or several species of bacteria; however, by amplicon sequencing, it was shown that up to 31-52 bacteria species could be detected in one myxomycete, suggesting that the bacterial diversity associated with myxomycetes was likely to be underestimated. To fill this gap and characterize myxomycetes' microbiota and functional traits, the diversity and functional characteristics of microbiota associated with the plasmodia of six myxomycetes species were investigated by metagenomic sequencing. The results indicate that the plasmodia harbored diverse microbial communities, including eukaryotes, viruses, archaea, and the dominant bacteria. The associated microbiomes represented more than 22.27% of the plasmodia genome, suggesting that these microbes may not merely be parasitic or present as food but rather may play functional roles within the plasmodium. The six myxomycetes contained similar bacteria, but the bacteria community compositions in each myxomycete were species-specific. Functional analysis revealed a highly conserved microbial functional profile across the six plasmodia, suggesting they may serve a specific function for the myxomycetes. While the host-specific selection may shape the microbial community compositions within plasmodia, functional redundancy ensures functional stability across different myxomycetes.}, }
@article {pmid39769095, year = {2024}, author = {Mohan, B and Majeed, A and Thingujam, D and Burton, SS and Cowart, KE and Pajerowska-Mukhtar, KM and Mukhtar, MS}, title = {Amplicon Sequencing Analysis of Submerged Plant Microbiome Diversity and Screening for ACC Deaminase Production by Microbes.}, journal = {International journal of molecular sciences}, volume = {25}, number = {24}, pages = {}, doi = {10.3390/ijms252413330}, pmid = {39769095}, issn = {1422-0067}, support = {IOS-2038872//National Science Foundation/ ; 2418230//National Science Foundation/ ; }, mesh = {*Carbon-Carbon Lyases/genetics/metabolism ; *Microbiota/genetics ; *Plants/microbiology ; Bacteria/genetics/classification/enzymology ; Metagenomics/methods ; Phylogeny ; Biodiversity ; }, abstract = {Submerged plants can thrive entirely underwater, playing a crucial role in maintaining water quality, supporting aquatic organisms, and enhancing sediment stability. However, they face multiple challenges, including reduced light availability, fluctuating water conditions, and limited nutrient access. Despite these stresses, submerged plants demonstrate remarkable resilience through physiological and biochemical adaptations. Additionally, their interactions with microbial communities are increasingly recognized as pivotal in mitigating these environmental stresses. Understanding the diversity of these microbial communities is crucial for comprehending the complex interactions between submerged plants and their environments. This research aims to identify and screen microbes from submerged plant samples capable of producing 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase and to explore microbial diversity through metagenomic analysis. Microbes were isolated and screened for ACC deaminase production, and metagenomic techniques, including co-occurrence network analysis, were used to examine microbial diversity and interactions within the communities. ACC deaminase-producing microbes can significantly enhance plant metabolism under stress conditions. The identification of the culturable bacteria revealed that most of these microbes belong to the genera Pseudomonas, Bacillus, and Acinetobacter. A total of 177 microbial strains were cultured, with molecular identification revealing 79 reductant, 86 non-reductant, and 12 uncultured strains. Among 162 samples screened for ACC deaminase activity, 50 tested positive. To further understand microbial dynamics, samples were collected from both natural sources and artificial pond reservoirs to assess the impact of the location on flood-associated microbiomes in submerged plants. Metagenomic analysis was conducted on both the epiphytic and endophytic samples. By exploring the overall composition and dynamics of microbial communities associated with submerged plants, this research seeks to deepen our understanding of plant-microbe interactions in aquatic environments. The microbial screening helped to identify the diverse microbes associated with ACC deaminase activity in submerged plants and amplicon sequencing analysis paved the way towards identifying the impact of the location in shaping the microbiome and the diversity associated with endophytic and epiphytic microbes. Co-occurrence network analysis further highlighted the intricate interactions within these microbial communities. Notably, ACC deaminase activity was observed in plant-associated microbes across different locations, with distinct variations between epiphytic and endophytic populations as identified through co-occurrence network analysis.}, }
@article {pmid39768398, year = {2024}, author = {Al-Awthan, YS and Mir, R and Alatawi, FA and Alatawi, AS and Almutairi, FM and Khafaga, T and Shohdi, WM and Fakhry, AM and Alharbi, BM}, title = {Metagenome Analysis Identified Novel Microbial Diversity of Sandy Soils Surrounded by Natural Lakes and Artificial Water Points in King Salman Bin Abdulaziz Royal Natural Reserve, Saudi Arabia.}, journal = {Life (Basel, Switzerland)}, volume = {14}, number = {12}, pages = {}, pmid = {39768398}, issn = {2075-1729}, abstract = {BACKGROUND: Soil microbes play a vital role in the ecosystem as they are able to carry out a number of vital tasks. Additionally, metagenomic studies offer valuable insights into the composition and functional potential of soil microbial communities. Furthermore, analyzing the obtained data can improve agricultural restoration practices and aid in developing more effective environmental management strategies.
METHODOLOGY: In November 2023, sandy soil samples were collected from ten sites of different geographical areas surrounding natural lakes and artificial water points in the Tubaiq conservation area of King Salman Bin Abdulaziz Royal Natural Reserve (KSRNR), Saudi Arabia. In addition, genomic DNA was extracted from the collected soil samples, and 16S rRNA sequencing was conducted using high-throughput Illumina technology. Several computational analysis tools were used for gene prediction and taxonomic classification of the microbial groups.
RESULTS: In this study, sandy soil samples from the surroundings of natural and artificial water resources of two distinct natures were used. Based on 16S rRNA sequencing, a total of 24,563 OTUs were detected. The metagenomic information was then categorized into 446 orders, 1036 families, 4102 genera, 213 classes, and 181 phyla. Moreover, the phylum Pseudomonadota was the most dominant microbial community across all samples, representing an average relative abundance of 34%. In addition, Actinomycetes was the most abundant class (26%). The analysis of clustered proteins assigned to COG categories provides a detailed understanding of the functional capabilities and adaptation of microbial communities in soil samples. Amino acid metabolism and transport were the most abundant categories in the soil environment.
CONCLUSIONS: Metagenome analysis of sandy soils surrounding natural lakes and artificial water points in the Tubaiq conservation area of KSRNR (Saudi Arabia) has unveils rich microbial activity, highlighting the complex interactions and ecological roles of microbial communities in these environments.}, }
@article {pmid39768341, year = {2024}, author = {Maffia, A and Scotti, R and Wood, T and Muscolo, A and Lepore, A and Acocella, E and Celano, G}, title = {Transforming Agricultural and Sulfur Waste into Fertilizer: Assessing the Short-Term Effects on Microbial Biodiversity via a Metagenomic Approach.}, journal = {Life (Basel, Switzerland)}, volume = {14}, number = {12}, pages = {}, pmid = {39768341}, issn = {2075-1729}, support = {FARB2023//University of Salerno and the doctoral research funds of the Mediterranean University of Reggio Calabria./ ; }, abstract = {Fungi and soil bacteria are vital for organic matter decomposition and biogeochemical cycles, but excessive synthetic fertilizer use contributes to soil degradation and loss of biodiversity. Despite this, about 97% of soil microorganisms are unculturable, making them difficult to study. Metagenomics offers a solution, enabling the direct extraction of DNA from soil to uncover microbial diversity and functions. This study utilized metagenomics to analyze the rhizosphere of two-year-old Tonda di Giffoni hazelnut saplings treated with synthetic NPK, composted olive pomace, and an innovative fertilizer derived from sulfur-based agro-industrial waste stabilized with bentonite clay. Using 16S rDNA for bacteria and ITS2 for fungi, Illumina sequencing provided insights into microbial responses to different fertilizer treatments. The results highlighted a significant increase in the abundance of beneficial microorganisms such as Thiobacillus, Pseudoxanthomonas, and Thermomyces, especially when organic materials were included. Additionally, microbial biodiversity improved with organic inputs, as shown by increased species richness (Chao1) and diversity (Bray-Curtis) greater than 20% compared with NPK and unfertilized soils (CTR). These findings emphasize the importance of organic fertilization in enhancing soil microbial health, offering a sustainable approach to improving soil quality and hazelnut productivity.}, }
@article {pmid39766799, year = {2024}, author = {Xu, X and Gao, X and Gui, C and Wang, H and Liu, X and Wu, G}, title = {Metagenomic Insights into the Enhancement of Bioavailable Nitrogen in Continuous Cropping Soil Through the Application of Traditional Chinese Medicine Residue Following Fumigation.}, journal = {Genes}, volume = {15}, number = {12}, pages = {}, pmid = {39766799}, issn = {2073-4425}, support = {32060639//National Natural Science Foundation of China/ ; 32060640//National Natural Science Foundation of China/ ; 32260704//National Natural Science Foundation of China/ ; 202105AC160037//Reserve Talents Project for Yunnan Young and Middle-aged Academic and Technical Leaders c/ ; 202205AC160077//Reserve Talents Project for Yunnan Young and Middle-aged Academic and Technical Leadersc/ ; NA//Hunan Engineering Research Center for Green Prevention and Control of Soil-borne Diseases/ ; NA//Hunan Engineering Research Center for Research and Development of plant resources in Nanling area, Hunan Province/ ; }, mesh = {*Soil Microbiology ; *Fumigation/methods ; *Nitrogen/metabolism ; *Rhizosphere ; *Soil/chemistry ; *Fertilizers/analysis ; Metagenomics/methods ; Medicine, Chinese Traditional/methods ; Bacteria/genetics/drug effects/growth & development ; Microbiota/drug effects ; Metagenome ; Capsicum/growth & development/microbiology/drug effects/genetics ; }, abstract = {Background/Objectives: Chemical fumigation can effectively inhibit the occurrence of soil-borne diseases; however, this approach can negatively affect the structure of the soil microbial community. The combination of soil fumigant and organic fertilizer application thus represents a widely adopted strategy in agricultural practice. Traditional Chinese medicine residue (TCMR) is a high-quality organic fertilizer; however, the impact of post-fumigation TCMR application on keystone taxa and their functional traits remains uncertain. Methods: This study examined the effects of five fertilization treatments on the diversity, key species, and related functional genes of microbial communities in rhizosphere soil of continuous cropping pepper. Results: Chemical fumigation followed by TCMR application markedly enhanced soil nutrient content in the rhizosphere and significantly influenced microbial community composition as well as functional gene patterns associated with microbial nitrogen cycling. It was also strongly correlated with soil bioavailable nitrogen content. The abundance of keystone bacterial species (Pseudomonadota, Actinomycetota, and Bacillota) substantially increased following TCMR application, alongside a notable rise in Ascomycota abundance within the fungal community. This shift contributed to an increase in beneficial bacterial abundance while reducing that of harmful bacteria. Additionally, TCMR addition affected the abundance of denitrification and DNRA genes involved in nitrogen cycling; specifically, nirB and nirK were strongly associated with soil organic nitrogen content. Conclusions: The combined application of chemical fumigants and TCMR modified the composition of keystone microbial community species by influencing rhizosphere soil TN and other nutrients, and these alterations were linked to multiple nitrogen-cycling functional genes.}, }
@article {pmid39763701, year = {2025}, author = {Hereira-Pacheco, S and Arias-Del Razo, I and Miranda-Carrazco, A and Dendooven, L and Estrada-Torres, A and Navarro-Noya, YE}, title = {Metagenomic analysis of fungal assemblages at a regional scale in high-altitude temperate forest soils: alternative methods to determine diversity, composition and environmental drivers.}, journal = {PeerJ}, volume = {13}, number = {}, pages = {e18323}, pmid = {39763701}, issn = {2167-8359}, mesh = {*Soil Microbiology ; *Forests ; *Metagenomics/methods ; *Fungi/genetics/classification/isolation & purification ; *Altitude ; Mexico ; Mycobiome/genetics ; Biodiversity ; }, abstract = {BACKGROUND: Understanding the diversity and distribution of fungal communities at a regional scale is important since fungi play a crucial role in ecosystem functioning. Our study used environmental metagenomics to determine fungal communities in mountainous forest soils in the central highlands of Mexico.
METHODS: We used four different bioinformatic workflows to profile fungal assemblages, i.e., Geneious+UNITE, single- and paired-end microbial community profiling (MiCoP), and Kraken2.
RESULTS: The workflows yielded different results; one detected a higher abundance of ectomycorrhizal (EcM) and saprophytic fungi, while the other identified more saprophytic and pathogenic fungi. Environmental, vegetation, and geographical factors determined the spatial distribution of soil fungi at a regional scale. Potential hydrogen (pH), calcium (Ca), magnesium (Mg), and silt content were detected as common drivers of fungal communities across different datasets enriched towards a functional guild. Vegetation traits were found to be more influential in shaping symbiotrophic fungi composition than saprotrophic and pathogenic fungi. This highlights the importance of considering vegetation traits when studying fungal community diversity and distribution. Clustering patterns of sampling points near the volcanoes indicated shared environmental and vegetation characteristics. A weak but significant distance decay in taxonomic similarity revealed that dispersal limitation contributed to fungal community composition, although it was not the primary factor in this study. Overall, this study provides important insights into the challenges and opportunities of studying fungal communities at a regional scale using metagenomic data.}, }
@article {pmid39762979, year = {2025}, author = {Oh, S and Kim, J and Shin, CM and Lee, HJ and Lee, HS and Park, KU}, title = {Metagenomic characterization of oral microbiome signatures to predict upper gastrointestinal and pancreaticobiliary cancers: a case-control study.}, journal = {Journal of translational medicine}, volume = {23}, number = {1}, pages = {20}, pmid = {39762979}, issn = {1479-5876}, support = {16-2021-0007//Seoul National University Bundang Hospital/ ; }, mesh = {Humans ; Case-Control Studies ; *Metagenomics/methods ; *Pancreatic Neoplasms/microbiology/diagnosis ; Female ; Male ; Middle Aged ; *Microbiota/genetics ; Mouth/microbiology ; RNA, Ribosomal, 16S/genetics ; Aged ; Metagenome ; Saliva/microbiology ; Biliary Tract Neoplasms/microbiology/diagnosis ; Gastrointestinal Neoplasms/microbiology/diagnosis ; }, abstract = {BACKGROUND: This study investigated the oral microbiome signatures associated with upper gastrointestinal (GI) and pancreaticobiliary cancers.
METHODS: Saliva samples from cancer patients and age- and sex-matched healthy controls were analyzed using 16S rRNA-targeted sequencing, followed by comprehensive bioinformatics analysis.
RESULTS: Significant dissimilarities in microbial composition were observed between cancer patients and controls across esophageal cancer (EC), gastric cancer (GC), biliary tract cancer (BC), and pancreatic cancer (PC) groups (R[2] = 0.067, = 0.075, = 0.068, and = 0.044; p = 0.001, = 0.001, = 0.002, and = 0.004, respectively). Additionally, the oral microbiome composition significantly differed by the four cancer sites (p = 0.001 for EC vs. GC, EC vs. BC, EC vs. PC, GC vs. BC, and GC vs. PC; p = 0.013 for BC vs. PC). We built oral metagenomic classifiers to predict cancer and selected specific microbial taxa with diagnostic properties. For EC, the classifier differentiated cancer patients and controls with good accuracy (area under the curve [AUC] = 0.791) and included three genera: Akkermansia, Escherichia-Shigella, and Subdoligranulum. For GC, the classifier exhibited high discriminative power (AUC = 0.961); it included five genera (Escherichia-Shigella, Gemella, Holdemanella, Actinomyces, and Stomatobaculum) and three species (Eubacterium sp. oral clone EI074, Ruminococcus sp. Marseille-P328, and Leptotrichia wadei F0279). However, microbial taxa with diagnostic features for BC and PC were not identified.
CONCLUSIONS: These findings suggested that the oral microbiome composition may serve as an indicator of tumorigenesis in upper GI and pancreaticobiliary cancers. The development of oral metagenomic classifiers for EC and GC demonstrates the potential value of microbial biomarkers in cancer screening.}, }
@article {pmid39762302, year = {2025}, author = {Kim, MJ and Song, MH and Ji, YS and Park, JW and Shin, YK and Kim, SC and Kim, G and Cho, B and Park, H and Ku, JL and Jeong, SY}, title = {Cell free supernatants of Bifidobacterium adolescentis and Bifidobacterium longum suppress the tumor growth in colorectal cancer organoid model.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {935}, pmid = {39762302}, issn = {2045-2322}, support = {2021M3H9A1030151//National Research Foundation, South Korea/ ; }, mesh = {Humans ; *Colorectal Neoplasms/microbiology/pathology/metabolism ; *Bifidobacterium longum/metabolism ; *Organoids/microbiology/metabolism ; *Gastrointestinal Microbiome ; *Bifidobacterium adolescentis/metabolism ; Female ; Male ; Probiotics ; Middle Aged ; Aged ; Cell Proliferation ; Cell Line, Tumor ; }, abstract = {The probiotic gut microbiome and its metabolites are pivotal in regulating host metabolism, inflammation, and immunity. Host genetics, colonization at birth, the host lifestyle, and exposure to diseases and drugs determine microbial composition. Dysbiosis and disruption of homeostasis in the beneficial microbiome have been reported to be involved in the tumorigenesis and progression of colorectal cancer (CRC). However, the influence of bacteria-secreted metabolites on CRC growth is yet to be fully elucidated. In this study, we compared the microbial composition of CRC patients to healthy controls to identify distinct patterns of microbiota-derived metabolites in CRC patients. Metagenomic analysis demonstrated that beneficial bacteria strains; Blautia producta, Bifidobacterium adolescentis, and Bifidobacterium longum decreased, while Parabacteroides distasonis and Bacteroides ovatus were more prevalent in the CRC patient group. Treatment of cancer organoid lines with microbial culture supernatants from Blautia producta, Bifidobacterium adolescentis, and Bifidobacterium longum showed remarkable inhibition of cancer growth. This study demonstrates that the bacterial metabolites depleted in CRC patients may inhibit cancer growth and highlights the effects of microbiome-derived metabolites on CRC growth.}, }
@article {pmid39762227, year = {2025}, author = {Ding, J and Liu, F and Zeng, J and Gu, H and Huang, J and Wu, B and Shu, L and Yan, Q and He, Z and Wang, C}, title = {Depth heterogeneity of lignin-degrading microbiome and organic carbon processing in mangrove sediments.}, journal = {NPJ biofilms and microbiomes}, volume = {11}, number = {1}, pages = {5}, pmid = {39762227}, issn = {2055-5008}, mesh = {*Geologic Sediments/microbiology ; *Lignin/metabolism ; *Microbiota ; *Carbon/metabolism ; *Wetlands ; *Metagenomics/methods ; Bacteria/genetics/classification/metabolism/isolation & purification ; Biomass ; Metagenome ; Sequence Analysis, DNA ; }, abstract = {Mangrove ecosystems are globally recognized for their blue carbon (C) sequestration capacity. Lignocellulosic detritus constitutes the primary C input to mangrove sediments, but the microbial processes involved in its bioprocessing remain unclear. Using lignocellulosic analysis and metagenomic sequencing across five 100-cm sediment cores, we found a high proportion of lignin (95.0-97.7%) within sediments' lignocellulosic detritus, with a small fraction of lignin-degrading genes (1.24-1.98%) of lignin-degrading genes within the carbohydrate-active enzyme coding genes. Depth stratification was observed in genes and microbial communities involved in lignin depolymerization and mineralization of lignin monomer derivatives. Further microbe-centered analyses of biomass production rates and adaptive metabolism revealed diminished microbial C use efficiency potential and augmented "enzyme latch" with increasing sediment depths. These findings enhance our understanding of sedimentary organic C cycling and storage in coastal blue C ecosystems.}, }
@article {pmid39762111, year = {2025}, author = {Al-Shakhshir, S and Quraishi, MN and Mullish, B and Patel, A and Vince, A and Rowe, A and Homer, V and Jackson, N and Gyimah, D and Shabir, S and Manzoor, S and Cooney, R and Alrubaiy, L and Quince, C and van Schaik, W and Hares, M and Beggs, AD and Efstathiou, E and Rimmer, P and Weston, C and Iqbal, T and Trivedi, PJ}, title = {FAecal micRobiota transplantation in primary sclerosinG chOlangitis (FARGO): study protocol for a randomised, multicentre, phase IIa, placebo-controlled trial.}, journal = {BMJ open}, volume = {15}, number = {1}, pages = {e095392}, doi = {10.1136/bmjopen-2024-095392}, pmid = {39762111}, issn = {2044-6055}, mesh = {Adult ; Female ; Humans ; Male ; *Cholangitis, Sclerosing/therapy ; Clinical Trials, Phase II as Topic ; *Fecal Microbiota Transplantation/methods ; Gastrointestinal Microbiome ; Inflammatory Bowel Diseases/therapy/microbiology ; Multicenter Studies as Topic ; Randomized Controlled Trials as Topic ; Treatment Outcome ; }, abstract = {INTRODUCTION: Primary sclerosing cholangitis (PSC) is the classical hepatobiliary manifestation of inflammatory bowel disease (IBD). The strong association between gut and liver inflammation has driven several pathogenic hypotheses to which the intestinal microbiome is proposed to contribute. Pilot studies of faecal microbiota transplantation (FMT) in PSC and IBD are demonstrated to be safe and associated with increased gut bacterial diversity. However, the longevity of such changes and the impact on markers of disease activity and disease progression have not been studied. The aim of this clinical trial is to determine the effects of repeated FMT as a treatment for PSC-IBD.
METHODS AND ANALYSIS: FAecal micRobiota transplantation in primary sclerosinG chOlangitis (FARGO) is a phase IIa randomised placebo-controlled trial to assess the efficacy and safety of repeated colonic administration of FMT in patients with non-cirrhotic PSC-IBD. Fifty-eight patients will be recruited from six sites across England and randomised in a 1:1 ratio between active FMT or FMT placebo arms. FMT will be manufactured by the University of Birmingham Microbiome Treatment Centre, using stool collected from rigorously screened healthy donors. A total of 8 weekly treatments will be delivered; the first through colonoscopic administration (week 1) and the remaining seven via once-weekly enema (up to week 8). Participants will then be followed on a 12-weekly basis until week 48 from the first treatment visit. The primary efficacy outcome will be to determine the effect of FMT on serum alkaline phosphatase values over time (end of study at 48 weeks). Key secondary outcomes will be to evaluate the impact of FMT on other liver biochemical parameters, PSC risk scores, circulating and imaging markers of liver fibrosis, health-related quality of life measures, IBD activity and the incidence of PSC-related clinical events. Key translational objectives will be to identify mucosal metagenomic, metatranscriptomic, metabolomic and immunological pathways associated with the administration of FMT.
ETHICS AND DISSEMINATION: The protocol was approved by the South Central-Hampshire B Research Ethics Committee (REC 23/SC/0147). Participants will be required to provide written informed consent. The results of this trial will be disseminated through national and international presentations and peer-reviewed publications.
TRIAL REGISTRATION NUMBER: The trial was registered at ClinicalTrials.gov on 23 February 2024 (NCT06286709). Weblink: Study Details | FAecal Microbiota Transplantation in primaRy sclerosinG chOlangitis | ClinicalTrials.gov.}, }
@article {pmid39762107, year = {2025}, author = {Weldegebreal, F and Ayana, DA and Wilfong, T and Dheresa, M and Yadeta, TA and Negesa, AS and Demmu, YM and Tesfa, T and Alemu, TN and Eticha, TG and Geremew, A and Roba, KT and Abdissa, A and Assefa, N and Negash, AA and Cools, P and Tura, AK}, title = {Relationship between vaginal and gut microbiome and pregnancy outcomes in eastern Ethiopia: a protocol for a longitudinal maternal-infant cohort study (the EthiOMICS study).}, journal = {BMJ open}, volume = {15}, number = {1}, pages = {e092461}, doi = {10.1136/bmjopen-2024-092461}, pmid = {39762107}, issn = {2044-6055}, mesh = {Humans ; Female ; Ethiopia ; Pregnancy ; *Gastrointestinal Microbiome/genetics ; *Vagina/microbiology ; Infant, Newborn ; Longitudinal Studies ; *Pregnancy Outcome ; Infant ; Feces/microbiology ; Research Design ; Milk, Human/microbiology ; Adult ; }, abstract = {INTRODUCTION: Although evidence exists on the impact of microbiota on pregnancy outcomes in many high-resource settings, there is a lack of research in many low-resource settings like Ethiopia. This study aims to fill this gap by studying the gut and vaginal microbiota changes throughout pregnancy and assess how these changes relate to pregnancy outcomes among a cohort of pregnant women in eastern Ethiopia.
METHODS AND ANALYSIS: Vaginal and stool samples will be collected using DNA/RNA Shield Collection kits three times starting at 12-22 weeks, 28-36 weeks and at birth (within 7 days). Postnatally, newborns' skin swabs (at birth) and rectal swabs will be obtained until 2 years of age. Moreover, breast milk samples at birth and 6 months and environmental samples (water, indoor air and soil) will be collected at enrolment, birth, 6, 12 and 24 months post partum. DNA will be extracted using Roche kits. Metagenomic sequencing will be performed to identify metataxonomic profiling and assess variations in microbial profiles, and α and β diversity of the microbiota. Information on socioeconomic, behavioural, household and biological factors will be collected at enrolment. The collected data will be coded, entered into EpiData 3.1 and analysed using Stata 17.
ETHICS AND DISSEMINATION: The Institutional Health Research Ethics Review Committee (Ref No. IHRERC/033/2022) of Haramaya University, Ethiopia has approved this study ethically. Written informed consent regarding the study and sample storage for biobanking will be obtained from all participants. Results will be published in international peer-reviewed journals, and summaries will be provided to the study funders. Clinical study data will be submitted to Data Compass (https://datacompass.lshtm.ac.uk/), and molecular profiles of the microbiome and whole-genome sequences will be submitted to the European Nucleotide Archive (https://www. ebi.ac.uk/ena). Requests for data should be directed to daberaf@gmail.com. The decision to share data will be made by the study steering committee under the College of Health and Medical Sciences, Haramaya University, Ethiopia.}, }
@article {pmid39761113, year = {2025}, author = {Kardailsky, A and Durán-Vinet, B and Nester, G and Ayad, ME and Raes, EJ and Jeunen, GJ and Miller, AK and McVey, P and Corrigan, S and Fraser, M and Goncalves, P and Burnell, S and Bennett, A and Rauschert, S and Bayer, PE}, title = {Monitoring the Land and Sea: Enhancing Efficiency Through CRISPR-Cas Driven Depletion and Enrichment of Environmental DNA.}, journal = {The CRISPR journal}, volume = {}, number = {}, pages = {}, doi = {10.1089/crispr.2024.0050}, pmid = {39761113}, issn = {2573-1602}, abstract = {Characterizing biodiversity using environmental DNA (eDNA) represents a paradigm shift in our capacity for biomonitoring complex environments, both aquatic and terrestrial. However, eDNA biomonitoring is limited by biases toward certain species and the low taxonomic resolution of current metabarcoding approaches. Shotgun metagenomics of eDNA enables the collection of whole ecosystem data by sequencing all molecules present, allowing characterization and identification. Clustered regularly interspaced short palindromic repeats (CRISPR) and the CRISPR-associated proteins (Cas)-based methods have the potential to improve the efficiency of eDNA metagenomic sequencing of low-abundant target organisms and simplify data analysis by enrichment of target species or nontarget DNA depletion before sequencing. Implementation of CRISPR-Cas in eDNA has been limited due to a lack of interest and support in the past. This perspective synthesizes current approaches of CRISPR-Cas to study underrepresented taxa and advocate for further application and optimization of depletion and enrichment methods of eDNA using CRISPR-Cas, holding promise for eDNA biomonitoring.}, }
@article {pmid39758340, year = {2024}, author = {Shang, X and Fu, Y and Wang, Y and Yan, S}, title = {Ramulus Mori (Sangzhi) alkaloids ameliorate high-fat diet induced obesity in rats by modulating gut microbiota and bile acid metabolism.}, journal = {Frontiers in endocrinology}, volume = {15}, number = {}, pages = {1506430}, pmid = {39758340}, issn = {1664-2392}, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Diet, High-Fat/adverse effects ; *Obesity/metabolism/drug therapy ; Rats ; Male ; *Bile Acids and Salts/metabolism ; *Rats, Sprague-Dawley ; *Alkaloids/pharmacology ; Lipid Metabolism/drug effects ; Liver/metabolism/drug effects ; Receptors, G-Protein-Coupled/metabolism ; }, abstract = {OBJECTIVE: The objective of this study is to investigate the ability of Ramulus Mori (Sangzhi) alkaloid tablets (SZ-A) to ameliorate obesity and lipid metabolism disorders in rats subjected to a high-fat diet (HFD) through metagenomics, untargeted lipidomics, targeted metabolism of bile acid (BA), and BA pathways, providing a novel perspective on the management of metabolic disorders.
METHODS: In this research, HFD-fed rats were concurrently administered SZ-A orally. We measured changes in body weight (BW), blood lipid profiles, and liver function to assess therapeutic effects. Liver lipid status was visualized through H&E and Oil Red O. Gut microbiota composition was elucidated using metagenomics. The LC-MS-targeted metabolomics approach was utilized to define the fecal BA profiles. Furthermore, the lipid metabolomics of adipose tissue samples was investigated using an LC-MS analysis platform. The expression levels of the BA receptor were determined by western blotting. Additionally, serum insulin (INS), glucagon-like peptide-1 (GLP-1), and inflammatory cytokines were quantified using an ELISA kit. The integrity of the colonic epithelial barrier was assessed using immunofluorescence.
RESULTS: SZ-A notably decreased BW and blood lipid levels in obese rats while also alleviating liver injury. Additionally, SZ-A reduced the serum levels of leptin (LEP), INS, and GLP-1, indicating its potential to modulate key metabolic hormones. Most notably, SZ-A substantially improved gut microbiota composition. Specifically, it reshaped the gut microbiota structure in HFD-fed rats by increasing the relative abundance of beneficial bacteria, such as Bacteroides, while decreasing the populations of potentially harmful bacteria, such as Dorea and Blautia. At the BA level, SZ-A decreased the levels of harmful BAs, including hyodeoxycholic acid (HDCA), deoxycholic acid (DCA), 12-keto lithocholic acid (12-KLCA), lithocholic acid (LCA), and muricholic acid (MDCA). Between the model group and SZ-A, 258 differentially abundant metabolites were detected, with 72 upregulated and 186 downregulated. Furthermore, these BAs are implicated in the activation of the FXR-FGF15 and TGR5-GLP-1 pathways in the intestine. This activation helps to alleviate HFD-fed intestinal inflammation and restore intestinal barrier damage by modulating inflammatory cytokines and bolstering the intestinal barrier's capabilities.
CONCLUSIONS: Our findings indicate that SZ-A effectively modulates BW, serum lipid profiles, and liver function in HFD-fed rats. Moreover, SZ-A exerts a positive influence on inflammatory cytokines, thereby mitigating inflammation and promoting the restoration of the intestinal barrier. Significantly, our research indicates that adjusting the gut microbiome and BA levels could serve as an effective approach for both preventing and treating obesity and related metabolic dyslipidemia.}, }
@article {pmid39754646, year = {2025}, author = {Shaffer, M and North, D and Bibby, K}, title = {Evaluating Nanotrap Microbiome Particles as A Wastewater Viral Concentration Method.}, journal = {Food and environmental virology}, volume = {17}, number = {1}, pages = {10}, pmid = {39754646}, issn = {1867-0342}, support = {1748019//National Science Foundation/ ; }, mesh = {*Wastewater/virology/microbiology ; *Microbiota ; *Viruses/isolation & purification/classification/genetics ; Metagenomics/methods ; Bacteria/isolation & purification/classification/genetics/virology ; Tobamovirus/isolation & purification/genetics/classification ; }, abstract = {Wastewater-based surveillance has emerged as a powerful approach to monitoring infectious diseases within a community. Typically, wastewater samples are concentrated before viral analyses to improve sensitivity. Current concentration methods vary in time requirements, costs, and efficiency. Here, we evaluated the concentration efficiency and bias of a novel viral concentration approach, Nanotrap Microbiome Particles (NMP), in wastewater. NMP concentration efficiency was target-specific, with significantly lower concentrations of the bacterial indicator HF183 and viral indicator Carjivirus (formerly crAssphage) relative to direct extraction (1.2 × 10[5] vs. 3.4 × 10[5] GC/mL and 2.0 × 10[5] vs. 1.2 × 10[5] GC/mL, respectively), but significantly higher concentrations of the viral fecal indicator Pepper Mild Mottle Virus (PMMoV) relative to direct extraction (1.4 × 10[5] vs. 8.4 × 10[3] GC/mL). Targeted metagenomic sequencing showed that NMP resulted in significantly more unique species reads per sample than direct extractions (p < 0.001) by detecting species that went undetected by direct extractions. Key viral families identified with high abundances were Adenoviridae, Caliciviridae, Herpesviridae, Papillomaviridae, and Polyomaviridae. NMP showed differential ability for concentrating clinically relevant viral families, suggesting that the technology should be evaluated and optimized for specific viral targets before implementation.}, }
@article {pmid39754220, year = {2025}, author = {Karwowska, Z and Aasmets, O and , and Kosciolek, T and Org, E}, title = {Effects of data transformation and model selection on feature importance in microbiome classification data.}, journal = {Microbiome}, volume = {13}, number = {1}, pages = {2}, pmid = {39754220}, issn = {2049-2618}, mesh = {Humans ; *Machine Learning ; *Gastrointestinal Microbiome/genetics ; *Algorithms ; *Metagenomics/methods ; Microbiota/genetics ; Bacteria/classification/genetics ; Biomarkers ; Metagenome ; }, abstract = {BACKGROUND: Accurate classification of host phenotypes from microbiome data is crucial for advancing microbiome-based therapies, with machine learning offering effective solutions. However, the complexity of the gut microbiome, data sparsity, compositionality, and population-specificity present significant challenges. Microbiome data transformations can alleviate some of the aforementioned challenges, but their usage in machine learning tasks has largely been unexplored.
RESULTS: Our analysis of over 8500 samples from 24 shotgun metagenomic datasets showed that it is possible to classify healthy and diseased individuals using microbiome data with minimal dependence on the choice of algorithm or transformation. Presence-absence transformations performed comparably to abundance-based transformations, and only a small subset of predictors is necessary for accurate classification. However, while different transformations resulted in comparable classification performance, the most important features varied significantly, which highlights the need to reevaluate machine learning-based biomarker detection.
CONCLUSIONS: Microbiome data transformations can significantly influence feature selection but have a limited effect on classification accuracy. Our findings suggest that while classification is robust across different transformations, the variation in feature selection necessitates caution when using machine learning for biomarker identification. This research provides valuable insights for applying machine learning to microbiome data and identifies important directions for future work.}, }
@article {pmid39753925, year = {2025}, author = {Bora, SS and Ronghang, R and Das, P and Naorem, RS and Hazarika, DJ and Gogoi, R and Banu, S and Barooah, M}, title = {Endophytic Microbial Community Structure and Dynamics Influence Agarwood Formation in Aquilaria malaccensis Lam.}, journal = {Current microbiology}, volume = {82}, number = {2}, pages = {66}, pmid = {39753925}, issn = {1432-0991}, mesh = {*Thymelaeaceae/microbiology ; *Bacteria/classification/genetics/isolation & purification ; *Endophytes/genetics/classification/isolation & purification ; *Fungi/genetics/classification/isolation & purification ; Microbiota ; Metagenomics ; Wood/microbiology ; Metagenome ; }, abstract = {Aquilaria malaccensis Lam., an Agarwood-producing tree native to Southeast Asia, secretes oleoresin, a resin with diverse applications, in response to injuries. To explore the role of endosphere microbial communities during Agarwood development, we utilized a metagenomics approach across three stages: non-symptomatic (NC), symptomatic early (IN), and symptomatic mature (IN1). The NC metagenome was dominated by Bacillus (19.15%), Klebsiella (13.25%), and Pantoea (12.46%) among bacteria and Saccharomyces (15.92%) among fungi. Notably, bacterial chemotaxis pathway genes were more prevalent in NC (2.14%) compared to IN (0.92%) and IN1 (1.16%), suggesting microbial chemotactic behavior. In the IN stage, Klebsiella (27.05%) and Saccharomyces (34.81%) were the dominant genera. The IN1 metagenome featured Pantoea (8.92%) and Neurospora (8.24%) as leading bacterial and fungal genera, respectively. Functional genes associated with defense mechanisms, lipid transport, and secondary metabolite biosynthesis were increasingly represented in IN1, indicating an enhanced microbial response as infection progresses. Ecological indices, including a high Shannon-Wiener index (H' = 4.467) and Simpson's dominance (1 - D = 0.9697), alongside Pielou's evenness index (J = 0.7034), highlighted a dynamic and diverse microbial community at the mature infection stage, reflecting the complex interactions within the Aquilaria endosphere during Agarwood formation.}, }
@article {pmid39753565, year = {2025}, author = {Chen, YC and Su, YY and Chu, TY and Wu, MF and Huang, CC and Lin, CC}, title = {PreLect: Prevalence leveraged consistent feature selection decodes microbial signatures across cohorts.}, journal = {NPJ biofilms and microbiomes}, volume = {11}, number = {1}, pages = {3}, pmid = {39753565}, issn = {2055-5008}, support = {NSTC 112-2221-E-A49 -106 -MY3//Ministry of Science and Technology, Taiwan (Ministry of Science and Technology of Taiwan)/ ; NSTC 109-2221-E-010 -014 -MY3//Ministry of Science and Technology, Taiwan (Ministry of Science and Technology of Taiwan)/ ; NSTC 109-2221-E-010 -014 -MY3//Ministry of Science and Technology, Taiwan (Ministry of Science and Technology of Taiwan)/ ; NSTC 112-2221-E-A49 -106 -MY3//Ministry of Science and Technology, Taiwan (Ministry of Science and Technology of Taiwan)/ ; NSTC 109-2221-E-010 -014 -MY3//Ministry of Science and Technology, Taiwan (Ministry of Science and Technology of Taiwan)/ ; NSTC 109-2221-E-010 -014 -MY3//Ministry of Science and Technology, Taiwan (Ministry of Science and Technology of Taiwan)/ ; NSTC 109-2221-E-010 -014 -MY3//Ministry of Science and Technology, Taiwan (Ministry of Science and Technology of Taiwan)/ ; MOHW112-TDU-B-222-124013//Ministry of Health and Welfare (Ministry of Health and Welfare, Taiwan)/ ; MOHW111-TDU-B-221-114007//Ministry of Health and Welfare (Ministry of Health and Welfare, Taiwan)/ ; MOHW112-TDU-B-222-124013//Ministry of Health and Welfare (Ministry of Health and Welfare, Taiwan)/ ; MOHW111-TDU-B-221-114007//Ministry of Health and Welfare (Ministry of Health and Welfare, Taiwan)/ ; }, mesh = {Humans ; *Colorectal Neoplasms/microbiology ; Microbiota ; Bacteria/genetics/classification/isolation & purification ; Machine Learning ; Gastrointestinal Microbiome ; Cohort Studies ; Glycerophospholipids ; Computational Biology/methods ; Lipopolysaccharides ; Metagenomics/methods ; }, abstract = {The intricate nature of microbiota sequencing data-high dimensionality and sparsity-presents a challenge in identifying informative and reproducible microbial features for both research and clinical applications. Addressing this, we introduce PreLect, an innovative feature selection framework that harnesses microbes' prevalence to facilitate consistent selection in sparse microbiota data. Upon rigorous benchmarking against established feature selection methodologies across 42 microbiome datasets, PreLect demonstrated superior classification capabilities compared to statistical methods and outperformed machine learning-based methods by selecting features with greater prevalence and abundance. A significant strength of PreLect lies in its ability to reliably identify reproducible microbial features across varied cohorts. Applied to colorectal cancer, PreLect identifies key microbes and highlights crucial pathways, such as lipopolysaccharide and glycerophospholipid biosynthesis, in cancer progression. This case study exemplifies PreLect's utility in discerning clinically relevant microbial signatures. In summary, PreLect's accuracy and robustness make it a significant advancement in the analysis of complex microbiota data.}, }
@article {pmid39749666, year = {2024}, author = {Defazio, G and Tangaro, MA and Pesole, G and Fosso, B}, title = {kMetaShot: a fast and reliable taxonomy classifier for metagenome-assembled genomes.}, journal = {Briefings in bioinformatics}, volume = {26}, number = {1}, pages = {}, pmid = {39749666}, issn = {1477-4054}, support = {CN_00000013//National Centre on High-Performance Computing, Big Data and Quantum Computing/ ; PNC0000002//Complementary National Plan PNC-I.1/ ; CUP H93C22000560003//Life Science Hub Puglia/ ; }, mesh = {*Metagenome ; *Software ; *Metagenomics/methods ; *Algorithms ; High-Throughput Nucleotide Sequencing/methods ; Computational Biology/methods ; Microbiota/genetics ; }, abstract = {The advent of high-throughput sequencing (HTS) technologies unlocked the complexity of the microbial world through the development of metagenomics, which now provides an unprecedented and comprehensive overview of its taxonomic and functional contribution in a huge variety of macro- and micro-ecosystems. In particular, shotgun metagenomics allows the reconstruction of microbial genomes, through the assembly of reads into MAGs (metagenome-assembled genomes). In fact, MAGs represent an information-rich proxy for inferring the taxonomic composition and the functional contribution of microbiomes, even if the relevant analytical approaches are not trivial and still improvable. In this regard, tools like CAMITAX and GTDBtk have implemented complex approaches, relying on marker gene identification and sequence alignments, requiring a large processing time. With the aim of deploying an effective tool for fast and reliable MAG taxonomic classification, we present here kMetaShot, a taxonomy classifier based on k-mer/minimizer counting. We benchmarked kMetaShot against CAMITAX and GTDBtk by using both in silico and real mock communities and demonstrated how, while implementing a fast and concise algorithm, it outperforms the other tools in terms of classification accuracy. Additionally, kMetaShot is an easy-to-install and easy-to-use bioinformatic tool that is also suitable for researchers with few command-line skills. It is available and documented at https://github.com/gdefazio/kMetaShot.}, }
@article {pmid39748884, year = {2024}, author = {Zhou, H and Pei, Y and Xie, Q and Nie, W and Liu, X and Xia, H and Jiang, J}, title = {Diagnosis and insight into the unique lung microbiota of pediatric pulmonary tuberculosis patients by bronchoalveolar lavage using metagenomic next-generation sequencing.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1492881}, pmid = {39748884}, issn = {2235-2988}, mesh = {Humans ; *Tuberculosis, Pulmonary/diagnosis/microbiology ; Female ; *Bronchoalveolar Lavage Fluid/microbiology ; *High-Throughput Nucleotide Sequencing ; Male ; Child ; *Microbiota/genetics ; *Lung/microbiology ; Child, Preschool ; *Metagenomics/methods ; Sensitivity and Specificity ; Adolescent ; Mycobacterium tuberculosis/genetics/isolation & purification ; Infant ; Bronchoalveolar Lavage ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: Although previous studies have reported the dysregulation of respiratory tract microbiota in infectious diseases, insufficient data exist regarding respiratory microbiota imbalances in the lower respiratory tracts of children with pulmonary tuberculosis (PTB). In this study, we assessed the value of mNGS in the pathogen diagnosis and microbiome analysis of PTB patients using bronchoalveolar lavage fluid (BALF) samples.
METHODS: A total of 64 participants, comprising 43 pediatric PTB and 21 pediatric pneumonia patients were recruited in the present study. BALF samples were collected from the above participants. Parallel comparisons between mNGS and conventional microbial test (CMT) pathogen detection were performed. Moreover, the diversity and structure of all 64 patients' lung BALF microbiomes were explored using the mNGS data.
RESULTS: Comparing to the final clinical diagnosis, mNGS in BALF samples produced a sensitivity of 46.51%, which was lower than that of TB-PCR (55.00%) and Xpert (55.00%). The diagnostic efficacy of PTB can be highly enhanced by mNGS combined with TB-PCR (AUC=0.8140, P<0.0001). There were no significant differences in the diversity either between patients with TB and pneumonia. Positive mNGS pathogen results in pediatric PTB patients significantly affect the β-diversity of the pulmonary microbiota. In addition, significant taxonomic differences were found in BALF specimens from patients with PTB and pneumonia, both of which have unique bacterial compositions.
CONCLUSIONS: mNGS is valuable in the etiological diagnosis of PTB, and can reveal pulmonary microecological characteristics. For pediatric PTB patients, the mNGS should be implemented early and complementary to CMTs.}, }
@article {pmid39748068, year = {2025}, author = {Li, S and Ma, X and Mei, H and Chang, X and He, P and Sun, L and Xiao, H and Wang, S and Li, R}, title = {Association between gut microbiota and short-chain fatty acids in children with obesity.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {483}, pmid = {39748068}, issn = {2045-2322}, support = {2019ZYYD051//the Special Projects for the Central Government to Guide the Development of Local Science and Technology/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; Child ; Male ; *Fatty Acids, Volatile/metabolism/blood ; Female ; Adolescent ; *Pediatric Obesity/microbiology/metabolism/blood ; Case-Control Studies ; Feces/microbiology ; Metabolome ; Metagenomics/methods ; Body Mass Index ; }, abstract = {The gut microbiome and its metabolites may be important role in regulating the pathogenesis of obesity. This study aimed to characterize the gut microbiome and short-chain fatty acid (SCFA) metabolome in obese children. This case-control study recruited children aged 7‒14 years and divided them into a normal group (NG) and an obese group (OG) based on their body mass index. Whole-genome shotgun metagenomic analysis was performed on fecal samples from the OG and NG groups to characterize the signatures and functional potential of the gut microbiota. Serum metabolite profiles were analyzed using high-performance liquid chromatography/mass spectrometry (LC/MS). The Statistical Package for the Social Sciences (SPSS, version 26) and R software were used for data analysis. A total of 99 children were recruited, with 49 in the OG and 50 in the NG. At the phylum level, Proteobacteria were significantly more abundant in children in the OG than those in the NG. At the genus level, Oscillibacter and Alistipes were significantly lower in children in the OG than those in the NG. Caproate levels significantly increased, whereas butyrate and isobutyrate levels decreased in children in the OG than those in the NG. Kyoto encyclopedia of genes and genomes (KEGG) functional analysis revealed 28 enriched KEGG pathways, of which/with the phosphotransferase system (PTS) and enhanced biofilm formation by Escherichia coli were particularly significant in the OG. Spearman's correlation analysis indicated that the genus Oscillibacter and species Clostridium_sp._CAG:302 connect serum metabolites and the gut microbiota in childhood obesity. Childhood obesity is correlated with the symbiotic status of the gut microbiota. The microbiota influences human metabolism via specific pathways, particularly butyrate, caproate, and the genus Oscillibacter, all closely associated with obesity.}, }
@article {pmid39747535, year = {2025}, author = {Wongsamart, R and Somboonna, N and Cheibchalard, T and Klankeo, P and Ruampatana, J and Nuntapaitoon, M}, title = {Probiotic Bacillus licheniformis DSMZ 28710 improves sow milk microbiota and enhances piglet health outcomes.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {17}, pmid = {39747535}, issn = {2045-2322}, support = {764002-DT//Ratchadapisek Sompoch Endowment Fund 2021/ ; 764002-DT//Ratchadapisek Sompoch Endowment Fund 2021/ ; //the Second Century Fund (C2F)/ ; //the Second Century Fund (C2F)/ ; //the Second Century Fund (C2F)/ ; //the Second Century Fund (C2F)/ ; CU_FRB65_hea(68)_131_23_61//Thailand Research Fund, Thailand Science Research and Innovation Fund Chulalongkorn University/ ; FOOD_FF_68_013_3100_003//Thailand Research Fund, Thailand Science Research and Innovation Fund Chulalongkorn University/ ; }, mesh = {Animals ; *Probiotics/administration & dosage ; Swine ; *Milk/microbiology ; *Microbiota ; *Bacillus licheniformis ; RNA, Ribosomal, 16S/genetics ; Female ; Colostrum/microbiology ; Dietary Supplements ; Animal Feed ; }, abstract = {Maintaining a diverse and balanced sow milk microbiome is essential to piglet development. Thus, this study aimed to examine the effects of probiotic Bacillus licheniformis supplementation on the microbiome composition of sow colostrum and milk, and to review associated health findings in piglets. B. licheniformis DSMZ 28710 was supplemented at 10 g/day as feed additive before predicted farrowing until weaning by top dressing. Colostrum and milk samples were collected for metagenomic DNA extraction, 16s rRNA sequencing, and bioinformatics analyses for bacterial microbiota diversity. Results indicated that the supplementation increased the abundances of beneficial bacteria, such as Lactobacillus, Pediococcus, Bacteroides, and Bifidobacterium, while decreasing the abundances of pathogenic bacteria, such as Staphylococcus aureus, Enterobacteriaceae, and Campylobacter in the colostrum. The supplementation increased diversity while maintaining richness and evenness. Moreover, the rise in predicted microbial community metabolic function in membrane transport pathways provides crucial evidence showing that the supplementation is potentially beneficial to piglets, as these pathways are important for providing nutrients and immunity to offspring. This research highlights the importance of microbiome composition in sow milk and the potential of B. licheniformis supplementation as a means to improve piglet health and development.}, }
@article {pmid39747287, year = {2025}, author = {Delgadillo, DR and Borelli, JL and Mayer, EA and Labus, JS and Cross, MP and Pressman, SD}, title = {Biological, environmental, and psychological stress and the human gut microbiome in healthy adults.}, journal = {Scientific reports}, volume = {15}, number = {1}, pages = {362}, pmid = {39747287}, issn = {2045-2322}, mesh = {Humans ; *Gastrointestinal Microbiome ; Female ; Adult ; *Stress, Psychological/microbiology ; Male ; *RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; Phylogeny ; Middle Aged ; Metagenome ; }, abstract = {Emerging research suggests that the gut microbiome plays a crucial role in stress. We assess stress-microbiome associations in two samples of healthy adults across three stress domains (perceived stress, stressful life events, and biological stress /Respiratory Sinus Arrhythmia; RSA). Study 1 (n = 62; mean-age = 37.3 years; 68% female) and Study 2 (n = 74; mean-age = 41.6 years; female only) measured RSA during laboratory stressors and used 16S rRNA pyrosequencing to classify gut microbial composition from fecal samples. Phylogenetic Investigation of Communities by Reconstruction of Unobserved States was used to predict functional pathways of metagenomes. Results showed differences in beta diversity between high and low stressful life events groups across both studies. Study 1 revealed differences in beta diversity between high and low RSA groups. In Study 1, the low perceived stress group was higher in alpha diversity than the high perceived stress group. Levels of Clostridium were negatively associated with RSA in Study 1 and levels Escherichia/Shigella were positively associated with perceived stress in Study 2. Associations between microbial functional pathways (L-lysine production and formaldehyde absorption) and RSA are discussed. Findings suggest that certain features of the gut microbiome are differentially associated with each stress domain.}, }
@article {pmid39746973, year = {2025}, author = {Inskeep, WP and Jay, ZJ and McKay, LJ and Dlakić, M}, title = {Respiratory processes of early-evolved hyperthermophiles in sulfidic and low-oxygen geothermal microbial communities.}, journal = {Nature communications}, volume = {16}, number = {1}, pages = {277}, pmid = {39746973}, issn = {2041-1723}, support = {1950770//National Science Foundation (NSF)/ ; }, mesh = {Hot Springs/microbiology ; *Pyrobaculum/classification/enzymology/genetics ; *Microbiota ; *Hot Temperature ; *Bacteria/classification/enzymology/genetics ; Anaerobiosis ; Electron Transport ; *Sulfur/metabolism ; *Arsenic/metabolism ; *Cytochrome b Group/metabolism ; *Oxidoreductases/metabolism ; Geothermal Energy ; Phylogeny ; Energy Metabolism ; }, abstract = {Thermophilic microbial communities growing in low-oxygen environments often contain early-evolved archaea and bacteria, which hold clues regarding mechanisms of cellular respiration relevant to early life. Here, we conducted replicate metagenomic, metatranscriptomic, microscopic, and geochemical analyses on two hyperthermophilic (82-84 °C) filamentous microbial communities (Conch and Octopus Springs, Yellowstone National Park, WY) to understand the role of oxygen, sulfur, and arsenic in energy conservation and community composition. We report that hyperthermophiles within the Aquificota (Thermocrinis), Pyropristinus (Caldipriscus), and Thermoproteota (Pyrobaculum) are abundant in both communities; however, higher oxygen results in a greater diversity of aerobic heterotrophs. Metatranscriptomics revealed major shifts in respiratory pathways of keystone chemolithotrophs due to differences in oxygen versus sulfide. Specifically, early-evolved hyperthermophiles express high levels of high-affinity cytochrome bd and CydAA' oxidases in suboxic sulfidic environments and low-affinity heme Cu oxidases under microaerobic conditions. These energy-conservation mechanisms using cytochrome oxidases in high-temperature, low-oxygen habitats likely played a crucial role in the early evolution of microbial life.}, }
@article {pmid39744910, year = {2024}, author = {de Moura Barbosa Leite, D and de Paula, TS and Hajdu, E}, title = {The complete mitochondrial genome of the deep-sea methanotrophic sponges Hymedesmia methanophila and Iophon methanophila: leveraging 'waste' in metagenomic data.}, journal = {Journal of genetics}, volume = {103}, number = {}, pages = {}, pmid = {39744910}, issn = {0973-7731}, mesh = {*Genome, Mitochondrial ; Animals ; *Porifera/microbiology/genetics ; *Phylogeny ; *Metagenomics/methods ; Methane/metabolism ; Metagenome ; High-Throughput Nucleotide Sequencing ; DNA, Mitochondrial/genetics ; RNA, Transfer/genetics ; }, abstract = {A significant proportion of next-generation sequencing (NGS) data ends up not being used since they comprise information out-of-scope of the primary studies. This 'waste' of potential can be harnessed to explore organellar genomes, such as the mitochondrial DNA, and be used for evolutionary, conservation and biodiversity research. We present the complete mitochondrial genomes of the deep-sea methanotrophic sponges Hymedesmia methanophila and Iophon methanophila (Demospongiae, Poecilosclerida) retrieved from previously published whole metagenome sequencing data. The predicted mitogenome of H. methanophila (18,657 bp) and I. methanophila (18,718 bp) present the characteristic arrangement observed among Poecilosclerida sponges. These mtDNAs encode the usual set of 14 proteins, two ribosomal RNA, and 24 or 23 transfer RNA genes, respectively, with intergenic regions amounting ~5% of their total length. The overall similarity of these mitogenomes to those of phylogenetic relatives, both in organization and divergence, suggests that neither their extremophilic habitat in asphalt seeps within the deep sea nor their symbiotic association with methaneoxidizing bacteria imposed a major influence on the evolution of their mitochondrial genome. This research shows how metagenomic data can be leveraged to extract additional genetic knowledge from primary metagenome sources, and by exploiting previously unexplored sequencing data, valuable information can be unlocked to shed light on the evolutionary dynamics of diverse organisms inhabiting extreme environments.}, }
@article {pmid39744158, year = {2024}, author = {Jiménez-Arroyo, C and Molinero, N and Sabater, C and Margolles, A and Terrón-Camero, LC and Andrés-León, E and Ramos, M and Del Val, M and Moreno-Arribas, MV}, title = {Gut microbiome and clinical and lifestyle host factors associated with recurrent positive RT-PCR for SARS-CoV-2.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1494193}, pmid = {39744158}, issn = {2235-2988}, mesh = {Humans ; *COVID-19/microbiology/virology/diagnosis ; *Gastrointestinal Microbiome/genetics ; *SARS-CoV-2/genetics/isolation & purification ; Male ; Female ; Middle Aged ; *Feces/microbiology/virology ; Adult ; Metagenomics/methods ; Life Style ; Aged ; }, abstract = {BACKGROUND: SARS-CoV-2 and COVID-19 are still active in the population. Some patients remained PCR-positive for more than 4 weeks, called "persistently PCR-positive". Recent evidence suggests a link between the gut microbiota and susceptibility to COVID-19, although no studies have explored persistent PCR conditions. We aimed to evaluate the relationship between persistent positive SARS-CoV-2 RT-PCR, the gut microbiome, and individual host determinants.
METHODS: A shotgun metagenomic analysis was conducted on fecal samples from 28 individuals affected by COVID-19. Patients were divided into two groups: those who had cleared the virus within 30 days (designated as the control group) (n = 15), and those who remained PCR-positive beyond 30 days (called the PCR+ group) (n = 13). We also investigated the correlation between prolonged viral clearance and several additional factors, including clinical parameters, immune responses, microbial metabolites, and dietary habits.
RESULTS: The composition and functionality of the microbiome varied based on the duration of positivity as determined by PCR. Compared to the control group, the persistent PCR+ group exhibited elevated pathogen levels and augmented diversity in functional gene families (p-value < 0.05). A multi-omics analysis integrating metagenomics, metabolites, and metadata also revealed the specific contribution of certain blood markers in this group, including basophils, IgM, IgG (both general and specific for SARS-CoV-2), and markers of liver damage. Unhealthy diet was identified as a significant factor influencing the duration of PCR positivity.
CONCLUSIONS: These findings indicate that the gut microbiome may play a role in delayed viral clearance and persistent positive RT-PCR results. Our study also contributes to the understanding of the role of host factors as mediators linking the gut microbiota and disease outcomes. Further large-scale studies must confirm these data; however, they suggest the relevance of monitoring microbiome changes in the early post-viral years to control SARS-CoV-2 and providing individual healthcare support.}, }
@article {pmid39743584, year = {2025}, author = {Ezzat, L and Peter, H and Bourquin, M and Busi, SB and Michoud, G and Fodelianakis, S and Kohler, TJ and Lamy, T and Geers, A and Pramateftaki, P and Baier, F and Marasco, R and Daffonchio, D and Deluigi, N and Wilmes, P and Styllas, M and Schön, M and Tolosano, M and De Staercke, V and Battin, TJ}, title = {Diversity and biogeography of the bacterial microbiome in glacier-fed streams.}, journal = {Nature}, volume = {}, number = {}, pages = {}, pmid = {39743584}, issn = {1476-4687}, abstract = {The rapid melting of mountain glaciers and the vanishing of their streams is emblematic of climate change[1,2]. Glacier-fed streams (GFSs) are cold, oligotrophic and unstable ecosystems in which life is dominated by microbial biofilms[2,3]. However, current knowledge on the GFS microbiome is scarce[4,5], precluding an understanding of its response to glacier shrinkage. Here, by leveraging metabarcoding and metagenomics, we provide a comprehensive survey of bacteria in the benthic microbiome across 152 GFSs draining the Earth's major mountain ranges. We find that the GFS bacterial microbiome is taxonomically and functionally distinct from other cryospheric microbiomes. GFS bacteria are diverse, with more than half being specific to a given mountain range, some unique to single GFSs and a few cosmopolitan and abundant. We show how geographic isolation and environmental selection shape their biogeography, which is characterized by distinct compositional patterns between mountain ranges and hemispheres. Phylogenetic analyses furthermore uncovered microdiverse clades resulting from environmental selection, probably promoting functional resilience and contributing to GFS bacterial biodiversity and biogeography. Climate-induced glacier shrinkage puts this unique microbiome at risk. Our study provides a global reference for future climate-change microbiology studies on the vanishing GFS ecosystem.}, }
@article {pmid39741524, year = {2024}, author = {Khatiebi, S and Kiprotich, K and Onyando, Z and Mwaura, J and Wekesa, C and Chi, CN and Mulambalah, C and Okoth, P}, title = {High-Throughput Shotgun Metagenomics of Microbial Footprints Uncovers a Cocktail of Noxious Antibiotic Resistance Genes in the Winam Gulf of Lake Victoria, Kenya.}, journal = {Journal of tropical medicine}, volume = {2024}, number = {}, pages = {7857069}, pmid = {39741524}, issn = {1687-9686}, abstract = {Background: A diverse range of pollutants, including heavy metals, agrochemicals, pharmaceutical residues, illicit drugs, personal care products, and other anthropogenic contaminants, pose a significant threat to aquatic ecosystems. The Winam Gulf of Lake Victoria, heavily impacted by surrounding human activities, faces potential contamination from these pollutants. However, studies exploring the presence of antibiotic resistance genes (ARGs) in the lake remain limited. In the current study, a shotgun metagenomics approach was employed to identify ARGs and related pathways. Genomic DNA was extracted from water and sediment samples and sequenced using the high-throughput Illumina NovaSeq platform. Additionally, phenotypic antibiotic resistance was assessed using the disk diffusion method with commonly used antibiotics. Results: The analysis of metagenomes sequences from the Gulf ecosystem and Comprehensive Antibiotic Resistance Database (CARD) revealed worrying levels of ARGs in the lake. The study reported nine ARGs from the 37 high-risk resistant gene families previously documented by the World Health Organization (WHO). Proteobacteria had the highest relative abundance of antibiotic resistance (53%), Bacteriodes (4%), Verrucomicrobia (2%), Planctomycetes Chloroflexi, Firmicutes (2%), and other unclassified bacteria (39%). Genes that target protection, replacement, change, and antibiotic-resistant efflux were listed in order of dominance. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed antibiotic resistance to beta-lactamase and vancomycin. Phenotypic resistance to vancomycin, tetracycline, sulfamethoxazole, erythromycin, trimethoprim, tetracycline, and penicillin was reported through the zone of inhibition. Conclusions: This study highlights that the Winam Gulf of Lake Victoria in Kenya harbors a diverse array of antibiotic-resistant genes, including those conferring multidrug resistance. These findings suggest that the Gulf could be serving as a reservoir for more antibiotic-resistant genes, posing potential risks to both human health and aquatic biodiversity. The insights gained from this research can guide policy development for managing antibiotic resistance in Kenya.}, }
@article {pmid39741321, year = {2024}, author = {Shao, L and Cai, G and Fu, J and Zhang, W and Ye, Y and Ling, Z and Ye, S}, title = {Gut microbial 'TNFα-sphingolipids-steroid hormones' axis in children with autism spectrum disorder: an insight from meta-omics analysis.}, journal = {Journal of translational medicine}, volume = {22}, number = {1}, pages = {1165}, pmid = {39741321}, issn = {1479-5876}, support = {LY22C010001//Natural Science Foundation of Zhejiang Province/ ; 2022KY1451//Zhejiang Provincial Medical and Health Science and Technology Plan/ ; 2022KY971//Zhejiang Provincial Medical and Health Science and Technology Plan/ ; 31870839//National Natural Science Foundation of China/ ; }, mesh = {Humans ; *Autism Spectrum Disorder/microbiology/blood/metabolism ; *Gastrointestinal Microbiome ; *Tumor Necrosis Factor-alpha/metabolism/blood ; *Sphingolipids/blood/metabolism ; Child ; *Steroids/blood/metabolism ; Metabolomics ; Male ; Female ; Hormones/blood/metabolism ; Metagenomics ; Child, Preschool ; Dysbiosis/microbiology ; Feces/microbiology ; }, abstract = {BACKGROUND: Autism spectrum disorder (ASD) is a persistent neurodevelopmental disorder affecting brains of children. Mounting evidences support the associations between gut microbial dysbiosis and ASD, whereas detailed mechanisms are still obscure.
METHODS: Here we probed the potential roles of gut microbiome in ASD using fecal metagenomics and metabolomics.
RESULTS: Children with ASD were found to be associated with augmented serum cytokines milieu, especially TNFα. Metagenomic analysis generated 29 differential species and 18 dysregulated functional pathways such as Bifidobacterium bifidum, Segatella copri, and upregulated 'Sphingolipid metabolism' in children with ASD. Metabolomics revealed steroid hormone dysgenesis in children with ASD with lower abundances of metabolites such as estriol, estradiol and deoxycorticosterone. A three-way association analysis showed positive correlations between TNFα and microbial function potentials such as 'Bacterial toxins' and 'Lysosome', indicating the contribution of microbial dysbiosis to neuroinflammation. TNFα also correlated positively with 'Sphingolipid metabolism', which further showed negative correlations with metabolites estriol and deoxycorticosterone. Such results, in consistent with current findings, revealed the contribution of increased TNFα to upregulated sphingolipid metabolism, which further impaired steroid hormone biosynthesis.
CONCLUSION: Our study proposed the gut microbial 'TNFα-sphingolipids-steroid hormones' axis in children with ASD, which may provide new perspectives for developing gut microbiome-based treatments in the future.}, }
@article {pmid39738315, year = {2024}, author = {Ecklu-Mensah, G and Miller, R and Maseng, MG and Hawes, V and Hinz, D and Kim, C and Gilbert, JA}, title = {Modulating the human gut microbiome and health markers through kombucha consumption: a controlled clinical study.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {31647}, pmid = {39738315}, issn = {2045-2322}, mesh = {Adult ; Female ; Humans ; Male ; Middle Aged ; *Biomarkers ; Diet, Western/adverse effects ; Feces/microbiology ; *Gastrointestinal Microbiome ; Probiotics/administration & dosage ; Kombucha Tea ; Cholesterol, HDL/blood ; Insulin Resistance ; Inflammation ; }, abstract = {Fermented foods are becoming more popular due to their purported links to metabolic health and the gut microbiome. However, direct clinical evidence for the health claims is lacking. Here, we describe an eight-week clinical trial that explored the effects of a four-week kombucha supplement in healthy individuals consuming a Western diet, randomized into the kombucha (n = 16) or control (n = 8) group. We collected longitudinal stool and blood samples to profile the human microbiome and inflammation markers. We did not observe significant changes in either biochemical parameters or levels of circulating markers of inflammation across the entire cohort. However, paired analysis between baseline and end of intervention time points within kombucha or control groups revealed increases in fasting insulin and in HOMA-IR in the kombucha group whereas reductions in HDL cholesterol were associated with the control group. Shotgun metagenomic analysis revealed the relative abundance of Weizmannia, a kombucha-enriched probiotic and several SCFA producing taxa to be overrepresented in consumers at the end of the intervention. Collectively, in our healthy cohort consuming a Western diet, a short-term kombucha intervention induced modest impacts on human gut microbiome composition and biochemical parameters, which may be attributed to relatively small number of participants and the extensive inter-participant variability.}, }
@article {pmid39738309, year = {2024}, author = {Tawfiq, R and Niu, K and Hoehndorf, R and Kulmanov, M}, title = {DeepGOMeta for functional insights into microbial communities using deep learning-based protein function prediction.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {31813}, pmid = {39738309}, issn = {2045-2322}, support = {URF/1/4675-01-01, URF/1/4355-01- 01, URF/1/4697-01-01, URF/1/5041-01- 01, REI/1/5334-01-01, FCC/1/1976-46-01, and FCC/1/1976- 34-01//King Abdullah University of Science and Technology (KAUST) Office of Sponsored Research (OSR)/ ; URF/1/4675-01-01, URF/1/4355-01- 01, URF/1/4697-01-01, URF/1/5041-01- 01, REI/1/5334-01-01, FCC/1/1976-46-01, and FCC/1/1976- 34-01//King Abdullah University of Science and Technology (KAUST) Office of Sponsored Research (OSR)/ ; URF/1/4675-01-01, URF/1/4355-01- 01, URF/1/4697-01-01, URF/1/5041-01- 01, REI/1/5334-01-01, FCC/1/1976-46-01, and FCC/1/1976- 34-01//King Abdullah University of Science and Technology (KAUST) Office of Sponsored Research (OSR)/ ; URF/1/4675-01-01, URF/1/4355-01- 01, URF/1/4697-01-01, URF/1/5041-01- 01, REI/1/5334-01-01, FCC/1/1976-46-01, and FCC/1/1976- 34-01//King Abdullah University of Science and Technology (KAUST) Office of Sponsored Research (OSR)/ ; }, mesh = {*Deep Learning ; *Microbiota ; Gene Ontology ; Computational Biology/methods ; Proteins/metabolism ; Bacteria/metabolism/genetics ; Bacterial Proteins/metabolism/genetics ; Software ; }, abstract = {Analyzing microbial samples remains computationally challenging due to their diversity and complexity. The lack of robust de novo protein function prediction methods exacerbates the difficulty in deriving functional insights from these samples. Traditional prediction methods, dependent on homology and sequence similarity, often fail to predict functions for novel proteins and proteins without known homologs. Moreover, most of these methods have been trained on largely eukaryotic data, and have not been evaluated on or applied to microbial datasets. This research introduces DeepGOMeta, a deep learning model designed for protein function prediction as Gene Ontology (GO) terms, trained on a dataset relevant to microbes. The model is applied to diverse microbial datasets to demonstrate its use for gaining biological insights. Data and code are available at https://github.com/bio-ontology-research-group/deepgometa.}, }
@article {pmid39738126, year = {2024}, author = {Zhang, S and Song, W and Marinos, G and Waschina, S and Zimmermann, J and Kaleta, C and Thomas, T}, title = {Genome-scale metabolic modelling reveals interactions and key roles of symbiont clades in a sponge holobiont.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {10858}, pmid = {39738126}, issn = {2041-1723}, mesh = {*Symbiosis ; *Porifera/microbiology/metabolism ; Animals ; *Microbiota/genetics ; *Metabolic Networks and Pathways/genetics ; Bacteria/metabolism/genetics/classification ; Phylogeny ; Genome ; Genome, Bacterial ; Models, Biological ; Metagenomics/methods ; }, abstract = {Sponges harbour complex microbiomes and as ancient metazoans and important ecosystem players are emerging as powerful models to understand the evolution and ecology of symbiotic interactions. Metagenomic studies have previously described the functional features of sponge symbionts, however, little is known about the metabolic interactions and processes that occur under different environmental conditions. To address this issue, we construct here constraint-based, genome-scale metabolic networks for the microbiome of the sponge Stylissa sp. Our models define the importance of sponge-derived nutrients for microbiome stability and discover how different organic inputs can result in net heterotrophy or autotrophy of the symbiont community. The analysis further reveals the key role that a newly discovered bacterial taxon has in cross-feeding activities and how it dynamically adjusts with nutrient inputs. Our study reveals insights into the functioning of a sponge microbiome and provides a framework to further explore and define metabolic interactions in holobionts.}, }
@article {pmid39732868, year = {2024}, author = {Liu, Y and Wang, F and Zhou, Z and Liu, B and Wu, Z and Pan, X}, title = {Profiling and comprehensive analysis of microbiome and ARGs of nurses and nursing workers in China: a cross-sectional study.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {31301}, pmid = {39732868}, issn = {2045-2322}, support = {2018YFC2000500//National Key Research and Development Program of China/ ; }, mesh = {Humans ; Cross-Sectional Studies ; China/epidemiology ; *Nurses ; *Microbiota/genetics ; Female ; Adult ; Male ; Feces/microbiology ; Cross Infection/microbiology/epidemiology ; Gastrointestinal Microbiome ; Hand/microbiology ; Bacteria/genetics/isolation & purification/drug effects/classification ; Metagenomics/methods ; Hand Hygiene ; }, abstract = {Hospital-acquired infection (HAI) and antimicrobial resistance (AMR) represent major challenges in healthcare system. Despite numerous studies have assessed environmental and patient samples, very few studies have explored the microbiome and resistome profiles of medical staff including nursing workers. This cross-sectional study was performed in a tertiary hospital in China and involved 25 nurses (NSs), 25 nursing workers (NWs), and 55 non-medical control (NC). Stool samples from all participants and hand samples (i.e., the microbiome sample from hand skin, which were collected by swabbing both hands with a sponge-swab soaked with neutralized buffer and centrifuging the liquid buffer) from NSs and NWs were collected for metagenomic analysis. Metagenomic analysis revealed that medical staff exhibited lower abundances of beneficial species such as Blautia, and Bifidobacterium in the gut microbiome. However, an important potential pathogen, Staphylococcus haemolyticus, was enriched in the hands of NWs, suggesting a considerable prevalence of pathogenesis and multi-drug resistance. Accordantly, ARG analysis revealed worse hand hygiene among NWs than among NSs, characterized by a higher diversity of ARGs and a higher abundance of ARGs conferring multi-drug resistance including mdtF, acrB, AcrF and evgS. This study provides a comprehensive overview of the microbial and ARG profiles in the gut and hands of NSs and NWs. The higher abundance of potential pathogens and diverse multi-drug resistant ARGs in NWs hands indicates insufficient hand hygiene and a higher risk of HAI in this subgroup. This study is the first to highlight the critical need to improve hand hygiene among NWs, thus mitigating the risks of AMR and HAI.}, }
@article {pmid39732792, year = {2024}, author = {Pan, J and Zhang, X and Shi, D and Tian, X and Xu, L and Lu, X and Dong, M and Yao, P and Pan, Z and Ling, Z and Wu, N and Yao, H}, title = {Short-chain fatty acids play a key role in antibody response to SARS-CoV-2 infection in people living with HIV.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {31211}, pmid = {39732792}, issn = {2045-2322}, support = {SYS202202//Shandong Provincial Laboratory Project/ ; 2022ZFJH003//Fundamental Research Funds for the Central Universities/ ; 2022R52029//Zhejiang Plan for the Special Support for Top-notch Talents/ ; }, mesh = {Humans ; *Fatty Acids, Volatile/metabolism ; *Gastrointestinal Microbiome/immunology ; *HIV Infections/immunology/virology/microbiology ; *COVID-19/immunology/blood/virology ; *SARS-CoV-2/immunology ; Male ; Female ; Middle Aged ; *Antibodies, Viral/blood/immunology ; Adult ; Antibody Formation/immunology ; }, abstract = {High SARS-CoV-2-specific antibody levels can protect against SARS-CoV-2 reinfection. The gut microbiome can affect a host's immune response. However, its role in the antibody response to SARS-CoV-2 in people living with HIV (PLWH) remains poorly understood. Here, we categorised PLWH and healthy individuals into high- and low-antibody-response groups. Shotgun metagenomic sequencing and targeted metabolomic assays were used to investigate the differences in the gut microbiome and metabolic functions between the high- and low-antibody-response groups. PLWH demonstrated a higher abundance of short-chain fatty acid (SCFA)-producing species, accompanied by high serum levels of several SCFAs, in the high-antibody-response group than in the low-antibody-response group. In contrast, healthy individuals demonstrated higher enrichment of pilus-bearing bacterial species, with flagella-expressing genes, in the high-antibody-response group than in the low-antibody-response group. Therefore, gut-microbiota-derived SCFAs play a key role in antibody responses in PLWH but not in healthy individuals. Our results afford a novel understanding of how the gut microbiome and its metabolites are associated with host immunity. Moreover, they may facilitate the exploration of modalities to prevent SARS-CoV-2 reinfection through various gut-microbiota-targeted interventions tailored to different populations.}, }
@article {pmid39732609, year = {2025}, author = {Tegegne, HA and Savidge, TC}, title = {Leveraging human microbiomes for disease prediction and treatment.}, journal = {Trends in pharmacological sciences}, volume = {46}, number = {1}, pages = {32-44}, doi = {10.1016/j.tips.2024.11.007}, pmid = {39732609}, issn = {1873-3735}, mesh = {Humans ; *Microbiota ; Precision Medicine/methods ; RNA, Ribosomal, 16S/genetics ; Metagenomics ; Computational Biology ; Animals ; }, abstract = {The human microbiome consists of diverse microorganisms that inhabit various body sites. As these microbes are increasingly recognized as key determinants of health, there is significant interest in leveraging individual microbiome profiles for early disease detection, prevention, and drug efficacy prediction. However, the complexity of microbiome data, coupled with conflicting study outcomes, has hindered its integration into clinical practice. This challenge is partially due to demographic and technological biases that impede the development of reliable disease classifiers. Here, we examine recent advances in 16S rRNA and shotgun-metagenomics sequencing, along with bioinformatics tools designed to enhance microbiome data integration for precision diagnostics and personalized treatments. We also highlight progress in microbiome-based therapies and address the challenges of establishing causality to ensure robust diagnostics and effective treatments for complex diseases.}, }
@article {pmid39731160, year = {2024}, author = {Virtanen, S and Saqib, S and Kanerva, T and Ventin-Holmberg, R and Nieminen, P and Holster, T and Kalliala, I and Salonen, A}, title = {Metagenome-validated combined amplicon sequencing and text mining-based annotations for simultaneous profiling of bacteria and fungi: vaginal microbiota and mycobiota in healthy women.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {273}, pmid = {39731160}, issn = {2049-2618}, mesh = {Humans ; *Vagina/microbiology ; Female ; *RNA, Ribosomal, 16S/genetics ; *Fungi/genetics/classification/isolation & purification ; *Bacteria/genetics/classification/isolation & purification ; *Microbiota/genetics ; *Metagenome ; *Data Mining ; Metagenomics/methods ; High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; Mycobiome ; Healthy Volunteers ; DNA, Bacterial/genetics ; }, abstract = {BACKGROUND: Amplicon sequencing of kingdom-specific tags such as 16S rRNA gene for bacteria and internal transcribed spacer (ITS) region for fungi are widely used for investigating microbial communities. So far most human studies have focused on bacteria while studies on host-associated fungi in health and disease have only recently started to accumulate. To enable cost-effective parallel analysis of bacterial and fungal communities in human and environmental samples, we developed a method where 16S rRNA gene and ITS1 amplicons were pooled together for a single Illumina MiSeq or HiSeq run and analysed after primer-based segregation. Taxonomic assignments were performed with Blast in combination with an iterative text-extraction-based filtration approach, which uses extensive literature records from public databases to select the most probable hits that were further validated by shotgun metagenomic sequencing.
RESULTS: Using 50 vaginal samples, we show that the combined run provides comparable results on bacterial composition and diversity to conventional 16S rRNA gene amplicon sequencing. The text-extraction-based taxonomic assignment-guided tool provided ecosystem-specific bacterial annotations that were confirmed by shotgun metagenomic sequencing (VIRGO, MetaPhlAn, Kraken2). Fungi were identified in 39/50 samples with ITS sequencing while in the metagenome data fungi largely remained undetected due to their low abundance and database issues. Co-abundance analysis of bacteria and fungi did not show strong between-kingdom correlations within the vaginal ecosystem of healthy women.
CONCLUSION: Combined amplicon sequencing for bacteria and fungi provides a simple and cost-effective method for simultaneous analysis of microbiota and mycobiota within the same samples. Conventional metagenomic sequencing does not provide sufficient fungal genome coverage for their reliable detection in vaginal samples. Text extraction-based annotation tool facilitates ecosystem-specific characterization and interpretation of microbial communities by coupling sequence homology to microbe metadata readily available through public databases. Video Abstract.}, }
@article {pmid39731152, year = {2024}, author = {Liang, L and Kong, C and Li, J and Liu, G and Wei, J and Wang, G and Wang, Q and Yang, Y and Shi, D and Li, X and Ma, Y}, title = {Distinct microbes, metabolites, and the host genome define the multi-omics profiles in right-sided and left-sided colon cancer.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {274}, pmid = {39731152}, issn = {2049-2618}, support = {No. 22PJD013//Shanghai Pujiang Program/ ; Nos. 81920108026 and 82372594//National Natural Science Foundation of China/ ; No.23410710500//Shanghai Science and Technology Development Foundation/ ; }, mesh = {Humans ; *Colonic Neoplasms/microbiology/genetics/metabolism ; *Gastrointestinal Microbiome/genetics ; Male ; *RNA, Ribosomal, 16S/genetics ; Female ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Middle Aged ; Metabolomics ; Metabolome ; Feces/microbiology ; Aged ; Exome Sequencing ; Metagenomics/methods ; Multiomics ; }, abstract = {BACKGROUND: Studies have reported clinical heterogeneity between right-sided colon cancer (RCC) and left-sided colon cancer (LCC). However, none of these studies used multi-omics analysis combining genetic regulation, microbiota, and metabolites to explain the site-specific difference.
METHODS: Here, 494 participants from a 16S rRNA gene sequencing cohort (50 RCC, 114 LCC, and 100 healthy controls) and a multi-omics cohort (63 RCC, 79 LCC, and 88 healthy controls) were analyzed. 16S rRNA gene, metagenomic sequencing, and metabolomics analyses of fecal samples were evaluated to identify tumor location-related bacteria and metabolites. Whole-exome sequencing (WES) and transcriptome sequencing (RNA-seq) were conducted to obtain the mutation burden and genomic expression pattern.
RESULTS: We found unique profiles of the intestinal microbiome, metabolome, and host genome between RCC and LCC. The bacteria Flavonifractor plautii (Fp) and Fusobacterium nucleatum, the metabolites L-phenylalanine, and the host genes PHLDA1 and WBP1 were the key omics features of RCC; whereas the bacteria Bacteroides sp. A1C1 (B.A1C1) and Parvimonas micra, the metabolites L-citrulline and D-ornithine, and the host genes TCF25 and HLA-DRB5 were considered the dominant omics features in LCC. Multi-omics correlation analysis indicated that RCC-enriched Fp was related to the accumulation of the metabolite L-phenylalanine and the suppressed WBP1 signal in RCC patients. In addition, LCC-enriched B.A1C1 was associated with the accumulation of the metabolites D-ornithine and L-citrulline as well as activation of the genes TCF25, HLA-DRB5, and AC079354.1.
CONCLUSION: Our findings identify previously unknown links between intestinal microbiota alterations, metabolites, and host genomics in RCC vs. LCC, suggesting that it may be possible to treat colorectal cancer (CRC) by targeting the gut microbiota-host interaction. Video Abstract.}, }
@article {pmid39724227, year = {2024}, author = {Shahid, U and Hooi, SL and Lim, SY and Mohd Aris, A and Khor, BC and Ayub, Q and Tan, HS}, title = {Metagenomic surveillance of microbial community and antibiotic resistant genes associated with Malaysian wastewater during the COVID-19 pandemic.}, journal = {Current genetics}, volume = {71}, number = {1}, pages = {1}, pmid = {39724227}, issn = {1432-0983}, mesh = {*Wastewater/microbiology ; *COVID-19/epidemiology ; Malaysia/epidemiology ; *Metagenomics/methods ; *SARS-CoV-2/genetics ; Humans ; Drug Resistance, Microbial/genetics ; Pandemics ; Microbiota/genetics ; Metagenome ; Bacteria/genetics/classification/drug effects ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; Gene Transfer, Horizontal ; }, abstract = {Wastewater is a reservoir of pathogens and hotspots for disseminating antibiotic resistance genes across species. The metagenomic surveillance of wastewater provides insight into the native microbial community, antibiotic-resistance genes (ARGs) and mobile genetic elements. t. The COVID-19 pandemic has caused wider dissemination of ARGs and resistant bacteria in wastewater. Although immensely significant, no research has been performed on the Malaysian wastewater microbial community and ARGs or their correlation with COVID-19 infections. This study utilised a 16S metagenomics approach to characterise the microbial community in Malaysian wastewater during high and low-case phases of the pandemic. Bacteria belonging to Bacteriodales, Bacillales, Actinomycetales and opportunistic pathogens-Arcobacters, Flavobacteria, and Campylobacterales, Neisseriales, were enriched during higher COVID-19 pandemic (active cases). Additionally, copy number profiling of ARGs in water samples showed the prevalence of elements conferring resistance to antibiotics like sulphonamides, cephalosporins, and colistin. The high prevalence of intI1 and other ion-based transporters in samples highlights an extensive risk of horizontal gene transfer to previously susceptible species. Our study emphasises the importance of wastewater surveillance in understanding microbial community dynamics and ARG dissemination, particularly during public health crises like the COVID-19 pandemic.}, }
@article {pmid39724159, year = {2024}, author = {Ulbrich, J and Jobe, NE and Jones, DS and Kieft, TL}, title = {Cave Pools in Carlsbad Caverns National Park Contain Diverse Bacteriophage Communities and Novel Viral Sequences.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {163}, pmid = {39724159}, issn = {1432-184X}, support = {NCKRI-NMT Internal Seed Grant Program//National Cave and Karst Research Institute/ ; }, mesh = {*Caves ; *Parks, Recreational ; *Bacteriophages/genetics/isolation & purification/classification ; *Bacteria/genetics/classification/isolation & purification/virology ; *RNA, Ribosomal, 16S/genetics ; California ; Metagenome ; Phylogeny ; Virome ; Biodiversity ; }, abstract = {Viruses are the most abundant biological entities on Earth, and they play a critical role in the environment and biosphere where they regulate microbial populations and contribute to nutrient cycling. Environmental viruses have been the most studied in the ocean, but viral investigations have now spread to other environments. Here, viral communities were characterized in four cave pools in Carlsbad Caverns National Park to test the hypotheses that (i) viral abundance is ten-fold higher than prokaryotic cell abundance in cavern pools, (ii) cavern pools contain novel viral sequences, and (iii) viral communities in pools from developed portions of the cave are distinct from those of pools in undeveloped parts of the same cave. The relationship between viral and microbial abundance was determined through direct epifluorescence microscopy counts. Viral metagenomes were constructed to examine viral diversity among pools, identify novel viruses, and characterize auxiliary metabolic genes (AMGs). Bacterial communities were characterized by 16S rRNA gene amplicon sequencing. Epifluorescence microscopy showed that the ratio of viral-like particles (VLPs) to microorganisms was approximately 22:1 across all sites. Viral communities from pools with higher tourist traffic were more similar to each other than to those from less visited pools, although surprisingly, viruses did not follow the same pattern as bacterial communities, which reflected pool geochemistry. Bacterial hosts predicted from viral sequences using iPHoP showed overlap with both rare and abundant genera and families in the 16S rRNA gene dataset. Gene-sharing network analysis revealed high viral diversity compared to a reference viral database as well as to other aquatic environments. AMG presence showed variation in metabolic potential among the four pools. Overall, Carlsbad Cavern harbors novel viruses with substantial diversity among pools within the same system, indicating that caves are likely an important repository for unexplored viromes.}, }
@article {pmid39722590, year = {2025}, author = {Wu, WK and Lo, YL and Chiu, JY and Hsu, CL and Lo, IH and Panyod, S and Liao, YC and Chiu, THT and Yang, YT and Kuo, HC and Zou, HB and Chen, YH and Chuang, HL and Yen, JJY and Wang, JT and Chiu, HM and Hsu, CC and Kuo, CH and Sheen, LY and Kao, HL and Wu, MS}, title = {Gut microbes with the gbu genes determine TMAO production from L-carnitine intake and serve as a biomarker for precision nutrition.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2446374}, doi = {10.1080/19490976.2024.2446374}, pmid = {39722590}, issn = {1949-0984}, mesh = {*Methylamines/metabolism ; *Gastrointestinal Microbiome ; *Carnitine/metabolism ; Humans ; *Biomarkers/analysis ; Male ; *Bacteria/genetics/classification/metabolism/isolation & purification ; *Feces/microbiology ; Female ; Animals ; Adult ; Mice ; Multigene Family ; Middle Aged ; Metagenomics ; Precision Medicine ; }, abstract = {Gut microbial metabolism of L-carnitine, which leads to the production of detrimental trimethylamine N-oxide (TMAO), offers a plausible link between red meat consumption and cardiovascular risks. Several microbial genes, including cntA/B, the cai operon, and the recently identified gbu gene cluster, have been implicated in the conversion of dietary L-carnitine into TMA(O). However, the key microbial genes and associated gut microbes involved in this pathway have not been fully explored. Utilizing the oral carnitine challenge test (OCCT), which specifically measures TMAO production from L-carnitine intake and identifies TMAO producer phenotypes, we compared the abundance of microbial genes between low- and high-TMAO producers across three independent cohorts. Our findings consistently revealed that the gbu gene cluster, rather than cntA/B or the cai operon, was significantly enriched in high-TMAO producers. We further analyzed 292 paired multi-omic datasets from OCCT and shotgun metagenomic sequencing, which demonstrated a significant positive correlation between the abundance of fecal gbu genes and L-carnitine-induced TMAO production, with gbuB showing the strongest correlation. Interestingly, these fecal gbu genes were found to increase with L-carnitine supplementation and decrease with a plant-based diet. Notably, we verified a previously uncultured gbu-containing bacterium, JAGTTR01 sp018223385, as the major contributor to TMA formation in the human gut. We isolated these gbu-containing gut microbes and confirmed their role in TMA/TMAO production using anaerobic incubation and a gnotobiotic mouse model. Using an in-house collection of gbu-containing isolates, we developed a qPCR-based method to quantify fecal gbuB and validated its correlation with L-carnitine-mediated TMAO production as measured by OCCT. Overall, these findings suggest that gbu-containing gut microbes are crucial for TMAO increases following L-carnitine intake and may serve as biomarkers or targets for personalized nutrition.}, }
@article {pmid39722539, year = {2025}, author = {Zepeda-Rivera, MA and Eisele, Y and Baryiames, A and Wu, H and Mengoni, C and Piccinno, G and McMahon, EF and LaCourse, KD and Jones, DS and Hauner, H and Minot, SS and Segata, N and Dewhirst, FE and Johnston, CD and Bullman, S}, title = {Fusobacterium sphaericum sp. nov., isolated from a human colon tumor adheres to colonic epithelial cells and induces IL-8 secretion.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2442522}, doi = {10.1080/19490976.2024.2442522}, pmid = {39722539}, issn = {1949-0984}, mesh = {Humans ; *Interleukin-8/metabolism/genetics ; *Colonic Neoplasms/microbiology/pathology ; *Fusobacterium/isolation & purification/genetics ; *Epithelial Cells/microbiology ; *Phylogeny ; Bacterial Adhesion ; Colon/microbiology/pathology ; Feces/microbiology ; Adenocarcinoma/microbiology/pathology ; Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; Genome, Bacterial ; }, abstract = {Cancerous tissue is a largely unexplored microbial niche that provides a unique environment for the colonization and growth of specific bacterial communities, and with it, the opportunity to identify novel bacterial species. Here, we report distinct features of a novel Fusobacterium species, F. sphaericum sp. nov. (Fs), isolated from primary colon adenocarcinoma tissue. We acquire the complete closed genome and associated methylome of this organism and phylogenetically confirm its classification into the Fusobacterium genus, with F. perfoetens as its closest neighbor. Fs is phenotypically and genetically distinct, with morphological analysis revealing its coccoid shape, that while similar to F. perfoetens is rare for most Fusobacterium members. Fs displays a metabolic profile and antibiotic resistance repertoire consistent with other Fusobacterium species. In vitro, Fs has adherent and immunomodulatory capabilities, as it intimately associates with human colon cancer epithelial cells and promotes IL-8 secretion. An analysis of the prevalence and abundance of Fs in > 20,000 human metagenomic samples shows that it is a rarely detected member within human stool with variable relative abundance, found in both healthy controls and patients with colorectal cancer (CRC). Our study sheds light on a novel bacterial species isolated directly from the human CRC tumor niche and given its in vitro interaction with cancer epithelial cells suggests that its role in human health and disease warrants further investigation.}, }
@article {pmid39720963, year = {2024}, author = {Guha, SK and Niyogi, S}, title = {Microbial Dynamics in COVID-19: Unraveling the Impact of Human Microbiome on Disease Susceptibility and Therapeutic Strategies.}, journal = {Current microbiology}, volume = {82}, number = {1}, pages = {59}, pmid = {39720963}, issn = {1432-0991}, mesh = {Humans ; *COVID-19/microbiology/virology ; *SARS-CoV-2 ; *Microbiota ; *Dysbiosis/microbiology ; Disease Susceptibility ; Probiotics/therapeutic use ; Gastrointestinal Microbiome ; }, abstract = {This review explores the bidirectional relationship between the human microbiome and SARS-CoV-2 infection, elucidating its implications for COVID-19 susceptibility, severity, and therapeutic strategies. Metagenomic analyses reveal notable alterations in microbiome composition associated with SARS-CoV-2 infection, impacting disease severity and clinical outcomes. Dysbiosis within the respiratory, gastrointestinal, oral, and skin microbiomes exacerbates COVID-19 pathology through immune dysregulation and inflammatory pathways. Understanding these microbial shifts is pivotal for devising targeted therapeutic interventions. Notably, co-infection of oral pathogens with SARS-CoV-2 worsens lung pathology, while gut microbiome dysbiosis influences viral susceptibility and severity. Potential therapeutic approaches targeting the microbiome include probiotics, antimicrobial agents, and immunomodulatory strategies. This review underscores the importance of elucidating host-microbiota interactions to advance precision medicine and public health initiatives in combating COVID-19 and other infectious diseases.}, }
@article {pmid39719706, year = {2025}, author = {Zhang, AN and Gaston, JM and Cárdenas, P and Zhao, S and Gu, X and Alm, EJ}, title = {CRISPR-Cas spacer acquisition is a rare event in human gut microbiome.}, journal = {Cell genomics}, volume = {5}, number = {1}, pages = {100725}, doi = {10.1016/j.xgen.2024.100725}, pmid = {39719706}, issn = {2666-979X}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *CRISPR-Cas Systems/genetics ; Gene Transfer, Horizontal/genetics ; Bacteriophages/genetics ; Bifidobacterium longum/genetics ; Metagenome/genetics ; Clustered Regularly Interspaced Short Palindromic Repeats/genetics ; Genome, Bacterial/genetics ; }, abstract = {Host-parasite relationships drive the evolution of both parties. In microbe-phage dynamics, CRISPR functions as an adaptive defense mechanism, updating immunity via spacer acquisition. Here, we investigated these interactions within the human gut microbiome, uncovering low frequencies of spacer acquisition at an average rate of one spacer every ∼2.9 point mutations using isolates' whole genomes and ∼2.7 years using metagenome time series. We identified a highly prevalent CRISPR array in Bifidobacterium longum spreading via horizontal gene transfer (HGT), with six spacers found in various genomic regions in 15 persons from the United States and Europe. These spacers, targeting two prominent Bifidobacterium phages, comprised 76% of spacer occurrence of all spacers targeting these phages in all B. longum populations. This result suggests that HGT of an entire CRISPR-Cas system introduced three times more spacers than local CRISPR-Cas acquisition in B. longum. Overall, our findings identified key ecological and evolutionary factors in prokaryote adaptive immunity.}, }
@article {pmid39719433, year = {2024}, author = {Jia, M and Fan, Y and Ma, Q and Yang, D and Wang, Y and He, X and Zhao, B and Zhan, X and Qi, Z and Ren, Y and Dong, Z and Zhu, F and Wang, W and Gao, Y and Ma, X}, title = {Gut microbiota dysbiosis promotes cognitive impairment via bile acid metabolism in major depressive disorder.}, journal = {Translational psychiatry}, volume = {14}, number = {1}, pages = {503}, pmid = {39719433}, issn = {2158-3188}, support = {82230044//National Science Foundation of China | Key Programme/ ; 82171505//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; *Depressive Disorder, Major/metabolism/microbiology ; *Bile Acids and Salts/metabolism ; Male ; Female ; *Dysbiosis/metabolism/complications ; *Cognitive Dysfunction/metabolism/etiology/microbiology ; Adult ; Middle Aged ; Feces/microbiology ; Metabolomics ; Case-Control Studies ; Brain-Gut Axis ; }, abstract = {Evidence suggests that complex interactions among the gut microbiome, metabolic abnormalities, and brain have important etiological and therapeutic implications in major depressive disorder (MDD). However, the influence of microbiome-gut-brain cross-talk on cognitive impairment in MDD remains poorly characterized. We performed serum metabolomic profiling on 104 patients with MDD and 77 healthy controls (HCs), and also performed fecal metagenomic sequencing on a subset of these individuals, including 79 MDD patients and 60 HCs. The findings were validated in a separate cohort that included 40 patients with MDD and 40 HCs using serum-targeted metabolomics. Abnormal bile acid metabolism was observed in patients with MDD, which is related to cognitive dysfunction. The following gut microbiota corresponded to changes in bile acid metabolism and enzyme activities involved in the bile acid metabolic pathway, including Lachnospiraceae (Blautia_massiliensis, Anaerostipes_hadrus, Dorea_formicigenerans, and Fusicatenibacter_saccharivorans), Ruminococcaceae (Ruminococcus_bromii, Flavonifractor_plautii, and Ruthenibacterium_lactatiformans), and Escherichia_coli. Furthermore, a combinatorial marker classifier that robustly differentiated patients with MDD from HCs was identified. In conclusion, this study provides insights into the gut-brain interactions in the cognitive phenotype of MDD, indicating a potential therapeutic strategy for MDD-associated cognitive impairment by targeting the gut microbiota and bile acid metabolism.}, }
@article {pmid39716092, year = {2024}, author = {Chapman, JA and Wroot, E and Brown, T and Beck, LC and Embleton, ND and Berrington, JE and Stewart, CJ}, title = {Characterising the metabolic functionality of the preterm neonatal gut microbiome prior to the onset of necrotising enterocolitis: a pilot study.}, journal = {BMC microbiology}, volume = {24}, number = {1}, pages = {533}, pmid = {39716092}, issn = {1471-2180}, mesh = {Humans ; *Enterocolitis, Necrotizing/microbiology/metabolism ; *Gastrointestinal Microbiome ; Pilot Projects ; Infant, Newborn ; *Infant, Premature ; Female ; Male ; Bacteria/classification/metabolism/isolation & purification/genetics ; Feces/microbiology ; Case-Control Studies ; Metagenome ; }, abstract = {BACKGROUND: Necrotising enterocolitis (NEC) is a devastating bowel disease that primarily occurs in infants born prematurely and is associated with abnormal gut microbiome development. While gut microbiome compositions associated with NEC have been well studied, there is a lack of experimental work investigating microbiota functions and their associations with disease onset. The aim of this pilot study was to characterise the metabolic functionality of the preterm gut microbiome prior to the onset of NEC compared with healthy controls.
RESULTS: Eight NEC infants were selected of median gestation 26.5 weeks and median day of life (DOL) of NEC onset 20, with one sample used per infant, collected within one to eight days (median four) before NEC onset. Each NEC case was matched to a control infant based on gestation and sample DOL, the main driver of microbiome composition in this population, giving a total cohort of 16 infants for this study. Dietary exposures were well matched. The microbiota of NEC and control infants showed similar wide-ranging metabolic functionalities. All 94 carbon sources were utilised to varying extents but NEC and control samples clustered separately by supervised ordination based on carbon source utilisation profiles. For a subset of eight samples (four NEC, four control) for which pre-existing metagenome data was available, microbiome composition was found to correlate significantly with metabolic activity measured on Biolog plates (p = 0.035). Comparisons across all 16 samples showed the NEC microbiota to have greater utilisation of carbon sources that are the products of proteolytic fermentation, specifically amino acids. In pairwise comparisons, L-methionine was highly utilised in NEC samples, but poorly utilised in controls (p = 0.043). Carbon sources identified as discriminatory for NEC also showed a greater enrichment for established markers of inflammatory disease, such as inflammatory bowel disease, irritable bowel syndrome and diverticular disease.
CONCLUSIONS: Before NEC onset, the preterm gut microbiota showed greater metabolic utilisation of amino acids, potentially indicating a shift from predominantly saccharolytic to proteolytic fermentation. Products of amino acid breakdown could therefore act as biomarkers for NEC development. A larger study is warranted, ideally with infants from multiple sites.}, }
@article {pmid39716039, year = {2025}, author = {Du, Q and Liu, X and Zhang, R and Hu, G and Liu, Q and Wang, R and Ma, W and Hu, Y and Fan, Z and Li, J}, title = {Placental and Fetal Microbiota in Rhesus Macaque: A Case Study Using Metagenomic Sequencing.}, journal = {American journal of primatology}, volume = {87}, number = {1}, pages = {e23718}, doi = {10.1002/ajp.23718}, pmid = {39716039}, issn = {1098-2345}, support = {//This work was supported by the National Natural Science Foundation of China (32171607)/ ; }, mesh = {Animals ; *Macaca mulatta/microbiology ; Female ; Pregnancy ; *Fetus/microbiology ; *Placenta/microbiology ; *Microbiota ; *Metagenomics ; Umbilical Cord/microbiology ; Gastrointestinal Microbiome ; }, abstract = {Recent evidence challenging the notion of a sterile intrauterine environment has sparked research into the origins and effects of fetal microbiota on immunity development during gestation. Rhesus macaques (RMs) serve as valuable nonhuman primate models due to their similarities to humans in development, placental structure, and immune response. In this study, metagenomic analysis was applied to the placenta, umbilical cord, spleen, gastrointestinal tissues of an unborn RM fetus, and the maternal intestine, revealing the diversity and functionality of microbes in these tissues. Additionally, gut metagenomic data of adult Rhesus macaques from our previous study, along with data from a human fetus obtained from public databases, were included for comparison. We observed substantial microbial sharing between the mother and fetus, with the microbial composition of the placenta and umbilical cord more closely resembling that of the fetal organs than the maternal intestine. Notably, compared with other adult RMs, there was a clear convergence between maternal and fetal microbiota, alongside distinct differences between the microbiota of adults and the fetus, which underscores the unique microbial profiles in fetal environments. Furthermore, the fetal microbiota displayed a less developed carbohydrate metabolism capacity than adult RMs. It also shared antibiotic resistance genes with both maternal and adult RM microbiomes, indicating potential vertical transmission. Comparative analysis of the metagenomes between the RM fetus and a human fetus revealed significant differences in microbial composition and genes, yet also showed similarities in certain abundant microbiota. Collectively, our results contribute to a more comprehensive understanding of the intrauterine microbial environment in macaques.}, }
@article {pmid39715919, year = {2024}, author = {Jiang, ZB and Zhang, H and Tian, JJ and Guo, HH and Zhou, LR and Ma, XL}, title = {The Microbial Diversity of Biological Moss Crust: Application in Saline-Alkali Soil Management.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {162}, pmid = {39715919}, issn = {1432-184X}, support = {82160672//the National Natural Science Foundation of China/ ; 2022AAC05041 and 2023AAC05048//Outstanding Youth Program of Ningxia Natural Science Foundation/ ; 2021BEB04019//the Key R&D Projects in Ningxia/ ; 2021AAC03210 and 2019AAC03113//the Ningxia Natural Science Foundation/ ; }, mesh = {*Soil/chemistry ; *Soil Microbiology ; *Bryophyta/microbiology ; China ; Biodiversity ; Alkalies/analysis ; Salinity ; Bacteria/classification/genetics/isolation & purification/metabolism ; Chlorophyll/analysis ; }, abstract = {Soil salinization poses a substantial threat to global food security, particularly under the influence of climate change, and is recognized as one of the most urgent challenges in land degradation. This study aims to elucidate the challenges associated with managing arid and semi-arid saline-alkali lands in China's Ningxia province and propose feasible solutions. To assess moss crust colonization, we measured changes in organic matter and chlorophyll levels. Additionally, we investigated the impact of an interlayer composed of Goji berry root bark using liquid chromatography-mass spectrometry analysis, biological enzyme activity analysis, and metagenomic sequencing. A total of 45 endophytes were isolated from the moss crust. The most significant colonization of moss crusts was observed when the Goji berry root bark was used as the interlayer, resulting in a significant increase in chlorophyll content. Several responses were identified as pivotal factors facilitating moss crust growth when the Goji berry root bark was used as the interlayer. In saline-alkali soil, the Goji berry root bark interlayer increased the activities of sucrase, urease, and alkaline phosphatase. Metagenomic data analysis revealed variations in the relative abundance of microorganisms at the phylum level, although these differences were not statistically significant. Evaluation of the impact of physical isolation and moss crust transplantation on the ecological restoration of saline-alkali soil using liquid chromatography-tandem mass spectrometry and metagenomic sequencing indicated that the Goji berry root bark as a physical isolation method promotes moss crust colonization in saline-alkali soil and increases soil organic matter and nutrient elements, offering valuable insights for the ecological management of saline-alkali land and serving as a reference for future research in this field.}, }
@article {pmid39714548, year = {2024}, author = {Wang, W and Zhang, Z and Sun, M and Li, C and Yan, M and Wang, C}, title = {Mechanism of decolorization and degradation of direct brown D3G by a halo-thermophilic consortium.}, journal = {Extremophiles : life under extreme conditions}, volume = {29}, number = {1}, pages = {11}, pmid = {39714548}, issn = {1433-4909}, support = {22B610001//the Key Scientific Research Project in Colleges and Universities of Henan Province of China/ ; HDXJJG2023-058//the teaching reform project of Henan University/ ; }, mesh = {*Azo Compounds/metabolism/chemistry ; Microbial Consortia ; Biodegradation, Environmental ; Halomonas/metabolism ; Coloring Agents/metabolism/chemistry ; Laccase/metabolism ; Bacillus/metabolism ; }, abstract = {Azo dye wastewater has garnered significant attention from researchers because of its association with high-temperature, high-salt, and high-alkali conditions. In this study, consortium ZZ efficiently decolorized brown D3G under halophilic and thermophilic conditions. he results indicated that consortium ZZ, which was mainly dominated by Marinobacter, Bacillus, and Halomonas, was achieved decolorization rates ranging from 1 to 10% at temperatures between 40 °C and 50 °C, while maintaining a pH range of 7 to 10 for direct brown D3G degradation. Through the comprehensive utilization of UV-vis spectral analysis, Fourier transform infrared (FTIR), gas chromatography mass spectrometric (GC-MS) techniques, as well as metagenomic analysis, the decolorization and degradation pathway of direct brown by consortium ZZ was proposed. The azo dye reductase, lignin peroxidase, and laccase were also highly expressed in the decolorization process. Additionally, phytotoxicity tests using seeds of Cucumis sativus and Oryza sativa revealed that the intermediates generated showed no significant toxicity compared with distilled water. This investigation elucidated the pivotal contribution of consortium ZZ to azo dye degradation and provided novel theoretical insights along with practical guidance for azo dye treatment at halo-thermophilic conditions.}, }
@article {pmid39713824, year = {2024}, author = {Karesh, WB}, title = {Shifting from wildlife disease threats to wildlife health.}, journal = {Revue scientifique et technique (International Office of Epizootics)}, volume = {Special Edition}, number = {}, pages = {141-144}, doi = {10.20506/rst.SE.3568}, pmid = {39713824}, issn = {0253-1933}, mesh = {Animals ; *Animals, Wild ; Humans ; Zoonoses/prevention & control ; Conservation of Natural Resources ; Animal Diseases/prevention & control/epidemiology ; }, abstract = {The evolution of wildlife disease management and surveillance, as documented in the World Organisation for Animal Health's Scientific and Technical Review, reflects a deepening understanding of the links between wildlife health, ecosystem integrity and human well-being. Early work, beginning with the World Assembly of Delegates in 1954, primarily focused on diseases like rabies. This focus expanded over time to include broader concerns such as the impacts of climate change, habitat loss and increased human-wildlife interactions on wildlife health. By the late 20th century, the emphasis had shifted towards improved practices for wildlife disease control and the development of advanced diagnostic methods and vaccines. Articles in the Review highlight the growing complexity of wildlife diseases and the need for holistic management strategies. The adoption in recent years of cutting-edge technologies like CRISPR-Cas systems and metagenomics points to a future of more proactive and integrated approaches to wildlife disease management. There is still a need to address not just the consequences of wildlife diseases but also their anthropogenic drivers. The latest perspectives advocate for nature-based solutions, expanded partnerships and systems-level thinking to effectively tackle 21st-century challenges in wildlife and biodiversity conservation.}, }
@article {pmid39711113, year = {2025}, author = {Olivares, C and Ruppé, E and Ferreira, S and Corbel, T and Andremont, A and de Gunzburg, J and Guedj, J and Burdet, C}, title = {A modelling framework to characterize the impact of antibiotics on the gut microbiota diversity.}, journal = {Gut microbes}, volume = {17}, number = {1}, pages = {2442523}, doi = {10.1080/19490976.2024.2442523}, pmid = {39711113}, issn = {1949-0984}, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Anti-Bacterial Agents/pharmacology/administration & dosage ; *Feces/microbiology ; *Bacteria/classification/genetics/drug effects/isolation & purification ; *RNA, Ribosomal, 16S/genetics ; Adult ; Ceftazidime/pharmacology/administration & dosage ; Male ; Moxifloxacin/pharmacology/administration & dosage ; Drug Combinations ; Ceftriaxone/pharmacology/administration & dosage ; Female ; Azabicyclo Compounds/pharmacology/administration & dosage ; Biodiversity ; Young Adult ; Healthy Volunteers ; Piperacillin, Tazobactam Drug Combination ; }, abstract = {Metagenomic sequencing deepened our knowledge about the role of the intestinal microbiota in human health, and several studies with various methodologies explored its dynamics during antibiotic treatments. We compared the impact of four widely used antibiotics on the gut bacterial diversity. We used plasma and fecal samples collected during and after treatment from healthy volunteers assigned to a 5-day treatment either by ceftriaxone (1 g every 24 h through IV route), ceftazidime/avibactam (2 g/500 mg every 8 h through IV route), piperacillin/tazobactam (1 g/500 mg every 8 h through IV route) or moxifloxacin (400 mg every 24 h through oral route). Antibiotic concentrations were measured in plasma and feces, and bacterial diversity was assessed by the Shannon index from 16S rRNA gene profiling. The relationship between the evolutions of antibiotic fecal exposure and bacterial diversity was modeled using non-linear mixed effects models. We compared the impact of antibiotics on gut microbiota diversity by simulation, using various reconstructed pharmacodynamic indices. Piperacillin/tazobactam was characterized by the highest impact in terms of intensity of perturbation (maximal [IQR] loss of diversity of 27.3% [1.9; 40.0]), while moxifloxacin had the longest duration of perturbation, with a time to return to 95% of baseline value after the last administration of 13.2 d [8.3; 19.1]. Overall, moxifloxacin exhibited the highest global impact, followed by piperacillin/tazobactam, ceftazidime/avibactam and ceftriaxone. Their AUC between day 0 and day 42 of the change of diversity indices from day 0 were, respectively, -13.2 Shannon unit.day [-20.4; -7.9], -10.9 Shannon unit.day [-20.4; -0.6] and -10.1 Shannon unit.day [-18.3; -4.6]. We conclude that antibiotics alter the intestinal diversity to varying degrees, both within and between antibiotics families. Such studies are needed to help antibiotic stewardship in using the antibiotics with the lowest impact on the intestinal microbiota.}, }
@article {pmid39710013, year = {2025}, author = {He, B and Xu, S and Schooling, CM and Leung, GM and Ho, JWK and Au Yeung, SL}, title = {Gut microbiome and obesity in late adolescence: A case-control study in "Children of 1997" birth cohort.}, journal = {Annals of epidemiology}, volume = {101}, number = {}, pages = {58-66}, doi = {10.1016/j.annepidem.2024.12.009}, pmid = {39710013}, issn = {1873-2585}, mesh = {Humans ; *Gastrointestinal Microbiome ; Case-Control Studies ; Female ; Male ; Adolescent ; *Pediatric Obesity/microbiology/epidemiology ; *Feces/microbiology ; Diabetes Mellitus, Type 2/microbiology/epidemiology ; Birth Cohort ; Bacteroides/isolation & purification ; }, abstract = {PURPOSE: Although the gut microbiome is important in human health, its relation to adolescent obesity remains unclear. Here we assessed the associations of the gut microbiome with adolescent obesity in a case-control study.
METHODS: In the "Children of 1997" birth cohort, participants with and without obesity at ∼17.4 years were 1:1 matched on sex, physical activity, parental education and occupation (n = 312). Fecal gut microbiome composition and pathways were assessed via shotgun metagenomic sequencing. The association of microbiota species with obesity was evaluated using conditional logistic regression. We explored the association of the obesity-relevant species with adolescent metabolomics using multivariable linear regression, and causal relationships with type 2 diabetes using Mendelian randomization analysis.
RESULTS: Gut microbiota in the adolescents with obesity exhibited lower richness (p = 0.031) and evenness (p = 0.014) compared to controls. Beta diversity revealed differences in the microbiome composition in two groups (p = 0.034). Lower relative abundance of Clostridium spiroforme, Clostridium phoceensis and Bacteroides uniformis were associated with higher obesity risk (q<0.15). Lower Bacteroides uniformis was associated with higher branched-chain amino acid, potentially contributing to higher type 2 diabetes risk.
CONCLUSION: Adolescents with obesity had a distinct gut microbiota profile compared to the controls, possibly linked to metabolic pertubation and related diseases.}, }
@article {pmid39709651, year = {2025}, author = {Cheng, E and Hung, SC and Lin, TY}, title = {Association of trimethylamine N-oxide and metabolites with kidney function decline in patients with chronic kidney disease.}, journal = {Clinical nutrition (Edinburgh, Scotland)}, volume = {44}, number = {}, pages = {239-247}, doi = {10.1016/j.clnu.2024.12.001}, pmid = {39709651}, issn = {1532-1983}, mesh = {Humans ; *Methylamines/blood ; Female ; *Renal Insufficiency, Chronic/blood/physiopathology ; Male ; Aged ; *Gastrointestinal Microbiome/physiology ; *Glomerular Filtration Rate ; Prospective Studies ; *Carnitine/blood ; Middle Aged ; *Choline/blood ; Kidney/physiopathology ; Disease Progression ; Betaine/blood/analogs & derivatives ; }, abstract = {BACKGROUND: Trimethylamine N-oxide (TMAO) is a gut microbial metabolite derived from dietary l-carnitine and choline. High plasma TMAO levels are associated with cardiovascular disease and overall mortality, but little is known about the associations of TMAO and related metabolites with the risk of kidney function decline among patients with chronic kidney disease (CKD).
METHODS: We prospectively followed 152 nondialysis patients with CKD stages 3-5 and measured plasma TMAO and related metabolites (trimethylamine [TMA], choline, carnitine, and γ-butyrobetaine) via liquid chromatography‒mass spectrometry. An estimated glomerular filtration rate (eGFR) slope >3 ml/min/per 1.73 m[2] per year was defined as a rapid decline. We performed logistic regression to determine the probability of rapid or slow eGFR decline, with each metabolite as the main predictor. The gut microbiota was profiled via whole metagenomic sequencing.
RESULTS: The participants had a median age of 66 years, 41.4 % were women, 39.5 % had diabetes, and the median eGFR was 23 mL/min/1.73 m[2]. A rapid decrease in the eGFR occurred in 65 patients (42.8 %) over a median follow-up of 3.3 years. After adjustment for baseline eGFR, proteinuria, and clinical factors, plasma TMAO levels were independently associated with increased odds of rapid eGFR decline (odds ratio, 2.42; 95 % CI, 1.36-4.32), whereas plasma TMA, choline, carnitine, and γ-butyrobetaine levels were not. Patients who exhibited rapid eGFR decline had a distinct gut microbial composition characterized by increased α-diversity and an abundance of TMA-producing bacteria, including those of the genera Desulfovibrio and Collinsella tanakaei, as well as increased expression of the TMA-producing enzymes bbuA and cutC.
CONCLUSION: Our findings suggest the relevance of plasma TMAO in the progression of kidney disease among patients with CKD.}, }
@article {pmid39709594, year = {2025}, author = {Smith, MZ and York, M and Townsend, KS and Martin, LM and Gull, T and Coghill, LM and Ericsson, AC and Johnson, PJ}, title = {Effects of orally administered clioquinol on the fecal microbiome of horses.}, journal = {Journal of veterinary internal medicine}, volume = {39}, number = {1}, pages = {e17276}, pmid = {39709594}, issn = {1939-1676}, mesh = {Animals ; Horses ; *Feces/microbiology ; *Clioquinol/pharmacology/administration & dosage ; Female ; Male ; Administration, Oral ; Prospective Studies ; Gastrointestinal Microbiome/drug effects ; RNA, Ribosomal, 16S/genetics ; Cohort Studies ; }, abstract = {BACKGROUND: Whereas restoration of fecal consistency after treatment with clioquinol for chronic diarrhea and free fecal water syndrome has been attributed to its antiprotozoal properties, actions of clioquinol on the colonic bacterial microbiota have not been investigated.
OBJECTIVES: Characterize the dynamics of fecal microbial diversity before, during, and after PO administration of clioquinol to healthy horses.
STUDY DESIGN: Experimental prospective cohort study using a single horse group.
METHODS: Eight healthy adult horses received PO clioquinol (10 g, daily) for 7 days. Feces were obtained daily for 7 days before, during, and after conclusion of treatment, and again 3 months later. Libraries of 16S rRNA V4 region amplicons generated from fecal DNA were sequenced using the Illumina sequencing platform. Bioinformatic analysis was undertaken with QIIME2 and statistical analyses included analysis of variance (ANOVA) and permutational multivariate ANOVA (PERMANOVA).
RESULTS: The richness and composition of the fecal microbiome was altered after administration of clioquinol, reaching a maximum effect by the fifth day of administration. Changes included a 90% decrease in richness, and compensatory expansion of facultative anaerobes including Streptococcaceae, Enterococcaceae, and Enterobacteriaceae. Multiple horses had Salmonella cultured from feces.
MAIN LIMITATIONS: Limitations including lack of control group and modest sample size are obviated by robust longitudinal study design and strong effect size associated with drug exposure.
CONCLUSIONS: Clioquinol has broad-spectrum antibacterial effects on the fecal microbiome of horses, but spares certain bacterial families including several pathogens and pathobionts. Clioquinol should be used with caution in horses, in an environment free of contamination with fecal pathogens.}, }
@article {pmid39709449, year = {2024}, author = {Dos Santos, SJ and Copeland, C and Macklaim, JM and Reid, G and Gloor, GB}, title = {Vaginal metatranscriptome meta-analysis reveals functional BV subgroups and novel colonisation strategies.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {271}, pmid = {39709449}, issn = {2049-2618}, support = {20170705//Weston Family Foundation/ ; }, mesh = {Humans ; Female ; *Vagina/microbiology ; *Vaginosis, Bacterial/microbiology ; *Microbiota/genetics ; *Transcriptome ; *Bacteria/genetics/classification/isolation & purification ; Biofilms/growth & development ; Metagenomics/methods ; }, abstract = {BACKGROUND: The application of '-omics' technologies to study bacterial vaginosis (BV) has uncovered vast differences in composition and scale between the vaginal microbiomes of healthy and BV patients. Compared to amplicon sequencing and shotgun metagenomic approaches focusing on a single or few species, investigating the transcriptome of the vaginal microbiome at a system-wide level can provide insight into the functions which are actively expressed and differential between states of health and disease.
RESULTS: We conducted a meta-analysis of vaginal metatranscriptomes from three studies, split into exploratory (n = 42) and validation (n = 297) datasets, accounting for the compositional nature of sequencing data and differences in scale between healthy and BV microbiomes. Conducting differential expression analyses on the exploratory dataset, we identified a multitude of strategies employed by microbes associated with states of health and BV to evade host cationic antimicrobial peptides (CAMPs); putative mechanisms used by BV-associated species to resist and counteract the low vaginal pH; and potential approaches to disrupt vaginal epithelial integrity so as to establish sites for adherence and biofilm formation. Moreover, we identified several distinct functional subgroups within the BV population, distinguished by genes involved in motility, chemotaxis, biofilm formation and co-factor biosynthesis. After defining molecular states of health and BV in the validation dataset using KEGG orthology terms rather than community state types, differential expression analysis confirmed earlier observations regarding CAMP resistance and compromising epithelial barrier integrity in healthy and BV microbiomes and also supported the existence of motile vs. non-motile subgroups in the BV population. These findings were independent of the enzyme classification system used (KEGG or EggNOG).
CONCLUSIONS: Our findings highlight a need to focus on functional rather than taxonomic differences when considering the role of microbiomes in disease and identify pathways for further research as potential BV treatment targets. Video Abstract.}, }
@article {pmid39708838, year = {2024}, author = {Luo, Q and Zhang, S and Butt, H and Chen, Y and Jiang, H and An, L}, title = {PhyImpute and UniFracImpute: two imputation approaches incorporating phylogeny information for microbial count data.}, journal = {Briefings in bioinformatics}, volume = {26}, number = {1}, pages = {}, pmid = {39708838}, issn = {1477-4054}, support = {R01ES027013//National Institute of Health/ ; ARZT-1361620-H22-149//United States Department of Agriculture/ ; }, mesh = {*Phylogeny ; Algorithms ; Humans ; Computational Biology/methods ; Microbiota/genetics ; }, abstract = {Sequencing-based microbial count data analysis is a challenging task due to the presence of numerous non-biological zeros, which can impede downstream analysis. To tackle this issue, we introduce two novel approaches, PhyImpute and UniFracImpute, which leverage similar microbial samples to identify and impute non-biological zeros in microbial count data. Our proposed methods utilize the probability of non-biological zeros and phylogenetic trees to estimate sample-to-sample similarity, thus addressing this challenge. To evaluate the performance of our proposed methods, we conduct experiments using both simulated and real microbial data. The results demonstrate that PhyImpute and UniFracImpute outperform existing methods in recovering the zeros and empowering downstream analyses such as differential abundance analysis, and disease status classification.}, }
@article {pmid39707929, year = {2024}, author = {Shahzaib, M and Muaz, M and Zubair, MH and Kayani, MUR}, title = {MiCK: a database of gut microbial genes linked with chemoresistance in cancer patients.}, journal = {Database : the journal of biological databases and curation}, volume = {2024}, number = {}, pages = {}, pmid = {39707929}, issn = {1758-0463}, mesh = {Humans ; *Neoplasms/genetics/drug therapy ; *Gastrointestinal Microbiome/genetics ; *Drug Resistance, Neoplasm/genetics ; *Databases, Genetic ; }, abstract = {Cancer remains a global health challenge, with significant morbidity and mortality rates. In 2020, cancer caused nearly 10 million deaths, making it the second leading cause of death worldwide. The emergence of chemoresistance has become a major hurdle in successfully treating cancer patients. Recently, human gut microbes have been recognized for their role in modulating drug efficacy through their metabolites, ultimately leading to chemoresistance. The currently available databases are limited to knowledge regarding the interactions between gut microbiome and drugs. However, a database containing the human gut microbial gene sequences, and their effect on the efficacy of chemotherapy for cancer patients has not yet been developed. To address this challenge, we present the Microbial Chemoresistance Knowledgebase (MiCK), a comprehensive database that catalogs microbial gene sequences associated with chemoresistance. MiCK contains 1.6 million sequences of 29 gene types linked to chemoresistance and drug metabolism, curated manually from recent literature and sequence databases. The database can support downstream analysis as it provides a user-friendly web interface for sequence search and download functionalities. MiCK aims to facilitate the understanding and mitigation of chemoresistance in cancers by serving as a valuable resource for researchers. Database URL: https://microbialchemreskb.com/.}, }
@article {pmid39707568, year = {2024}, author = {Yang, X and Yuan, R and Yang, S and Dai, Z and Di, N and Yang, H and He, Z and Wei, M}, title = {A salt-tolerant growth-promoting phyllosphere microbial combination from mangrove plants and its mechanism for promoting salt tolerance in rice.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {270}, pmid = {39707568}, issn = {2049-2618}, mesh = {*Oryza/microbiology/growth & development ; *Salt Tolerance ; *Plant Leaves/microbiology ; Microbiota ; Rhizosphere ; Pantoea/genetics ; Soil Microbiology ; Bacillus/genetics/isolation & purification/physiology ; Bacteria/genetics/classification/isolation & purification ; Wetlands ; Rhizophoraceae/microbiology ; Quorum Sensing ; }, abstract = {BACKGROUND: Mangrove plants growing in the high salt environment of coastal intertidal zones colonize a variety of microorganisms in the phyllosphere, which have potential salt-tolerant and growth-promoting effects. However, the characteristics of microbial communities in the phyllosphere of mangrove species with and without salt glands and the differences between them remain unknown, and the exploration and the agricultural utilization of functional microbial resources from the leaves of mangrove plants are insufficient.
RESULTS: In this study, we examined six typical mangrove species to unravel the differences in the diversity and structure of phyllosphere microbial communities between mangrove species with or without salt glands. Our results showed that a combination of salt-tolerant growth-promoting strains of Pantoea stewartii A and Bacillus marisflavi Y25 (A + Y25) was constructed from the phyllosphere of mangrove plants, which demonstrated an ability to modulate osmotic substances in rice and regulate the expression of salt-resistance-associated genes. Further metagenomic analysis revealed that exogenous inoculation with A + Y25 increased the rice rhizosphere's specific microbial taxon Chloroflexi, thereby elevating microbial community quorum sensing and ultimately enhancing ionic balance and overall microbial community function to aid salt resistance in rice.
CONCLUSIONS: This study advances our understanding of the mutualistic and symbiotic relationships between mangrove species and their phyllosphere microbial communities. It offers a paradigm for exploring agricultural beneficial microbial resources from mangrove leaves and providing the potential for applying the salt-tolerant bacterial consortium to enhance crop adaptability in saline-alkaline land. Video Abstract.}, }
@article {pmid39707567, year = {2024}, author = {Feng, X and Xing, P and Tao, Y and Wang, X and Wu, QL and Liu, Y and Luo, H}, title = {Functional traits and adaptation of lake microbiomes on the Tibetan Plateau.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {264}, pmid = {39707567}, issn = {2049-2618}, support = {2023A1515012162//Basic and Applied Basic Research Foundation of Guangdong Province/ ; 2022M712195//the China Postdoctoral Science Foundation/ ; 2019QZKK0503//the Second Tibetan Plateau Scientific Expedition and Research Program/ ; 2019QZKK0503//the Second Tibetan Plateau Scientific Expedition and Research Program/ ; 2019QZKK0503//the Second Tibetan Plateau Scientific Expedition and Research Program/ ; U2102216//the National Natural Science Foundation of China/ ; 92251304//the National Natural Science Foundation of China/ ; 92251304//the National Natural Science Foundation of China/ ; AoE/M-403/16//the Hong Kong Research Grants Council Area of Excellence Scheme/ ; }, mesh = {*Lakes/microbiology ; Tibet ; *Microbiota/genetics ; *Phylogeny ; *Bacteria/classification/genetics ; Metagenome ; Salinity ; Climate Change ; Ecosystem ; Adaptation, Physiological ; }, abstract = {BACKGROUND: Tibetan Plateau is credited as the "Third Pole" after the Arctic and the Antarctic, and lakes there represent a pristine habitat ideal for studying microbial processes under climate change.
RESULTS: Here, we collected 169 samples from 54 lakes including those from the central Tibetan region that was underrepresented previously, grouped them to freshwater, brackish, and saline lakes, and generated a genome atlas of the Tibetan Plateau Lake Microbiome. This genomic atlas comprises 8271 metagenome-assembled genomes featured by having significant phylogenetic and functional novelty. The microbiomes of freshwater lakes are enriched with genes involved in recalcitrant carbon degradation, carbon fixation, and energy transformation, whereas those of saline lakes possess more genes that encode osmolyte transport and synthesis and enable anaerobic metabolism. These distinct metabolic features match well with the geochemical properties including dissolved organic carbon, dissolved oxygen, and salinity that distinguish between these lakes. Population genomic analysis suggests that microbial populations in saline lakes are under stronger functional constraints than those in freshwater lakes. Although microbiomes in the Tibet lakes, particularly the saline lakes, may be subject to changing selective regimes due to ongoing warming, they may also benefit from the drainage reorganization and metapopulation reconnection.
CONCLUSIONS: Altogether, the Tibetan Plateau Lake Microbiome atlas serves as a valuable microbial genetic resource for biodiversity conservation and climate research. Video Abstract.}, }
@article {pmid39707560, year = {2024}, author = {Wang, H and Sun, C and Li, Y and Chen, J and Zhao, XM and Chen, WH}, title = {Complementary insights into gut viral genomes: a comparative benchmark of short- and long-read metagenomes using diverse assemblers and binners.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {260}, pmid = {39707560}, issn = {2049-2618}, support = {T2225015//National Natural Science Foundation of China/ ; 32070660//National Natural Science Foundation of China/ ; 2020YFA0712403//National Key Research and Development Program of China/ ; 2019YFA0905600//National Key Research and Development Program of China/ ; 82161138017//NNSF-VR Sino-Swedish Joint Research Programme/ ; }, mesh = {*Genome, Viral/genetics ; Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Gastrointestinal Microbiome/genetics ; *Metagenome/genetics ; *Feces/virology ; Metagenomics/methods ; Virome/genetics ; Viruses/genetics/classification ; Benchmarking ; Sequence Analysis, DNA/methods ; }, abstract = {BACKGROUND: Metagenome-assembled viral genomes have significantly advanced the discovery and characterization of the human gut virome. However, we lack a comparative assessment of assembly tools on the efficacy of viral genome identification, particularly across next-generation sequencing (NGS) and third-generation sequencing (TGS) data.
RESULTS: We evaluated the efficiency of NGS, TGS, and hybrid assemblers for viral genome discovery using 95 viral-like particle (VLP)-enriched fecal samples sequenced on both Illumina and PacBio platforms. MEGAHIT, metaFlye, and hybridSPAdes emerged as the optimal choices for NGS, TGS, and hybrid datasets, respectively. Notably, these assemblers recovered distinct viral genomes, demonstrating a remarkable degree of complementarity. By combining individual assembler results, we expanded the total number of nonredundant high-quality viral genomes by 4.83 ~ 21.7-fold compared to individual assemblers. Among them, viral genomes from NGS and TGS data have the least overlap, indicating the impact of data type on viral genome recovery. We also evaluated four binning methods, finding that CONCOCT incorporated more unrelated contigs into the same bins, while MetaBAT2, AVAMB, and vRhyme balanced inclusiveness and taxonomic consistency within bins.
CONCLUSIONS: Our findings highlight the challenges in metagenome-driven viral discovery, underscoring tool limitations. We advocate for combined use of multiple assemblers and sequencing technologies when feasible and highlight the urgent need for specialized tools tailored to gut virome assembly. This study contributes essential insights for advancing viral genome research in the context of gut metagenomics. Video Abstract.}, }
@article {pmid39707557, year = {2024}, author = {Santamarina-García, G and Yap, M and Crispie, F and Amores, G and Lordan, C and Virto, M and Cotter, PD}, title = {Shotgun metagenomic sequencing reveals the influence of artisanal dairy environments on the microbiomes, quality, and safety of Idiazabal, a raw ewe milk PDO cheese.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {262}, pmid = {39707557}, issn = {2049-2618}, support = {IT1568-22//Eusko Jaurlaritza/ ; IT1568-22//Eusko Jaurlaritza/ ; IT1568-22//Eusko Jaurlaritza/ ; PIF19/31//Euskal Herriko Unibertsitatea/ ; }, mesh = {*Cheese/microbiology ; Animals ; *Milk/microbiology ; *Microbiota ; *Metagenomics ; Sheep/microbiology ; *Bacteria/classification/genetics/isolation & purification ; Female ; Dairying ; Food Microbiology ; Metagenome ; }, abstract = {BACKGROUND: Numerous studies have highlighted the impact of bacterial communities on the quality and safety of raw ewe milk-derived cheeses. Despite reported differences in the microbiota among cheese types and even producers, to the best of our knowledge, no study has comprehensively assessed all potential microbial sources and their contributions to any raw ewe milk-derived cheese, which could suppose great potential for benefits from research in this area. Here, using the Protected Designation of Origin Idiazabal cheese as an example, the impact of the environment and practices of artisanal dairies (including herd feed, teat skin, dairy surfaces, and ingredients) on the microbiomes of the associated raw milk, whey, and derived cheeses was examined through shotgun metagenomic sequencing.
RESULTS: The results revealed diverse microbial ecosystems across sample types, comprising more than 1300 bacterial genera and 3400 species. SourceTracker analysis revealed commercial feed and teat skin as major contributors to the raw milk microbiota (45.6% and 33.5%, respectively), being a source of, for example, Lactococcus and Pantoea, along with rennet contributing to the composition of whey and cheese (17.4% and 41.0%, respectively), including taxa such as Streptococcus, Pseudomonas_E or Lactobacillus_H. Functional analysis linked microbial niches to cheese quality- and safety-related metabolic pathways, with brine and food contact surfaces being most relevant, related to genera like Brevibacterium, Methylobacterium, or Halomonas. With respect to the virulome (virulence-associated gene profile), in addition to whey and cheese, commercial feed and grass were the main reservoirs (related to, e.g., Brevibacillus_B or CAG-196). Similarly, grass, teat skin, or rennet were the main contributors of antimicrobial resistance genes (e.g., Bact-11 or Bacteriodes_B). In terms of cheese aroma and texture, apart from the microbiome of the cheese itself, brine, grass, and food contact surfaces were key reservoirs for hydrolase-encoding genes, originating from, for example, Lactococcus, Lactobacillus, Listeria or Chromohalobacter. Furthermore, over 300 metagenomic assembled genomes (MAGs) were generated, including 60 high-quality MAGs, yielding 28 novel putative species from several genera, e.g., Citricoccus, Corynebacterium, or Dietzia.
CONCLUSION: This study emphasizes the role of the artisanal dairy environments in determining cheese microbiota and, consequently, quality and safety. Video Abstract.}, }
@article {pmid39707494, year = {2024}, author = {Li, C and Liu, K and Gu, C and Li, M and Zhou, P and Chen, L and Sun, S and Li, X and Wang, L and Ni, W and Li, M and Hu, S}, title = {Gastrointestinal jumbo phages possess independent synthesis and utilization systems of NAD.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {268}, pmid = {39707494}, issn = {2049-2618}, mesh = {*Bacteriophages/genetics/classification/isolation & purification ; Animals ; *Genome, Viral/genetics ; *NAD/metabolism ; *Phylogeny ; Humans ; Gastrointestinal Microbiome ; Swine ; Sheep ; Metagenomics ; Horses ; Cattle ; Bacteria/virology/genetics ; Deer/virology ; DNA Replication ; }, abstract = {BACKGROUND: Jumbo phages, phages with genomes > 200 kbp, contain some unique genes for successful reproduction in their bacterial hosts. Due to complex and massive genomes analogous to those of small-celled bacteria, how jumbo phages complete their life cycle remains largely undefined.
RESULTS: In this study, we assembled 668 high-quality jumbo phage genomes from over 15 terabytes (TB) of intestinal metagenomic data from 955 samples of 5 animal species (cow, sheep, pig, horse, and deer). Within them, we obtained a complete genome of 716 kbp in length, which is the largest phage genome so far reported in the gut environments. Interestingly, 174 out of the 668 jumbo phages were found to encode all genes required for the synthesis of NAD[+] by the salvage pathway or Preiss-Handler pathway, referred to as NAD-jumbo phage. Besides synthesis genes of NAD[+], these NAD-jumbo phages also encode at least 15 types of NAD[+]-consuming enzyme genes involved in DNA replication, DNA repair, and counterdefense, suggesting that these phages not only have the capacity to synthesize NAD[+] but also redirect NAD[+] metabolism towards phage propagation need in hosts. Phylogenetic analysis and environmental survey indicated NAD-jumbo phages are widely present in the Earth's ecosystems, including the human gut, lakes, salt ponds, mine tailings, and seawater.
CONCLUSION: In summary, this study expands our understanding of the diversity and survival strategies of phages, and an in-depth study of the NAD-jumbo phages is crucial for understanding their role in ecological regulation. Video Abstract.}, }
@article {pmid39707478, year = {2024}, author = {He, Z and Hou, Y and Li, Y and Bei, Q and Li, X and Zhu, YG and Liesack, W and Rillig, MC and Peng, J}, title = {Increased methane production associated with community shifts towards Methanocella in paddy soils with the presence of nanoplastics.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {259}, pmid = {39707478}, issn = {2049-2618}, mesh = {*Methane/metabolism ; *Soil Microbiology ; *Soil/chemistry ; *Oryza/microbiology ; Microbiota ; Polyethylene ; Soil Pollutants ; Metagenomics ; Archaea/metabolism/genetics/classification ; Carbon/metabolism ; Plastics ; }, abstract = {BACKGROUND: Planetary plastic pollution poses a major threat to ecosystems and human health in the Anthropocene, yet its impact on biogeochemical cycling remains poorly understood. Waterlogged rice paddies are globally important sources of CH4. Given the widespread use of plastic mulching in soils, it is urgent to unravel whether low-density polyethylene (LDPE) will affect the methanogenic community in flooded paddy soils. Here, we employed a combination of process measurements, short-chain and long-chain fatty acid (SCFAs and LCFAs) profiling, Fourier-transform ion cyclotron resonance mass spectrometry, quantitative PCR, metagenomics, and mRNA profiling to investigate the impact of LDPE nanoplastics (NPs) on dissolved organic carbon (DOC) and CH4 production in both black and red paddy soils under anoxic incubation over a 160-day period.
RESULTS: Despite significant differences in microbiome composition between the two soil types, both exhibited similar results to NPs exposure. NPs induced a change in DOC content and CH4 production up to 1.8-fold and 10.1-fold, respectively. The proportion of labile dissolved organic matter decreased, while its recalcitrance increased. Genes associated with the degradation of complex carbohydrates and aromatic carbon were significantly enriched. The elevated CH4 production was significantly correlated to increases in both the PCR-quantified mcrA gene copy numbers and the metagenomic methanogen-to-bacteria abundance ratio. Notably, the latter was linked to an enrichment of the hydrogenotrophic methanogenesis pathway. Among 391 metagenome-assembled genomes (MAGs), the abundance of several Syntrophomonas and Methanocella MAGs increased concomitantly, suggesting that the NPs treatments stimulated the syntrophic oxidation of fatty acids. mRNA profiling further identified Methanosarcinaceae and Methanocellaceae to be the key players in the NPs-induced CH4 production.
CONCLUSIONS: The specific enrichment of Syntrophomonas and Methanocella indicates that LDPE NPs stimulate the syntrophic oxidation of LCFAs and SCFAs, with Methanocella acting as the hydrogenotrophic methanogen partner. Our findings enhance the understanding of how LDPE NPs affect the methanogenic community in waterlogged paddy soils. Given the importance of this ecosystem, our results are crucial for elucidating the mechanisms that govern carbon fluxes, which are highly relevant to global climate change.}, }
@article {pmid39706917, year = {2024}, author = {Chang, WS and Harvey, E and Mahar, JE and Firth, C and Shi, M and Simon-Loriere, E and Geoghegan, JL and Wille, M}, title = {Improving the reporting of metagenomic virome-scale data.}, journal = {Communications biology}, volume = {7}, number = {1}, pages = {1687}, pmid = {39706917}, issn = {2399-3642}, mesh = {Animals ; Humans ; Genome, Viral ; Metagenome ; *Metagenomics/methods ; *Virome/genetics ; *Viruses/genetics/classification ; }, abstract = {Over the last decade metagenomic sequencing has facilitated an increasing number of virome-scale studies, leading to an exponential expansion in understanding of virus diversity. This is partially driven by the decreasing costs of metagenomic sequencing, improvements in computational tools for revealing novel viruses, and an increased understanding of the key role that viruses play in human and animal health. A central concern associated with this remarkable increase in the number of virome-scale studies is the lack of broadly accepted "gold standards" for reporting the data and results generated. This is of particular importance for animal virome studies as there are a multitude of nuanced approaches for both data presentation and analysis, all of which impact the resulting outcomes. As such, the results of published studies can be difficult to contextualise and may be of reduced utility due to reporting deficiencies. Herein, we aim to address these reporting issues by outlining recommendations for the presentation of virome data, encouraging a transparent communication of findings that can be interpreted in evolutionary and ecological contexts.}, }
@article {pmid39705954, year = {2024}, author = {Basile, A and Riggio, FP and Tescari, M and Chebbi, A and Sodo, A and Bartoli, F and Imperi, F and Caneva, G and Visca, P}, title = {Metagenome-resolved functional traits of Rubrobacter species implicated in rosy discoloration of ancient frescoes in two Georgian Cathedrals.}, journal = {The Science of the total environment}, volume = {958}, number = {}, pages = {178135}, doi = {10.1016/j.scitotenv.2024.178135}, pmid = {39705954}, issn = {1879-1026}, abstract = {Pink biofilm formation on stone monuments and mural paintings poses serious harm to cultural heritage preservation. Pink biofilms are globally widespread and recalcitrant to eradication, often causing recurrences after restoration. Yet, the ecological drivers of pink biofilm formation and the metabolic functions sustaining the growth of pigment-producing biodeteriogens remain unclear. In this study, a combined approach integrating physicochemical investigations, scanning electron microscopy, 16S rRNA sequence-based analysis of the prokaryotic community, metagenomic deep sequencing, and metabolic profiling, was applied to determine the etiology of rosy discoloration of ancient frescoes in the Gelati and the Martvili Cathedrals (Georgia). Martvili samples showed greater diversity than Gelati samples, though Actinomycetota predominated in both samples. Rubrobacter-related sequences were detected in all sampling sites, showing an overwhelming abundance in Gelati samples. Reconstruction of metagenome-assembled genomes (MAGs) and phylogenetic analyses highlighted significant intra-genus diversity for Rubrobacter-related sequences, most of which could not be assigned to any formally described Rubrobacter species. Metabolic profiling of the Gelati metagenomes suggests that carbon-fixing autotrophic bacteria and proteinaceous substances in the plaster could contribute to sustaining the chemoorganotrophic members of the community. Complete pathways for β-carotene and bacterioruberin synthesis were identified in Rubrobacter MAGs, consistent with the Raman spectroscopy-based detection of these pigments in fresco samples. Gene clusters for the synthesis of secondary metabolites endowed with antibiotic activity were predicted from the annotation of Rubrobacter MAGs, along with genes conferring resistance to several antimicrobials and biocides. In conclusion, genome-resolved metagenomics provided robust evidence of a causal relationship between contamination by Rubrobacter-related carotenoid-producing bacteria and the rosy discoloration of Georgian frescoes, with relevant implications for rational biodeteriogen-targeted restoration strategies.}, }
@article {pmid39705480, year = {2024}, author = {Lu, S and Sun, L and Cao, L and Zhao, M and Guo, Y and Li, M and Duan, S and Zhai, Y and Zhang, X and Wang, Y and Gai, W and Cui, X}, title = {Analysis of lung microbiota in pediatric pneumonia patients using BALF metagenomic next-generation sequencing: A retrospective observational study.}, journal = {Medicine}, volume = {103}, number = {51}, pages = {e40860}, pmid = {39705480}, issn = {1536-5964}, support = {202139//Clinical Medical peronnel training programs/ ; }, mesh = {Child ; Child, Preschool ; Female ; Humans ; Infant ; Male ; *Bronchoalveolar Lavage Fluid/microbiology ; *High-Throughput Nucleotide Sequencing/methods ; *Lung/microbiology ; *Metagenomics/methods ; *Microbiota/genetics ; *Pneumonia/genetics/microbiology ; Pneumonia, Mycoplasma/microbiology/diagnosis ; Retrospective Studies ; Severity of Illness Index ; }, abstract = {The contribution of the lung microbiota to pneumonia in children of varying severity remains poorly understood. This study utilized metagenomic next-generation sequencing (mNGS) technology to elucidate the characteristics of lung microbiota and their association with disease severity. This retrospective study analyzed bronchoalveolar lavage fluid (BALF) mNGS data of 92 children diagnosed with pneumonia between January 2021 and July 2022. A comparative analysis of the lung microbiota was conducted between the severe pneumonia (SP) (n = 44) and non-severe pneumonia (NSP) (n = 48) groups. Compared to conventional microbiological tests (CMT), mNGS had a higher positivity rate in etiology detection (68% vs 100%). In the NSP group, the predominant type of infection was Mycoplasma pneumoniae single infection, whereas in the SP group, the main type involved a combination of M pneumoniae and bacterial infection. The top 3 identified microbial taxa in both the groups were M pneumoniae, Rothia mucilaginosa, and Schaalia odontolyticus. Although there were no significant differences in the α and β diversity of the lung microbiota between the SP and NSP groups, the abundance of M pneumoniae was higher in the SP group (P = .053). Spearman analysis indicated a highly significant positive correlation between the abundance of Prevotella melaninogenica and M pneumoniae (P < .001). Our analysis identified an association between M pneumoniae infections and disease severity. This study provides a foundation for a better understanding of the pathogenesis of pediatric pneumonia and the relationship between microorganisms.}, }
@article {pmid39705298, year = {2024}, author = {Oliveira, V and Cleary, DFR and Polónia, ARM and Huang, YM and Rocha, U and Voogd, NJ and Gomes, NCM}, title = {Unravelling a Latent Pathobiome Across Coral Reef Biotopes.}, journal = {Environmental microbiology}, volume = {26}, number = {12}, pages = {e70008}, doi = {10.1111/1462-2920.70008}, pmid = {39705298}, issn = {1462-2920}, support = {VH-NG-1248 Micro "BigData"//Helmholtz Young Investigator Grant/ ; MNPH 104403//Marine National Parks Headquarter, Taiwan/ ; MOST 105-2621-B-346-002//Ministry of Science and Technology, Taiwan/ ; DOI: 10.54499/DL57/2016/CP1482/CT0109//Foundation for Science and Technology/ ; PTDC/BIA29/MIC/6473/2014 - POCI-01-0145-FEDER-01//Foundation for Science and Technology/ ; SFRH/BPD/117563/2016//Foundation for Science and Technology/ ; UIDP/50017/2020 + UIDB/50017/2020 + LA/P/0094/2020//Foundation for Science and Technology/ ; }, mesh = {*Coral Reefs ; Animals ; *Anthozoa/microbiology ; *Bacteria/genetics/classification ; *Microbiota ; Virulence Factors/genetics ; }, abstract = {Previous studies on disease in coral reef organisms have neglected the natural distribution of potential pathogens and the genetic factors that underlie disease incidence. This study explores the intricate associations between hosts, microbial communities, putative pathogens, antibiotic resistance genes (ARGs) and virulence factors (VFs) across diverse coral reef biotopes. We observed a substantial compositional overlap of putative bacterial pathogens, VFs and ARGs across biotopes, consistent with the 'everything is everywhere, but the environment selects' hypothesis. However, flatworms and soft corals deviated from this pattern, harbouring the least diverse microbial communities and the lowest diversity of putative pathogens and ARGs. Notably, our study revealed a significant congruence between the distribution of putative pathogens, ARGs and microbial assemblages across different biotopes, suggesting an association between pathogen and ARG occurrence. This study sheds light on the existence of this latent pathobiome, the disturbance of which may contribute to disease onset in coral reef organisms.}, }
@article {pmid39702650, year = {2024}, author = {Vriend, EMC and Galenkamp, H and Herrema, H and Nieuwdorp, M and van den Born, BH and Verhaar, BJH}, title = {Machine learning analysis of sex and menopausal differences in the gut microbiome in the HELIUS study.}, journal = {NPJ biofilms and microbiomes}, volume = {10}, number = {1}, pages = {152}, pmid = {39702650}, issn = {2055-5008}, support = {189235//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; 09150182010020/ZONMW_/ZonMw/Netherlands ; 101141346/ERC_/European Research Council/International ; }, mesh = {*Gastrointestinal Microbiome ; Humans ; Female ; *Machine Learning ; Male ; Middle Aged ; *Menopause ; Aged ; Sex Factors ; Metagenomics/methods ; Adult ; Cohort Studies ; Bacteria/classification/genetics/isolation & purification ; Feces/microbiology ; }, abstract = {Sex differences in the gut microbiome have been examined previously, but results are inconsistent, often due to small sample sizes. We investigated sex and menopausal differences in the gut microbiome in a large multi-ethnic population cohort study, including 5166 participants. Using machine learning models, we revealed modest associations between sex and menopausal status, and gut microbiota composition (AUC 0.61-0.63). After adjustments for age, cardiovascular risk factors, and diet, a part of the associations of the highest-ranked gut microbes with sex were attenuated, but most associations remained significant. In contrast, most associations with menopausal status were driven by age and lost significance after adjustment. Using pathway analyses on metagenomic data, we identified sex differences in vitamin B6 synthesis and stachyose degradation pathways. Since some of sex differences in gut microbiome composition and function could not be explained by covariates, we recommend sex stratification in future microbiome studies.}, }
@article {pmid39702405, year = {2024}, author = {Soufi, HH and Porch, R and Korchagina, MV and Abrams, JA and Schnider, JS and Carr, BD and Williams, MA and Louca, S}, title = {Taxonomic variability and functional stability across Oregon coastal subsurface microbiomes.}, journal = {Communications biology}, volume = {7}, number = {1}, pages = {1663}, pmid = {39702405}, issn = {2399-3642}, mesh = {Oregon ; *Microbiota/genetics ; *Geologic Sediments/microbiology ; *RNA, Ribosomal, 16S/genetics ; Bacteria/genetics/classification ; Phylogeny ; Metagenomics/methods ; Biodiversity ; }, abstract = {The factors shaping microbial communities in marine subsurface sediments remain poorly understood. Here, we analyzed the microbiome of subsurface sediments within a depth range of 1.6-1.9 m, at 10 locations along the Oregon coast. We used metagenomics to reconstruct the functional structure and 16S rRNA gene amplicon sequencing to estimate the taxonomic composition of microbial communities, accompanied by physicochemical measurements. Functional community structure, in terms of the proportions of various gene groups, was remarkably stable across samples, despite the latter covering a region spanning over 300 km. In contrast, taxonomic composition was highly variable, especially at the level of amplicon sequence variants (ASVs) and operational taxonomic units (OTUs). Mantel correlation tests between compositional dissimilarities and geographic distances revealed only a moderate influence of distance on composition. Regression models predicting taxonomic dissimilarities and considering up to 20 physicochemical variables as predictors, almost always failed to select a significant predictor, suggesting that variation in local conditions does not explain the high taxonomic variability. Permutation null models of community assembly revealed that taxa tend to strongly segregate, i.e., exclude each other. We conclude that biological interactions are important drivers of taxonomic variation in subsurface sediments, and that this variation can decouple from functional structure.}, }
@article {pmid39702006, year = {2024}, author = {Demirkan, A and van Dongen, J and Finnicum, CT and Westra, HJ and Jankipersadsing, S and Willemsen, G and Ijzerman, RG and Boomsma, DI and Ehli, EA and Bonder, MJ and Fu, J and Franke, L and Wijmenga, C and de Geus, EJC and Kurilshikov, A and Zhernakova, A}, title = {Linking the gut microbiome to host DNA methylation by a discovery and replication epigenome-wide association study.}, journal = {BMC genomics}, volume = {25}, number = {1}, pages = {1224}, pmid = {39702006}, issn = {1471-2164}, mesh = {*DNA Methylation ; *Gastrointestinal Microbiome/genetics ; Humans ; *Epigenome ; *Genome-Wide Association Study ; Male ; Female ; RNA, Ribosomal, 16S/genetics ; CpG Islands/genetics ; Middle Aged ; Adult ; Netherlands ; }, abstract = {Microbiome influences multiple human systems, but its effects on gene methylation is unknown. We investigated the relations between gene methylation in blood and the abundance of common gut bacteria profiled by 16s rRNA gene sequencing in two population-based Dutch cohorts: LifeLines-Deep (LLD, n = 616, discovery) and the Netherlands Twin Register (NTR, n = 296, replication). In LLD, we also explored microbial pathways using data generated by shotgun metagenomic sequencing (n = 683). Methylation in both cohorts was profiled in blood samples using the Illumina 450K array. Discovery and replication analysis identified two independent CpGs associated with the genus Eggerthella: cg16586104 (Pmeta-analysis = 3.21 × 10[-11]) and cg12234533 (Pmeta-analysis = 4.29 × 10[-10]). We also show that microbiome can mediate the effect of environmental factors on host gene methylation. In this first association study linking epigenome to microbiome, we found and replicated the associations of two CpGs to the abundance of genus Eggerthella and identified microbiome as a mediator of the exposome. These associations are observational and suggest further investigation in larger and longitudinal set-ups.}, }
@article {pmid39701966, year = {2024}, author = {Oskolkov, N and Sandionigi, A and Götherström, A and Canini, F and Turchetti, B and Zucconi, L and Mimmo, T and Buzzini, P and Borruso, L}, title = {Unraveling the ancient fungal DNA from the Iceman gut.}, journal = {BMC genomics}, volume = {25}, number = {1}, pages = {1225}, pmid = {39701966}, issn = {1471-2164}, mesh = {*DNA, Ancient/analysis ; Humans ; *DNA, Fungal/genetics ; Metagenomics/methods ; Gastrointestinal Microbiome/genetics ; Gastrointestinal Tract/microbiology ; Mummies/microbiology ; Computational Biology/methods ; Fungi/genetics/classification ; }, abstract = {BACKGROUND: Fungal DNA is rarely reported in metagenomic studies of ancient samples. Although fungi are essential for their interactions with all kingdoms of life, limited information is available about ancient fungi. Here, we explore the possibility of the presence of ancient fungal species in the gut of Ötzi, the Iceman, a naturally mummified human found in the Tyrolean Alps (border between Italy and Austria).
METHODS: A robust bioinformatic pipeline has been developed to detect and authenticate fungal ancient DNA (aDNA) from muscle, stomach, small intestine, and large intestine samples.
RESULTS: We revealed the presence of ancient DNA associated with Pseudogymnoascus genus, with P. destructans and P. verrucosus as possible species, which were abundant in the stomach and small intestine and absent in the large intestine and muscle samples.
CONCLUSION: We suggest that Ötzi may have consumed these fungi accidentally, likely in association with other elements of his diet, and they persisted in his gut after his death due to their adaptability to harsh and cold environments. This suggests the potential co-occurrence of ancient humans with opportunistic fungal species and proposes and validates a conservative bioinformatic approach for detecting and authenticating fungal aDNA in historical metagenomic samples.}, }
@article {pmid39701829, year = {2025}, author = {McAlister, JS and Blum, MJ and Bromberg, Y and Fefferman, NH and He, Q and Lofgren, E and Miller, DL and Schreiner, C and Candan, KS and Szabo-Rogers, H and Reed, JM}, title = {An interdisciplinary perspective of the built-environment microbiome.}, journal = {FEMS microbiology ecology}, volume = {101}, number = {1}, pages = {}, pmid = {39701829}, issn = {1574-6941}, support = {CCF 2200140//U.S. National Science Foundation/ ; }, mesh = {*Microbiota ; *Built Environment ; Humans ; Interdisciplinary Research ; }, abstract = {The built environment provides an excellent setting for interdisciplinary research on the dynamics of microbial communities. The system is simplified compared to many natural settings, and to some extent the entire environment can be manipulated, from architectural design to materials use, air flow, human traffic, and capacity to disrupt microbial communities through cleaning. Here, we provide an overview of the ecology of the microbiome in the built environment. We address niche space and refugia, population, and community (metagenomic) dynamics, spatial ecology within a building, including the major microbial transmission mechanisms, as well as evolution. We also address landscape ecology, connecting microbiomes between physically separated buildings. At each stage, we pay particular attention to the actual and potential interface between disciplines, such as ecology, epidemiology, materials science, and human social behavior. We end by identifying some opportunities for future interdisciplinary research on the microbiome of the built environment.}, }
@article {pmid39701698, year = {2024}, author = {Bao, YY and Li, MX and Gao, XX and Wei, WJ and Huang, WJ and Lin, LZ and Wang, H and Zheng, NN and Li, HK}, title = {[Astragalus polysaccharides improve adipose tissue aging in naturally aged mice via indole-3-lactic acid].}, journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica}, volume = {49}, number = {22}, pages = {5998-6007}, doi = {10.19540/j.cnki.cjcmm.20240508.401}, pmid = {39701698}, issn = {1001-5302}, mesh = {Animals ; Mice ; *Aging/drug effects ; *Adipose Tissue/drug effects/metabolism ; *Polysaccharides/pharmacology ; *Indoles/pharmacology ; Male ; *Astragalus Plant/chemistry ; 3T3-L1 Cells ; Humans ; Adipocytes/drug effects/metabolism/cytology ; Mice, Inbred C57BL ; Cellular Senescence/drug effects ; Drugs, Chinese Herbal/pharmacology/administration & dosage ; Gastrointestinal Microbiome/drug effects ; }, abstract = {Plant polysaccharides are effective components that widely present in traditional Chinese medicine(TCM), exhibiting rich biological activities. However, as most plant polysaccharides cannot be directly absorbed and utilized by the human digestive system, it is now believed that their mode of action mainly involves interaction with intestinal microbiota, leading to the production of functional small molecules. The efficacy of Astragalus polysaccharide(APS) is extensive, including weight loss, improvement of fatty liver, reduction of blood lipids, and enhancement of insulin sensitivity, which may also be related to the regulation of intestinal microbiota. Adipose tissue senescence is an important characteristic of the physiological aging process in the body, often occurring prior to the aging of other important organs. Its main features include the accumulation of senescent cells and exacerbation of inflammation within the tissue. Therefore, to explore the potential protective effects of APS on aging, the improvement of adipose tissue aging phenotype in naturally aging mice was observed using APS, and combined with metagenomic metabolomics, corresponding microbial metabolic functional molecules were identified. Furthermore, functional tests in cell aging models were conducted. The results showed that APS significantly improved the adipocyte aging characteristics of naturally aging mice: specifically reducing aging-induced adipocyte hypertrophy; decreasing the protein expression of aging markers cyclin-dependent kinase inhibitor p21(P21) and multiple tumor suppressor 1(P16); lowering the tissue inflammation reaction. Metagenomic metabolomic analysis of serum from mice in each group revealed that APS significantly increased the content of indole-3-lactic acid(ILA) in naturally aging mice. Further in vitro studies showed that ILA could improve the aging of 3T3-L1 mouse embryonic fibroblasts induced by bleomycin, reduce the protein expression of the aging marker P21, alleviate inflammation, and enhance the ability of preadipocytes to mature. Therefore, APS had the efficacy of protecting naturally aging mice, and its action may be related to the increase in the intestinal microbiota metabolite ILA. This study suggested that TCM may serve as an important entry point for explaining the mechanism of action of TCM by regulating intestinal microbiota and their functional metabolites.}, }
@article {pmid39696556, year = {2024}, author = {Amano, Y and Sachdeva, R and Gittins, D and Anantharaman, K and Lei, S and Valentin-Alvarado, LE and Diamond, S and Beppu, H and Iwatsuki, T and Mochizuki, A and Miyakawa, K and Ishii, E and Murakami, H and Jaffe, AL and Castelle, C and Lavy, A and Suzuki, Y and Banfield, JF}, title = {Diverse microbiome functions, limited temporal variation and substantial genomic conservation within sedimentary and granite rock deep underground research laboratories.}, journal = {Environmental microbiome}, volume = {19}, number = {1}, pages = {105}, pmid = {39696556}, issn = {2524-6372}, support = {JPJ007597//The Ministry of Economy, Trade and Industry of Japan/ ; 19K05342//the Japan Society for the Promotion of Science/ ; OCE2049478//National Science Foundation/ ; DE-AC02-05CH11231//the Watershed Function Scientific Focus Area funded by the U.S. Department of Energy/ ; 2230766//NSF "Four Networks for Geologic Hydrogen Storage"/ ; }, abstract = {BACKGROUND: Underground research laboratories (URLs) provide a window on the deep biosphere and enable investigation of potential microbial impacts on nuclear waste, CO2 and H2 stored in the subsurface. We carried out the first multi-year study of groundwater microbiomes sampled from defined intervals between 140 and 400 m below the surface of the Horonobe and Mizunami URLs, Japan.
RESULTS: We reconstructed draft genomes for > 90% of all organisms detected over a four year period. The Horonobe and Mizunami microbiomes are dissimilar, likely because the Mizunami URL is hosted in granitic rock and the Horonobe URL in sedimentary rock. Despite this, hydrogen metabolism, rubisco-based CO2 fixation, reduction of nitrogen compounds and sulfate reduction are well represented functions in microbiomes from both URLs, although methane metabolism is more prevalent at the organic- and CO2-rich Horonobe URL. High fluid flow zones and proximity to subsurface tunnels select for candidate phyla radiation bacteria in the Mizunami URL. We detected near-identical genotypes for approximately one third of all genomically defined organisms at multiple depths within the Horonobe URL. This cannot be explained by inactivity, as in situ growth was detected for some bacteria, albeit at slow rates. Given the current low hydraulic conductivity and groundwater compositional heterogeneity, ongoing inter-site strain dispersal seems unlikely. Alternatively, the Horonobe URL microbiome homogeneity may be explained by higher groundwater mobility during the last glacial period. Genotypically-defined species closely related to those detected in the URLs were identified in three other subsurface environments in the USA. Thus, dispersal rates between widely separated underground sites may be fast enough relative to mutation rates to have precluded substantial divergence in species composition. Species overlaps between subsurface locations on different continents constrain expectations regarding the scale of global subsurface biodiversity.
CONCLUSIONS: Our analyses reveal microbiome stability in the sedimentary rocks and surprising microbial community compositional and genotypic overlap over sites separated by hundreds of meters of rock, potentially explained by dispersal via slow groundwater flow or during a prior hydrological regime. Overall, microbiome and geochemical stability over the study period has important implications for underground storage applications.}, }
@article {pmid39695983, year = {2024}, author = {Su, L and Guo, J and Shi, W and Tong, W and Li, X and Yang, B and Xiang, Z and Qin, C}, title = {Metagenomic analysis reveals the community composition of the microbiome in different segments of the digestive tract in donkeys and cows: implications for microbiome research.}, journal = {BMC microbiology}, volume = {24}, number = {1}, pages = {530}, pmid = {39695983}, issn = {1471-2180}, support = {2021YFF0702900//National Key Research and Development Program of China/ ; 2023-PT180-01//Non-profit Central Research Institute Fund of Chinese Academy of Medical Sciences/ ; 2021-I2M-1-039, 2021-I2M-1-034//CAMS initiative for Innovative Medicine of China/ ; }, mesh = {Animals ; *Equidae/microbiology ; Cattle/microbiology ; *Metagenomics/methods ; *Gastrointestinal Microbiome/genetics ; *Feces/microbiology ; *Bacteria/classification/genetics/isolation & purification ; *Gastrointestinal Tract/microbiology ; Sequence Analysis, DNA/methods ; Metagenome ; Bacteroidetes/genetics/isolation & purification/classification ; }, abstract = {INTRODUCTION: The intestinal microbiota plays a crucial role in health and disease. This study aimed to assess the composition and functional diversity of the intestinal microbiota in donkeys and cows by examining samples collected from different segments of the digestive tract using two distinct techniques: direct swab sampling and faecal sampling.
RESULTS: In this study, we investigated and compared the effects of multiple factors on the composition and function of the intestinal microbial community. Approximately 300 GB of metagenomic sequencing data from 91 samples obtained from various segments of the digestive tract were used, including swabs and faecal samples from monogastric animals (donkeys) and polygastric animals (cows). We assembled 4,004,115 contigs for cows and 2,938,653 contigs for donkeys, with a total of 9,060,744 genes. Our analysis revealed that, compared with faecal samples, swab samples presented a greater abundance of Bacteroidetes, whereas faecal samples presented a greater abundance of Firmicutes. Additionally, we observed significant variations in microbial composition among different digestive tract segments in both animals. Our study identified key bacterial species and pathways via different methods and provided evidence that multiple factors can influence the microbial composition. These findings provide new insights for the accurate characterization of the composition and function of the gut microbiota in microbiome research.
CONCLUSIONS: The results obtained by both sampling methods in the present study revealed that the composition and function of the intestinal microbiota in donkeys and cows exhibit species-specific and region-specific differences. These findings highlight the importance of using standardized sampling protocols to ensure accurate and consistent characterization of the intestinal microbiota in various animal species. The implications and underlying mechanisms of these associations provide multiple perspectives for future microbiome research.}, }
@article {pmid39695885, year = {2024}, author = {Galic, I and Bez, C and Bertani, I and Venturi, V and Stankovic, N}, title = {Herbicide-treated soil as a reservoir of beneficial bacteria: microbiome analysis and PGP bioinoculants in maize.}, journal = {Environmental microbiome}, volume = {19}, number = {1}, pages = {107}, pmid = {39695885}, issn = {2524-6372}, support = {451-03-47/2023-01/ 200042//Ministarstvo Prosvete, Nauke i Tehnološkog Razvoja/ ; 451-03-47/2023-01/ 200042//Ministarstvo Prosvete, Nauke i Tehnološkog Razvoja/ ; Research and Training Grant 1818//FEMS/ ; }, abstract = {BACKGROUND: Herbicides are integral to agricultural weed management but can adversely affect non-target organisms, soil health, and microbiome. We investigated the effects of herbicides on the total soil bacterial community composition using 16S rRNA gene amplicon community profiling. Further, we aimed to identify herbicide-tolerant bacteria with plant growth-promoting (PGP) capabilities as a mitigative strategy for these negative effects, thereby promoting sustainable agricultural practices.
RESULTS: A bacterial community analysis explored the effects of long-term S-metolachlor application on soil bacterial diversity, revealing that the herbicide's impact on microbial communities is less significant than the effects of temporal factors (summer vs. winter) or agricultural practices (continuous maize cultivation vs. maize-winter wheat rotation). Although S-metolachlor did not markedly alter the overall bacteriome structure in our environmental context, the application of enrichment techniques enabled the selection of genera such as Pseudomonas, Serratia, and Brucella, which were rare in metagenome analysis of soil samples. Strain isolation revealed a rich source of herbicide-tolerant PGP bacteria within the culturable microbiome fraction, termed the high herbicide concentration tolerant (HHCT) bacterial culture collection. Within the HHCT collection, we isolated 120 strains that demonstrated significant in vitro PGP and biocontrol potential, and soil quality improvement abilities. The most promising HHCT isolates were combined into three consortia, each exhibiting a comprehensive range of plant-beneficial traits. We evaluated the efficacy and persistence of these multi-strain consortia during 4-week in pot experiments on maize using both agronomic parameters and 16S rRNA gene community analysis assessing early-stage plant development, root colonization, and rhizosphere persistence. Notably, 7 out of 10 inoculated consortia partners successfully established themselves and persisted in the maize root microbiome without significantly altering host root biodiversity. Our results further evidenced that all three consortia positively impacted both seed germination and early-stage plant development, increasing shoot biomass by up to 47%.
CONCLUSIONS: Herbicide-treated soil bacterial community analysis revealed that integrative agricultural practices can suppress the effects of continuous S-metolachlor application on soil microbial diversity and stabilize microbiome fluctuations. The HHCT bacterial collection holds promise as a source of beneficial bacteria that promote plant fitness while maintaining herbicide tolerance.}, }
@article {pmid39695297, year = {2024}, author = {Conteville, LC and Silva, JVD and Andrade, BGN and Coutinho, LL and Palhares, JCP and Regitano, LCA}, title = {Recovery of metagenome-assembled genomes from the rumen and fecal microbiomes of Bos indicus beef cattle.}, journal = {Scientific data}, volume = {11}, number = {1}, pages = {1385}, pmid = {39695297}, issn = {2052-4463}, mesh = {Animals ; Cattle/microbiology ; *Feces/microbiology ; *Metagenome ; *Rumen/microbiology ; *Phylogeny ; Gastrointestinal Microbiome ; Brazil ; Male ; Archaea/genetics/classification ; Bacteria/genetics/classification ; Microbiota ; }, abstract = {Nelore is a Bos indicus beef breed that is well-adapted to tropical environments and constitutes most of the world's largest commercial cattle herd: the Brazilian bovine herd. Despite its significance, microbial genome recovery from ruminant microbiomes has largely excluded representatives from Brazilian Nelore cattle. To address this gap, this study presents a comprehensive dataset of microbial genomes recovered from the rumen and feces of 52 Brazilian Nelore bulls. A total of 1,526 non-redundant metagenome-assembled genomes (MAGs) were recovered from their gastrointestinal tract, with 497 ruminal and 486 fecal classified as high-quality. Phylogenetic analysis revealed that the bacterial MAGs fall into 12 phyla, with Firmicutes and Bacteroidota being the most predominant, while all archaeal MAGs belong to the genus Methanobrevibacter. The exploration of these microbial genomes will provide valuable insights into the metabolic potential and functional roles of individual microorganisms within host-microbiome interactions, contributing to a better understanding of the microbiome's roles in bovine performance.}, }
@article {pmid39695203, year = {2024}, author = {Jeon, J and Park, Y and Lee, DH and Kim, JH and Jin, YK and Hong, JK and Lee, YM}, title = {Microbial profiling of the East Siberian Sea sediments using 16S rRNA gene and metagenome sequencing.}, journal = {Scientific data}, volume = {11}, number = {1}, pages = {1350}, pmid = {39695203}, issn = {2052-4463}, mesh = {*Geologic Sediments/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Metagenome ; *Archaea/genetics/classification ; *Bacteria/genetics/classification ; Arctic Regions ; Microbiota ; Oceans and Seas ; Siberia ; }, abstract = {The Arctic Ocean is experiencing significant global warming, leading to reduced sea-ice cover, submarine permafrost thawing, and increased river discharge. The East Siberian Sea (ESS) undergoes more significant terrestrial inflow from coastal erosion and river runoff than other Arctic seas. Despite extensive research on environmental changes, microbial communities and their functions in the ESS, which are closely related to environmental conditions, remain largely unexplored. Here, we investigated microbial communities in ESS surface sediments spanning latitudes from 73°N to 77°N using 16S rRNA amplicon sequencing, and reconstructed 211 metagenome-assembled genomes (MAGs) using shotgun metagenome sequencing. Taxonomic analysis identified 209 bacterial MAGs, with the predominant phyla Pseudomonadota (n = 82), Actinobacteriota (n = 38), Desulfobacterota (n = 23), along with 2 archaeal MAGs of Thermoproteota. Notably, 86% of the MAGs (n = 183) could not be classified into known species, indicating the potential presence of novel and unidentified microorganisms in the ESS. This dataset provides invaluable information on the microbial diversity and ecological functions in the rapidly changing ESS.}, }
@article {pmid39693444, year = {2024}, author = {Ruff, SE and de Angelis, IH and Mullis, M and Payet, JP and Magnabosco, C and Lloyd, KG and Sheik, CS and Steen, AD and Shipunova, A and Morozov, A and Reese, BK and Bradley, JA and Lemonnier, C and Schrenk, MO and Joye, SB and Huber, JA and Probst, AJ and Morrison, HG and Sogin, ML and Ladau, J and Colwell, F}, title = {A global comparison of surface and subsurface microbiomes reveals large-scale biodiversity gradients, and a marine-terrestrial divide.}, journal = {Science advances}, volume = {10}, number = {51}, pages = {eadq0645}, pmid = {39693444}, issn = {2375-2548}, mesh = {*Microbiota/genetics ; *Biodiversity ; *Archaea/genetics/classification ; *Phylogeny ; *Bacteria/genetics/classification ; Metagenome ; Seawater/microbiology ; Ecosystem ; }, abstract = {Subsurface environments are among Earth's largest habitats for microbial life. Yet, until recently, we lacked adequate data to accurately differentiate between globally distributed marine and terrestrial surface and subsurface microbiomes. Here, we analyzed 478 archaeal and 964 bacterial metabarcoding datasets and 147 metagenomes from diverse and widely distributed environments. Microbial diversity is similar in marine and terrestrial microbiomes at local to global scales. However, community composition greatly differs between sea and land, corroborating a phylogenetic divide that mirrors patterns in plant and animal diversity. In contrast, community composition overlaps between surface to subsurface environments supporting a diversity continuum rather than a discrete subsurface biosphere. Differences in microbial life thus seem greater between land and sea than between surface and subsurface. Diversity of terrestrial microbiomes decreases with depth, while marine subsurface diversity and phylogenetic distance to cultured isolates rivals or exceeds that of surface environments. We identify distinct microbial community compositions but similar microbial diversity for Earth's subsurface and surface environments.}, }
@article {pmid39688845, year = {2024}, author = {Oteo-García, G and Mutti, G and Caldon, M and Oosthuitzen, O and ManfrediniK, M and Capelli, C}, title = {Reconstructing micro-evolutionary dynamics shaping local variation in southern African populations using genomics, metagenomics and personal metadata.}, journal = {Journal of anthropological sciences = Rivista di antropologia : JASS}, volume = {102}, number = {}, pages = {123-143}, doi = {10.4436/JASS.10204}, pmid = {39688845}, issn = {2037-0644}, mesh = {Humans ; Namibia ; *Metagenomics ; *Saliva/microbiology/virology ; *Microbiota/genetics ; Male ; Female ; Adult ; Lesotho ; Genomics ; Genetic Variation ; Young Adult ; Middle Aged ; Adolescent ; Black People/genetics ; }, abstract = {Geography is a well-known factor shaping genetic variation in human populations. However, the potential role played by cultural variables remains much understudied. This study investigates the impact of socio-cultural variables on genomic similarity and the saliva microbiome, using data from populations in Lesotho and Namibia. Geographic distance within Lesotho increases genetic differentiation, while shared clan affiliation surprisingly increases it. In Namibia, ethnicity is the predominant factor influencing genetic affinity. Saliva metagenomic data shows a negative correlation between age and alpha diversity, with notable differences in host-interacting taxa and viral load. These findings highlight the role of geography in shaping genetic affinity even at small scales and the complex influences of cultural factors. The saliva microbiome appears primarily affected by unrecorded individual behaviors rather than geographic or cultural variables. At population-level these oral microbiomes reveal insights into some dietary habits, oral health, and also the communal viral load, which appears to have greater incidence in Lesotho possibly related to the long-term effects of the HIV epidemic in the country.}, }
@article {pmid39684893, year = {2024}, author = {Parkar, N and Young, W and Olson, T and Hurst, C and Janssen, P and Spencer, NJ and McNabb, WC and Dalziel, JE}, title = {Peripherally Restricted Activation of Opioid Receptors Influences Anxiety-Related Behaviour and Alters Brain Gene Expression in a Sex-Specific Manner.}, journal = {International journal of molecular sciences}, volume = {25}, number = {23}, pages = {}, pmid = {39684893}, issn = {1422-0067}, support = {C10X1706//Ministry of Business, Innovation and Employment/ ; }, mesh = {Animals ; Male ; Female ; *Anxiety/metabolism ; Rats ; *Loperamide/pharmacology ; *Brain/metabolism/drug effects ; *Rats, Sprague-Dawley ; *Receptors, Opioid/metabolism/genetics ; Behavior, Animal/drug effects ; Gastrointestinal Microbiome/drug effects ; Hippocampus/metabolism/drug effects ; Enteric Nervous System/metabolism ; Gene Expression Regulation/drug effects ; Sex Factors ; Sex Characteristics ; }, abstract = {Although effects of stress-induced anxiety on the gastrointestinal tract and enteric nervous system (ENS) are well studied, how ENS dysfunction impacts behaviour is not well understood. We investigated whether ENS modulation alters anxiety-related behaviour in rats. We used loperamide, a potent μ-opioid receptor agonist that does not cross the blood-brain barrier, to manipulate ENS function and assess changes in behaviour, gut and brain gene expression, and microbiota profile. Sprague Dawley (male/female) rats were acutely dosed with loperamide (subcutaneous) or control solution, and their behavioural phenotype was examined using open field and elevated plus maze tests. Gene expression in the proximal colon, prefrontal cortex, hippocampus, and amygdala was assessed by RNA-seq and caecal microbiota composition determined by shotgun metagenome sequencing. In female rats, loperamide treatment decreased distance moved and frequency of supported rearing, indicating decreased exploratory behaviour and increased anxiety, which was associated with altered hippocampal gene expression. Loperamide altered proximal colon gene expression and microbiome composition in both male and female rats. Our results demonstrate the importance of the ENS for communication between gut and brain for normo-anxious states in female rats and implicate corticotropin-releasing hormone and gamma-aminobutyric acid gene signalling pathways in the hippocampus. This study also sheds light on sexually dimorphic communication between the gut and the brain. Microbiome and colonic gene expression changes likely reflect localised effects of loperamide related to gut dysmotility. These results suggest possible ENS pharmacological targets to alter gut to brain signalling for modulating mood.}, }
@article {pmid39684853, year = {2024}, author = {Tynior, W and Kłósek, M and Salatino, S and Cuber, P and Hudy, D and Nałęcz, D and Chan, YT and Gustave, C and Strzelczyk, JK}, title = {Metagenomic Analysis of the Buccal Microbiome by Nanopore Sequencing Reveals Structural Differences in the Microbiome of a Patient with Molar Incisor Hypomineralization (MIH) Compared to a Healthy Child-Case Study.}, journal = {International journal of molecular sciences}, volume = {25}, number = {23}, pages = {}, pmid = {39684853}, issn = {1422-0067}, support = {PCN-1-111/N/2/O//Medical University of Silesia/ ; }, mesh = {Humans ; *Microbiota/genetics ; *Metagenomics/methods ; *Nanopore Sequencing/methods ; *Dental Enamel Hypoplasia/microbiology/genetics ; Child ; Mouth Mucosa/microbiology/pathology ; Male ; Female ; Bacteria/genetics/classification/isolation & purification ; Case-Control Studies ; Metagenome ; Incisor/microbiology ; Molar Hypomineralization ; }, abstract = {Molar incisor hypomineralization (MIH) is a qualitative developmental defect that affects the enamel tissue of permanent molars and can also occur in permanent incisors. Enamel affected by MIH has reduced hardness, increased porosity, and a higher organic content than unaffected enamel. These characteristics predispose the enamel to accumulation of bacteria and a higher prevalence of caries lesions. Through a groundbreaking metagenomic analysis of the buccal mucosal sample from a patient with MIH, we explored the intricacies of its microbiome compared to a healthy control using state-of-the-art nanopore long-read sequencing. Out of the 210 bacterial taxa identified in the MIH microbiome, we found Streptococcus and Haemophilus to be the most abundant genera. The bacteria with the highest read counts in the patient with MIH included Streptococcus mitis, Haemophilus parainfluenzae, Streptococcus pneumoniae, Rothia dentocariosa, and Gemella haemolysans. Our results revealed a striking contrast between healthy and MIH affected children, with a higher dominance and number of pathogenic species (S. pneumoniae, H. influenzae, and N. meningitidis) and reduced diversity in the MIH-affected patient. This distinct microbial profile not only sheds light on MIH-affected patients, but paves the way for future research, inspiring deeper understanding and larger scale studies.}, }
@article {pmid39684458, year = {2024}, author = {Salini, A and Zuliani, L and Gonnelli, PM and Orlando, M and Odoardo, A and Ragno, D and Aulitto, M and Zaccone, C and Fusco, S}, title = {Plastic-Degrading Microbial Consortia from a Wastewater Treatment Plant.}, journal = {International journal of molecular sciences}, volume = {25}, number = {23}, pages = {}, pmid = {39684458}, issn = {1422-0067}, support = {CUP B53D23015130001//MUR - Italian Ministry of University and Research in the framework of the Next Generation EU action/ ; }, mesh = {*Microbial Consortia ; *Wastewater/microbiology ; *Biodegradation, Environmental ; Sewage/microbiology ; Plastics/metabolism ; Bacteria/metabolism/classification/genetics/isolation & purification ; Microbiota ; }, abstract = {Plastic waste pollution has become a global crisis, with millions of tons of plastic expected to accumulate in landfills and in natural environments, posing a serious threat to wildlife and human health. As current recycling methods remain inefficient, there is an urgent need for innovative enzymatic solutions to break down plastics and enable a circular economy approach. In this study, we explore the plastic-degrading potential of microorganisms enriched from activated sludge (AS) sourced from a municipal wastewater treatment plant (WWTP)-a known microplastic-contaminated industrial niche. Five microbial consortia (i.e., microbiomes) were enriched under selective pressure using low-carbon conditions and high concentrations of polyester polymers, including post-consumer PET, post-consumer PLA, and virgin PLA. Enrichment was performed for 100 days at 37 °C and 50 °C, followed by microbiomes isolation and metagenomic analysis to identify plastic-active bacteria and their enzymes. The results revealed that PLA polymers, but not post-consumer PET, were effectively degraded by the microbiomes, as confirmed by nuclear magnetic resonance (NMR) and gel permeation chromatography (GPC), showing significant molecular weight reduction compared to the abiotic controls. Microbial community analysis highlighted a distinct enrichment profile driven by the polymer composition and the temperature. At 50 °C, the Bacillales order became the predominant population, whereas at 37 °C, a more diverse community within the Proteobacteria and Actinobacteria phyla were selected. Nonetheless, the enriched microbial communities at both temperatures included phyla with members known for polyester degradation. Moreover, at 50 °C, enrichment of putative PET/PLA hydrolases was also observed. These findings suggest that AS microorganisms are a reservoir of polyester-active enzymes, particularly PLA-depolymerases, and hold promise for advancing biotechnological strategies to mitigate plastic pollution through re- and up-cycling.}, }
@article {pmid39684246, year = {2024}, author = {Domínguez-Pino, M and Mellado, S and Cuesta, CM and Grillo-Risco, R and García-García, F and Pascual, M}, title = {Metagenomics Reveals Sex-Based Differences in Murine Fecal Microbiota Profiles Induced by Chronic Alcohol Consumption.}, journal = {International journal of molecular sciences}, volume = {25}, number = {23}, pages = {}, pmid = {39684246}, issn = {1422-0067}, support = {2023-I024//the Spanish Ministry of Health-PNSD/ ; CIAICO/2021/203//GVA/ ; RD21/0009/0005//the Primary Addiction Care Research Network/ ; pro-ject IMPaCT-Data, exp. IMP/00019//FGG and RGR were supported by and partially funded by the Institute of Health Carlos III/ ; PID2023-146865OB-I00 and PID2021-124430OA-I00//MCIN/AEI/10.13039/501100011033/ FEDER/ ; }, mesh = {Animals ; Female ; Male ; *Feces/microbiology ; Mice ; *Gastrointestinal Microbiome/drug effects ; *Toll-Like Receptor 4/genetics/metabolism ; *Metagenomics/methods ; *Mice, Knockout ; *RNA, Ribosomal, 16S/genetics ; *Ethanol/adverse effects ; Alcohol Drinking/adverse effects ; Mice, Inbred C57BL ; Sex Factors ; Dysbiosis/microbiology/chemically induced ; Sex Characteristics ; }, abstract = {Chronic ethanol exposure induces an inflammatory response within the intestinal tract, compromising mucosal and epithelial integrity and leading to dysbiosis of the gut microbiome. However, the specific roles of the gut microbiota in mediating ethanol-induced effects, as well as their interactions with the immune system, remain poorly characterized. This study aimed to evaluate sex-based differences in fecal microbiota profiles induced by chronic alcohol consumption and to assess whether TLR4 is involved in these effects. We analyzed the 16S rRNA gene sequencing of fecal samples from male and female wild-type (WT) and TLR4-knockout (TLR4-KO) mice with and without chronic ethanol exposure over a three-month period. Our findings provide evidence, for the first time, that male mice are more susceptible to the effects of ethanol on the fecal microbiota, since ethanol exposure induced greater alterations in the Gram-negative and -positive bacteria with immunogenic capacity in the WT male mice than in the female mice. We also demonstrate that the absence of immune receptor TLR4 leads to different microbiota in both sexes, showing anti-inflammatory and protective properties for intestinal barrier function and resulting in a phenotype more resistant to ethanol's effects. These findings may open new avenues for understanding the relationship between gut microbiota profiles and inflammation in the digestive system induced by chronic alcohol consumption.}, }
@article {pmid39683635, year = {2024}, author = {Ouédraogo, LO and Deng, L and Ouattara, CA and Compaoré, A and Ouédraogo, M and Argaw, A and Lachat, C and Houpt, ER and Saidi, Q and Haerynck, F and Sonnenburg, J and Azad, MB and Tavernier, SJ and Bastos-Moreira, Y and Toe, LC and Dailey-Chwalibóg, T}, title = {Describing Biological Vulnerability in Small, Vulnerable Newborns in Urban Burkina Faso (DenBalo): Gut Microbiota, Immune System, and Breastmilk Assembly.}, journal = {Nutrients}, volume = {16}, number = {23}, pages = {}, pmid = {39683635}, issn = {2072-6643}, support = {INV-035474 & INV-036154/GATES/Bill & Melinda Gates Foundation/United States ; }, mesh = {Humans ; Burkina Faso ; Female ; Infant, Newborn ; *Gastrointestinal Microbiome ; *Milk, Human/immunology ; Prospective Studies ; *Vagina/microbiology/immunology ; *Immune System ; Pregnancy ; Breast Feeding ; Infant, Small for Gestational Age ; Adult ; }, abstract = {Background: Small vulnerable newborns (SVNs), including those born preterm, small for gestational age, or with low birth weight, are at higher risk of neonatal mortality and long-term health complications. Early exposure to maternal vaginal microbiota and breastfeeding plays a critical role in the development of the neonatal microbiota and immune system, especially in low-resource settings like Burkina Faso, where neonatal mortality rates remain high. Objectives: The DenBalo study aims to investigate the role of maternal and neonatal factors, such as vaginal and gut microbiota, immune development, and early nutrition, in shaping health outcomes in SVNs and healthy infants. Methods: This prospective cohort observational study will recruit 141 mother-infant pairs (70 SVNs and 71 healthy controls) from four health centers in Bobo-Dioulasso, Burkina Faso. The mother-infant pairs will be followed for six months with anthropometric measurements and biospecimen collections, including blood, breast milk, saliva, stool, vaginal swabs, and placental biopsies. Multi-omics approaches, encompassing metagenomics, metabolomics, proteomics, and immune profiling, will be used to assess vaginal and gut microbiota composition and functionality, immune cell maturation, and cytokine levels at critical developmental stages. Conclusions: This study will generate comprehensive data on how microbiota, metabolomic, and proteomic profiles, along with immune system development, differ between SVNs and healthy infants. These findings will guide targeted interventions to improve neonatal health outcomes and reduce mortality, particularly in vulnerable populations.}, }
@article {pmid39682735, year = {2024}, author = {Hemmati, MA and Monemi, M and Asli, S and Mohammadi, S and Foroozanmehr, B and Haghmorad, D and Oksenych, V and Eslami, M}, title = {Using New Technologies to Analyze Gut Microbiota and Predict Cancer Risk.}, journal = {Cells}, volume = {13}, number = {23}, pages = {}, pmid = {39682735}, issn = {2073-4409}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Neoplasms/microbiology ; Machine Learning ; High-Throughput Nucleotide Sequencing/methods ; Metagenomics/methods ; }, abstract = {The gut microbiota significantly impacts human health, influencing metabolism, immunological responses, and disease prevention. Dysbiosis, or microbial imbalance, is linked to various diseases, including cancer. It is crucial to preserve a healthy microbiome since pathogenic bacteria, such as Escherichia coli and Fusobacterium nucleatum, can cause inflammation and cancer. These pathways can lead to the formation of tumors. Recent advancements in high-throughput sequencing, metagenomics, and machine learning have revolutionized our understanding of the role of gut microbiota in cancer risk prediction. Early detection is made easier by machine learning algorithms that improve the categorization of cancer kinds based on microbiological data. Additionally, the investigation of the microbiome has been transformed by next-generation sequencing (NGS), which has made it possible to fully profile both cultivable and non-cultivable bacteria and to understand their roles in connection with cancer. Among the uses of NGS are the detection of microbial fingerprints connected to treatment results and the investigation of metabolic pathways implicated in the development of cancer. The combination of NGS with machine learning opens up new possibilities for creating customized medicine by enabling the development of diagnostic tools and treatments that are specific to each patient's microbiome profile, even in the face of obstacles like data complexity. Multi-omics studies reveal microbial interactions, biomarkers for cancer detection, and gut microbiota's impact on cancer progression, underscoring the need for further research on microbiome-based cancer prevention and therapy.}, }
@article {pmid39681310, year = {2024}, author = {Tobar, Z and Lee, KY and Gaa, ME and Moore, BP and Li, X and Pitesky, ME}, title = {Evaluation of 16s Long Read Metabarcoding for Characterizing the Microbiome and Salmonella Contamination of Retail Poultry Meat.}, journal = {Journal of food protection}, volume = {88}, number = {2}, pages = {100434}, doi = {10.1016/j.jfp.2024.100434}, pmid = {39681310}, issn = {1944-9097}, abstract = {The traditional gold standard for detection of Salmonella in meat products is bacterial culture with enrichment. While this method is highly sensitive, it is slow and provides an incomplete assessment of isolate taxonomy in positive samples. This study presents a novel PCR-based detection assay which amplifies the 16s-ITS-23s region which is an approximately 2,500 base pair region of the larger ribosomal rrn operon. Intra-assay variation was assessed by splitting each biological sample into 3 technical replicates. Limits of detection (LOD) were assessed by utilizing a serial dilution of a pure culture of Salmonella enterica subsp. enterica serovar Heidelberg spiked into either sterile 1 × PBS or 1 × PBS rinsate of a Salmonella culture-negative chicken meat sample. Results indicate the 16s metabarcoding assay evaluated here could not be reliably used for the detection of Salmonella in adulterated retail meat samples as the LOD observed, 4.70 log colony forming units (CFU)/ml, is above the expected concentration of Salmonella in retail poultry meat samples which previous studies have shown range from under 1 to 2 log CFU/ml. However, due to greater taxonomic resolution afforded by using 16s long reads, the assay allowed alpha diversity assessment of the microbiome of raw poultry meat with the ability to assign taxonomy to the species and strain level for some amplicon sequence variants (ASV). This indicates this process may have value characterizing biodiversity and pathogen contamination of poultry samples in earlier steps of the poultry meat production process where bacterial contamination concentrations are likely to be higher.}, }
@article {pmid39679737, year = {2024}, author = {Zhao, H and Wang, T}, title = {Debiased high-dimensional regression calibration for errors-in-variables log-contrast models.}, journal = {Biometrics}, volume = {80}, number = {4}, pages = {}, doi = {10.1093/biomtc/ujae153}, pmid = {39679737}, issn = {1541-0420}, mesh = {Humans ; Calibration ; *Models, Statistical ; Gastrointestinal Microbiome ; Computer Simulation ; Regression Analysis ; Bias ; Linear Models ; Biometry/methods ; Data Interpretation, Statistical ; Metagenomics/methods/statistics & numerical data ; }, abstract = {Motivated by the challenges in analyzing gut microbiome and metagenomic data, this work aims to tackle the issue of measurement errors in high-dimensional regression models that involve compositional covariates. This paper marks a pioneering effort in conducting statistical inference on high-dimensional compositional data affected by mismeasured or contaminated data. We introduce a calibration approach tailored for the linear log-contrast model. Under relatively lenient conditions regarding the sparsity level of the parameter, we have established the asymptotic normality of the estimator for inference. Numerical experiments and an application in microbiome study have demonstrated the efficacy of our high-dimensional calibration strategy in minimizing bias and achieving the expected coverage rates for confidence intervals. Moreover, the potential application of our proposed methodology extends well beyond compositional data, suggesting its adaptability for a wide range of research contexts.}, }
@article {pmid39679619, year = {2024}, author = {Steinbach, E and Belda, E and Alili, R and Adriouch, S and Dauriat, CJG and Donatelli, G and Dumont, JL and Pacini, F and Tuszynski, T and Pelloux, V and Jacques, F and Creusot, L and Coles, E and Taillandier, P and Vazquez Gomez, M and Masi, D and Mateo, V and André, S and Kordahi, M and Rouault, C and Zucker, JD and Sokol, H and Genser, L and Chassaing, B and Le Roy, T and Clément, K}, title = {Comparative analysis of the duodenojejunal microbiome with the oral and fecal microbiomes reveals its stronger association with obesity and nutrition.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2405547}, pmid = {39679619}, issn = {1949-0984}, mesh = {Humans ; *Obesity/microbiology ; *Feces/microbiology ; Female ; Male ; Middle Aged ; *Gastrointestinal Microbiome ; Adult ; *Duodenum/microbiology ; *Bacteria/classification/isolation & purification/genetics/metabolism ; Jejunum/microbiology ; Mouth/microbiology ; Nutritional Status ; }, abstract = {The intestinal microbiota is increasingly recognized as a crucial player in the development and maintenance of various chronic conditions, including obesity and associated metabolic diseases. While most research focuses on the fecal microbiota due to its easier accessibility, the small intestine, as a major site for nutrient sensing and absorption, warrants further investigation to determine its microbiota composition and functions. Here, we conducted a clinical research project in 30 age- and sex-matched participants with (n = 15) and without (n = 15) obesity. Duodenojejunal fluid was obtained by aspiration during endoscopy. Phenotyping included clinical variables related to metabolic status, lifestyle, and psychosocial factors using validated questionnaires. We performed metagenomic analyses of the oral, duodenojejunal, and fecal microbiome, alongside metabolomic data from duodenojejunal fluid and feces, integrating these data with clinical and lifestyle information. Our results highlight significant associations between duodenojejunal microbiota composition and usual dietary intake, as well as clinical phenotypes, with larger effect sizes than the associations between these variables and fecal microbiota. Notably, we found that the duodenojejunal microbiota of patients with obesity exhibited higher diversity and showed distinct differences in the abundance of several duodenojejunal microbiota species compared with individuals without obesity. Our findings support the relevance of studying the role of the small intestinal microbiota in the pathogenesis of nutrition-related diseases.}, }
@article {pmid39679617, year = {2024}, author = {McAdams, ZL and Gustafson, KL and Russell, AL and Self, R and Petry, AL and Lever, TE and Ericsson, AC}, title = {Supplier-origin gut microbiomes affect host body weight and select autism-related behaviors.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2385524}, pmid = {39679617}, issn = {1949-0984}, mesh = {*Gastrointestinal Microbiome ; Animals ; Mice ; Male ; *Autism Spectrum Disorder/microbiology ; *Body Weight ; Female ; *Behavior, Animal ; Disease Models, Animal ; Humans ; Brain-Gut Axis/physiology ; Bacteria/classification/isolation & purification/genetics ; Autistic Disorder/microbiology/psychology ; }, abstract = {Autism spectrum disorders (ASD) are complex human neurodiversities increasing in prevalence within the human population. In search of therapeutics to improve quality-of-life for ASD patients, the gut microbiome (GM) has become a promising target as a growing body of work supports roles for the complex community of microorganisms in influencing host behavior via the gut-brain-axis. However, whether naturally-occurring microbial diversity within the host GM affects these behaviors is often overlooked. Here, we applied a model of population-level differences in the GM to a classic ASD model - the BTBR T[+] Itpr3[tf]/J mouse - to assess how complex GMs affect host behavior. Leveraging the naturally occurring differences between supplier-origin GMs, our data demonstrate that differing, complex GMs selectively effect host ASD-related behavior - especially neonatal ultrasonic communication - and reveal a male-specific effect on behavior not typically observed in this strain. We then identified that the body weight of BTBR mice is influenced by the postnatal GM which was potentially mediated by microbiome-dependent effects on energy harvest in the gut. These data provide insight into how variability within the GM affects host behavior and growth, thereby emphasizing the need to incorporate microbial diversity within the host GM as an experimental factor in biomedical research.}, }
@article {pmid39679616, year = {2024}, author = {Seki, D and Kirkegaard, R and Osvatic, J and Hausmann, B and Séneca, J and Pjevac, P and Berger, A and J Hall, L and Wisgrill, L and Berry, D}, title = {Gut microbiota genome features associated with brain injury in extremely premature infants.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2410479}, pmid = {39679616}, issn = {1949-0984}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {*Gastrointestinal Microbiome ; Humans ; Infant, Newborn ; *Infant, Extremely Premature ; *Brain Injuries/microbiology/genetics ; *Feces/microbiology ; Female ; Male ; Bacteria/genetics/classification/isolation & purification/metabolism ; Genome, Bacterial ; Cohort Studies ; }, abstract = {Severe brain damage is common among premature infants, and the gut microbiota has been implicated in its pathology. Although the order of colonizing bacteria is well described, the mechanisms underlying aberrant assembly of the gut microbiota remain elusive. Here, we employed long-read nanopore sequencing to assess abundances of microbial species and their functional genomic potential in stool samples from a cohort of 30 extremely premature infants. We identify several key microbial traits significantly associated with severe brain damage, such as the genomic potential for nitrate respiration and iron scavenging. Members of the Enterobacteriaceae were prevalent across the cohort and displayed a versatile metabolic potential, including pathogenic and nonpathogenic traits. Predominance of Enterobacter hormaechei and Klebsiella pneumoniae were associated with an overall loss of genomic functional redundancy as well as poor neurophysiological outcome. These findings reveal microbial traits that may be involved in exacerbating brain injury in extremely premature infants and provide suitable targets for therapeutic interventions.}, }
@article {pmid39678952, year = {2024}, author = {Sinha, T and Talukdar, NC}, title = {Phylum Level Diversity of Plant Interior Bacteria in Seeds, Supernatant and Pellet Phases of Seed Suspension of Mustard Plant.}, journal = {Indian journal of microbiology}, volume = {64}, number = {4}, pages = {1587-1597}, pmid = {39678952}, issn = {0046-8991}, abstract = {Our previous study explored the bacterial endophytic diversity in a certain quantity of mustard seeds using culture dependent method by development of new isolation strategies. No bacterial colony was initially observed in supernatant obtained after centrifugation of mustard seed suspension. This was later overcome by usage of surfactant whereas pellet part showed presence of bacterial colonies on media. In our present study, presence of bacteria was examined in supernatant and whether the diversity was similar to that of pellet and seeds by culture independent approach. In addition, growth of bacterial colonies on media is explained using GC-MS. In this study, Proteobacteria was the dominant bacterial phyla followed by Firmicutes in pellet, supernatant and seed. This indicated that bacteria were present in supernatant but may not be viable when plated on media. This is either due to antimicrobial compounds or oil-imposed difficulty during their isolation which might have hindered their survival. GC-MS study revealed the presence of compounds with antimicrobial property as suggested by previous literature. Our research conducts fundamental investigations to address the primary objective of understanding the bacterial diversity in mustard seed, pellet, and supernatant. Further research using workflows of metagenomics and metabolomics approaches can enrich our understanding ofthe diversity of microorganisms in seeds.}, }
@article {pmid39676101, year = {2024}, author = {Wang, C and Zhang, C and He, S and Wang, Q and Gao, H}, title = {The microbiome alterations of supragingival plaque among adolescents using clear aligners: a metagenomic sequencing analysis.}, journal = {Progress in orthodontics}, volume = {25}, number = {1}, pages = {48}, pmid = {39676101}, issn = {2196-1042}, support = {PY2023038//Science research cultivation program of stomatological hospital, Southern medical university/ ; PY2023043//Science research cultivation program of stomatological hospital, Southern medical university/ ; B2023274//Guangdong Medical Research Fund/ ; B2022013//Guangdong Medical Research Fund/ ; }, mesh = {Humans ; Adolescent ; *Dental Plaque/microbiology ; Male ; *Microbiota ; Female ; *Biofilms ; Child ; *Capnocytophaga ; Neisseria ; Metagenomics/methods ; Virulence Factors/genetics ; }, abstract = {BACKGROUND: White spot lesions (WSLs) may develop in adolescents undergoing clear aligner (CA) therapy with poor oral hygiene. The specific effects of CAs on the microbial composition and functional characteristics of supragingival plaques remain unclear. The present study investigated the shift in the supragingival microbial community induced by CAs in adolescents through metagenomic technology.
METHODS: Fifteen adolescents (12-15 years old) with Invisalign appliances were recruited. Supragingival plaque specimens were obtained twice, before treatment (T1) and three months after treatment (T2). All the bacterial plaque specimens were analyzed for microbial communities and functions using metagenomic analyses.
RESULTS: A total of 2,840,242,722 reads disclosed 180 phyla, 3,975 genera, and 16,497 microbiome species. During the first three months, the microbial community was relatively stable. The genus level revealed a higher relative abundance of Capnocytophaga, Neisseria, and Arachnia in the T2 period. Furthermore, the functional analysis suggested that the relative abundances of folate biosynthesis, biotin metabolism and biofilm formation-vibrio cholerae were increased in the T2 period compared to the T1 period. Finally, virulence factor analysis demonstrated that the relative abundance of genes associated with type IV pili (VF0082) and polar flagella (VF0473) was higher in the T2 period than in the T1 period.
CONCLUSION: In adolescents undergoing CA therapy with poor plaque control, caries progresses quickly within three months and noticeable WSLs develop on the tooth surface. Although the microbial community remained relatively steady and CA therapy did not cause significant changes in the overall functional gene composition in the first three months, virulence factors, including type IV pili and flagella, were more abundant and actively contributed to microorganism adhesion and biofilm formation.}, }
@article {pmid39674265, year = {2024}, author = {Ravishankar, S and Perez, V and Davidson, R and Roca-Rada, X and Lan, D and Souilmi, Y and Llamas, B}, title = {Filtering out the noise: metagenomic classifiers optimize ancient DNA mapping.}, journal = {Briefings in bioinformatics}, volume = {26}, number = {1}, pages = {}, pmid = {39674265}, issn = {1477-4054}, support = {CE170100015//Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage/ ; GA204260//NHMRC SYNERGY/ ; //Australian Government Research Training Program Scholarship/ ; //Portuguese National Funds/ ; }, mesh = {*DNA, Ancient/analysis ; *Metagenomics/methods ; *Sequence Analysis, DNA/methods ; Humans ; High-Throughput Nucleotide Sequencing/methods ; Metagenome ; Workflow ; DNA Contamination ; }, abstract = {Contamination with exogenous DNA presents a significant challenge in ancient DNA (aDNA) studies of single organisms. Failure to address contamination from microbes, reagents, and present-day sources can impact the interpretation of results. Although field and laboratory protocols exist to limit contamination, there is still a need to accurately distinguish between endogenous and exogenous data computationally. Here, we propose a workflow to reduce exogenous contamination based on a metagenomic classifier. Unlike previous methods that relied exclusively on DNA sequencing reads mapping specificity to a single reference genome to remove contaminating reads, our approach uses Kraken2-based filtering before mapping to the reference genome. Using both simulated and empirical shotgun aDNA data, we show that this workflow presents a simple and efficient method that can be used in a wide range of computational environments-including personal machines. We propose strategies to build specific databases used to profile sequencing data that take into consideration available computational resources and prior knowledge about the target taxa and likely contaminants. Our workflow significantly reduces the overall computational resources required during the mapping process and reduces the total runtime by up to ~94%. The most significant impacts are observed in low endogenous samples. Importantly, contaminants that would map to the reference are filtered out using our strategy, reducing false positive alignments. We also show that our method results in a negligible loss of endogenous data with no measurable impact on downstream population genetics analyses.}, }
@article {pmid39673707, year = {2024}, author = {Huang, KD and Müller, M and Sivapornnukul, P and Bielecka, AA and Amend, L and Tawk, C and Lesker, TR and Hahn, A and Strowig, T}, title = {Dietary selective effects manifest in the human gut microbiota from species composition to strain genetic makeup.}, journal = {Cell reports}, volume = {43}, number = {12}, pages = {115067}, doi = {10.1016/j.celrep.2024.115067}, pmid = {39673707}, issn = {2211-1247}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Diet ; Adult ; Male ; Bacteria/genetics/classification ; Female ; Genetic Variation ; Middle Aged ; }, abstract = {Diet significantly influences the human gut microbiota, a key player in health. We analyzed shotgun metagenomic sequencing data from healthy individuals with long-term dietary patterns-vegan, flexitarian, or omnivore-and included detailed dietary surveys and blood biomarkers. Dietary patterns notably affected the bacterial community composition by altering the relative abundances of certain species but had a minimal impact on microbial functional repertoires. However, diet influenced microbial functionality at the strain level, with diet type linked to strain genetic variations. We also found molecular signatures of selective pressure in species enriched by specific diets. Notably, species enriched in omnivores exhibited stronger positive selection, such as multiple iron-regulating genes in the meat-favoring bacterium Odoribacter splanchnicus, an effect that was also validated in independent cohorts. Our findings offer insights into how diet shapes species and genetic diversity in the human gut microbiota.}, }
@article {pmid39671861, year = {2025}, author = {Buzzanca, D and Giordano, M and Chiarini, E and Ferrocino, I and Cocolin, L and Zeppa, G and Alessandria, V}, title = {Delving into Roccaverano PDO cheese: A comprehensive examination of microbial diversity and flavour profiles compared to non-PDO cheeses.}, journal = {International journal of food microbiology}, volume = {429}, number = {}, pages = {111014}, doi = {10.1016/j.ijfoodmicro.2024.111014}, pmid = {39671861}, issn = {1879-3460}, mesh = {*Cheese/microbiology ; *Volatile Organic Compounds/analysis ; *Taste ; Italy ; *Microbiota ; Humans ; Food Microbiology ; Flavoring Agents/analysis ; Bacteria/classification/isolation & purification/genetics ; Fungi/isolation & purification/classification/genetics ; Odorants/analysis ; Gas Chromatography-Mass Spectrometry ; }, abstract = {Roccaverano Protected Designation of Origin (PDO) is a fresh soft cheese produced in Roccaverano area (Italy). This study aimed to evaluate Roccaverano PDO microbiota, together with aromatic profile and sensory analysis to be compared with 15 non-PDO cheeses of the same type. Microbiota was evaluated through shotgun metagenomics sequencing, while GC-MS analysis was conducted to study volatile organic compounds (VOCs) presence and concentration. Sensory analyses were conducted through ONAF (Italian National Organization of Cheese Tasters) evaluation parameters followed by flash profile sensory analysis of selected cheeses. The results demonstrated Lactococcus lactis predominance in both non-PDO and PDO cheeses, while Streptococcus thermophilus was more abundant in non-PDO group. A higher abundance of Kluyveromyces lactis was observed in Roccaverano PDO, which exhibited greater fungal diversity compared to non-PDO cheeses. Metagenome-Assembled Genomes of 26 L. lactis and 19 Leuconostoc mesenteroides showed absence of significant differences in terms of average nucleotide identity and pangenomes partitions. The ONAF sensory evaluation demonstrated a higher average score of Roccaverano PDO group. Flash profile analysis demonstrated that lactic aroma/odour, acid, astringent, vegetal odour, exotic fruit and fermented aroma, hazelnut flavour and sweet were associated with high ONAF scores. The concentration of butanoic acid, 2-methyl-, ethyl ester and butanoic acid, 3-methyl- (sweat, acid, rancid related) were higher in PDO cheeses, while reads related to butanoate metabolism were less abundant compared to non-PDO samples. Several fungal species (included K. lactis) were associated with astringents, acid and chalky flavours. Roccaverano PDO demonstrates unique characteristics even maintaining a certain degree of variability between samples.}, }
@article {pmid39669269, year = {2024}, author = {Lee, KH and Kim, YO and Dho, SH and Yong, JJH and Oh, HS and Lee, JH and Yang, SJ and Cha, I and Chun, J and Lee, EH and Jeong, SJ and Woo, W and Choi, JP and Han, SH and Choi, GB and Huh, JR and Kim, LK and Song, YG}, title = {Altered gut microbiome in convalescent patients with coronavirus disease 2019.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1455295}, pmid = {39669269}, issn = {2235-2988}, mesh = {Humans ; *COVID-19/microbiology ; *Gastrointestinal Microbiome ; Male ; Female ; *Feces/microbiology/virology ; Middle Aged ; Prospective Studies ; *SARS-CoV-2/isolation & purification ; Longitudinal Studies ; *RNA, Ribosomal, 16S/genetics ; Adult ; Severity of Illness Index ; Convalescence ; Bacteria/classification/isolation & purification/genetics ; Aged ; }, abstract = {INTRODUCTION: Coronavirus disease 2019 (COVID-19) alters the gut microbiome. This study aimed to assess the association between the disease severity of COVID-19 and changes in stool microbes through a seven-month follow-up of stool collection.
METHODS: We conducted a multicentre, prospective longitudinal study of 58 COVID-19 patients and 116 uninfected controls. Differences in the gut microbiota were analysed using 16S ribosomal RNA sequencing. The first stool samples were collected at an early convalescent phase of COVID-19, and the second sample was collected at least seven months after COVID-19 infection.
RESULTS AND DISCUSSION: At the order level, Eubacteriales and Bifidobacteriales decreased, while Bacteroidales and Burkholderiales increased in the COVID-19 group compared to the controls. Alpha diversity also decreased in COVID-19 patients compared to controls, with imperfect recovery of the gut microbiome after seven months. The compositional change in the gut microbiome between the early and late convalescent phases was largest in the moderate and severe groups. The severity of COVID-19 was the most influential clinical variable for microbiome composition (Sum of Sqs = 0.686, P = 0.006), and its effect persisted even after partialling out other effects such as antibiotic use and age. Thus, our study indicates a possible interaction between respiratory viral infection and the composition of the gut microbiota community, warranting future mechanistic and prospective longitudinal studies. Additionally, we were able to detect microbiome changes in patients who were re-infected with SARS-CoV-2. Notably, the dominant bacteria in the re-infected group were Lachnospiraceae and Faecalimonas umbilicata, compared to the one-time infected group.}, }
@article {pmid39660920, year = {2025}, author = {Zavarzina, DG and Maslov, AA and Merkel, AY and Kharitonova, NA and Klyukina, AA and Baranovskaya, EI and Baydariko, EA and Potapov, EG and Zayulina, KS and Bychkov, AY and Chernyh, NA and Bonch-Osmolovskaya, EA and Gavrilov, SN}, title = {Analogs of Precambrian microbial communities formed de novo in Caucasian mineral water aquifers.}, journal = {mBio}, volume = {16}, number = {1}, pages = {e0283124}, pmid = {39660920}, issn = {2150-7511}, mesh = {*Groundwater/microbiology/chemistry ; *Mineral Waters/microbiology ; *Bacteria/genetics/classification/metabolism/isolation & purification ; Microbiota ; Archaea/genetics/classification/metabolism ; Phylogeny ; Metagenomics ; }, abstract = {The microbiome of deep continental aquifers is considered the most slowly evolving part of the biosphere. The Yessentukskoye Mineral Water Basin (YMWB), located in the pre-Caucasus region, contains three closely spaced but distinct aquifers, the Upper Cretaceous, the Lower Cretaceous, and the Upper Jurassic, which represent unique objects for subsurface biosphere research due to gas-hydrogeochemical and thermal anomalies of the area. We analyzed the geological and hydrogeochemical parameters of the three aquifers and a recharge area of the YMWB and investigated their microbial communities using metagenomic and cultivation-based approaches within a long-term survey. Correlation analysis of the obtained data revealed stable and highly stratified microbial communities inhabiting four distinct ecosystems. Their structure and the metabolic traits of their prokaryotic populations were similar to those presumed to have dominated the Earth's biosphere during several critical periods of its evolutionary history, that is, the Early Archean, the period of banded iron formations accumulation, and the Great Oxidation Event. Among the YMWB strata, the Upper Jurassic aquifer, supersaturated with CO2, influenced by magmatic activity, and highly enriched with thermophilic autotrophic hydrogenotrophic acetogens, turned out to be the first described modern ecosystem based on the primary production by a process predicted to support the Last Universal Common Ancestor (LUCA). The characterization of the YMWB microbial communities reveals a contemporary model environment of the early stages of Earth's development and thus contributes to the understanding of the evolutionary traits in microbial populations that may have played a critical role in the formation of the modern biosphere.IMPORTANCEContinental subsurface environments are estimated to harbor up to one-fifth of the planet's total biomass, representing the most stable and slowly evolving part of the biosphere. Among the deep subsurface inhabitants, the microbial communities of drinking mineral waters remain the least studied. Our interdisciplinary study of the Yessentukskoye Mineral Water Basin shows how hydrochemical and hydrodynamic factors shape different subsurface ecosystems, whose microbial populations influence the composition of mineral waters. A comprehensive analysis reveals the similarity of these ecosystems to those predicted for the early Earth. The deepest of the studied aquifers is the first described modern ecosystem with the most probable primary producer performing hydrogenotrophic acetogenesis. Thus, our results contribute to the understanding of the genesis of modern drinking water resources and expand the knowledge of the evolutionary traits that may have played a critical role in the formation of the Earth's biosphere.}, }
@article {pmid39660898, year = {2025}, author = {Su, G and Huang, P and Liu, D and Xing, G and Guo, R and Li, S and Fan, S and Cheng, L and Yan, Q and Yang, W}, title = {Gut mycobiome alterations and network interactions with the bacteriome in patients with atherosclerotic cardiovascular disease.}, journal = {Microbiology spectrum}, volume = {13}, number = {1}, pages = {e0218224}, pmid = {39660898}, issn = {2165-0497}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Mycobiome ; Male ; Female ; *Bacteria/classification/genetics/isolation & purification ; Middle Aged ; *Fungi/classification/genetics/isolation & purification ; Aged ; *Atherosclerosis/microbiology ; Cardiovascular Diseases/microbiology ; Metagenomics ; Feces/microbiology ; }, abstract = {The connection between the gut mycobiome and atherosclerotic cardiovascular disease (ACVD) is largely uncharted. In our study, we compared the gut fungal communities of 214 ACVD patients with those of 171 healthy controls using shotgun metagenomic sequencing and examined their interactions with gut bacterial communities and network key taxa. The gut mycobiome composition in ACVD patients is significantly different, showing a rise in opportunistic pathogens like Candida albicans, Exophiala spinifera, and Malassezia restricta, with Exophiala and Malassezia showing the most significant changes (Wilcoxon rank-sum test, P < 0.001, fold change >10). Network analysis revealed a less interconnected and more uneven gut microbial network in ACVD patients. Network key taxa identified in the ACVD gut microbiome network include Malassezia globosa c182, Nakaseomyces glabratus c88, Malassezia arunalokei c192, and Penicillium sumatraense c22. Predictive models that integrated both bacterial and fungal taxa enhanced prediction accuracy, underscoring the critical role of gut fungi in ACVD. Our findings offer a thorough understanding of the link between the gut mycobiome and ACVD progression, which is vital for directing future therapeutic research.IMPORTANCEACVD is a leading cause of death and morbidity worldwide. While the role of the gut microbiome in ACVD development is recognized, the contribution of the gut mycobiome remains largely unexplored. Our study reveals significant alterations in the gut mycobiome of ACVD patients and identifies key fungal taxa associated with the disease. These findings underscore the importance of the gut mycobiome in the pathogenesis of ACVD and offer new avenues for developing preventive and therapeutic strategies targeting the gut fungal community. Our results provide valuable insights into the complex interplay between gut fungi and bacteria in ACVD, paving the way for novel therapeutic approaches.}, }
@article {pmid39660058, year = {2024}, author = {Boer, MD and Melkonian, C and Zafeiropoulos, H and Haas, AF and Garza, DR and Dutilh, BE}, title = {Improving genome-scale metabolic models of incomplete genomes with deep learning.}, journal = {iScience}, volume = {27}, number = {12}, pages = {111349}, pmid = {39660058}, issn = {2589-0042}, abstract = {Deciphering microbial metabolism is essential for understanding ecosystem functions. Genome-scale metabolic models (GSMMs) predict metabolic traits from genomic data, but constructing GSMMs for uncultured bacteria is challenging due to incomplete metagenome-assembled genomes, resulting in many gaps. We introduce the deep neural network guided imputation of reactomes (DNNGIOR), which uses AI to improve gap-filling by learning from the presence and absence of metabolic reactions across diverse bacterial genomes. Key factors for prediction accuracy are: (1) reaction frequency across all bacteria and (2) phylogenetic distance of the query to the training genomes. DNNGIOR predictions achieve an average F1 score of 0.85 for reactions present in over 30% of training genomes. DNNGIOR guided gap-filling was 14 times more accurate for draft reconstructions and 2-9 times for curated models than unweighted gap-filling.}, }
@article {pmid39658189, year = {2024}, author = {Dufault-Thompson, K and Levy, S and Hall, B and Jiang, X}, title = {Bilirubin reductase shows host-specific associations in animal large intestines.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, pmid = {39658189}, issn = {1751-7370}, mesh = {Animals ; *Phylogeny ; *Gastrointestinal Microbiome ; *Intestine, Large/microbiology ; *Oxidoreductases Acting on CH-CH Group Donors/genetics/metabolism ; Bilirubin/metabolism ; Heme/metabolism ; Bacteria/genetics/classification/isolation & purification/enzymology ; Metagenomics ; }, abstract = {Animal gastrointestinal tracts contain diverse metabolites, including various host-derived compounds that gut-associated microbes interact with. Here, we explore the diversity and evolution of bilirubin reductase, a bacterial enzyme that metabolizes the host-derived tetrapyrrole bilirubin, performing a key role in the animal heme degradation pathway. Through an analysis of the bilirubin reductase phylogeny and predicted structures, we found that the enzyme family can be divided into three distinct clades with different structural features. Using these clade definitions, we analyzed metagenomic sequencing data from multiple animal species, finding that bilirubin reductase is significantly enriched in the large intestines of animals and that the clades exhibit differences in distribution among animals. Combined with phylogenetic signal analysis, we find that the bilirubin reductase clades exhibit significant associations with specific animals and animal physiological traits like gastrointestinal anatomy and diet. These patterns demonstrate that bilirubin reductase is specifically adapted to the anoxic lower gut environment of animals and that its evolutionary history is complex, involving adaptation to a diverse collection of animals harboring bilirubin-reducing microbes. The findings suggest that bilirubin reductase evolution has been shaped by the host environment, providing a new perspective on heme metabolism in animals and highlighting the importance of the microbiome in animal physiology and evolution.}, }
@article {pmid39657789, year = {2025}, author = {Zdouc, MM and Blin, K and Louwen, NLL and Navarro, J and Loureiro, C and Bader, CD and Bailey, CB and Barra, L and Booth, TJ and Bozhüyük, KAJ and Cediel-Becerra, JDD and Charlop-Powers, Z and Chevrette, MG and Chooi, YH and D'Agostino, PM and de Rond, T and Del Pup, E and Duncan, KR and Gu, W and Hanif, N and Helfrich, EJN and Jenner, M and Katsuyama, Y and Korenskaia, A and Krug, D and Libis, V and Lund, GA and Mantri, S and Morgan, KD and Owen, C and Phan, CS and Philmus, B and Reitz, ZL and Robinson, SL and Singh, KS and Teufel, R and Tong, Y and Tugizimana, F and Ulanova, D and Winter, JM and Aguilar, C and Akiyama, DY and Al-Salihi, SAA and Alanjary, M and Alberti, F and Aleti, G and Alharthi, SA and Rojo, MYA and Arishi, AA and Augustijn, HE and Avalon, NE and Avelar-Rivas, JA and Axt, KK and Barbieri, HB and Barbosa, JCJ and Barboza Segato, LG and Barrett, SE and Baunach, M and Beemelmanns, C and Beqaj, D and Berger, T and Bernaldo-Agüero, J and Bettenbühl, SM and Bielinski, VA and Biermann, F and Borges, RM and Borriss, R and Breitenbach, M and Bretscher, KM and Brigham, MW and Buedenbender, L and Bulcock, BW and Cano-Prieto, C and Capela, J and Carrion, VJ and Carter, RS and Castelo-Branco, R and Castro-Falcón, G and Chagas, FO and Charria-Girón, E and Chaudhri, AA and Chaudhry, V and Choi, H and Choi, Y and Choupannejad, R and Chromy, J and Donahey, MSC and Collemare, J and Connolly, JA and Creamer, KE and Crüsemann, M and Cruz, AA and Cumsille, A and Dallery, JF and Damas-Ramos, LC and Damiani, T and de Kruijff, M and Martín, BD and Sala, GD and Dillen, J and Doering, DT and Dommaraju, SR and Durusu, S and Egbert, S and Ellerhorst, M and Faussurier, B and Fetter, A and Feuermann, M and Fewer, DP and Foldi, J and Frediansyah, A and Garza, EA and Gavriilidou, A and Gentile, A and Gerke, J and Gerstmans, H and Gomez-Escribano, JP and González-Salazar, LA and Grayson, NE and Greco, C and Gomez, JEG and Guerra, S and Flores, SG and Gurevich, A and Gutiérrez-García, K and Hart, L and Haslinger, K and He, B and Hebra, T and Hemmann, JL and Hindra, H and Höing, L and Holland, DC and Holme, JE and Horch, T and Hrab, P and Hu, J and Huynh, TH and Hwang, JY and Iacovelli, R and Iftime, D and Iorio, M and Jayachandran, S and Jeong, E and Jing, J and Jung, JJ and Kakumu, Y and Kalkreuter, E and Kang, KB and Kang, S and Kim, W and Kim, GJ and Kim, H and Kim, HU and Klapper, M and Koetsier, RA and Kollten, C and Kovács, ÁT and Kriukova, Y and Kubach, N and Kunjapur, AM and Kushnareva, AK and Kust, A and Lamber, J and Larralde, M and Larsen, NJ and Launay, AP and Le, NT and Lebeer, S and Lee, BT and Lee, K and Lev, KL and Li, SM and Li, YX and Licona-Cassani, C and Lien, A and Liu, J and Lopez, JAV and Machushynets, NV and Macias, MI and Mahmud, T and Maleckis, M and Martinez-Martinez, AM and Mast, Y and Maximo, MF and McBride, CM and McLellan, RM and Bhatt, KM and Melkonian, C and Merrild, A and Metsä-Ketelä, M and Mitchell, DA and Müller, AV and Nguyen, GS and Nguyen, HT and Niedermeyer, THJ and O'Hare, JH and Ossowicki, A and Ostash, BO and Otani, H and Padva, L and Paliyal, S and Pan, X and Panghal, M and Parade, DS and Park, J and Parra, J and Rubio, MP and Pham, HT and Pidot, SJ and Piel, J and Pourmohsenin, B and Rakhmanov, M and Ramesh, S and Rasmussen, MH and Rego, A and Reher, R and Rice, AJ and Rigolet, A and Romero-Otero, A and Rosas-Becerra, LR and Rosiles, PY and Rutz, A and Ryu, B and Sahadeo, LA and Saldanha, M and Salvi, L and Sánchez-Carvajal, E and Santos-Medellin, C and Sbaraini, N and Schoellhorn, SM and Schumm, C and Sehnal, L and Selem, N and Shah, AD and Shishido, TK and Sieber, S and Silviani, V and Singh, G and Singh, H and Sokolova, N and Sonnenschein, EC and Sosio, M and Sowa, ST and Steffen, K and Stegmann, E and Streiff, AB and Strüder, A and Surup, F and Svenningsen, T and Sweeney, D and Szenei, J and Tagirdzhanov, A and Tan, B and Tarnowski, MJ and Terlouw, BR and Rey, T and Thome, NU and Torres Ortega, LR and Tørring, T and Trindade, M and Truman, AW and Tvilum, M and Udwary, DW and Ulbricht, C and Vader, L and van Wezel, GP and Walmsley, M and Warnasinghe, R and Weddeling, HG and Weir, ANM and Williams, K and Williams, SE and Witte, TE and Rocca, SMW and Yamada, K and Yang, D and Yang, D and Yu, J and Zhou, Z and Ziemert, N and Zimmer, L and Zimmermann, A and Zimmermann, C and van der Hooft, JJJ and Linington, RG and Weber, T and Medema, MH}, title = {MIBiG 4.0: advancing biosynthetic gene cluster curation through global collaboration.}, journal = {Nucleic acids research}, volume = {53}, number = {D1}, pages = {D678-D690}, pmid = {39657789}, issn = {1362-4962}, support = {//Conahcyt Mexico International PhD Studentship/ ; 32170080//National Natural Science Foundation of China/ ; 547394769//German Research Foundation/ ; 101066127//European Union/ ; NNF19SA0059360//Novo Nordisk Foundation INTERACT/ ; //Swedish Pharmaceutical Society PostDoc/ ; F32AT011475/AT/NCCIH NIH HHS/United States ; //Werner Siemens Foundation/ ; 027/E5/PG.02.00.PL/2024//Ministry of Education/ ; ANR-17-EUR-0007//EUR Saclay Plant Sciences-SPS/ ; PROYEXCEL_00012//Spanish "Junta de Andalucía"/ ; 1347411//CONAHCYT/ ; IM230100154//Australian Research Council Industry Fellowship/ ; 1229222N//Research Foundation-Flanders (FWO)/ ; R01 GM146224/GM/NIGMS NIH HHS/United States ; //Swiss Federal Government/ ; OSF.23.1.044//NWO Open Science Project 'BiG-CODEC'/ ; //NWO Merian/ ; 024.004.014//MiCRop Consortium/ ; CZIF2022-007203//Chan Zuckerberg Initiative Foundation/ ; BB/T007222/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; DP230102668//Australian Research Council Discovery Project/ ; 57/0009//Ministry of Education and Science of Ukraine/ ; //Delta Stewardship Council Delta Science Program/ ; T32 GM136629/GM/NIGMS NIH HHS/United States ; //Basic Science Research Program/ ; R01-GM146224/GM/NIGMS NIH HHS/United States ; K12 GM068524/GM/NIGMS NIH HHS/United States ; AUFF-E-2022-9-42//AUFF/ ; 10062709//UK Innovation Funding Agency (UKRI)/ ; CBET-2032243//U.S. National Science Foundation/ ; //University of Illinois/ ; //HZI POF IV Cooperativity and Creativity Project Call/ ; //Horizon Europe Marie Skłodowska-Curie Actions Postdoctoral Fellowship/ ; NE/T010959/1//Signals in the Soil/ ; ANR-24-CE20-7299-01//Agence Nationale de la Recherche/ ; DNRF137//Danish National Research Foundation/ ; OCENW.GROOT.2019.063//NWO-XL/ ; BB/V005723/2//BBSRC/ ; 101087181//EU/ ; 101000392//Horizon 2020/ ; 101072485//European Union's Horizon/ ; 10.55776/P 34036//Austrian Science Fund/ ; EP/X03142X/1//United Kingdom Research and Innovation/ ; 23/01956-2//São Paulo Research Foundation/ ; //Department of Biotechnology/ ; 222676//USDA Evans-Allen Research/ ; //Saarland University/ ; 102022750//SINTEF/ ; //Hans Fischer Society/ ; 21K06336//KAKENHI/ ; CF22-1239//Carlsberg Foundation/ ; ANR-22-CE44-0011-01 UMISYN//Agence Nationale de la Recherche/ ; 495740318//German Research Foundation/ ; 802736//European Union Horizon 2020/ ; //Strathclyde University Global Research Scholarship/ ; NNF22OC0079021//Novo Nordisk Foundation Postdoctoral Fellowship/ ; 101055020-COMMUNITY//ERC Advanced/ ; 101099528//European Innovation Council/ ; GNT2021638//National Health and Medical Research Council/ ; 757173//Consejo Nacional de Ciencia y Tecnología/ ; NA22NOS4200050//NERRS/ ; 865738/ERC_/European Research Council/International ; DGE 2241144//NSF GRFP/ ; //National Research Fund of Ukraine/ ; RYC2020-029240-I//Ministerio de Ciencia, Innovación y Universidades/ ; MR/V022334/1//UKRI Future Leaders Fellowship/ ; 102029187//SEP AGREE/ ; NNF22OC0078997//Novo Nodisk Foundation/ ; F31 ES036421/ES/NIEHS NIH HHS/United States ; KICH1.LWV04.21.013//NWO/ ; DM60066//Italian Ministry of Research/ ; 101117891-MeDiSyn//ERC Starting/ ; //European Union's Horizon 2020 Research/ ; NRF 2018R1A5A2023127//Korea Government (MSIT)/ ; PS00349981//Fulbright/ ; NRF-2020R1A6A1A03044512//Korean Government (MSIT)/ ; 735867//Consejo Nacional de Ciencia y Tecnología/ ; 3141-00013A//Innovation Fund Denmark/ ; CFB 2.0//Novo Nordisk Foundation/ ; 21/07038-0//São Paulo Research Foundation/ ; 2021YFA0909500//National Key Research and Development Program of China/ ; 101072485//European Union's Horizon Europe/ ; OCENW.XL21.XL21.088//NWO-XL/ ; //University Grants Commission/ ; //Natural Science and Research Council of Canada/ ; TTU 09.826//German Center for Infection Research/ ; //European Regional Development Fund/ ; 101072485//Horizon Europe Marie Skłodowska-Curie/ ; DNRF137//Danish National Research Foundation CeMiSt/ ; BB/X010953/1//Growing Health Institute Strategic Programme/ ; BB/X01097X/1//BBSRC Institute Strategic Program/ ; 802736//European Union's Horizon 2020/ ; //Alexander von Humboldt-Stiftung/ ; //UK Government Department for Environment, Food & Rural Affairs (DEFRA) Global Centre on Biodiversity for the Climate/ ; //Shanghai Pilot Program for Basic Research - Shanghai Jiao Tong University/ ; 102024676-14//POS BIOINFO 2024/ ; MR/W011247/1//UKRI Future Leaders Fellowship/ ; DGE 21-46756//National Science Foundation Graduate Research Fellowship/ ; 101106349//Marie Sklodowska-Curie/ ; T32-GM136629//Chemical-Biology Interface Training/ ; //University of Sydney/ ; 101000794//SECRETed EU Project Horizon 2020/ ; 2022R1C1C2004118//National Research Foundation of Korea/ ; //Indonesia Endowment Fund for Education Agency (LPDP)/ ; 101130799//European Union's Horizon/ ; 852600//Innovation Program ERC St/ ; //National Agri-Food Biotechnology Institute/ ; //German Academic Scholarship Foundation/ ; 205320_219638/SNSF_/Swiss National Science Foundation/Switzerland ; EXC-2124/1-09.029_0//Cluster of Excellence: Controlling Microbes to Fight Infection/ ; F32 AT011475/AT/NCCIH NIH HHS/United States ; 398967434-TRR 261//Deutsche Forschungsgemeinschaft/ ; 212747/SNSF_/Swiss National Science Foundation/Switzerland ; K445/2022//Leibniz Association/ ; NRF-RS-2024-00352229//Ministry of Science and ICT/ ; //Natural Sciences and Engineering Research Council of Canada Discovery/ ; VI.Veni.202.130//NWO Talent/ ; 106/IV/KS/11/2023//National Research and Innovation Agency/ ; T32GM136583/NH/NIH HHS/United States ; DE-AC02-05CH11231//U.S. Department of Energy/ ; }, mesh = {*Multigene Family ; *Databases, Genetic ; Biosynthetic Pathways/genetics ; Molecular Sequence Annotation ; Biological Products/metabolism/chemistry ; Data Curation ; }, abstract = {Specialized or secondary metabolites are small molecules of biological origin, often showing potent biological activities with applications in agriculture, engineering and medicine. Usually, the biosynthesis of these natural products is governed by sets of co-regulated and physically clustered genes known as biosynthetic gene clusters (BGCs). To share information about BGCs in a standardized and machine-readable way, the Minimum Information about a Biosynthetic Gene cluster (MIBiG) data standard and repository was initiated in 2015. Since its conception, MIBiG has been regularly updated to expand data coverage and remain up to date with innovations in natural product research. Here, we describe MIBiG version 4.0, an extensive update to the data repository and the underlying data standard. In a massive community annotation effort, 267 contributors performed 8304 edits, creating 557 new entries and modifying 590 existing entries, resulting in a new total of 3059 curated entries in MIBiG. Particular attention was paid to ensuring high data quality, with automated data validation using a newly developed custom submission portal prototype, paired with a novel peer-reviewing model. MIBiG 4.0 also takes steps towards a rolling release model and a broader involvement of the scientific community. MIBiG 4.0 is accessible online at https://mibig.secondarymetabolites.org/.}, }
@article {pmid39654977, year = {2024}, author = {Wu, J and Wang, D and He, WJ and Li, JY and Mo, X and Li, YJ}, title = {Allergen-specific sublingual immunotherapy altered gut microbiota in patients with allergic rhinitis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1454333}, pmid = {39654977}, issn = {2235-2988}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Sublingual Immunotherapy/methods ; *Rhinitis, Allergic/therapy/microbiology/immunology ; Male ; Female ; Adult ; *Feces/microbiology ; Allergens/immunology ; Young Adult ; Animals ; Middle Aged ; Antigens, Dermatophagoides/immunology ; Dermatophagoides farinae/immunology ; Treatment Outcome ; Adolescent ; Metagenomics/methods ; }, abstract = {INTRODUCTION: Allergen-specific immunotherapy (AIT) induces long-term immune tolerance to allergens and is effective for treating allergic rhinitis (AR). However, the impact of sublingual immunotherapy (SLIT) on gut microbiota from AR patients and its correlation with treatment efficacy remains unclear.
METHODS: In the present study, we enrolled 24 AR patients sensitized to Dermatophagoides farinae (Der-f) and 6 healthy donors (HD). All AR patients received SLIT treatment using standardized Der-f drops. Stool samples were collected from AR patients before treatment, and 1- and 3-months post-treatment, as well as from HD, for metagenomic sequencing analysis.
RESULTS: AR patients had significantly lower richness and diversity in gut microbiota compared to HD, with notable alterations in composition and function. Besides, three months post-SLIT treatment, significant changes in gut microbiota composition at the genus and species levels were observed in AR patients. Streptococcus parasanguinis_B and Streptococcus parasanguinis, which were significantly lower in AR patients compared to HD, increased notably after three months of treatment. LEfSe analysis identified these species as markers distinguishing HD from AR patients and AR patients pre- from post-SLIT treatment. Furthermore, changes in the relative abundance of S. parasanguinis_B were negatively correlated with changes in VAS scores but positively correlated with changes in RCAT scores, suggesting a positive correlation with effective SLIT treatment.
DISCUSSION: SLIT treatment significantly alters the gut microbiota of AR patients, with S. parasanguinis_B potentially linked to its effectiveness. This study offers insights into SLIT mechanisms and suggests that specific strains may serve as biomarkers for predicting SLIT efficacy and as modulators for improving SLIT efficacy.}, }
@article {pmid39654975, year = {2024}, author = {Jarmukhanov, Z and Mukhanbetzhanov, N and Vinogradova, E and Kozhakhmetov, S and Kushugulova, A}, title = {Gut metagenomic features of frailty.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1486579}, pmid = {39654975}, issn = {2235-2988}, mesh = {*Gastrointestinal Microbiome/genetics ; Humans ; *Frailty/microbiology/metabolism ; Male ; Female ; Aged ; Middle Aged ; *Feces/microbiology ; *Metagenomics/methods ; Kazakhstan ; Adult ; Metagenome ; Bacteria/classification/genetics/isolation & purification/metabolism ; Aged, 80 and over ; Metabolic Networks and Pathways/genetics ; }, abstract = {This study investigates the relationship between frailty severity and gut microbiome characteristics in adults in Kazakhstan. We analyzed 158 participants across four frailty severity (mild to very severe) using metagenomic sequencing of stool samples. Frailty was significantly correlated with age, weight, and functional measures like walking speed and grip strength. Microbial diversity decreased significantly with increasing frailty. Beta diversity analysis revealed distinct clustering patterns based at phylum level. Taxonomically, we observed a significant inverse correlation between Firmicutes abundance and frailty. Classes like Clostridia and Erysipelotrichia decreased with frailty, while Bacteroidia and Actinobacteria increased. At the family level, Oscillospiraceae showed a positive correlation with frailty. Functionally, we identified significant correlations between frailty measures and specific metabolic pathways. The frailty index negatively correlated with pathways involved in cobalamin, arginine and molybdenum cofactor biosynthesis and positively correlated with folate biosynthesis. Physical performance measures strongly correlated with pathways related to nucleotide biosynthesis, and one-carbon metabolism. We propose these identified features may constitute a "frailty-associated metabolic signature" in the gut microbiome. This signature suggests multiple interconnected mechanisms through which the microbiome may influence frailty development, including modulation of inflammation, alterations in energy metabolism, and potential impacts on muscle function through microbial metabolites.}, }
@article {pmid39653697, year = {2024}, author = {Palladino, G and Nanetti, E and Scicchitano, D and Cinti, N and Foresto, L and Cozzi, A and Gonzalez Vara Rodriguez, A and Interino, N and Fiori, J and Turroni, S and Candela, M and Rampelli, S}, title = {Zonation of the Vitis vinifera microbiome in Vino Nobile di Montepulciano PDO production area.}, journal = {Communications biology}, volume = {7}, number = {1}, pages = {1626}, pmid = {39653697}, issn = {2399-3642}, support = {818290//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; }, mesh = {*Vitis/microbiology ; *Microbiota/genetics ; Italy ; *Wine/microbiology ; Soil Microbiology ; Bacteria/genetics/classification/metabolism/isolation & purification ; Fungi/genetics/classification/metabolism ; Rhizosphere ; }, abstract = {The microbial dimension of the terroir is crucial for wine quality, as microbiomes contribute to plant biofertilization, stress tolerance and pathogen suppression. While microbial terroir can act as a biological signature at large scale, data for local contexts is lacking, hindering the characterization of regional microbial diversity in vineyards. Here, we define the microbial terroir of vineyards across the 12 sub-areas (Additional Geographic Units -AGUs) of the "Consorzio del Vino Nobile di Montepulciano DOCG" PDO area (Italy), a world-renowned wine-producing region. Rhizospheres of Vitis vinifera cultivar Sangiovese and soil samples were collected throughout the 2022 viticultural season and analyzed through an integrated metabarcoding/shotgun metagenomic approach, targeting bacteria and fungi. Wine metabolomics was also perfomed, projecting compositional and functional variations of the microbial terroir at the AGUs level into a corresponding variation in the product metabolic profile. Our findings reveal a unique taxonomic configuration of the Vino Nobile di Montepulciano terroir compared to other vineyards, with microbiomes being "AGU-specific" in taxonomic abundances and plant growth-promoting functions, confirming the potential relevance of characterizing and preserving the microbial terroir to safeguard high-quality traditional wines.}, }
@article {pmid39653684, year = {2024}, author = {Chen, Y and Yang, C and Deng, Z and Xiang, T and Tan, J and Xu, J and Sun, D and Luo, F}, title = {Alterations of gut virome with close interaction in the progression of estrogen deficiency-induced osteoporosis.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2437250}, pmid = {39653684}, issn = {1949-0984}, mesh = {*Gastrointestinal Microbiome ; Animals ; Female ; *Virome ; Mice ; *Osteoporosis/virology ; Humans ; *Estrogens/metabolism ; Ovariectomy ; Bacteria/classification/genetics/isolation & purification/metabolism ; Mice, Inbred C57BL ; Disease Models, Animal ; Disease Progression ; }, abstract = {Previous research has established a link between gut microbiota and osteoporosis (OP) advancement. However, there remains a limited understanding of the crucial contribution of the gut virome in the onset and progression of OP. We employed metagenomic shotgun sequencing and gut virome sequencing to process the ovariectomy (OVX)-induced OP murine model, which revealed significant disparities in bacteriome and virome compositions between subjects with OP and healthy controls. One hundred and seventy-four altered viral strains were identified to participate in the multifaceted regulation of bone loss, involving immune modulation, microbial metabolic activity, and intricate host-virus dynamics. Our findings suggested that the gut virome may influence bone metabolism, potentially altering the balance of bone-modulating compounds like short-chain fatty acids. This comprehensive analysis of the gut virome in OP highlighted the diagnostic potential of combined gut viral and bacterial biomarkers for OP.}, }
@article {pmid39648978, year = {2025}, author = {Ribero, MN and Schiaffino, MR and Filloy, J}, title = {Grassland Afforestation Drives Biotic Homogenisation of Soil Microbial Communities at a Regional Scale.}, journal = {Molecular ecology}, volume = {34}, number = {2}, pages = {e17617}, doi = {10.1111/mec.17617}, pmid = {39648978}, issn = {1365-294X}, support = {2018//Secretaría de Ciencia y Técnica, Universidad de Buenos Aires/ ; //Neotropical Grassland Conservancy/ ; PICT 2017//Agencia Nacional de Promoción Científica y Tecnológica/ ; //Consejo Nacional de Investigaciones Científicas y Técnicas/ ; }, mesh = {*Soil Microbiology ; *Grassland ; *Biodiversity ; Argentina ; *Microbiota/genetics ; *Fungi/genetics/classification ; Bacteria/genetics/classification ; RNA, Ribosomal, 16S/genetics ; Soil/chemistry ; }, abstract = {Grassland afforestation poses a threat to biodiversity beyond land-use conversion. Diversity patterns are shaped by temporal dynamics, particularly, time since afforestation can decline beta diversity and lead to biotic homogenisation. Our study examines the effect of grassland afforestation on soil prokaryotic and fungal beta diversity. We evaluate the contributions of colonisation and extinction processes to beta diversity, as well as the replacement of endemic species by ubiquitous ones. Along a 200 km climatic gradient in Argentina's Pampas region, we analysed grasslands and mature eucalypt plantations at different times since afforestation. Soil samples were collected at each site and analysed using 16S (V3-V4) and ITS2 amplicon sequencing to identify prokaryotic and fungal communities, respectively. The analyses revealed biotic homogenisation at the transition from grassland to newly planted stands, evidenced by a decrease in intratreatment beta diversity. Increasing time since afforestation did not exacerbate this decline. However, our findings indicate that there are different responses between prokaryotes and fungi. The homogenisation of prokaryotes in young stands is due to the low heterogeneity in colonising communities. On the other hand, the decline in fungal beta diversity is likely caused by other mechanisms beyond extinction or replacement. The study highlights the impacts of the afforestation process on the beta diversity of soil microbial communities of grasslands, affecting taxonomic groups in different ways. Although microbial diversity may be partially restored in time in eucalypt plantations, it is important to investigate its underlying mechanisms and the ecological implications for microbial diversity and its spatial distribution.}, }
@article {pmid39647426, year = {2024}, author = {Ge, H and Li, C and Huang, C and Zhao, L and Cong, B and Liu, S}, title = {Bacterial community composition and metabolic characteristics of three representative marine areas in northern China.}, journal = {Marine environmental research}, volume = {204}, number = {}, pages = {106892}, doi = {10.1016/j.marenvres.2024.106892}, pmid = {39647426}, issn = {1879-0291}, abstract = {Bacteria are essential components of ecosystems, participating in nutrient cycling and biogeochemical processes, and playing a crucial role in maintaining the stability of marine ecosystems. However, the biogeographic distribution patterns of bacterial diversity and metabolic functions in the estuarine and coastal areas of northern China remain unclear. Here, we used metagenomic sequencing to investigate the bacterial community composition and metabolic functions in sediments from the adjacent waters of the Yellow River Estuary, the Yellow Sea Cold Water Mass, and the adjacent waters of the Yangtze River Estuary. Among the 9164 species that were found, the most dominant microbial communities are Pseudomonadota, Actinomycetota, Bacteroidota, and Bacillota, but there are significant differences in the species composition in these three typical habitats. Amino acid metabolism and carbohydrate metabolic pathways were highly enriched. Glycoside hydrolases (GHs) predominate in carbon metabolism across all samples. In nitrogen metabolic pathway, genes related to organic degradation and synthesis are more abundant in the Yellow River Estuary than the other two habitats. In sulfur metabolic pathway, genes involved in assimilatory sulfate reduction are significantly enriched. Assimilatory sulfate reduction might be crucial for sulfur metabolism in coastal regions, with a full assimilatory nitrate reduction pathway found in Desulfobacterota. This research offers insights into the compositional diversity, metabolic functions, and biogeographic distribution patterns of bacterial communities in sediments from typical marine areas of northern China.}, }
@article {pmid39647412, year = {2024}, author = {He, T and Xie, J and Jin, L and Zhao, J and Zhang, X and Liu, H and Li, XD}, title = {Seasonal dynamics of the phage-bacterium linkage and associated antibiotic resistome in airborne PM2.5 of urban areas.}, journal = {Environment international}, volume = {194}, number = {}, pages = {109155}, doi = {10.1016/j.envint.2024.109155}, pmid = {39647412}, issn = {1873-6750}, mesh = {*Bacteriophages/genetics ; *Particulate Matter ; China ; *Bacteria/genetics/drug effects ; *Seasons ; Humans ; Air Microbiology ; Cities ; Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology ; Air Pollutants/analysis ; Metagenomics ; Drug Resistance, Bacterial/genetics ; Microbiota ; }, abstract = {Inhalable microorganisms in airborne fine particulate matter (PM2.5), including bacteria and phages, are major carriers of antibiotic resistance genes (ARGs) with strong ecological linkages and potential health implications for urban populations. A full-spectrum study on ARG carriers and phage-bacterium linkages will shed light on the environmental processes of antibiotic resistance from airborne dissemination to the human lung microbiome. Our metagenomic study reveals the seasonal dynamics of phage communities in PM2.5, their impacts on clinically important ARGs, and potential implications for the human respiratory microbiome in selected cities of China. Gene-sharing network comparisons show that air harbours a distinct phage community connected to human- and water-associated viromes, with 57 % of the predicted hosts being potential bacterial pathogens. The ARGs of common antibiotics, e.g., peptide and tetracycline, dominate both the antibiotic resistome associated with bacteria and phages in PM2.5. Over 60 % of the predicted hosts of vARG-carrying phages are potential bacterial pathogens, and about 67 % of these hosts have not been discovered as direct carriers of the same ARGs. The profiles of ARG-carrying phages are distinct among urban sites, but show a significant enrichment in abundance, diversity, temperate lifestyle, and matches of CRISPR (short for 'clustered regularly interspaced short palindromic repeats') to identified bacterial genomes in winter and spring. Moreover, phages putatively carry 52 % of the total mobile genetic element (MGE)-ARG pairs with a unique 'flu season' pattern in urban areas. This study highlights the role that phages play in the airborne dissemination of ARGs and their delivery of ARGs to specific opportunistic pathogens in human lungs, independent of other pathways of horizontal gene transfer. Natural and anthropogenic stressors, particularly wind speed, UV index, and level of ozone, potentially explained over 80 % of the seasonal dynamics of phage-bacterial pathogen linkages on antibiotic resistance. Therefore, understanding the phage-host linkages in airborne PM2.5, the full-spectrum of antibiotic resistomes, and the potential human pathogens involved, will be of benefit to protect human health in urban areas.}, }
@article {pmid39643877, year = {2024}, author = {Cui, Z and Wang, S and Niu, J and Ma, J and Yang, H}, title = {Bifidobacterium species serve as key gut microbiome regulators after intervention in gestational diabetes mellitus.}, journal = {BMC microbiology}, volume = {24}, number = {1}, pages = {520}, pmid = {39643877}, issn = {1471-2180}, support = {22cz020401-4811009//National High Level Hospital Clinical Research/ ; 81830044//National Natural Science Foundation of China/ ; 2021YFC2700700//National Key Research and Development Program of China/ ; }, mesh = {Humans ; *Diabetes, Gestational/microbiology/metabolism/blood ; Pregnancy ; *Gastrointestinal Microbiome/genetics ; Female ; *Bifidobacterium/genetics ; Adult ; *Feces/microbiology ; Fatty Acids, Volatile/metabolism ; Dysbiosis/microbiology ; Genome-Wide Association Study ; Metagenome ; }, abstract = {Gut microbiome dysbiosis is associated with gestational diabetes mellitus (GDM), and its modulation represents a promising approach for enhancing glycemic control. In this study, we aimed to discover specific alterations in the gut microbiome through lifestyle management. We performed metagenome sequencing on fecal samples and measured short-chain fatty acid (SCFA) in plasma samples from 27 well-controlled GDM pregnancies before and after glycemic control. At the same time, 38 normal glucose tolerance (NGT) samples served as controls. Additionally, we employed two-sample Mendelian Randomization (MR) to validate our findings against Genome-Wide Association Study (GWAS) database. Our dynamic analysis revealed Bifidobacterium genus increased in GDM patients after intervention. The MR analysis confirmed that the family of Bifidobacteriaceae (OR 0.929, 95% CI, 0.886-0.975; P = 0.003) was the only negatively associated family with GDM. Further analysis indicated the increased abundance of Bifidobacterium species were negatively correlated with glycemic traits (Spearman rho mean - 0.32 ± 0.34) but positively correlated with plasma SCFA levels (Spearman rho mean 0.24 ± 0.19). Functional analysis revealed that the quorum-sensing pathway had the strongest effect on the ability of Bifidobacterium to promote glucose homeostasis (Spearman rho = -0.34), suggesting its role in regulating intestinal microbiota. Finally, the multivariable MR analysis demonstrated that two pathways, COLANSYN PWY and PWY 7323, responsible for cell surface compound synthesis in gram-negative bacteria, mediated 14.83% (P = 0.017) and 16.64% (P = 0.049) of the protective effects of Bifidobacteriaceae against GDM, respectively. In summary, Bifidobacterium is an effective gut microbiota regulator for GDM-related glucose homeostasis.}, }
@article {pmid39643362, year = {2024}, author = {Shen, C and Yu, Y and Zhang, X and Zhang, H and Chu, M and Yuan, B and Guo, Y and Li, Y and Zhou, J and Mao, J and Xu, X}, title = {The dynamic of physicochemical properties, volatile compounds and microbial community during the fermentation of Chinese rice wine with diverse cereals.}, journal = {Food research international (Ottawa, Ont.)}, volume = {198}, number = {}, pages = {115319}, doi = {10.1016/j.foodres.2024.115319}, pmid = {39643362}, issn = {1873-7145}, mesh = {Amino Acids/analysis/metabolism ; Bacteria/classification/metabolism ; Edible Grain/chemistry/microbiology ; Esters/analysis/metabolism ; *Fermentation ; Gas Chromatography-Mass Spectrometry ; Microbiota ; *Odorants/analysis ; *Oryza/chemistry ; Taste ; *Volatile Organic Compounds/analysis ; *Wine/analysis/microbiology ; }, abstract = {This study investigates the impact of liquid state fermentation on the key flavor compounds and microbial community structure in Chinese rice wine brewed from five different raw materials: buckwheat, sorghum, japonica rice, glutinous rice, and black rice. Using HS-SPME-GC-MS and HPLC, the volatile compounds were analyzed across various grain liquefaction methods, detecting 82 volatiles, including esters, alcohols, aldehydes, and acids. The concentration of flavor compounds such as esters, amino acids, phenolic acids, and organic acids varied significantly depending on the raw material used. Based on odor activity values, 31 key compounds were identified, including 15 ethyl esters, like ethyl laurate, responsible for the unique and complex aroma of the rice wines. Bitter amino acids, making up over 50 % of the total amino acids, were predominant. Among the varieties, the buckwheat-fermented wine exhibited the highest ester content (27.39 mg/L), nearly double that of other samples, along with elevated amino acids (1.47 mg/mL) and phenolic acids (904.29 mg/L). Black rice ranked second in amino acid content (0.93 mg/mL), while glutinous rice had the highest organic acid content (239.76 mg/mL). Metagenomic sequencing on the fifth day of fermentation revealed significant differences in microbial community structure among the raw materials. Saccharomyces, Aspergillus, Thermomyces, Epicoccus, and Albertella were dominant fungi, while Weissella, Thermoactinomyces, Bacillus, and Saccharopolyspora were dominant bacteria. Sensory analysis showed that buckwheat-fermented rice wine was distinguished by its honey, floral, creamy, and umami attributes, while balancing alcohol, acidity, bitterness, and Qu aroma. The results demonstrate the significant influence of raw material selection and liquefaction method on both flavor profile and microbial diversity in Chinese rice wine.}, }
@article {pmid39643360, year = {2024}, author = {Li, N and Xu, W and Meng, L and Zhao, Y and Zhao, X and Zheng, N and Zhang, Y and Wang, J}, title = {Metagenomics reveals differences in spore-forming bacterial diversity in raw milk in different regions and seasons in China.}, journal = {Food research international (Ottawa, Ont.)}, volume = {198}, number = {}, pages = {115317}, doi = {10.1016/j.foodres.2024.115317}, pmid = {39643360}, issn = {1873-7145}, mesh = {*Seasons ; Animals ; *Milk/microbiology ; China ; *Spores, Bacterial/genetics ; *Metagenomics ; Food Microbiology ; Bacteria/genetics/classification/isolation & purification ; Biodiversity ; }, abstract = {The spore-forming bacteria in the dairy industry are notable for their spores resilience and capacity to survive heating processes, allowing them to germinate and enter the vegetative stage, potentially leading to spoilage of the milk. Additionally, these spores can form biofilms, becoming a persistent source of contamination in processing environments. In this study, we collected a total of 165 raw milk from six different parts in China in spring, summer, autumn, and winter, respectively. Metagenomics sequencing method was used to explore and compare the differences in spore-forming bacterial composition and diversity in raw milk samples. Among these samples, four genera and 207 species of spore-forming bacteria were identified, with the genus Bacillus and the species Paenibacillus darwinianus dominant. Seasonal variations had a greater impact on the composition and abundance of spore-forming bacteria in raw milk than regional differences. Notable, raw milk samples collected during the spring and summer exhibited a higher number of unique spore-forming bacterial species compared to those collected in other seasons. Moreover, different regions and seasons have their own dominant bacteria. Metabolism of cofactors and vitamins, energy metabolism, carbohydrate metabolism, and amino acid metabolism were the main metabolic pathways. Hence, specific strategies need to be adopted to prevent and control spore-forming bacteria in raw milk in different regions and seasons.}, }
@article {pmid39643345, year = {2024}, author = {Jian, C and Sun, M and Ma, T and Wang, W and Lv, B and Wang, J and Su, X and Li, S and Guo, Y}, title = {Revealing the formation mechanisms of key flavor components during the fermentation of bamboo shoots by combining flavoromics and metagenomics.}, journal = {Food research international (Ottawa, Ont.)}, volume = {198}, number = {}, pages = {115361}, doi = {10.1016/j.foodres.2024.115361}, pmid = {39643345}, issn = {1873-7145}, mesh = {*Fermentation ; *Metagenomics ; *Taste ; *Volatile Organic Compounds/analysis/metabolism ; *Odorants/analysis ; *Metabolomics ; Flavoring Agents/metabolism ; Plant Shoots ; Fermented Foods/microbiology ; Bacteria/genetics/classification/metabolism ; Food Microbiology ; Amino Acids/analysis/metabolism ; Microbiota ; }, abstract = {Microbial metabolism plays a critical role in the flavor development of Guangxi fermented bamboo shoots (GFBS). To clarify the role of microorganisms in flavor formation and predict the metabolic pathways of key characteristic flavor compounds, this study employed metabolomics, Odor Activity Value (OAV), and Taste Activity Value (TAV) calculations, integrated with Partial Least Squares Discriminant Analysis (PLS-DA), to investigate changes in GFBS flavors-represented by volatile flavor compounds, organic acids, and free amino acids-across a 30-day fermentation period. Metagenomic datasets were used to identify taxonomic and functional changes in the microbial community. As a result, 26 characteristic flavor compounds (OAV or TAV > 1) were identified in mature GFBS, and 23 differential flavor compounds were identified at different fermentation stages using PLS-DA (VIP > 1.2). The top 10 microbial genera associated with these characteristic flavor compounds were identified, including Acinetobacter, Enterobacter, Raoultella, Enterococcus, Klebsiella, Lactococcus, Leuconostoc, Weissella, Lactiplantibacillus and Limosilactobacillus. Based on these findings, a predictive metabolic network of key flavor compounds in GFBS was constructed, providing a comprehensive understanding of the diverse metabolic roles of microorganisms during fermentation. This work lays a theoretical foundation for the standardized production and quality control of GFBS flavor.}, }
@article {pmid39643336, year = {2024}, author = {Li, T and Cao, W and Li, D and Wei, C and Yan, Y and Zeng, X}, title = {Metagenomic insights into quorum sensing-associated microbial profiling and its correlations with flavor compounds of Maotai-flavor liquor: A case study of stacking fermented grains.}, journal = {Food research international (Ottawa, Ont.)}, volume = {198}, number = {}, pages = {115324}, doi = {10.1016/j.foodres.2024.115324}, pmid = {39643336}, issn = {1873-7145}, mesh = {*Quorum Sensing ; *Fermentation ; *Flavoring Agents/metabolism ; *Metagenomics/methods ; Taste ; Food Microbiology ; Bacteria/genetics/metabolism/classification ; Fungi/genetics/metabolism ; Edible Grain/microbiology ; Alcoholic Beverages/microbiology ; Microbiota ; }, abstract = {Stacking fermentation is typical process of Maotai-flavor Baijiu and microbial composition determine content of flavors. To date, the knowledge on the driving force of microbial composition was as yet unknown. Since quorum sensing molecule (QSM) plays an important role in modifying microbial interactions. Therefore, the objectives of the present study were: (1) to describe the microbial profile associated with QSM in stacking grains using metagenomics; (2) to elucidate how QSM shapes microbial interactions and accordingly regulates flavor synthesis. Results indicated that bacterial QSM including AI-2, DSF, and AHL as well as fungal QSM aromatic alcohols and farnesol were prevalent in the stacking fermented grains. Thereinto, AI-2 might be an important driving force of microbial composition due to its highest abundance. AI-2 in Limosilactobacillus fermentum, Pediococcus pentosaceus, and Weissella cibaria perhaps modified microbial interactions together with fungal QSM in Schizosaccharomyces pombe and Pichia membranifaciens. The role of AI-2 was much higher than that of fungal QSM. Furthermore, QSM indirectly influenced the synthesis of important flavors such as ethyl lactate, phenylethanol, and ethyl phenylacetate through the dynamic of microbial composition. Together, this current study for the first time explored the effects of QSM on microbial composition and flavor synthesis in the Baijiu field.}, }
@article {pmid39642431, year = {2024}, author = {Bertini, F and Catania, V and Scirè Calabrisotto, L and Dara, M and Bisanti, L and La Corte, C and Staropoli, M and Piazzese, D and Parisi, MG and Parrinello, D and Cammarata, M}, title = {A multi-comprehensive approach to assess the responses of the Mediterranean mussel Mytilus galloprovincialis (Lamarck, 1919) to a simulation of a diesel-oil mixture spill.}, journal = {Aquatic toxicology (Amsterdam, Netherlands)}, volume = {279}, number = {}, pages = {107188}, doi = {10.1016/j.aquatox.2024.107188}, pmid = {39642431}, issn = {1879-1514}, abstract = {Oil spills are a major cause of pollution impacting marine ecosystems. In this work, the effects of short-term exposure to three different concentrations of a hydrocarbon mixture (HC), that simulated the action of such an event, were investigated on Mytilus galloprovincialis specimens. Physiological effects were measured using a battery of biomarkers consisting of cellular activity (phagocytosis), immune-related enzymes, chaperonins (HSP70 and HSC70), and histomorphological alterations. Different concentrations of HC led to a significant decrease in phagocytosis, especially following high concentrations. Immune-related enzymes evaluated in hemolymph and digestive gland extract showed up-regulation, suggesting the activation of antioxidant, detoxicant, and inflammatory responses. Morphological alterations of digestive gland tubules were observed after exposure to the HC. HSP70 and HSC70 activity was up regulated following the treatments, indicating their involvement in maintaining organism homeostasis. In addition, the diversity and composition of hemolymph and digestive gland microbiota exposed to HC were analyzed by automated ribosomal intergenic spacer analysis (ARISA) and a Next Generation Sequencing (NGS) approach to evaluate the connection with hydrocarbon contamination. Metagenomic analysis revealed significant differences in the hemolymph and digestive gland microbiota composition between mussels exposed and unexposed to HC. Exposure to increasing HC concentrations had a positive effect on microbial diversity with clear adaptative responses, and an increase in the relative abundance of several known degrading bacterial genera, including Alcanivorax, Roseovarius, Pseudomonas, Vibrio, Oleibacter. These results show the utility of a multi-comprehensive approach to evaluating functional adaptation in terms of immunological dysfunctions and microbiota alteration in the sentinel organism M. galloprovincialis.}, }
@article {pmid39641169, year = {2025}, author = {Yang, J and Lei, OK and Bhute, S and Kris-Etherton, PM and Lichtenstein, AH and Matthan, NR and Petersen, KS and Sabaté, J and Reboussin, DM and Lovato, L and Vitolins, MZ and Rajaram, S and Jacobs, JP and Huang, J and Taw, M and Yang, S and Li, Z}, title = {Impact of daily avocado consumption on gut microbiota in adults with abdominal obesity: an ancillary study of HAT, a randomized controlled trial.}, journal = {Food & function}, volume = {16}, number = {1}, pages = {168-180}, doi = {10.1039/d4fo03806a}, pmid = {39641169}, issn = {2042-650X}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Persea ; Female ; Male ; Adult ; Middle Aged ; *Obesity, Abdominal/diet therapy/metabolism/microbiology ; Feces/microbiology ; Bacteria/classification/genetics/isolation & purification/metabolism ; Diet ; }, abstract = {Objectives: This study aimed to investigate short-term and long-term impact of avocado consumption without caloric restriction on the gut microbiota of free-living adults with abdominal obesity. Methods: The Habitual Diet and Avocado Trial (HAT) was a 26-week, multi-center, randomized, controlled trial involving 1008 individuals with abdominal obesity. Participants were randomly assigned to the Avocado Supplemented Diet Group (AVO), receiving one avocado per day, or the Habitual Diet group (HAB), maintaining their usual dietary habits. Fecal samples were collected at baseline, week 4 and week 26 from a subset of participants recruited at a University of California Los Angeles site (n = 230). Fecal microbiota was assessed with shotgun metagenomics sequencing. Alpha diversity was assessed using the Chao1 and Shannon indices; beta diversity was assessed using Bray-Curtis dissimilarity with significance determined by repeated measures permutational multivariat analysis of variance. Potential association of intervention at week 4 and 26 with alpha diversity, species and metabolic pathways was examined using linear mixed effect models. Results: Compared to the HAB group, the AVO group had higher alpha diversity by 4 weeks, which persisted through the 26-week study period. Exploratory analysis based on healthy eating index-2015 (HEI-2015) indicated that participants with a low HEI score at baseline (≤52.7), had an increase in alpha diversity in the AVO group vs. HAB group. The AVO group had a significant change in beta diversity at week 26 compared to the HAB group. At the species level, the AVO group had significantly increased Faecalibacterium prausnitzii and Bacterium AF16_15 at week 26 compared to the HAB group. Functional analysis showed no significant difference in metabolic pathways between the HAB and AVO groups. Conclusions: Our findings document a potentially favorable effect of avocados on gut microbiota diversity. The prebiotic potential of avocados is more pronounced in individuals with a low diet quality score. This trial is registered at clinicaltrials.gov as NCT03528031 (https://clinicaltrials.gov/study/NCT03528031).}, }
@article {pmid39640900, year = {2024}, author = {Pahirah, N and Narkwichean, A and Taweechotipatr, M and Wannaiampikul, S and Duang-Udom, C and Laosooksathit, W}, title = {Comparison of Gut Microbiomes Between Neonates Born by Cesarean Section and Vaginal Delivery: Prospective Observational Study.}, journal = {BioMed research international}, volume = {2024}, number = {}, pages = {8302361}, pmid = {39640900}, issn = {2314-6141}, mesh = {Humans ; *Cesarean Section ; *Gastrointestinal Microbiome ; Infant, Newborn ; Female ; Prospective Studies ; *Delivery, Obstetric ; Pregnancy ; *RNA, Ribosomal, 16S/genetics ; Male ; Feces/microbiology ; Thailand ; Bifidobacterium ; }, abstract = {Background: Balanced diversity and abundance of gut microbiome play important roles in human health, including neonatal health. Though not established, there is evidence that the delivery route could alter the diversity of neonatal gut microbiomes. Objective: The objective of the study was to investigate the differences in the gut microbiomes of neonates delivered via cesarean section compared to those born by vaginal delivery and to identify the predominant microbial taxa present in each group. Study Design: A prospective observational study of 281 healthy neonates born between February 2021 and April 2023 at Her Royal Highness Maha Chakri Sirindhorn Medical Center, Srinakharinwirot University, Thailand, was performed. The study population was divided into two groups: 139 neonates born via vaginal delivery and 141 neonates born via cesarean section. The microbiota composition of each neonate's fecal sample was identified by using 16S ribosomal ribonucleic acid metagenomic sequencing. Results: Neonates delivered vaginally exhibited a gut microbiome with higher abundance and diversity than those delivered by cesarean delivery. Bifidobacterium was the dominant genus in both groups. Bifidobacterium breve was the dominant species and was significantly higher in cesarean-delivered neonates compared to those delivered vaginally (24.0% and 9.2%, respectively) (p < 0.001). However, the taxonomy of only 89 (64.0%) and 44 (31.43%) fecal samples could be identified from the vaginal and cesarean delivery groups, respectively. Conclusion: Route of delivery is associated with neonatal gut microbiome abundance and diversity. Neonates delivered via vaginal delivery exhibited higher diversity but lower abundance of the dominant species in the gut microbiome. Trial Registration: Thai Clinical Trials Registry identifier: TCTR20221024003.}, }
@article {pmid39639355, year = {2024}, author = {Benga, L and Rehm, A and Gougoula, C and Westhoff, P and Wachtmeister, T and Benten, WPM and Engelhardt, E and Weber, APM and Köhrer, K and Sager, M and Janssen, S}, title = {The host genotype actively shapes its microbiome across generations in laboratory mice.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {256}, pmid = {39639355}, issn = {2049-2618}, mesh = {Animals ; Mice ; Female ; *Genotype ; *Mice, Inbred BALB C ; *Mice, Inbred C57BL ; *Microbiota ; Male ; Maternal Inheritance ; Embryo, Mammalian/microbiology ; Host Microbial Interactions ; Pregnancy ; }, abstract = {BACKGROUND: The microbiome greatly affects health and wellbeing. Evolutionarily, it is doubtful that a host would rely on chance alone to pass on microbial colonization to its offspring. However, the literature currently offers only limited evidence regarding two alternative hypotheses: active microbial shaping by host genetic factors or transmission of a microbial maternal legacy.
RESULTS: To further dissect the influence of host genetics and maternal inheritance, we collected two-cell stage embryos from two representative wild types, C57BL6/J and BALB/c, and transferred a mixture of both genotype embryos into hybrid recipient mice to be inoculated by an identical microbiome at birth.
CONCLUSIONS: Observing the offspring for six generations unequivocally emphasizes the impact of host genetic factors over maternal legacy in constant environments, akin to murine laboratory experiments. Interestingly, maternal legacy solely controlled the microbiome in the first offspring generation. However, current evidence supporting maternal legacy has not extended beyond this initial generation, resolving the aforementioned debate. Video Abstract.}, }
@article {pmid39639104, year = {2025}, author = {Knuth, MM and Campos, CV and Smith, K and Hutchins, EK and Lewis, S and York, M and Coghill, LM and Franklin, C and MacFarlane, AJ and Ericsson, AC and Magnuson, T and Ideraabdullah, F}, title = {Timing of standard chow exposure determines the variability of mouse phenotypic outcomes and gut microbiota profile.}, journal = {Lab animal}, volume = {54}, number = {1}, pages = {24-36}, pmid = {39639104}, issn = {1548-4475}, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Mice, Inbred C57BL ; Male ; Mice ; Female ; *Diet/veterinary ; Phenotype ; Time Factors ; Animal Feed/analysis ; }, abstract = {Standard chow diets influence reproducibility in animal model experiments because chows have different nutrient compositions, which can independently influence phenotypes. However, there is little evidence of the role of timing in the extent of variability caused by chow exposure. Here we measured the impact of different diets (5V5M, 5V0G, 2920X and 5058) and timing of exposure (adult exposure (AE), lifetime exposure (LE) and developmental exposure (DE)) on growth and development, metabolic health indicators and gut bacterial microbiota profiles across genetically identical C57BL/6J mice. Diet drove differences in macro- and micronutrient intake for all exposure models. AE had no effect on phenotypic outcomes. However, LE mice exhibited significant sex-dependent diet effects on growth, body weight and body composition. LE effects were mostly absent in the DE model, where mice were exposed to chow differences only from conception to weaning. Both AE and LE models exhibited similar diet-driven beta diversity profiles for the gut bacterial microbiota, with 5058 diet driving the most distinct profile. However, compared with AE, LE effects on beta diversity were sex dependent, and LE mice exhibited nine times more differentially abundant bacterial genera, the majority of which were inversely affected by 2920X and 5058 diets. Our findings demonstrate that LE to different chow diets has the greatest impact on the reproducibility of several experimental measures commonly used in preclinical mouse model studies. Importantly, weaning mice from different diets onto the same diet for maturation may be an effective way to reduce unwanted phenotypic variability among experimental models.}, }
@article {pmid39637857, year = {2024}, author = {Vaher, K and Cabez, MB and Parga, PL and Binkowska, J and van Beveren, GJ and Odendaal, ML and Sullivan, G and Stoye, DQ and Corrigan, A and Quigley, AJ and Thrippleton, MJ and Bastin, ME and Bogaert, D and Boardman, JP}, title = {The neonatal gut microbiota: A role in the encephalopathy of prematurity.}, journal = {Cell reports. Medicine}, volume = {5}, number = {12}, pages = {101845}, doi = {10.1016/j.xcrm.2024.101845}, pmid = {39637857}, issn = {2666-3791}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics/physiology ; Infant, Newborn ; Female ; Male ; *Infant, Premature ; Feces/microbiology ; Brain/pathology/microbiology ; Brain Diseases/microbiology/pathology ; Gestational Age ; Magnetic Resonance Imaging/methods ; Premature Birth/microbiology ; }, abstract = {Preterm birth correlates with brain dysmaturation and neurocognitive impairment. The gut microbiome associates with behavioral outcomes in typical development, but its relationship with neurodevelopment in preterm infants is unknown. We characterize fecal microbiome in a cohort of 147 neonates enriched for very preterm birth using 16S-based and shotgun metagenomic sequencing. Delivery mode strongly correlates with the preterm microbiome shortly after birth. Low birth gestational age, infant sex assigned at birth, and antibiotics associate with microbiome composition at neonatal intensive care unit discharge. We integrate these data with term-equivalent structural and diffusion brain MRI. Bacterial community composition associates with MRI features of encephalopathy of prematurity. Particularly, abundances of Escherichia coli and Klebsiella spp. correlate with microstructural parameters in deep and cortical gray matter. Metagenome functional capacity analyses suggest that these bacteria may interact with brain microstructure via tryptophan and propionate metabolism. This study indicates that the gut microbiome associates with brain development following preterm birth.}, }
@article {pmid39637856, year = {2025}, author = {Caty, SN and Alvarez-Buylla, A and Vasek, C and Tapia, EE and Martin, NA and McLaughlin, T and Golde, CL and Weber, PK and Mayali, X and Coloma, LA and Morris, MM and O'Connell, LA}, title = {Alkaloids are associated with increased microbial diversity and metabolic function in poison frogs.}, journal = {Current biology : CB}, volume = {35}, number = {1}, pages = {187-197.e8}, doi = {10.1016/j.cub.2024.10.069}, pmid = {39637856}, issn = {1879-0445}, mesh = {Animals ; *Alkaloids/metabolism ; *Microbiota ; *Anura/microbiology/metabolism ; Skin/microbiology/metabolism ; Bacteria/metabolism/classification/genetics/isolation & purification ; Poison Frogs ; }, abstract = {Shifts in host-associated microbiomes can impact both host and microbes.[1][,][2][,][3][,][4][,][5][,][6] It is of interest to understand how perturbations, like the introduction of exogenous chemicals,[7][,][8][,][9][,][10][,][11][,][12][,][13] impact microbiomes. In poison frogs (family Dendrobatidae), the skin microbiome is exposed to alkaloids that the frogs sequester for defense.[14][,][15][,][16][,][17][,][18][,][19] These alkaloids are antimicrobial[20][,][21][,][22]; however, their effect on the frogs' skin microbiome is unknown. To test this, we characterized microbial communities from field-collected dendrobatid frogs. Then, we conducted a laboratory experiment to monitor the effect of the alkaloid decahydroquinoline (DHQ) on the microbiome of two frog species with contrasting alkaloid loads in nature. In both datasets, we found that alkaloid-exposed microbiomes were more phylogenetically diverse, with an increase in diversity among rare taxa. To better understand the isolate-specific response to alkaloids, we cultured microbial isolates from poison frog skin and found that many isolates exhibited enhanced growth or were not impacted by the addition of DHQ. To further explore the microbial response to alkaloids, we sequenced the metagenomes from high- and low-alkaloid frogs and observed a greater diversity of genes associated with nitrogen and carbon metabolism in high-alkaloid frogs. From these data, we hypothesized that some strains may metabolize the alkaloids. We used stable isotope tracing coupled to nanoSIMS (nanoscale secondary ion mass spectrometry), which supported the idea that some of these isolates are able to metabolize DHQ. Together, these data suggest that poison frog alkaloids open new niches for skin-associated microbes with specific adaptations, such as alkaloid metabolism, that enable survival in this environment.}, }
@article {pmid39636804, year = {2024}, author = {Calderon, MS and Bustamante, DE and Perez, J and Fernandez-Güimac, SLJ and Mendoza, JE and Barboza, JI and Ayala, RY and Carrion, JV}, title = {Diversity and functional role of bacterial microbiota in spontaneous coffee fermentation in northern Peru using shotgun metagenomics.}, journal = {Journal of food science}, volume = {89}, number = {12}, pages = {9692-9710}, doi = {10.1111/1750-3841.17583}, pmid = {39636804}, issn = {1750-3841}, support = {//Consejo Nacional de Ciencia, Tecnología e Innovación Tecnológica/ ; N° 030-2018-FONDECYT-BM-IADT-MU//Peruvian CONCYTEC under the projects Metacafé/ ; N° PE501081184-2022-PROCIENCIA//Metacafé 2.0/ ; //Vicerrectorado de Investigación (VRIN) de la UNTRM/ ; }, mesh = {*Fermentation ; Peru ; *Coffee/microbiology ; *Metagenomics/methods ; *Bacteria/classification/genetics/isolation & purification ; *Microbiota ; Taste ; Coffea/microbiology ; Food Microbiology/methods ; }, abstract = {Peru is the ninth-largest coffee producer and the largest organic coffee exporter worldwide. Specific modifications in the microbial consortia during fermentation control the flavor of coffee. It is still unclear how fermentation duration affects microbial communities. This study aimed to provide insights into the diversity and functional behavior of the bacterial microbiome during coffee fermentation in northern Peru using shotgun metagenomics. Accordingly, metagenomic DNA was extracted and sequenced from samples of the liquid fraction during the short fermentation process (SFP) in Amazonas (6 and 12 h) and long fermentation process (LFP) in Cajamarca (6, 12, 18, 24, and 36 h). Our findings indicate that common (e.g., Acetobacter, Lactobacillus, Leuconostoc, and Weissella) and unique (e.g., Acidiphilium and Methylobacterium) acid-tolerant bacteria from the SFP and LFP play crucial roles and have a positive impact on the sensory qualities of coffee. Specifically, the LFP from San Ignacio might be associated with the high sensory quality of coffee based on the release of catalytic, hydrolase, oxidoreductase, transferase, and transporter enzymes in the InterPro and KEGG profiles. Additionally, these bacterial microorganisms metabolize several compounds (e.g., isoleucine, betaine, galactose, tryptophan, arginine, and cobalamin) into volatile compounds, mainly in the LFP, enhancing the flavor and aroma of coffees. This characteristic suggests that the LFP has a stronger effect on coffee quality than does the SFP on the basis of bacterial diversity and functional prediction. These findings provide new perspectives on the potential biotechnological uses of autochthonous microorganisms to produce superior-quality coffee beans from northern Peru.}, }
@article {pmid39635041, year = {2024}, author = {Dora, D and Revisnyei, P and Mihucz, A and Kiraly, P and Szklenarik, G and Dulka, E and Galffy, G and Lohinai, Z}, title = {Metabolic pathways from the gut metatranscriptome are associated with COPD and respiratory function in lung cancer patients.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1381170}, pmid = {39635041}, issn = {2235-2988}, mesh = {Humans ; *Pulmonary Disease, Chronic Obstructive/microbiology/metabolism/physiopathology ; *Gastrointestinal Microbiome/genetics ; *Metabolic Networks and Pathways/genetics ; *Lung Neoplasms/microbiology/genetics ; Male ; *Feces/microbiology ; Female ; Aged ; Middle Aged ; Carcinoma, Non-Small-Cell Lung/genetics/microbiology ; Transcriptome ; Metagenomics/methods ; Bacteria/genetics/classification/isolation & purification/metabolism ; Streptococcus/genetics/isolation & purification/metabolism ; }, abstract = {INTRODUCTION: Changes in the human gut microbiome have been linked to various chronic diseases, including chronic obstructive pulmonary disease (COPD). While substantial knowledge is available on the genomic features of fecal communities, little is known about the microbiome's transcriptional activity. Here, we analyzed the metatranscriptomic (MTR) abundance of MetaCyc pathways, SuperPathways, and protein domain families (PFAM) represented by the gut microbiome in a cohort of non-small cell lung cancer (NSCLC) patients with- or without COPD comorbidity.
METHODS: Fecal samples of 40 NSCLC patients with- or without COPD comorbidity were collected at the time of diagnosis. Data was preprocessed using the Metaphlan3/Humann3 pipeline and BioCyc[©] to identify metabolic SuperPathways. LEfSe analysis was conducted on Pathway- and PFAM abundance data to determine COPD- and non-COPD-related clusters.
RESULTS: Key genera Streptococcus, Escherichia, Gemella, and Lactobacillus were significantly more active transcriptionally compared to their metagenomic presence. LEfSe analysis identified 11 MetaCyc pathways that were significantly overrepresented in patients with- and without COPD comorbidity. According to Spearman's rank correlation, Smoking PY showed a significant negative correlation with Glycolysis IV, Purine Ribonucleoside Degradation and Glycogen Biosynthesis I, and a significant positive correlation with Superpathway of Ac-CoA Biosynthesis and Glyoxylate cycle, whereas forced expiratory volume in the first second (FEV1) showed a significant negative correlation with Glycolysis IV and a significant positive correlation with Glycogen Biosynthesis I. Furthermore, COPD patients showed a significantly increased MTR abundance in ~60% of SuperPathways, indicating a universally increased MTR activity in this condition. FEV1 showed a significant correlation with SuperPathways Carbohydrate degradation, Glycan biosynthesis, and Glycolysis. Taxonomic analysis suggested a more prominent MTR activity from multiple Streptococcus species, Enterococcus (E.) faecalis, E. faecium and Escherichia (E.) coli than expected from their metagenomic abundance. Multiple protein domain families (PFAMs) were identified as more associated with COPD, E. faecium, E.coli, and Streptococcus salivarius, contributing the most to these PFAMs.
CONCLUSION: Metatranscriptome analysis identified COPD-related subsets of lung cancer with potential therapeutic relevance.}, }
@article {pmid39632378, year = {2024}, author = {Li, Y and Hu, W and Lin, B and Ma, T and Zhang, Z and Hu, W and Zhou, R and Kwok, LY and Sun, Z and Zhu, C and Zhang, H}, title = {Omic characterizing and targeting gut dysbiosis in children with autism spectrum disorder: symptom alleviation through combined probiotic and medium-carbohydrate diet intervention - a pilot study.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2434675}, pmid = {39632378}, issn = {1949-0984}, mesh = {Humans ; *Autism Spectrum Disorder/diet therapy/microbiology ; Pilot Projects ; *Probiotics/administration & dosage ; *Gastrointestinal Microbiome ; *Dysbiosis/microbiology/diet therapy/therapy ; Male ; Child ; Female ; *Feces/microbiology/chemistry ; Child, Preschool ; Bacteria/classification/isolation & purification/genetics/metabolism ; Dietary Carbohydrates/metabolism/administration & dosage ; Bifidobacterium animalis ; }, abstract = {Autism spectrum disorder (ASD) currently lacks effective diagnostic and therapeutic approaches. Disruptions in the gut ecosystem have been observed in individuals with ASD, suggesting that targeting gut microbiota through probiotic and dietary supplementation may serve as a potential treatment strategy. This two-phase study aimed to characterize the fecal metagenome of children with ASD and investigate the beneficial effects of a combined probiotic and medium-carbohydrate intervention in ASD. Fecal metagenomes of children with ASD were compared to those of typically developing children, revealing intestinal dysbiosis in ASD, characterized by reduced levels of Prevotella sp. Dialister invisus, and Bacteroides sp. along with increased predicted abundances of inosine, glutamate, xanthine, and methylxanthine. The gut bacteriome and phageome exhibited high cooperativity. In a 3-month pilot study, Bifidobacterium animalis subsp. lactis Probio-M8 (Probio-M8) was administered alongside a medium-carbohydrate diet to Chinese children with ASD. The primary endpoint was the Childhood Autism Rating Scale (CARS), while the secondary endpoint was the Gastrointestinal Symptom Rating Scale (GSRS). A total of 72 autistic children were initially recruited for the intervention study, but only 53 completed the intervention. Probio-M8, in combination with dietary intervention, significantly improved CARS and GSRS scores, increased fecal levels of Bifidobacterium animalis, Akkermansia muciniphila, Fusicatenibacter saccharivorans, and Sutterella sp. while also reducing Blautia obeum (Benjamini-Hochberg corrected p ≤ 0.05 for all cases). The intervention also modulated fecal metabolites associated with the metabolism of amino acids (lysine), neurotransmitters (glutamate, γ-aminobutyric acid), polyunsaturated fatty acids (arachidonate, myristic acid), and vitamin B3. In conclusion, Probio-M8 combined with medium-carbohydrate diet effectively improved ASD symptoms, with associated changes in the gut microbiome and metabolome, supporting its potential as an adjunctive therapy for ASD.}, }
@article {pmid39631543, year = {2024}, author = {Qu, M and Zheng, Y and Cheng, Z and Shi, Y and Wang, W and Wu, X and Chen, J}, title = {Mechanism of chlorobenzene removal in biotrickling filter enhanced by non-thermal plasma: Insights from biodiversity and functional gene perspectives.}, journal = {Bioresource technology}, volume = {418}, number = {}, pages = {131931}, doi = {10.1016/j.biortech.2024.131931}, pmid = {39631543}, issn = {1873-2976}, abstract = {Biotrickling filter (BTF) technology is inefficient in the treatment of Cl-containing volatile organic compounds (VOCs) such as chlorobenzene (CB). This study adopted non-thermal plasma (NTP) as a pretreatment and conducted in-depth analyses, especially in microorganisms, to investigate strengthening mechanism of a NTP to a BTF in the process. The introduction of NTP enhance efficiency of CB removal from 65 % to 90 %, and CO2 generation from 60 % to 85 %. It is found that the protein content of the extracellular polymeric substances increases from 212 × 10[-3] mg·g[-1] filler to 299 × 10[-3] mg·g[-1] filler, thus CB capturing and utilization enhanced. Metagenomic analysis showed that bacteria with CB-degrading properties were enriched in BTF, and CB was involved in cellular metabolism as a carbon source. The presence of active substances from NTP is found to stimulate the ability of BTF treatment. The findings of this study will provide theoretical support for the application of NTP-BTF technology.}, }
@article {pmid39630952, year = {2024}, author = {Gao, F and Shen, Y and Wu, H and Laue, HE and Lau, FK and Gillet, V and Lai, Y and Shrubsole, MJ and Prada, D and Zhang, W and Liu, Z and Bellenger, JP and Takser, L and Baccarelli, AA}, title = {Associations of Stool Metal Exposures with Childhood Gut Microbiome Multiomics Profiles in a Prospective Birth Cohort Study.}, journal = {Environmental science & technology}, volume = {58}, number = {50}, pages = {22053-22063}, doi = {10.1021/acs.est.4c09642}, pmid = {39630952}, issn = {1520-5851}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Feces/microbiology ; Child ; *Metals ; Prospective Studies ; Female ; Male ; Birth Cohort ; Environmental Exposure ; Multiomics ; }, abstract = {Metal exposures are closely related to childhood developmental health. However, their effects on the childhood gut microbiome, which also impacts health, are largely unexplored using microbiome multiomics including the metagenome and metatranscriptome. This study examined the associations of fecal profiles of metal/element exposures with gut microbiome species and active functional pathways in 8- to 12-year-old children (N = 116) participating in the GESTation and Environment (GESTE) cohort study. We analyzed 19 stool metal and element concentrations (B, Na, Mg, Al, K, Ca, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, As, Mo, Cd, Ba, and Pb). Covariate-adjusted linear regression models identified several significant microbiome associations with continuous stool metal/element concentrations. For instance, Zn was positively associated with Turicibacter sanguinis (coef = 1.354, q-value = 0.039) and negatively associated with Eubacterium eligens (coef = -0.794, q-value = 0.044). Higher concentrations of Cd were associated with lower Eubacterium eligens (coef = -0.774, q-value = 0.045). Additionally, a total of 490 significant functional pathways such as biosynthesis and degradation/utilization/assimilation were identified, corresponding to different functions, including amino acid synthesis and carbohydrate degradation. Our results suggest links among metal exposures, pediatric gut microbiome multiomics, and potential health implications. Future work will further explore their relation to childhood health.}, }
@article {pmid39629792, year = {2024}, author = {González-García, S and Hamdan-Partida, A and Pérez-Ramos, J and Aguirre-Garrido, JF and Bustos-Hamdan, A and Bustos-Martínez, J}, title = {Comparison of the bacterial microbiome in the pharynx and nasal cavity of persistent, intermittent carriers and non-carriers of Staphylococcus aureus.}, journal = {Journal of medical microbiology}, volume = {73}, number = {12}, pages = {}, pmid = {39629792}, issn = {1473-5644}, mesh = {Humans ; *Pharynx/microbiology ; *Staphylococcus aureus/isolation & purification/genetics ; *Carrier State/microbiology ; *Nasal Cavity/microbiology ; *Microbiota ; *Staphylococcal Infections/microbiology ; Male ; Female ; Adult ; Young Adult ; RNA, Ribosomal, 16S/genetics ; DNA, Bacterial/genetics ; }, abstract = {Introduction. Staphylococcus aureus is a bacterium that colonizes various human sites. The pharynx has been considered as a site of little clinical relevance and little studied. Recently, it has been reported that S. aureus can colonize more the pharynx than the nose. In addition, S. aureus can persist in these sites for prolonged periods of time.Hypothesis. The composition of the pharyngeal and nasal microbiome will differ between persistent, intermittent carriers and non-carriers of S. aureus.Aim. Determine whether the pharyngeal and nasal microbiome is different between carriers and non-carriers of S. aureus.Methodology. S. aureus carriers were monitored by means of pharyngeal and nasal exudates of apparently healthy adult university students for 3 months. Samples from individuals of the same carrier type were pooled, and DNA was extracted and the 16S rRNA was sequenced. The sequences were analysed in MOTHUR v.1.48.0 software, by analysing the percentages of relative abundance in the STAMP 2.1.3 program, in addition to the predictive analysis of metabolic pathways in PICRUSt2.Results. A greater colonization of S. aureus was found in the pharynx than in the nose. The microbiomes of S. aureus carriers and non-carriers do not show significant differences. The main microbiome difference found was between pharyngeal and nasal microbiomes. No significant differences were found in the abundance of the genus Staphylococcus in pharyngeal and nasal S. aureus carriers and non-carriers. The nasal microbiome was found to have more variation compared to the pharyngeal microbiome, which appears to be more stable between individuals and pools. Predictive analysis of metabolic pathways showed a greater presence of Staphylococcus-associated pathways in the nose than in the pharynx.Conclusion. S. aureus can colonize and persist in the pharynx in equal or greater proportion than in the nose. No statistically significant differences were found in the microbiome of the pharyngeal and nasal carriers and non-carriers of S. aureus, but the pharyngeal and nasal microbiomes are different independent of the type of S. aureus carrier or non-carrier. Therefore, the microbiome apparently does not influence the persistence of S. aureus.}, }
@article {pmid39629129, year = {2024}, author = {Zhao, Q and Lu, Y and Duan, J and Du, D and Pu, Q and Li, F}, title = {Gut microbiota depletion and FXR inhibition exacerbates zonal hepatotoxicity of sunitinib.}, journal = {Theranostics}, volume = {14}, number = {18}, pages = {7219-7240}, pmid = {39629129}, issn = {1838-7640}, mesh = {Animals ; *Sunitinib/toxicity ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Chemical and Drug Induced Liver Injury/pathology/etiology ; *Liver/drug effects/pathology ; *Mice, Knockout ; *Receptors, Cytoplasmic and Nuclear/metabolism ; Male ; Hepatocytes/drug effects ; Mice, Inbred C57BL ; Endothelial Cells/drug effects ; Apoptosis/drug effects ; Bacteroidetes/drug effects ; Autophagy/drug effects ; }, abstract = {Rationale: Sunitinib is a small-molecule tyrosine kinase inhibitor associated with the side-effect of liver injury. The impaired cell type in liver and the hepatotoxicity mechanisms is still unclear. Methods: Spatial metabolomics, transmission electron microscopy, immunofluorescence co-staining, and isolation of bile duct cells and liver sinusoidal endothelial cells (LSECs) were used to evaluate the zonated hepatotoxicity of sunitinib. Farnesoid X receptor (FXR) conditional knockout mice, metagenomics analysis, bacteria clearance, bacterial culture, Parabacteroides distasonis and 3-oxolithocholic acid supplementation were used to evaluate the hepatotoxicity mechanisms of sunitinib. Results: Phenotype analysis found that hepatic autophagy, apoptosis, and mitochondrial injury were observed in vivo or in vitro after sunitinib treatment. By using spatial metabolomics and isolation of bile duct cells and LSECs, the zonated drug toxicity was observed around the portal vein. Hepatocytes, bile duct cells, and LSECs were damaged after sunitinib treatment. FXR inhibition and gut microbiota depletion aggravated sunitinib-induced liver injury. For diurnal variation, sunitinib-induced liver injury was enhanced at night compared with that at day, and FXR and gut microbiota participated in circadian rhythmic hepatotoxicity induced by sunitinib. Conclusions: Our data suggested activation of FXR and Parabacteroides distasonis supplementation may be used to improve sunitinib-induced hepatotoxicity.}, }
@article {pmid39628196, year = {2024}, author = {Li, ZX and Li, JH and Zhang, Q and Lu, JJ and Gao, CH and Jin, DS and Xu, MG}, title = {[Response and Assembly Process of Soil Microbial Communities Under Different Reclamation Measures].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {45}, number = {12}, pages = {7326-7336}, doi = {10.13227/j.hjkx.202312247}, pmid = {39628196}, issn = {0250-3301}, mesh = {*Soil Microbiology ; *Fungi/classification ; *Bacteria/classification/genetics/growth & development/isolation & purification ; Mining ; Nitrogen ; Soil/chemistry ; Phosphorus ; Environmental Restoration and Remediation/methods ; Microbiota ; Ecosystem ; }, abstract = {Reclamation is essential for restoring the ecological function of soil in mining areas. However, the microbiological mechanism of soil ecological function reconstruction under different reclamation measures still needs to be clarified. Clarifying the characteristics of soil bacterial and fungal communities, assembly mechanisms, and their relationship with physicochemical properties under different reclamation measures is crucial for reshaping the ecological stability of soil in mining areas. Metagenomic sequencing technology was combined with the null model and neutral model to analyze the differences in soil microbial diversity, community composition, network structure, and community assembly process between the reclaimed natural recovery area (LH) and the reclamation fertilization area (MM). The results suggested that: ① Compared with that in the LH treatment, the MM treatment significantly increased the soil nutrient content, and the total nitrogen (TN), total phosphorus (TP), available phosphorus (AP), and available potassium (AK) contents increased by 34.70%, 72.72%, 468.98%, and 45.74%, respectively (P<0.05). ② The dominant bacterial and fungal communities did not change under the LH and MM treatments; however, the abundance of bacterial communities changed significantly. Compared with that in the LH treatment, the relative abundance of Acidobacteria increased significantly by 5.4% in the MM treatment, while the relative abundance of Candidatus Rokubacteria decreased significantly by 235.72% (P<0.05). Under different reclamation measures, the indicator microorganisms of bacterial and fungal communities changed. ③ Compared with that in the LH treatment, the MM treatment increased the complexity of bacterial networks, decreased the complexity of fungal networks, and increased the number of soil bacterial nodes and links. The reclamation measures transformed the key bacterial groups from Proteobacteria to Candidatus Rokubacteria and Planctomycetes. The key group of fungi was Ascomycota. 4.) The deterministic process dominated the assembly of bacterial and fungal communities. Homogeneous selection contributed the most to the bacterial community assembly in the LH treatment, and heterogeneous selection contributed the most to the MM treatment. The fungal communities were all dominated by heterogeneous selection. These results provide new insights into the soil microbial community structure and ecological function restoration in coal mining subsidence reclamation areas.}, }
@article {pmid39626557, year = {2025}, author = {Peng, Q and Cheng, S and Huang, X and Pu, Y and Xie, G}, title = {Comprehensive multi-omics analysis of fermented Chinese artichoke: Insights from Flavoromics, metagenomics, and untargeted metabolomics.}, journal = {Food chemistry}, volume = {467}, number = {}, pages = {142278}, doi = {10.1016/j.foodchem.2024.142278}, pmid = {39626557}, issn = {1873-7072}, mesh = {*Fermentation ; *Metabolomics ; *Metagenomics ; *Flavoring Agents/metabolism/chemistry ; *Volatile Organic Compounds/metabolism/chemistry/analysis ; *Taste ; *Bacteria/metabolism/genetics/classification/isolation & purification ; *Cynara scolymus/chemistry/metabolism ; Microbiota ; Fermented Foods/analysis/microbiology ; Multiomics ; East Asian People ; }, abstract = {Fermented Chinese Artichoke, a traditional Chinese fermented vegetable, has a distinctive flavor profile shaped by its fermentation process. This study applied flavoromics, metagenomics, and untargeted metabolomics to comprehensively analyze flavor compounds, microbial communities, and metabolic transformations during fermentation. We identified 43 volatile organic compounds (VOCs), with Terpineol, 1-Hexanol, and Linalool as the predominant components. Metagenomic analysis highlighted Lactiplantibacillus plantarum, Priestia megaterium, and Pediococcus pentosaceus as the dominant species, while Lactiplantibacillus, Pediococcus, and Bacillus were key in flavor development. Untargeted metabolomics further revealed increases in organic acids, amino acids, and umami compounds, contributing to flavor enhancement. These findings offer valuable insights into flavor formation mechanisms in Fermented Chinese Artichoke and provide guidance for improving its industrial fermentation quality.}, }
@article {pmid39626551, year = {2025}, author = {Xu, C and Han, A and Tian, Y and Sun, S}, title = {Based on computer simulation and experimental verification: mining and characterizing novel antimicrobial peptides from soil microbiome.}, journal = {Food chemistry}, volume = {467}, number = {}, pages = {142275}, doi = {10.1016/j.foodchem.2024.142275}, pmid = {39626551}, issn = {1873-7072}, mesh = {*Soil Microbiology ; *Antimicrobial Peptides/chemistry/pharmacology ; Microbiota ; Anti-Bacterial Agents/pharmacology/chemistry ; Computer Simulation ; Microbial Sensitivity Tests ; Klebsiella pneumoniae/drug effects ; Staphylococcus aureus/drug effects/growth & development ; Molecular Docking Simulation ; Escherichia coli/drug effects/genetics ; Bacteria/drug effects/genetics ; Molecular Dynamics Simulation ; }, abstract = {Antimicrobial peptides (AMPs) show great promise for enhancing food safety and extending shelf life, but traditional screening methods are complex and costly. To address these issues, we developed a deep learning-based prediction pipeline to identify potential AMPs from soil metagenomic data, achieving high accuracy (92.71 %) and precision (91.29 %). Based on model scoring, surface charge, and Hemopred and ToxinPred screenings, we identified nine candidate peptides. Peptide P4 (GTAWRWHYRARS) showed the best binding affinity to MrkH in molecular docking studies and was validated through molecular dynamics simulations. The chemically synthesized P4 demonstrated significant antimicrobial activity against Klebsiella pneumoniae, Escherichia coli, and Staphylococcus aureus, indicating its potential as an effective alternative to traditional food antimicrobial agents. This study highlights the effectiveness of our integrated prediction pipeline for discovering new AMPs.}, }
@article {pmid39626421, year = {2024}, author = {Wang, J and Wu, D and Wu, Q and Chen, J and Zhao, Y and Wang, H and Liu, F and Yuan, Q}, title = {Vertical profiles of community and activity of methanotrophs in large lake and reservoir of Southwest China.}, journal = {The Science of the total environment}, volume = {957}, number = {}, pages = {177782}, doi = {10.1016/j.scitotenv.2024.177782}, pmid = {39626421}, issn = {1879-1026}, mesh = {China ; *Lakes/microbiology/chemistry ; *Methane/metabolism/analysis ; *Geologic Sediments/microbiology/chemistry ; Methylococcaceae/genetics/metabolism ; Oxidation-Reduction ; RNA, Ribosomal, 16S ; Environmental Monitoring ; Microbiota ; }, abstract = {Microbial methane oxidation plays a significant role in regulating methane emissions from lakes and reservoirs. However, the differences in methane oxidation activity and methanotrophic community between lakes and reservoirs remain inadequately characterized. In this study, sediment and water samples were collected from the large shallow lake (Dianchi) and deep reservoirs (Dongfeng and Hongjiadu) located in karst area, Southwest China. The results indicated that the rates of aerobic oxidation of methane (AeOM) in lake sediment ranged from 7.1 to 27.7 μg g[-1] d[-1], which was higher than that in reservoirs sediment (1.92 to 11.56 μg g[-1] d[-1]). Similarly, the average AeOM in the water column of lake (104.7 μg L[-1] d[-1]) was much higher than that of reservoirs (46 μg L[-1] d[-1]). The content of sediment organic carbon and dissolved inorganic carbon were important factors that influenced the rates of AeOM in sediment and water column, respectively. 16S rRNA genes sequencing revealed a higher relative abundance of methanotrophs in lake sediments compared to reservoir sediments. The dominant methanotrophic taxa in lake was Methylococcaceae (type Ib), while Methylomonadaceae (type Ia) was predominant in reservoirs. Meanwhile, anaerobic methane-oxidizing microorganisms Candidatus Methylomirabilis and Candidatus Methanoperedens were also abundant in sediments of reservoirs. However, metatranscriptomic analysis revealed that the type I methanotrophs, especially Methylobacter, was most active in the sediment of both lake and reservoir. Water depth and conductivity could be the key controlling factors of the structures of methanotrophic communities in sediment and water column, respectively. Metagenome-assembled genomes suggested that type I methanotrophs exhibited greater motility, as evidenced by a higher number of flagellar assembly genes, while type II methanotrophs demonstrated advantages in metabolic processes such as carbon, phosphorus, and methane metabolism.}, }
@article {pmid39625614, year = {2024}, author = {Saeng-Kla, K and Mhuantong, W and Termsaithong, T and Pinyakong, O and Sonthiphand, P}, title = {Biodegradation of Di-2-Ethylhexyl Phthalate by Mangrove Sediment Microbiome Impacted by Chronic Plastic Waste.}, journal = {Marine biotechnology (New York, N.Y.)}, volume = {27}, number = {1}, pages = {19}, pmid = {39625614}, issn = {1436-2236}, support = {FF-072/2567//Mahidol University (Fundamental Fund: fiscal year 2024 by National Science Research and Innovation Fund (NSRF)/ ; }, mesh = {*Diethylhexyl Phthalate/metabolism ; *Geologic Sediments/microbiology ; *Biodegradation, Environmental ; *Microbiota ; Water Pollutants, Chemical/metabolism ; Plastics/metabolism ; Gordonia Bacterium/metabolism/genetics ; Plasticizers/metabolism ; Wetlands ; Bacteria/metabolism/classification/genetics/isolation & purification ; }, abstract = {Plastic pollution through the leaching of di(2-ethylhexyl) phthalate (DEHP), a widely used plasticizer, has led to the emergence of mangrove pollution. This study aimed to assess the DEHP removal efficiency of indigenous mangrove sediment microbiomes and identify key DEHP degraders using microcosm construction and metagenomic analysis. During the 35-day incubation period, the indigenous mangrove sediment microbiome, affected by chronic plastic pollution, demonstrated a 99% degradation efficiency of 200 mg/kg DEHP. Spearman's correlation analysis suggested that Myxococcales, Methyloligellaceae, Mycobacterium, and Micromonospora were potentially responsible for DEHP degradation. Based on PICRUSt2, the DEHP-degrading pathway in the sediment was predicted to be an anaerobic process involving catechol metabolism through catC, pcaD, pcaI, pcaF, and fadA. Efficient bacterial isolates from the mangrove sediment, identified as Gordonia sp. and Gordonia polyisoprenivorans, were able to degrade DEHP (65-97%) within 7 days and showed the ability to degrade other phthalate esters (PAEs).}, }
@article {pmid39623529, year = {2024}, author = {Ma, J and Sun, S and Cheng, X and Meng, C and Zhao, H and Fu, W and Gao, Y and Ma, L and Yang, Z and Yao, H and Su, J}, title = {Unraveling the role of gut microbiome in predicting adverse events in neoadjuvant therapy for rectal cancer.}, journal = {Human vaccines & immunotherapeutics}, volume = {20}, number = {1}, pages = {2430087}, pmid = {39623529}, issn = {2164-554X}, mesh = {Adult ; Aged ; Female ; Humans ; Male ; Middle Aged ; Chemoradiotherapy/adverse effects/methods ; *Feces/microbiology ; *Gastrointestinal Microbiome ; Immunotherapy/methods/adverse effects ; Metabolome ; Metabolomics ; Metagenomics/methods ; *Neoadjuvant Therapy/adverse effects/methods ; *Rectal Neoplasms/therapy/microbiology ; }, abstract = {Some patients may develop adverse events during neoadjuvant chemoradiotherapy combined with immunotherapy, influencing response rates. The roles of intestinal microbiome and its metabolites in therapeutic adverse events remain unclear. We collected baseline fecal samples from 21 patients with adverse events (AE group) and 11 patients without adverse events (Non-AE group). Their microbiota and metabolome were characterized using metagenomic shotgun sequencing and untargeted metabolomics. At the species level, the gut microbiota in the Non-AE group exhibits significantly higher abundance of Clostridium sp. Alistipes sp. and lower abundance of Lachnoclostridium sp. Weissella cibaria, Weissella confusa, compared to the AE group (p < .05). A total of 58 discriminative metabolites were identified between groups. Beta-alanine metabolism was scattered. Boc-beta-cyano-L-alanine and CoQ9 were significantly increased in patients without adverse events, while linoleic acid increased in patients with adverse events. The increased Alistipes sp. in the Non-AE group was positively correlated with Boc-beta-cyano-L-alanine and negatively correlated with linoleic acid (p < .05). We constructed a combined microbiome-metabolite model to distinguish Non-AE and AE patients with an AUC of 0.963 via the random forest algorithm. Our findings provided a novel insight into the interplay of multispecies microbial cluster and metabolites of rectal patients with adverse events in neoadjuvant chemoradiotherapy combined with immunotherapy. These microbiota and metabolites deserve further investigations to reveal their roles in adverse events, providing clues for better treatment scenarios.Trial registration number: ClinicalTrials.gov identifier: NCT05368051.}, }
@article {pmid39621710, year = {2024}, author = {Mangoma, N and Zhou, N and Ncube, T}, title = {Metagenome-assembled genomes provide insight into the microbial taxonomy and ecology of the Buhera soda pans, Zimbabwe.}, journal = {PloS one}, volume = {19}, number = {12}, pages = {e0299620}, pmid = {39621710}, issn = {1932-6203}, mesh = {Zimbabwe ; *Metagenome ; *Phylogeny ; Metagenomics/methods ; Bacteria/genetics/classification ; Genome, Bacterial ; Ecosystem ; Microbiota/genetics ; Extreme Environments ; }, abstract = {The use of metagenomics has substantially improved our understanding of the taxonomy, phylogeny and ecology of extreme environment microbiomes. Advances in bioinformatics now permit the reconstruction of almost intact microbial genomes, called metagenome-assembled genomes (MAGs), from metagenomic sequence data, allowing for more precise cell-level taxonomic, phylogenetic and functional profiling of uncultured extremophiles. Here, we report on the recovery and characterisation of metagenome-assembled genomes from the Buhera soda pans located in eastern Zimbabwe. This ecosystem has not been studied despite its unique geochemistry and potential as a habitat for unique microorganisms. Metagenomic DNA from the soda pan was sequenced using the DNA Nanoball Sequencing (DNBSEQR) technique. Sequence analysis, done on the Knowledgebase (KBase) platform, involved quality assessment, read assembly, contig binning, and MAG extraction. The MAGs were subjected to taxonomic placement, phylogenetic profiling and functional annotation in order to establish their possible ecological roles in the soda pan ecosystem. A total of 16 bacterial MAGs of medium to high quality were recovered, all distributed among five phyla dominated by Pseudomonadota and Bacillota. Of the ten MAGs that were taxonomically classified up to genus level, five of them belonged to the halophilic/ haloalkaliphilic genera Alkalibacterium, Vibrio, Thioalkalivibrio, Cecembia and Nitrincola, underscoring the importance of haloalkaliphiles in the Buhera soda pans. Functional profiling revealed the possession of diverse carbohydrate-metabolising pathways by the MAGs, with glycolysis and the pentose phosphate pathways appearing to be key pathways in this ecosystem. Several MAGs possessed pathways that implicated them in some key aspects of the nitrogen and sulphur cycle. Some MAGs harboured both sulphate reduction and respiratory pathways, suggesting a possible mechanism of ATP biosynthesis through sulphate respiration. This study demonstrates the feasibility of the recovery and taxonomic and functional annotation of high quality microbial genomes from extreme environments, making it possible to establish the ecological roles and biotechnological potential of uncultured microorganisms.}, }
@article {pmid39621607, year = {2024}, author = {Deel, HL and Manter, DK and Moore, JM}, title = {Rethreading the needle: A novel molecular index of soil health (MISH) using microbial functional genes to predict soil health management.}, journal = {PloS one}, volume = {19}, number = {12}, pages = {e0314072}, pmid = {39621607}, issn = {1932-6203}, mesh = {*Soil Microbiology ; *Soil/chemistry ; *RNA, Ribosomal, 16S/genetics ; Metagenome ; Bacteria/genetics/classification/isolation & purification ; Microbiota/genetics ; Machine Learning ; Ecosystem ; Genes, Microbial ; }, abstract = {Soil health relies on the actions and interactions of an abundant and diverse biological community. Current soil health assessments rely heavily on a suite of soil biological, chemical, and physical indicators, often excluding molecular information. Soil health is critical for sustainable agricultural production, and a comprehensive understanding of how microbial communities provide ecosystem services can help guide management practices. To explore the role of microbial function in soil health, 536 soil samples were collected from 26 U.S. states, representing 52 different crops and grazing lands, and analyzed for various soil health indicators. The bacterial functional profile was characterized using 16S ribosomal RNA gene sequencing paired with PICRUSt2 to predict metagenome functions. Functional data were used as predictors in eXtreme Gradient Boosting (XGBoost), a powerful machine learning algorithm, and enzymes important to soil health indicators were compiled into a Molecular Index of Soil Health (MISH). The overall MISH score significantly correlated with non-molecular measures of soil health and management practice adoption. Additionally, several new enzymes were identified as potential targets to better understand microbial mediation of soil health. This low-cost, DNA-based approach to measuring soil health is robust and generalizable across climates.}, }
@article {pmid39621089, year = {2024}, author = {Singh, K and Gupta, JK and Chanchal, DK and Shinde, MG and Kumar, S and Jain, D and Almarhoon, ZM and Alshahrani, AM and Calina, D and Sharifi-Rad, J and Tripathi, A}, title = {Natural products as drug leads: exploring their potential in drug discovery and development.}, journal = {Naunyn-Schmiedeberg's archives of pharmacology}, volume = {}, number = {}, pages = {}, pmid = {39621089}, issn = {1432-1912}, abstract = {Natural products have been pivotal in drug discovery, offering a wealth of bioactive compounds that significantly contribute to therapeutic developments. Despite the rise of synthetic chemistry, natural products continue to play a crucial role due to their unique chemical structures and diverse biological activities. This study reviews and evaluates the potential of natural products in drug discovery and development, emphasizing the integration of traditional knowledge with modern drug discovery methodologies and addressing the associated challenges. A comprehensive literature search was conducted across PubMed/MedLine, Scopus, Web of Science, Google Scholar, and Cochrane Library, covering publications from 2000 to 2023. Inclusion criteria focused on studies related to natural products, bioactive compounds, medicinal plants, phytochemistry, and AI applications in drug discovery. Data were categorized into source, extraction methods, bioactivity assays, and technological advances. The current review underscores the historical and ongoing importance of natural products in drug discovery. Technological advancements in chromatographic and spectroscopic techniques have improved the isolation and structural elucidation of bioactive compounds. AI and machine learning have streamlined the identification and optimization of natural product leads. Challenges such as biodiversity sustainability and development complexities are discussed, alongside innovative approaches like biosynthetic engineering and metagenomics. Natural products remain a vital source of novel therapeutic agents, providing unique chemical diversity and specific biological activities. Integrating traditional knowledge with modern scientific methods is essential for maximizing the potential of natural products in drug discovery. Despite existing challenges, ongoing research and technological advancements are expected to enhance the efficiency and success of natural product-based drug development.}, }
@article {pmid39620486, year = {2024}, author = {Luo, Y and Sheikh, TMM and Li, X and Yuan, Y and Yao, F and Wang, M and Guo, X and Wu, J and Shafiq, M and Xie, Q and Jiao, X}, title = {Exploring the dynamics of gut microbiota, antibiotic resistance, and chemotherapy impact in acute leukemia patients: A comprehensive metagenomic analysis.}, journal = {Virulence}, volume = {15}, number = {1}, pages = {2428843}, pmid = {39620486}, issn = {2150-5608}, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Metagenomics ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; Male ; Female ; Adult ; Middle Aged ; Feces/microbiology ; Bacteria/genetics/drug effects/classification/isolation & purification ; Leukemia/drug therapy/microbiology/complications ; Drug Resistance, Microbial/genetics ; Aged ; Young Adult ; Antineoplastic Agents/adverse effects ; }, abstract = {Leukemia poses significant challenges to its treatment, and understanding its complex pathogenesis is crucial. This study used metagenomic sequencing to investigate the interplay between chemotherapy, gut microbiota, and antibiotic resistance in patients with acute leukemia (AL). Pre- and post-chemotherapy stool samples from patients revealed alterations in microbial richness, taxa, and antibiotic resistance genes (ARGs). The analysis revealed a decreased alpha diversity, increased dispersion in post-chemotherapy samples, and changes in the abundance of specific bacteria. Key bacteria such as Enterococcus, Klebsiella, and Escherichia coli have been identified as prevalent ARG carriers. Correlation analysis between gut microbiota and blood indicators revealed potential links between microbial species and inflammatory biomarkers, including C-reactive protein (CRP) and adenosine deaminase (ADA). This study investigated the impact of antibiotic dosage on microbiota and ARGs, revealing networks connecting co-occurring ARGs with microbial species (179 nodes, 206 edges), and networks associated with ARGs and antibiotic dosages (50 nodes, 50 edges). Antibiotics such as cephamycin and sulfonamide led to multidrug-resistant Klebsiella colonization. Our analyses revealed distinct microbial profiles with Salmonella enterica elevated post-chemotherapy in NF patients and Akkermansia muciniphila elevated pre-chemotherapy. These microbial signatures could inform strategies to modulate the gut microbiome, potentially mitigating the risk of neutropenic fever in patients undergoing chemotherapy. Finally, a comprehensive analysis of KEGG modules shed light on disrupted metabolic pathways after chemotherapy, providing insights into potential targets for managing side effects. Overall, this study revealed intricate relationships between gut microbiota, chemotherapy, and antibiotic resistance, providing new insights into improving therapy and enhancing patient outcomes.}, }
@article {pmid39620359, year = {2024}, author = {López-Agudelo, VA and Falk-Paulsen, M and Bharti, R and Rehman, A and Sommer, F and Wacker, EM and Ellinghaus, D and Luzius, A and Sievers, LK and Liebeke, M and Kaser, A and Rosenstiel, P}, title = {Defective Atg16l1 in intestinal epithelial cells links to altered fecal microbiota and metabolic shifts during pregnancy in mice.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2429267}, pmid = {39620359}, issn = {1949-0984}, mesh = {Animals ; Female ; Pregnancy ; *Gastrointestinal Microbiome ; Mice ; *Feces/microbiology ; *Autophagy-Related Proteins/genetics/metabolism ; Bacteria/classification/genetics/isolation & purification/metabolism ; RNA, Ribosomal, 16S/genetics ; Intestinal Mucosa/microbiology/metabolism ; Epithelial Cells/microbiology/metabolism ; Crohn Disease/microbiology/metabolism ; Mice, Inbred C57BL ; Metagenomics ; Chemokine CXCL1/genetics/metabolism ; }, abstract = {Throughout gestation, the female body undergoes a series of transformations, including profound alterations in intestinal microbial communities. Changes gradually increase toward the end of pregnancy and comprise reduced α-diversity of microbial communities and an increased propensity for energy harvest. Despite the importance of the intestinal microbiota for the pathophysiology of inflammatory bowel diseases, very little is known about the relationship between these microbiota shifts and pregnancy-associated complications of the disease. Here, we explored the longitudinal dynamics of gut microbiota composition and functional potential during pregnancy and after lactation in Atg16l1[∆IEC] mice carrying an intestinal epithelial deletion of the Crohn's disease risk gene Atg16l1. Using 16S rRNA amplicon and shotgun metagenomic sequencing, we demonstrated divergent temporal shifts in microbial composition between Atg16l1 wildtype and Atg16l1[∆IEC] pregnant mice in trimester 3, which was validated in an independent experiment. Observed differences included microbial genera implicated in IBD such as Lachnospiraceae, Roseburia, Ruminococcus, and Turicibacter. Changes partially recovered after lactation. Additionally, metagenomic and metabolomic analyses suggest an increased capacity for chitin degradation, resulting in higher levels of free N-acetyl-glucosamine products in feces, alongside reduced glucose and myo-inositol levels in serum around the time of delivery. On the host side, we found that the immunological response of Atg16l1[∆IEC] mice is characterized by higher colonic mRNA levels of TNFα and CXCL1 in trimester 3 and a lower weight of offspring at birth. Understanding pregnancy-dependent microbiome changes in the context of IBD may constitute the first step in the identification of fecal microbial biomarkers and microbiota-directed therapies that could help improve precision care for managing pregnancies in IBD patients.}, }
@article {pmid39619205, year = {2024}, author = {Hewson, I and Brandt, M and Budd, K and Breitbart, M and DeRito, C and Gittens, S and Henson, MW and Hylkema, A and Sevier, M and Souza, M and Vilanova-Cuevas, B and Von Hoene, S}, title = {Viral metagenomic investigation of two Caribbean echinoderms, Diadema antillarum (Echinoidea) and Holothuria floridana (Holothuria).}, journal = {PeerJ}, volume = {12}, number = {}, pages = {e18321}, pmid = {39619205}, issn = {2167-8359}, mesh = {Animals ; *Metagenomics ; Caribbean Region ; *Genome, Viral/genetics ; Echinodermata/virology ; Metagenome ; Holothuria/virology/genetics ; Coral Reefs ; Viruses/genetics/isolation & purification/classification ; Virome/genetics ; }, abstract = {BACKGROUND: Echinoderms play crucial roles in coral reef ecosystems, where they are significant detritivores and herbivores. The phylum is widely known for its boom and bust cycles, driven by food availability, predation pressure and mass mortalities. Hence, surveillance of potential pathogens and associates of grossly normal specimens is important to understanding their roles in ecology and mass mortality.
METHODS: We performed viral surveillance in two common coral reef echinoderms, Diadema antillarum and Holothuria floridana, using metagenomics. Urchin specimens were obtained during the 2022 Diadema antillarum scuticociliatosis mass mortality event from the Caribbean and grossly normal H. floridana specimens from a reef in Florida. Viral metagenomes were assembled and aligned against viral genomes and protein encoding regions. Metagenomic reads and previously sequenced transcriptomes were further investigated for putative viral elements by Kraken2.
RESULTS: D. antillarum was devoid of viruses typically seen in echinoderms, but H. floridana yielded viral taxa similar to those found in other sea cucumbers, including Pisoniviricetes (Picornaviruses), Ellioviricetes (Bunyaviruses), and Magsaviricetes (Nodaviruses). The lack of viruses detected in D. antillarum may be due to the large amount of host DNA in viral metagenomes, or because viruses are less abundant in D. antillarum tissues when compared to H. floridana tissues. Our results also suggest that RNA amplification approach may influence viral representation in viral metagenomes. While our survey was successful in describing viruses associated with both echinoderms, our results indicate that viruses are less pronounced in D. antillarum than in other echinoderms. These results are important in context of wider investigation on the association between viruses and D. antillarum mass mortalities, since the conventional method used in this study was unsuccessful.}, }
@article {pmid39616358, year = {2024}, author = {Dell'Olio, A and Scott, WT and Taroncher-Ferrer, S and San Onofre, N and Soriano, JM and Rubert, J}, title = {Tailored impact of dietary fibers on gut microbiota: a multi-omics comparison on the lean and obese microbial communities.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {250}, pmid = {39616358}, issn = {2049-2618}, support = {79441//'European Union's Horizon 2020 Research and Innovation programme' for the Marie Skłodowska-Curie/ ; RYC2018-024850-I//Spanish Ministry of Science and Innovation for the Ramón y Cajal fellowship/ ; }, mesh = {*Dietary Fiber/metabolism ; *Obesity/microbiology ; *Gastrointestinal Microbiome ; *Malus/microbiology ; Humans ; Bacteria/classification/genetics/metabolism/isolation & purification ; Metagenomics ; Pectins/metabolism ; Metabolomics ; Cellulose/metabolism ; Bioreactors/microbiology ; Multiomics ; }, abstract = {BACKGROUND: Previous studies have shown that microbial communities differ in obese and lean individuals, and dietary fiber can help reduce obesity-related conditions through diet-gut microbiota interactions. However, the mechanisms by which dietary fibers shape the gut microbiota still need to be elucidated. In this in vitro study, we examined how apple fibers affect lean and obese microbial communities on a global scale. We employed a high-throughput micro-matrix bioreactor system and a multi-omics approach to identify the key microorganisms and metabolites involved in this process.
RESULTS: Initially, metagenomics and metabolomics data indicated that obese and lean microbial communities had distinct starting microbial communities. We found that obese microbial community had different characteristics, including higher levels of Ruminococcus bromii and lower levels of Faecalibacterium prausnitzii, along with an increased Firmicutes:Bacteroides ratio. Afterward, we exposed obese and lean microbial communities to an apple as a representative complex food matrix, apple pectin as a soluble fiber, and cellulose as an insoluble fiber. Dietary fibers, particularly apple pectin, reduced Acidaminococcus intestini and boosted Megasphaera and Akkermansia in the obese microbial community. Additionally, these fibers altered the production of metabolites, increasing beneficial indole microbial metabolites. Our results underscored the ability of apple and apple pectin to shape the obese gut microbiota.
CONCLUSION: We found that the obese microbial community had higher branched-chain amino acid catabolism and hexanoic acid production, potentially impacting energy balance. Apple dietary fibers, especially pectin, influenced the obese microbial community, altering both species and metabolites. Notably, the apple pectin feeding condition affected species like Klebsiella pneumoniae and Bifidobacterium longum. By using genome-scale metabolic modeling, we discovered a mutualistic cross-feeding relationship between Megasphaera sp. MJR8396C and Bifidobacterium adolescentis. This in vitro study suggests that incorporating apple fibers into the diets of obese individuals can help modify the composition of gut bacteria and improve metabolic health. This personalized approach could help mitigate the effects of obesity. Video Abstract.}, }
@article {pmid39616151, year = {2024}, author = {Wang, J and Zhong, H and Chen, Q and Ni, J}, title = {Adaption mechanism and ecological role of CPR bacteria in brackish-saline groundwater.}, journal = {NPJ biofilms and microbiomes}, volume = {10}, number = {1}, pages = {141}, pmid = {39616151}, issn = {2055-5008}, support = {52070002, 51721006, 51925901//National Natural Science Foundation of China (National Science Foundation of China)/ ; 52209078//National Natural Science Foundation of China (National Science Foundation of China)/ ; 2023T160020//China Postdoctoral Science Foundation/ ; }, mesh = {*Groundwater/microbiology ; *Bacteria/genetics/classification/isolation & purification ; *Phylogeny ; Salinity ; Biodiversity ; Metagenome ; Adaptation, Physiological ; Nitrogen/metabolism ; Carbon/metabolism ; Sulfur/metabolism ; Metagenomics/methods ; Bacterial Physiological Phenomena ; }, abstract = {Candidate phyla radiation (CPR) constitutes a substantial fraction of bacterial diversity, yet their survival strategies and biogeochemical roles in brackish-saline groundwater remain unknown. By reconstructing 399 CPR metagenome-assembled genomes (MAGs) and 2007 non-CPR MAGs, we found that CPR, affiliated with 44 previously proposed phyla and 8 putative novel phyla, played crucial roles in maintaining the microbial stability and complexity in groundwater. Metabolic reconstructions revealed that CPR participated in diverse processes, including carbon, nitrogen, and sulfur cycles. Adaption of CPR to high-salinity conditions could be attributed to abundant genes associated with heat shock proteins, osmoprotectants, and sulfur reduction, as well as their cooperation with Co-CPR (non-CPR bacteria co-occurred with CPR) for metabolic support and resource exchange. Our study enhanced the understanding of CPR biodiversity in high-salinity groundwater, highlighting the collaborative roles of self-adaptive CPR bacteria and their reciprocal partners in coping with salinity stress, maintaining ecological stability, and mediating biogeochemical cycling.}, }
@article {pmid39615045, year = {2024}, author = {Valentino, V and De Filippis, F and Marotta, R and Pasolli, E and Ercolini, D}, title = {Genomic features and prevalence of Ruminococcus species in humans are associated with age, lifestyle, and disease.}, journal = {Cell reports}, volume = {43}, number = {12}, pages = {115018}, doi = {10.1016/j.celrep.2024.115018}, pmid = {39615045}, issn = {2211-1247}, mesh = {Humans ; *Ruminococcus/genetics ; *Life Style ; Genome, Bacterial ; Adult ; Gastrointestinal Microbiome/genetics ; Metagenome ; Phylogeny ; Genomics/methods ; Male ; Middle Aged ; Female ; Aged ; }, abstract = {The genus Ruminococcus is dominant in the human gut, but higher levels of some species, such as R. gnavus, R. torques, and R. bromii, have been linked to health or disease. In this study, we analyzed >9,000 Ruminococcus metagenome-assembled genomes (MAGs) reconstructed from >5,000 subjects and revealed significant links between the prevalence of some species/subspecies and geographic origin, age, lifestyle, and disease, with subspecies prevalent in specific subpopulations showing divergent metabolic potential. Furthermore, Ruminococcus species from Lachnospiraceae encoded for carbohydrate-active enzymes (CAZy) potentially involved in the metabolism of human N- and O-glycans, whereas those from Oscillospiraceae appear to be more adapted toward fiber metabolism. These new findings contribute to elucidating the potential functional role of Ruminococcus in specific lifestyles and diseases and to decipher the diversity and the adaptation of members of this genus to the human gut.}, }
@article {pmid39614549, year = {2024}, author = {Wicaksono, WA and Akinyemi, OE and Wassermann, B and Bickel, S and Suwanto, A and Berg, G}, title = {Traditionally produced tempeh harbors more diverse bacteria with more putative health-promoting properties than industrially produced tempeh.}, journal = {Food research international (Ottawa, Ont.)}, volume = {196}, number = {}, pages = {115030}, doi = {10.1016/j.foodres.2024.115030}, pmid = {39614549}, issn = {1873-7145}, mesh = {*Bacteria/genetics/classification/metabolism ; *Food Microbiology ; Humans ; Soy Foods/microbiology ; Fermentation ; Rhizopus/genetics/metabolism ; Hygiene ; Indonesia ; Microbiota ; Fermented Foods/microbiology ; }, abstract = {In recent years, there has been a significant shift towards industrialization in food production, resulting in the implementation of higher hygiene standards globally. Our study focused on examining the impact of hygiene standards on tempeh, a popular Rhizopus-based fermented soybean product native to Indonesia, and now famous around the world. We observed that tempeh produced with standardized hygiene measures exhibited a microbiome with comparable bacterial abundances but a markedly different community structure and function than traditionally produced tempeh. In detail, we found a decreased bacterial abundance of lactobacilli and enterobacteria, bacterial diversity, different indicator taxa, and significantly changed community structure in industrial tempeh. A similar picture was found for functional analysis: the quantity of bacterial genes was similar but qualitative changes were found for genes associated with human health. The resistome of tempeh varied based on its microbiome composition. The higher number of antimicrobial resistance genes in tempeh produced without standardized hygiene measures mainly belong to multidrug efflux pumps known to occur in plant-based food. Our findings were confirmed by functional insights into genomes and metagenome-assembled genomes from the dominant bacteria, e.g. Leuconostoc, Limosilactobacillus, Lactobacillus, Enterococcus, Paenibacillus, Azotobacter and Enterobacter. They harboured an impressive spectrum of genes important for human health, e.g. for production of vitamin B1, B7, B12, and K, iron and zinc transport systems and short chain fatty acid production. In conclusion, industrially produced tempeh harbours a less diverse microbiome than the traditional one. Although this ensures production at large scales as well as biosafety, in the long-term it can lead to potential effects for human gut health.}, }
@article {pmid39614478, year = {2024}, author = {Yu, H and Li, Z and Zheng, D and Chen, C and Ge, C and Tian, H}, title = {Exploring microbial dynamics and metabolic pathways shaping flavor profiles in Huangjiu through metagenomic analysis.}, journal = {Food research international (Ottawa, Ont.)}, volume = {196}, number = {}, pages = {115036}, doi = {10.1016/j.foodres.2024.115036}, pmid = {39614478}, issn = {1873-7145}, mesh = {*Taste ; *Metagenomics/methods ; *Fermentation ; *Wine/microbiology/analysis ; *Metabolic Networks and Pathways ; Microbiota/genetics ; Oryza/microbiology ; Flavoring Agents/metabolism ; Humans ; Food Microbiology ; Odorants/analysis ; Male ; }, abstract = {In the production of Huangjiu (Chinese rice wine), fermentation microbiota plays a crucial role in flavor formation. This study investigates the microbial dynamics and metabolic pathways that shape the flavor profiles of Huangjiu using different starters. Sensory evaluation and metabolite analysis of six starters revealed significant differences in ester, fruity, and sweet aromas. Saccharomyces, Aspergillus, and Rhizopus were identified as the dominant genera significantly impacting fermentation. Metagenomic species and functional gene annotations of Huangjiu starters elucidated the metabolic pathways for key flavor compounds synthesis pathways. Enzyme genes involved in these pathways were classified and annotated to microbial genera using the NR database, identifying 231 classes of relevant catalytic enzymes and 154 microbial genera. A metabolic relationship between flavor compound formation and different microbial genera was established using catalytic enzymes as a bridge. This study highlights the impact of starter composition on the final product and provides new insights for optimizing starters to enhance Huangjiu flavor quality.}, }
@article {pmid39614477, year = {2024}, author = {Yang, L and Fan, W and Xu, Y}, title = {Effects of storage period and season on the microecological characteristics of Jiangxiangxing high-temperature Daqu.}, journal = {Food research international (Ottawa, Ont.)}, volume = {196}, number = {}, pages = {115034}, doi = {10.1016/j.foodres.2024.115034}, pmid = {39614477}, issn = {1873-7145}, mesh = {*Seasons ; *Hot Temperature ; *Food Storage/methods ; *Microbiota ; Fermentation ; Bacteria/metabolism/classification ; Food Microbiology ; Metabolomics ; Proteomics ; China ; Metagenomics ; Camellia sinensis/microbiology/metabolism ; Fungi/metabolism/classification ; }, abstract = {Metagenomics, non-targeted metabolomics, and metaproteomics were employed to analyze the microecological succession of high-temperature Daqu during storage, elucidate the adaptation mechanism of the microbial community of Daqu to storage environments, and clarify the microecological characteristics of Daqu during different seasons. During storage, the relative abundances of Bacillus, Oceanobacillus, Staphylococcus, and Aspergillus in Daqu had significantly increased, while those of Kroppenstedtia, Saccharopolyspora, Thermoascus, and Thermomyces had significantly decreased. During the first 3 months of storage, compound metabolism of Daqu was primarily dominated by generation of small molecular substances and then shifted to metabolism of amino sugars. During the storage process, homogeneous selection (15.57 %) and homogeneous diffusion (14.86 %) of the microbial communities of Daqu were much larger than during the fermentation process, while the variable selection assembly (29.43 %) was smaller than during the fermentation process. Among the 2509 proteins identified in the four-season Daqu, bacterial protein expression was 1.46-fold greater than that of fungi. Seasonal factors influenced the function of Daqu by alterations to Bacillus subtilis, Oceanobacillus iheyensis, and Aspergillus nidulans and other microbial functions. Carbon and benzoic acid metabolism of Daqu was relatively increased during the spring, while metabolism of alkaloids and tyrosine was upregulated during the summer, amino acid synthesis and starch metabolism were enriched during the autumn, and peptidoglycan synthesis was relatively greater during the winter. Adjusting the moisture content of Daqu during the storage period was shown to reduce microecological differentiation caused by seasonal temperature variations.}, }
@article {pmid39614169, year = {2024}, author = {Tang, H and Du, S and Niu, Z and Zhang, D and Tang, Z and Chen, H and Chen, Z and Zhang, M and Xu, Y and Sun, Y and Fu, X and Norback, D and Shao, J and Zhao, Z}, title = {Nasal, dermal, oral and indoor dust microbe and their interrelationship in children with allergic rhinitis.}, journal = {BMC microbiology}, volume = {24}, number = {1}, pages = {505}, pmid = {39614169}, issn = {1471-2180}, mesh = {Humans ; *Dust/analysis ; Male ; Child ; Female ; *Rhinitis, Allergic/microbiology ; Case-Control Studies ; *RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/isolation & purification/genetics ; *Skin/microbiology ; *Mouth/microbiology ; *Microbiota ; Nasal Cavity/microbiology ; Air Pollution, Indoor/analysis ; Child, Preschool ; Metagenomics/methods ; Nose/microbiology ; }, abstract = {BACKGROUND: Allergic rhinitis (AR) subjects might have their microenvironment changed due to pathogenesis and living environment. Whether the nasal microbe in AR children differs from healthy subjects and how it interplays with dermal, oral and indoor dust microbe needs to be elucidated.
METHODS: In this case-control study, we analyzed and compared the bacterial characterization and associations in nasal, dermal, oral swab samples and dust samples in 62 children with physician-diagnosed AR(cases) and 51 age- and gender-matched healthy ones with no history of allergic diseases(controls). Full-length 16S rRNA sequencing(swabs) and shotgun metagenomics(dust) were applied. Bacterial diversity, composition, abundance difference characteristics and fast expectation-maximization for microbial source tracking(FEAST) analysis were performed and compared between cases and controls.
RESULTS: The α-diversity of dust microorganisms in AR was lower than that in control group (P = 0.034), and the β-diversity indices of microorganisms in nasal cavity (P = 0.020), skin (P = 0.001) and dust (P = 0.004) were significantly different from those in control group. At species levels, a total of 10, 15, 12, and 15 bacterial species were differentially enriched in either cases or controls in nasal, dermal, oral, and dust samples, respectively(Linear Discriminant Analysis(LDA) score > 2, P < 0.05). Staphylococcus epidermidis was the single species simultaneously more abundant in nasal, dermal and dust samples in AR children. By FEAST analysis, 8.85% and 10.11% of S. epidermidis in AR dermal and dust samples came from nasal cavity. These proportions were significantly higher than those in controls (2.70% and 3.86%) (P < 0.05). The same significantly higher transfer proportions(P < 0.05) were observed for Staphylococcus aureus enriched in the nasal cavity in AR children. Classification models by random forest regression at species levels showed, bacterial species enriched in indoor dust, nasal and dermal samples had substantial power in distinguishing AR children from healthy ones, with the highest power in the dust samples (AUC = 0.88) followed by nasal(AUC = 0.81) and dermal ones(AUC = 0.80).
CONCLUSIONS: Our study presented the microbial enrichment characteristics in AR children both in the living environment(dust) and body sites exposed to environment through inhalation(nasal cavity), contact(skin) and ingestion(oral cavity) pathways, respectively. Nasal S.epidermidis and S.aureus had dominant influences on dust and other body sites in AR children.}, }
@article {pmid39614167, year = {2024}, author = {Mangoma, N and Zhou, N and Ncube, T}, title = {Metagenomic insights into the microbial community of the Buhera soda pans, Zimbabwe.}, journal = {BMC microbiology}, volume = {24}, number = {1}, pages = {510}, pmid = {39614167}, issn = {1471-2180}, mesh = {Zimbabwe ; *Metagenomics ; *Bacteria/genetics/classification/isolation & purification/metabolism ; *Microbiota/genetics ; Salinity ; Phylogeny ; Hydrogen-Ion Concentration ; Archaea/genetics/classification/metabolism/isolation & purification ; Water Microbiology ; }, abstract = {BACKGROUND: Soda pans are unique, natural aquatic environments characterised by elevated salinity and alkalinity, creating a distinctive and often extreme geochemistry. The microbiomes of soda pans are unique, with extremophiles such as halophiles, alkaliphiles and haloalkaliphiles being important. Despite being dominated by mostly unculturable inhabitants, soda pans hold immense biotechnological potential. The application of modern "omics-based" techniques helps us better understand the ecology and true extend of the biotechnological potential of soda pan microbiomes. In this study, we used a shotgun metagenomic approach to determine the microbial diversity and functional profile of previously unexplored soda pans located in Buhera, Eastern Zimbabwe. A combination of titrimetry and inductively coupled plasma optical emission spectroscopy (ICP‒OES) was used to perform physico-chemical analysis of the soda pan water.
RESULTS: Physicochemical analysis revealed that the Buhera soda pans are highly alkaline, with a pH range of 8.74 to 11.03, moderately saline (2.94 - 7.55 g/L), and have high carbonate (3625 mg/L) and bicarbonate ion (1325 mg/L) alkalinity. High levels of sulphate, phosphate, chloride and fluoride ions were detected. Metagenomic analysis revealed that domain Bacteria dominated the soda pan microbial community, with Pseudomonadota and Bacillota being the dominant phyla. Vibrio was shown to be the predominant genus, followed by Clostridium, Candidatus Brevefilum, Acetoanaerobium, Thioalkalivibrio and Marinilactibacillus. Archaea were also detected, albeit at a low prevalence of 1%. Functional profiling revealed that the Buhera soda pan microbiome is functionally diverse, has hydrolytic-enzyme production potential and is capable of supporting a variety of geochemical cycles.
CONCLUSIONS: The results of this pioneering study showed that despite their extreme alkalinity and moderate salinity, the Buhera soda pans harbour a taxonomically and functionally diverse microbiome dominated by bacteria. Future work will aim towards establishing the full extent of the soda pan's biotechnological potential, with a particular emphasis on potential enzyme production.}, }
@article {pmid39612821, year = {2025}, author = {Rosenqvist, T and Hilding, J and Suarez, C and Paul, CJ}, title = {Microbial communities in slow sand filters for drinking water treatment adapt to organic matter altered by ozonation.}, journal = {Water research}, volume = {270}, number = {}, pages = {122843}, doi = {10.1016/j.watres.2024.122843}, pmid = {39612821}, issn = {1879-2448}, mesh = {*Ozone ; *Drinking Water/microbiology ; *Water Purification/methods ; *Filtration ; Sand ; Bacteria/genetics ; Microbiota ; }, abstract = {Changing natural organic matter quality from anthropogenic activity and stricter requirements for micropollutant removal challenges existing systems for drinking water production. Ozonation of water followed by biofiltration, such as passage through a slow sand filter (SSF), is a partial solution. Biofiltration relies on biofilms (microbial communities within extracellular matrices). However, the effects of ozonation on SSF microbial communities are unknown. In this study, genome-resolved and read-based metagenomics were used to compare the microbial communities of two full-scale SSFs employing conventional pre-treatment to a 20 m[2] SSF operated in parallel with ozonation as additional pre-treatment. The SSF microbial community receiving ozonated water was less diverse than those receiving non-ozonated water. Families Hyphomicrobiaceae, Acetobacteraceae, Sphingomonadaceae and Burkholderiaceae were more abundant when ozone was used, as were genes for metabolism of single-carbon organic compounds. Conversely, genes for metabolism of aromatic compounds and fatty acids were less abundant. Metagenome assembled genomes associated with the non-ozonated SSFs were enriched with several glycoside hydrolases, while those associated with the ozonated SSF were enriched with genes for 1-2 carbon compound metabolism. No indications of increased microbial risk (pathogens or antibiotic resistance genes) were detected as a consequence of ozonation. This study shows how microbial communities of SSFs adapt to changes in organic matter quality, highlighting the key role of biofilters for production of safe and sustainable drinking water in a changing climate.}, }
@article {pmid39611142, year = {2024}, author = {Zhang, L and Zhang, H and Su, S and Jia, Y and Liang, C and Fang, Y and Hong, D and Li, T and Ma, F}, title = {Risk factor assessment and microbiome analysis in peritoneal dialysis-related peritonitis reveal etiological characteristics.}, journal = {Frontiers in immunology}, volume = {15}, number = {}, pages = {1443468}, pmid = {39611142}, issn = {1664-3224}, mesh = {Humans ; *Peritonitis/microbiology/etiology/diagnosis ; *Peritoneal Dialysis/adverse effects ; Male ; Female ; Middle Aged ; Risk Factors ; *Gastrointestinal Microbiome ; Aged ; Risk Assessment ; Adult ; Metagenomics/methods ; High-Throughput Nucleotide Sequencing ; }, abstract = {BACKGROUND: Peritoneal dialysis-related peritonitis (PDRP) is one of the most common complications of peritoneal dialysis (PD). Understanding the risk factors and etiological characteristics is indispensable for infection prevention and improving the outcome and life quality.
METHODS: A total of 70 PD patients were separated into the PDRP group (n=25) and the control group (n=45). Variables, including gender, age, body mass index, primary diseases, and history of basic diseases, in the two groups were analyzed to assess the risk factors of PDRP. Metagenomic next-generation sequencing (mNGS) and microbial culture were compared in detecting pathogenic microorganisms. Gut microbiota analysis was performed in 35 PDRP patients based on mNGS data.
RESULTS: Dialysis time and times of dialysate change were the risk factors of PDRP, and times of dialysate change was the independent risk factor of PDRP (p = 0.046). mNGS produced higher sensitivity (65.79%) than microbial culture (36.84%) in identifying pathogenic microorganisms. Staphylococcus aureus and Klebsiella pneumoniae (four cases) were the most frequent pathogens causing PDRP, followed by Staphylococcus capitis (three cases). β diversity of the gut microbiota was significantly different between patients with fewer times of dialysate change (≤4) and more (>5), as well as between patients with gram-positive (G+) bacterial and gram-negative (G-) bacterial infection.
CONCLUSION: The dialysis time and times of dialysate changes not only are risk factors for peritonitis in PD patients but also stimulate significant changes in the gut microbiome structure in PDRP patients. These findings may provide a novel viewpoint for the management of patients with PDRP.}, }
@article {pmid39611041, year = {2024}, author = {Liu, L and Lian, ZH and Lv, AP and Salam, N and Zhang, JC and Li, MM and Sun, WM and Tan, S and Luo, ZH and Gao, L and Yuan, Y and Ming, YZ and OuYang, YT and Li, YX and Liu, ZT and Hu, CJ and Chen, Y and Hua, ZS and Shu, WS and Hedlund, BP and Li, WJ and Jiao, JY}, title = {Insights into chemoautotrophic traits of a prevalent bacterial phylum CSP1-3, herein Sysuimicrobiota.}, journal = {National science review}, volume = {11}, number = {11}, pages = {nwae378}, pmid = {39611041}, issn = {2053-714X}, abstract = {Candidate bacterial phylum CSP1-3 has not been cultivated and is poorly understood. Here, we analyzed 112 CSP1-3 metagenome-assembled genomes and showed they are likely facultative anaerobes, with 3 of 5 families encoding autotrophy through the reductive glycine pathway (RGP), Wood-Ljungdahl pathway (WLP) or Calvin-Benson-Bassham (CBB), with hydrogen or sulfide as electron donors. Chemoautotrophic enrichments from hot spring sediments and fluorescence in situ hybridization revealed enrichment of six CSP1-3 genera, and both transcribed genes and DNA-stable isotope probing were consistent with proposed chemoautotrophic metabolisms. Ancestral state reconstructions showed that the ancestors of phylum CSP1-3 may have been acetogens that were autotrophic via the RGP, whereas the WLP and CBB were acquired by horizontal gene transfer. Our results reveal that CSP1-3 is a widely distributed phylum with the potential to contribute to the cycling of carbon, sulfur and nitrogen. The name Sysuimicrobiota phy. nov. is proposed.}, }
@article {pmid39609882, year = {2024}, author = {Cloarec, LA and Bacchetta, T and Bruto, M and Leboulanger, C and Grossi, V and Brochier-Armanet, C and Flandrois, JP and Zurmely, A and Bernard, C and Troussellier, M and Agogué, H and Ader, M and Oger-Desfeux, C and Oger, PM and Vigneron, A and Hugoni, M}, title = {Lineage-dependent partitioning of activities in chemoclines defines Woesearchaeota ecotypes in an extreme aquatic ecosystem.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {249}, pmid = {39609882}, issn = {2049-2618}, mesh = {*Archaea/classification/genetics/metabolism ; *Lakes/microbiology ; *Phylogeny ; *Ecotype ; Ecosystem ; Metagenomics ; Microbiota ; Genome, Archaeal ; Water Microbiology ; Biodiversity ; }, abstract = {BACKGROUND: DPANN archaea, including Woesearchaeota, encompass a large fraction of the archaeal diversity, yet their genomic diversity, lifestyle, and role in natural microbiomes remain elusive. With an archaeal assemblage naturally enriched in Woesearchaeota and steep vertical geochemical gradients, Lake Dziani Dzaha (Mayotte) provides an ideal model to decipher their in-situ activity and ecology.
RESULTS: Using genome-resolved metagenomics and phylogenomics, we identified highly diversified Woesearchaeota populations and defined novel halophilic clades. Depth distribution of these populations in the water column showed an unusual double peak of abundance, located at two distinct chemoclines that are hotspots of microbial diversity in the water column. Genome-centric metatranscriptomics confirmed this vertical distribution and revealed a fermentative activity, with acetate and lactate as end products, and active cell-to-cell processes, supporting strong interactions with other community members at chemoclines. Our results also revealed distinct Woesearchaeota ecotypes, with different transcriptional patterns, contrasted lifestyles, and ecological strategies, depending on environmental/host conditions.
CONCLUSIONS: This work provides novel insights into Woesearchaeota in situ activity and metabolism, revealing invariant, bimodal, and adaptative lifestyles among halophilic Woesearchaeota. This challenges our precepts of an invariable host-dependent metabolism for all the members of this taxa and revises our understanding of their contributions to ecosystem functioning and microbiome assemblage. Video Abstract.}, }
@article {pmid39609616, year = {2024}, author = {Kim, M and Parrish, RC and Tisza, MJ and Shah, VS and Tran, T and Ross, M and Cormier, J and Baig, A and Huang, CY and Brenner, L and Neuringer, I and Whiteson, K and Harris, JK and Willis, AD and Lai, PS}, title = {Host DNA depletion on frozen human respiratory samples enables successful metagenomic sequencing for microbiome studies.}, journal = {Communications biology}, volume = {7}, number = {1}, pages = {1590}, pmid = {39609616}, issn = {2399-3642}, support = {R01 AI144119/AI/NIAID NIH HHS/United States ; R21 AI175965/AI/NIAID NIH HHS/United States ; R35 GM133420/GM/NIGMS NIH HHS/United States ; T32 HL116275/HL/NHLBI NIH HHS/United States ; }, mesh = {Humans ; *Metagenomics/methods ; *Microbiota/genetics ; *Sputum/microbiology ; *Cystic Fibrosis/microbiology ; Bronchoalveolar Lavage Fluid/microbiology ; Freezing ; Adult ; Cryopreservation ; Female ; High-Throughput Nucleotide Sequencing/methods ; Bacteria/genetics/isolation & purification/classification ; Sequence Analysis, DNA/methods ; Male ; Respiratory System/microbiology ; }, abstract = {Most respiratory microbiome studies use amplicon sequencing due to high host DNA. Metagenomics sequencing offers finer taxonomic resolution, phage assessment, and functional characterization. We evaluated five host DNA depletion methods on frozen nasal swabs from healthy adults, sputum from people with cystic fibrosis (pwCF), and bronchoalveolar lavage (BAL) from critically ill patients. Median sequencing depth was 76.4 million reads per sample. Untreated nasal, sputum, and BAL had 94.1%, 99.2%, and 99.7% host reads, respectively. Host depletion effects varied by sample type, generally increasing microbial reads, species and functional richness; this was mediated by higher effective sequencing depth. Rarefaction curves showed species richness saturation at 0.5-2 million microbial reads. Most methods did not change Morisita-Horn dissimilarity for BAL and nasal samples although the proportion of gram-negative bacteria decreased for sputum from pwCF. Freezing did not affect the viability of Staphylococcus aureus but reduced the viability of Pseudomonas aeruginosa and Enterobacter spp.; this was mitigated by adding a cryoprotectant. QIAamp-based host depletion minimally impacted gram-negative viability even in non-cryoprotected frozen isolates. While some host depletion methods may shift microbial composition, metagenomics sequencing without host depletion severely underestimates microbial diversity of respiratory samples due to shallow effective sequencing depth and is not recommended.}, }
@article {pmid39608999, year = {2024}, author = {Climacosa, FMM and Anlacan, VMM and Gordovez, FJA and Reyes, JCB and Tabios, IKB and Manalo, RVM and Cruz, JMC and Asis, JLB and Razal, RB and Abaca, MJM and Dacasin, AB and Espiritu, APN and Gapaz, NCLL and Lee Yu, MHL}, title = {Monitoring drug Efficacy through Multi-Omics Research initiative in Alzheimer's Disease (MEMORI-AD): A protocol for a multisite exploratory prospective cohort study on the drug response-related clinical, genetic, microbial and metabolomic signatures in Filipino patients with Alzheimer's disease.}, journal = {BMJ open}, volume = {14}, number = {11}, pages = {e078660}, pmid = {39608999}, issn = {2044-6055}, mesh = {Humans ; *Alzheimer Disease/drug therapy/genetics ; Philippines ; Prospective Studies ; Aged ; Cholinesterase Inhibitors/therapeutic use ; Rivastigmine/therapeutic use ; Donepezil/therapeutic use ; Cross-Sectional Studies ; Memantine/therapeutic use ; Male ; Female ; Metabolomics ; Gastrointestinal Microbiome/drug effects ; Multiomics ; }, abstract = {INTRODUCTION: Dementia is one of the leading causes of disability among older people aged 60 years and above, with majority eventually being diagnosed with Alzheimer's disease (AD). Pharmacological agents approved for dementia include acetylcholinesterase enzyme (AChE) inhibitors like rivastigmine, donepezil and galantamine and the N-methyl-D-aspartate (NMDA) receptor antagonist memantine, prescribed as monotherapy or in combination with each other, depending on the severity of disease. There is currently no available study demonstrating the clinical response to these drugs for AD in the Filipino population. Hence, this protocol aims to characterise the clinical, genetic, microbial and metabolic factors associated with drug responses to donepezil, rivastigmine and/or memantine for AD in a cohort of Filipinos with late-onset AD.
METHODS AND ANALYSIS: This protocol involves a multisite descriptive study that will use two study designs: (1) a descriptive, cross-sectional study to characterise the clinical profile of Filipino dementia patients with AD and (2) an exploratory prospective cohort study to investigate drug response-related genetic, gut microbiome and metabolome signatures of a subset of the recruited AD patients. At least 153 patients with mild or moderate AD aged 65 years old and above will be recruited regardless of their treatment status. A subset of these patients (n=60) who meet inclusion and exclusion criteria will be included further in the exploratory cohort study. These patients will be grouped according to their baseline medications and will be observed for treatment response in 6 months. The cognitive, functional and behavioural domains of patients and levels of functioning will be measured using different assessment tools. Drug responses of Filipino patients will then be investigated employing multi-omics technology to characterise genetic variations via whole exome sequencing, gut microbiome profile via shotgun metagenomic sequencing and metabolome profile via liquid chromatography with mass spectrometry.
ETHICS AND DISSEMINATION: The study has received ethical clearance from the Department of Health Single Joint Research Ethics Board (SJREB-2022-15). Results of psychometric scales will be made available to enrolled patients. The study results will be presented at national/international conferences and published in international peer-reviewed scientific journals, and summaries of the results will be provided to the study funders and institutional review boards of the three tertiary referral hospitals.
TRIAL REGISTRATION NUMBER: Philippine Health Research Registry ID PHRR230220-0054116; ClinicalTrials.gov ID NCT05801380.}, }
@article {pmid39608199, year = {2025}, author = {Bhat, AH and Malik, IM and Tak, H and Ganai, BA and Bharti, P}, title = {Host, parasite, and microbiome interaction: Trichuris ovis and its effect on sheep gut microbiota.}, journal = {Veterinary parasitology}, volume = {333}, number = {}, pages = {110356}, doi = {10.1016/j.vetpar.2024.110356}, pmid = {39608199}, issn = {1873-2550}, mesh = {Animals ; Sheep ; *Sheep Diseases/parasitology/microbiology ; *Gastrointestinal Microbiome ; *Trichuris ; *Host-Parasite Interactions ; *Trichuriasis/veterinary/parasitology/microbiology ; RNA, Ribosomal, 16S/genetics ; Cecum/microbiology/parasitology ; Bacteria/classification/genetics/isolation & purification ; }, abstract = {Sheep that are infected with gastrointestinal helminths experience a significant impact on their health and productivity. Among the helminths, nematodes like Haemonchus contortus, Oesophagostomum spp., Bunostomum trigonocephalum, Nematodirus battus, Trichostrongylus spp. and Teladorsagia circumcincta are particularly pathogenic. Understanding the interactions among parasites, hosts, and their microbiomes is crucial in developing new approaches in the management of parasites. This study examines the bacterial profile of Trichuris ovis, a highly prevalent nematode among Kashmir Merino sheep, and the influence of nematode infection on the caecal microbiome of its host. Sheep were selected based on T. ovis infection status, and samples were collected from infected and non-infected caecum. The 16S rRNA metagenomic analysis revealed distinct microbial communities in T. ovis, infected caecum, and non-infected caecum. Proteobacteria dominated the T. ovis microbiome, while infected caecum was rich in Bacteroidota and Spirochaetota, and non-infected caecum had a higher proportion of Firmicutes and Verrucomicrobiota. At the genus level, T. ovis was predominantly associated with Escherichia/Shigella, while infected caecum had higher proportions of Bacteroides, Prevotella, and Treponema. Non-infected caecum was characterized by WCHB1-41, Prevotella, and Succiniclasticum like genera. Alpha and beta diversity indicated significant differences in microbiome among the groups, with higher diversity observed in infected caecum. The study found T. ovis infection significantly alters the caecal microbiome of sheep, introducing potentially pathogenic bacteria and reducing beneficial ones. These findings underscore the complex relationship between host, parasite, and microbiome, highlighting the need for comprehensive strategies to manage helminth infections and their broader ecological impacts.}, }
@article {pmid39607975, year = {2024}, author = {Abbasi, AM and Nasir, S and Bajwa, AA and Akbar, H and Ali, MM and Rashid, MI}, title = {A comparative study of the microbiomes of the ticks Rhipicephalus microplus and Hyalomma anatolicum.}, journal = {Parasite (Paris, France)}, volume = {31}, number = {}, pages = {74}, pmid = {39607975}, issn = {1776-1042}, support = {HEC-GCF-273//Higher Education Commission, Pakistan/ ; }, mesh = {Animals ; *Rhipicephalus/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Ixodidae/microbiology ; *Microbiota ; Pakistan ; Phylogeny ; Symbiosis ; Female ; Gastrointestinal Microbiome ; Coxiella/genetics/isolation & purification/classification ; Bacteria/classification/genetics/isolation & purification ; }, abstract = {Hyalomma anatolicum and Rhipicephalus microplus are tick species that are important vectors of numerous pathogens affecting both humans and livestock. Endosymbionts, such as Coxiella-like endosymbionts (CLE), Francisella-like endosymbionts (FLE), and Candidatus Midichloria, play a crucial role in the physiology and vector competence of these ticks. In this study, we investigated the microbial composition of H. anatolicum and R. microplus from four geographically distinct regions of Pakistan to assess whether environmental differences influence their microbiomes. We analyzed the ticks' gut microbiome targeting the V3-V4 hypervariable region of 16S rRNA for Illumina 16S metagenome NGS sequencing and processed overall 144 ticks. Analysis of gut bacterial composition resulted in observation of 1200 R. microplus and 968 H. anatolicum unique amplicon sequencing variants (ASVs). Relative abundance, Alpha diversity (Shannon, Faith's phylogenetic distance) and beta diversity metrics (Bray-Curtis, Jaccard and UniFrac) were analyzed and revealed that H. anatolicum ticks have significantly unique and diverse microbial communities with Acinetobacter indicus and Francisella-like endosymbionts dominating as opposed to Candidatus Midichloria. Rhipicephalus microplus exhibited results consistent with the previous studies with no major changes in microbiome including Coxiella-like endosymbionts as the major contributor. These findings suggest that geographical and environmental factors play a significant role in shaping the tick microbiome, with potential consequences for disease transmission and tick survivability. Further research is needed to elucidate the functional roles of these microbial shifts and their impact on public health and livestock in affected regions.}, }
@article {pmid39604824, year = {2024}, author = {Li, X and Zhang, Z and Bai, H and Liu, Z}, title = {Analysis of vaginal microbiota during postpartum and postmenopausal periods based on metagenomics.}, journal = {BMC microbiology}, volume = {24}, number = {1}, pages = {501}, pmid = {39604824}, issn = {1471-2180}, mesh = {Humans ; Female ; *Vagina/microbiology ; *Postmenopause ; *Postpartum Period ; *Microbiota/genetics ; *Metagenomics/methods ; *Bacteria/genetics/classification/isolation & purification ; Adult ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: Postmenopausal and the postpartum periods are essential physiological phases that result in low estrogen levels in women; however, they are important to female reproductive health. Traditional as well as new detection methods (such as 16 S RNA sequencing) have limitations in detecting the composition of vaginal microbiota. Therefore, in this study, we used metagenomic detection technology to study the composition of vaginal microbiota in postmenopausal and postpartum women. Six women were randomly selected from each group (healthy women of childbearing age, postmenopausal group, and postpartum) for vaginal microecology, composition, α-diversity, linear discriminant analysis effect size (LEfSe), and Comprehensive Antibiotic Resistance Database (CARD) analyses.
RESULTS: We discovered that Lactobacillus dominance disappeared in postpartum and postmenopausal group women and that diversity increased. However, the proportions of Atopobium vaginae, Escherichia coli, and Streptococcus agalactiae significantly increased. Diversity was the highest in the postpartum period, with a significant increase in the proportions of A. vaginae, Gardnerella vaginalis, Prevotella, and occasionally, Chlamydia trachomatis. Linear discriminant analysis effect size analysis revealed that Lactobacillus crispatus and L. iners enrichment in the postpartum and menopausal periods was much lower than that in the childbearing age group. CARD analysis revealed that ABC-F ATP-binding cassette ribosomal protection protein subfamily gene abundance was significantly lower in the menopausal than in the childbearing age group, whereas the gimA family macrolide glycosyltransferase gene abundance was significantly higher.
CONCLUSIONS: The dominance of vaginal Lactobacillus in postpartum and menopausal women disappeared, while their diversity increased. In addition, the reproductive tract of postpartum women was susceptible to invasion by pathogenic microorganisms, which deserves clinical attention. When menopausal women receive treatment for vaginal infections, the likelihood that certain bacterial communities develop antibiotic resistance through ribosomal protection mechanisms is lower than that of women in the childbearing age, while the possibility of developing resistance to macrolides through glycosylation may increase. This, however, requires further research.}, }
@article {pmid39604809, year = {2025}, author = {Li, Q and Wu, D and Song, Y and Zhang, L and Wang, T and Chen, X and Zhang, M}, title = {In vivo mechanism of the interaction between trimethylamine lyase expression and glycolytic pathways.}, journal = {Food & function}, volume = {16}, number = {1}, pages = {87-101}, doi = {10.1039/d4fo03809f}, pmid = {39604809}, issn = {2042-650X}, mesh = {Animals ; *Glycolysis ; Mice ; *Gastrointestinal Microbiome ; Male ; Glycine/metabolism/pharmacology ; Mice, Inbred C57BL ; Lyases/metabolism/genetics ; Methylamines/metabolism ; Diet ; Bacteria/genetics/classification/metabolism ; RNA, Ribosomal, 16S/genetics ; Choline/metabolism ; }, abstract = {Recent studies confirmed that host-gut microbiota interactions modulate disease-linked metabolite TMA production via TMA lyase. However, microbial enzyme production mechanisms remain unclear. In the present study, we investigated the impact of dietary and intervention factors on gut microbiota, microbial gene expression, and the interplay between TMA lyase and glycolytic pathways in mice. Using 16S rRNA gene sequencing, metagenomics, and metabolomics, the gut microbiota composition and microbial functional gene expression profiles related to TMA lyase and glycolytic enzymes were determined. The results revealed that distinct diets and intervention factors altered gut microbiota, gene expression, and metabolites linked to glycine metabolism and glycolysis. Notably, an arabinoxylan-rich diet suppressed genes linked to choline, glycine, glycolysis, and TMA lyase, favoring glycine utilization via pyruvate pathways. Glycolytic inhibitors amplified these effects, mainly inhibiting pyruvate kinase. Our findings underscored the crosstalk between TMA lyase and glycolytic pathways, regulating glycine levels, and suggested avenues for targeted interventions and personalized diets to curb choline TMA lyase production.}, }
@article {pmid39604726, year = {2025}, author = {Chen-Liaw, A and Aggarwala, V and Mogno, I and Haifer, C and Li, Z and Eggers, J and Helmus, D and Hart, A and Wehkamp, J and Lamousé-Smith, ESN and Kerby, RL and Rey, FE and Colombel, JF and Kamm, MA and Olle, B and Norman, JM and Menon, R and Watson, AR and Crossett, E and Terveer, EM and Keller, JJ and Borody, TJ and Grinspan, A and Paramsothy, S and Kaakoush, NO and Dubinsky, MC and Faith, JJ}, title = {Gut microbiota strain richness is species specific and affects engraftment.}, journal = {Nature}, volume = {637}, number = {8045}, pages = {422-429}, pmid = {39604726}, issn = {1476-4687}, support = {R01 DK112978/DK/NIDDK NIH HHS/United States ; R01 DK124133/DK/NIDDK NIH HHS/United States ; }, mesh = {*Gastrointestinal Microbiome ; *Fecal Microbiota Transplantation ; Humans ; Animals ; *Species Specificity ; *Feces/microbiology ; Mice ; Metagenome ; Male ; Female ; Lakes/microbiology ; Bacteria/classification/genetics/isolation & purification ; Biodiversity ; Soil Microbiology ; }, abstract = {Despite the fundamental role of bacterial strain variation in gut microbiota function[1-6], the number of unique strains of a species that can stably colonize the human intestine is still unknown for almost all species. Here we determine the strain richness (SR) of common gut species using thousands of sequenced bacterial isolates with paired metagenomes. We show that SR varies across species, is transferable by faecal microbiota transplantation, and is uniquely low in the gut compared with soil and lake environments. Active therapeutic administration of supraphysiologic numbers of strains per species increases recipient SR, which then converges back to the population average after dosing is ceased. Stratifying engraftment outcomes by high or low SR shows that SR predicts microbial addition or replacement in faecal transplants. Together, these results indicate that properties of the gut ecosystem govern the number of strains of each species colonizing the gut and thereby influence strain addition and replacement in faecal microbiota transplantation and defined live biotherapeutic products.}, }
@article {pmid39604394, year = {2024}, author = {Akiyama, S and Nishijima, S and Kojima, Y and Kimura, M and Ohsugi, M and Ueki, K and Mizokami, M and Hattori, M and Tsuchiya, K and Uemura, N and Kawai, T and Bork, P and Nagata, N}, title = {Multi-biome analysis identifies distinct gut microbial signatures and their crosstalk in ulcerative colitis and Crohn's disease.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {10291}, pmid = {39604394}, issn = {2041-1723}, mesh = {Humans ; *Colitis, Ulcerative/microbiology/genetics/virology ; *Crohn Disease/microbiology ; *Gastrointestinal Microbiome/genetics ; *Feces/microbiology ; Male ; *Metagenomics/methods ; Female ; *Bacteriophages/genetics ; Adult ; Escherichia coli/genetics/metabolism ; Middle Aged ; Japan ; Fungi/genetics ; Bacteria/genetics/metabolism/classification ; Metagenome/genetics ; Saccharomyces cerevisiae/genetics ; Bifidobacterium/genetics ; Virome/genetics ; Enterococcus faecium/genetics/pathogenicity ; Fatty Acids, Volatile/metabolism ; Young Adult ; China ; Case-Control Studies ; }, abstract = {The integrative multi-kingdom interaction of the gut microbiome in ulcerative colitis (UC) and Crohn's disease (CD) remains underinvestigated. Here, we perform shotgun metagenomic sequencing of feces from patients with UC and CD, and healthy controls in the Japanese 4D cohort, profiling bacterial taxa, gene functions, and antibacterial genes, bacteriophages, and fungi. External metagenomic datasets from the US, Spain, the Netherlands, and China were analyzed to validate our multi-biome findings. We found that Enterococcus faecium and Bifidobacterium spp. were enriched in both diseases. Enriched Escherichia coli was characteristic of CD and was linked to numerous antibiotic resistance genes involved in efflux pumps and adherent-invasive Escherichia coli virulence factors. Virome changes correlated with shifts in the bacteriome, including increased abundances of phages encoding pathogenic genes. Saccharomyces paradoxus and Saccharomyces cerevisiae were enriched in UC and CD, respectively. Saccharomyces cerevisiae and Escherichia coli had negative associations with short-chain fatty acid (SCFA)-producing bacteria in CD. Multi-biome signatures and their interactions in UC and CD showed high similarities between Japan and other countries. Since bacteria, phages, and fungi formed multiple hubs of intra- or trans-kingdom networks with SCFA producers and pathobionts in UC and CD, an approach targeting the interaction network may hold therapeutic promise.}, }
@article {pmid39603713, year = {2024}, author = {Helfrich, PG and Feldman, J and Andrade-Barahona, E and Robertson, I and Foster, J and Hofacker, R and Dahlquist Selking, G and Sheik, CS and Cox, A}, title = {Aqueous copper geochemistry shapes the sediment microbial resistome in a recovering stream.}, journal = {Environmental microbiology reports}, volume = {16}, number = {6}, pages = {e70045}, pmid = {39603713}, issn = {1758-2229}, support = {800015-10297//Montana Department of Justice, Natural Resource Damage Program (NRDP) through the Butte Natural Resource Damage Restoration Council (BNRC)/ ; //Montana Tech Faculty Seed and Faculty Development Initiatives/ ; //Montana Tech Earth Science and Engineering Fellowship/ ; //Montana Water Center, Faculty Seed Grant/ ; }, mesh = {*Copper/metabolism ; *Geologic Sediments/microbiology/chemistry ; *Rivers/microbiology/chemistry ; *Bacteria/genetics/drug effects/classification/metabolism/isolation & purification ; Metagenome ; Water Pollutants, Chemical/metabolism ; Metagenomics ; Arsenic/metabolism ; Microbiota/genetics/drug effects ; }, abstract = {Aqueous metals are pervasive contaminants associated with historical mining. We produced and examined 16 metagenomes from a contaminated creek to investigate how anthropogenic metal contamination shapes the functional profiles of microbial communities. We then incorporated the metagenomic profiles and concurrently collected geochemical context into a multivariate model to examine correlations between stream geochemistry and microbial functional potential. Integrating the metagenomes with full geochemical profiles emphasised that even low metalloid concentrations shaped microbial functionality, seasonal shifts in copper bioavailability and arsenic exposure correlated with genetic variation, and copper resistomes were spatiotemporally distinct. This study provides new insights into microbial metabolic potential and microbe-metal(loid) interactions.}, }
@article {pmid39603473, year = {2025}, author = {Li, Y and Tao, C and Li, S and Chen, W and Fu, D and Jafvert, CT and Zhu, T}, title = {Feasibility study of machine learning to explore relationships between antimicrobial resistance and microbial community structure in global wastewater treatment plant sludges.}, journal = {Bioresource technology}, volume = {417}, number = {}, pages = {131878}, doi = {10.1016/j.biortech.2024.131878}, pmid = {39603473}, issn = {1873-2976}, mesh = {*Machine Learning ; *Sewage/microbiology ; *Wastewater/microbiology ; Water Purification/methods ; Feasibility Studies ; Bacteria/drug effects/genetics ; Drug Resistance, Microbial/genetics ; Microbiota/drug effects ; China ; Drug Resistance, Bacterial/genetics ; }, abstract = {Wastewater sludges (WSs) are major reservoirs and emission sources of antibiotic resistance genes (ARGs) in cities. Identifying antimicrobial resistance (AMR) host bacteria in WSs is crucial for understanding AMR formation and mitigating biological and ecological risks. Here 24 sludge data from wastewater treatment plants in Jiangsu Province, China, and 1559 sludge data from genetic databases were analyzed to explore the relationship between 7 AMRs and bacterial distribution. The results of the Procrustes and Spearman correlation analysis were unsatisfactory, with p-value exceeding the threshold of 0.05 and no strong correlation (r > 0.8). In contrast, explainable machine learning (EML) using SHapley Additive exPlanation (SHAP) revealed Pseudomonadota as a major contributor (39.3 %-74.2 %) to sludge AMR. Overall, the application of ML is promising in analyzing AMR-bacteria relationships. Given the different applicable occasions and advantages of various analysis methods, using ML as one of the correlation analysis tools is strongly recommended.}, }
@article {pmid39602306, year = {2024}, author = {Pasolli, E and Mauriello, IE and Avagliano, M and Cavaliere, S and De Filippis, F and Ercolini, D}, title = {Bifidobacteriaceae diversity in the human microbiome from a large-scale genome-wide analysis.}, journal = {Cell reports}, volume = {43}, number = {12}, pages = {115027}, doi = {10.1016/j.celrep.2024.115027}, pmid = {39602306}, issn = {2211-1247}, mesh = {Humans ; *Phylogeny ; *Microbiota/genetics ; Metagenome ; Genome, Bacterial ; Genome-Wide Association Study ; Probiotics ; }, abstract = {We performed a large-scale genome-wide analysis aiming to investigate the prevalence and strain-level diversity of Bifidobacteriaceae species in the human microbiome. We considered 9,528 publicly available human metagenomes and integrated them with 1,192 isolate genomes from different sources. The prevalence and abundance of Bifidobacteriaceae species in humans was linked to multiple host characteristics: they were reduced in older people and enriched in populations characterized by Westernized lifestyles with geography-specific patterns. Phylogenetic analysis highlighted 110 Bifidobacteriaceae species-level genome bins (SGBs), with 32 found in humans and 8 in food and probiotic sources. Functional annotation revealed a great diversity in carbohydrate-active enzyme families across these SGBs. We found potential subspecies for most of the SGBs prevalent in humans and identified patterns driven by age and geography. We provided evidence that strains used in probiotics were rarely identified in humans, with the only exception represented by Bifidobacterium animalis. We finally evaluated that the abundance of Bifidobacteriaceae species exhibited moderate and variable capabilities to predict health status in case-control studies.}, }
@article {pmid39601988, year = {2024}, author = {Rekadwad, BN and Shouche, YS and Jangid, K}, title = {Oil spill pollution and diversity analyses of resistant bacteria isolated from soil across the Arabian Sea and Bay of Bengal coastlines.}, journal = {Environmental monitoring and assessment}, volume = {196}, number = {12}, pages = {1265}, pmid = {39601988}, issn = {1573-2959}, mesh = {*Bacteria/classification/isolation & purification/genetics ; *Petroleum Pollution ; *Environmental Monitoring ; India ; *Soil Microbiology ; Biodiversity ; Bays/microbiology ; Drug Resistance, Bacterial ; }, abstract = {Pelagic transport causes oil pollution via international tanker routes in the open ocean across southern Asia and the Indian Territory. Nutrient-rich runoff from residential, commercial, and industrial wastes, oil tanker mishaps, and sailing flags have all resulted in pollution. The natural flow of ocean water from east to west dragged pollutants into Indian Territory. We have investigated that the severe deposition of oil spills and biohazardous wastes is causing faunal mortality. Microbiome analyses helped us understand the sample's microbial load. 16S amplicon metagenome analysis, followed by enumeration and confirmation using molecular methods, indicates the presence of diverse microbial profiles. The presence of non-native hydrocarbon- and AMR-resistant bacterial taxa, such as Brevundimonas, Staphylococcus spp., Mycolicibacterium, Spingomonas spp., Bacillus spp., Chitinophaga spp., Priestia spp., Domibacillus spp., Rossellomorea spp., and Acinetobacter spp., confirms the impacts of oil and urban pollution. This indicates that the coastal soil of Goa and Andhra Pradesh has hydrocarbon- and antibiotic-resistant bacteria, which confirms that the present pollution status and that high-traffic recreational activities put biodiversity and humans at risk of getting illnesses linked to antibiotic resistance.}, }
@article {pmid39601556, year = {2024}, author = {Yang, J and Wang, H and Lin, X and Liu, J and Feng, Y and Bai, Y and Liang, H and Hu, T and Wu, Z and Lai, J and Liu, J and Zou, Y and Wei, S and Yan, P}, title = {Gut microbiota dysbiosis induced by alcohol exposure in pubertal and adult mice.}, journal = {mSystems}, volume = {9}, number = {12}, pages = {e0136624}, pmid = {39601556}, issn = {2379-5077}, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Dysbiosis/chemically induced/microbiology ; Mice ; *Ethanol ; Male ; Mice, Inbred C57BL ; Metagenome/drug effects ; Liver/metabolism/drug effects/pathology ; Sexual Maturation/drug effects ; }, abstract = {UNLABELLED: Alcohol intake causes many diseases including neuropsychiatric symptoms, nutritional deficiency, progressive pancreatitis, liver cirrhosis, and ischemic heart disease. The gut microbiota changes significantly after alcohol exposure. Alcohol consumption tends to increase in underage and young people, but the feature of the gut microbiota in puberty remains largely unexplored. In this study, we conducted alcohol-exposed pubertal and adult mice model to investigate the intestinal damage and gut microbiota change. Interestingly, the responses of pubertal mice and adult mice after alcohol exposure were different. We found that alcohol dehydrogenase decreased and aldehyde dehydrogenase increased in the liver of pubertal mice, thus reducing the accumulation of toxic acetaldehyde. Furthermore, alcohol exposure caused less intestinal injury in pubertal mice. Through the analysis of metagenome assembly genome, we obtained many unrecognized bacterial genomes. Limosillactobacillus reuteri (cluster_56) and Lactobacillus intestinalis (cluster_57) were assembled from the samples of pubertal mice, which were involved in the production of indole acetic acid and the transformation of bile acids in response to alcohol exposure. This study provided a new insight to investigate the gut microbiota change and explained the difference of the gut microbiota after alcohol exposure between pubertal mice and adult mice.
IMPORTANCE: This study elucidates the significant impact of alcohol exposure on the gut microbiota and metabolic pathways in mice, highlighting the differential responses between adolescent and adult stages. Alcohol exposure was found to damage the intestinal barrier, alter the microbial composition by decreasing beneficial bacteria like Lactobacillus, and increase harmful bacteria such as Alistipes. The study also discovered unique microbial changes and resilience in pubertal mice. Species-level metagenomic analysis revealed specific microbial taxa and metabolic functions affected by alcohol. Metagenome-assembled genomes (MAGs) found many species that could not be annotated by conventional methods including many members of Lachnospiraceae, greatly expanding our understanding of the gut microbiota composition. These findings underscore the need for further research on alcohol's effects on various organs and the implications of microbial metabolites on disease progression.}, }
@article {pmid39601555, year = {2024}, author = {Gao, Y and Zhang, H and Zhu, D and Guo, L}, title = {Different artificial feeding strategies shape the diverse gut microbial communities and functions with the potential risk of pathogen transmission to captive Asian small-clawed otters (Aonyx cinereus).}, journal = {mSystems}, volume = {9}, number = {12}, pages = {e0095424}, pmid = {39601555}, issn = {2379-5077}, support = {561119219//Scientific research start-up foundation from Lanzhou University/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; *Otters/microbiology ; *Feces/microbiology ; *Animal Feed/analysis/microbiology ; Animals, Zoo/microbiology ; Diet/veterinary ; Bacteria/genetics/isolation & purification/classification ; Fatty Acids, Volatile/metabolism ; }, abstract = {UNLABELLED: Captive otters raised in zoos are fed different artificial diets, which may shape gut microbiota. The objective is to evaluate the impacts of two different artificial diets on microbial communities and function capabilities and short-chain fatty acid (SCFA) profiles in healthy otters' feces. A total of 16 Asian small-clawed otters in two groups (n = 8) were selected. Group A otters were fed raw loaches supplemented with commercial cat food (LSCF) diet, and group B otters were fed raw crucian diet. The communities and functional capabilities of microbiota in feces were assessed with metagenomic sequencing. Captive otters fed two kinds of diets possessed different gut microbial communities and functional capabilities. Various pathogenic bacteria, like Escherichia coli and Clostridium perfringens, were enriched in the samples from the two groups, respectively. Most of the differential pathways of nutrient metabolism were significantly enriched in group A, and the distributions of carbohydrate enzymes in the two groups significantly differed from each other. Multiple resistance genes markedly accumulated in fecal samples of the group A otters with LSCF diet. Higher concentrations of SCFAs were also observed in group A otters. Two feeding strategies were both likely to facilitate the colonization and expansion of various pathogenic bacteria and the accumulation of resistance genes in the intestines of captive otters, suggesting that risk of pathogen transmission existed in the current feeding process. Commercial cat food could supplement various nutrients and provide a substrate for the production of SCFAs, which might be beneficial for the otters' intestinal fermentation and metabolism.
IMPORTANCE: Captive otters fed with different diets possessed distinct gut microbial communities and functions, with the enrichment of several pathogens and multiple resistance genes in their gut microbiota. The current artificial feeding strategies had the possibility to accelerate the colonization and proliferation of various pathogenic bacteria in the intestines of otters and the spread of resistance genes, increasing the risk of diseases. In addition, supplementation with commercial cat food had benefits for otters' intestinal fermentation and the metabolism of gut microbiota.}, }
@article {pmid39601293, year = {2024}, author = {Liu, L and Cao, S and Lin, W and Gao, Z and Yang, L and Zhu, L and Yang, B and Zhang, G and Zhu, R and Wu, D}, title = {miMatch: a microbial metabolic background matching tool for mitigating host confounding in metagenomics research.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2434029}, pmid = {39601293}, issn = {1949-0984}, mesh = {*Metagenomics/methods ; Humans ; Gastrointestinal Microbiome ; Software ; Case-Control Studies ; Bacteria/genetics/classification/metabolism/isolation & purification ; Metagenome ; Propensity Score ; }, abstract = {Metagenomic research faces a persistent challenge due to the low concordance across studies. While matching host confounders can mitigate the impact of individual differences, the influence of factors such as genetics, environment, and lifestyle habits on microbial profiles makes it exceptionally challenging to create fully matched cohorts. The microbial metabolic background, which modulates microbial composition, reflects a cumulative impact of host confounders, serving as an ideal baseline for microbial sample matching. In this study, we introduced miMatch, an innovative metagenomic sample-matching tool that uses microbial metabolic background as a comprehensive reference for host-related variables and employs propensity score matching to build case-control pairs, even in the absence of host confounders. In the simulated datasets, miMatch effectively eliminated individual metabolic background differences, thereby enhancing the accuracy of identifying differential microbial patterns and reducing false positives. Moreover, in real metagenomic data, miMatch improved result consistency and model generalizability across cohorts of the same disease. A user-friendly web server (https://www.biosino.org/iMAC/mimatch) has been established to promote the integration of multiple metagenomic cohorts, strengthening causal relationships in metagenomic research.}, }
@article {pmid39599783, year = {2024}, author = {Vila-Nistal, M and Logares, R and Gasol, JM and Martinez-Garcia, M}, title = {Time Series Data Provide Insights into the Evolution and Abundance of One of the Most Abundant Viruses in the Marine Virosphere: The Uncultured Pelagiphages vSAG 37-F6.}, journal = {Viruses}, volume = {16}, number = {11}, pages = {}, pmid = {39599783}, issn = {1999-4915}, support = {PID2021-125175OB-I00//Agencia Estatal de Investigación/ ; CTM2015-70340-R//Agencia Estatal de Investigación/ ; RTI2018-101025-B-I00//Agencia Estatal de Investigación/ ; }, mesh = {*Seawater/virology ; *Metagenomics/methods ; Genome, Viral ; Phylogeny ; Evolution, Molecular ; Aquatic Organisms/virology ; Virome/genetics ; }, abstract = {Viruses play a pivotal role in ecosystems by influencing biochemical cycles and impacting the structure and evolution of their host cells. The widespread pelagiphages infect Pelagibacter spp., the most abundant marine microbe on Earth, and thus play a significant role in carbon transformation through the viral shunt. Among these viruses, the uncultured lytic pelagiphage vSAG 37-F6, uncovered by single-virus genomics, is likely the most numerous virus in the ocean. While previous research has delved into the diversity and spatial distribution of vSAG 37-F6, there is still a gap in understanding its temporal dynamics, hindering our insight into its ecological impact. We explored the temporal dynamics of vSAG 37-F6, assessing periodic fluctuations in abundance and evolutionary patterns using long- and short-term data series. In the long-term series (7 years), metagenomics showed negative selection acting on all viral genes, with a highly conserved overall diversity over time composed of a pool of yearly emergent, highly similar novel strains that exhibited a seasonal abundance pattern with two peaks during winter and fall and a decrease in months with higher UV radiation. Most non-synonymous polymorphisms occurred in structural viral proteins located in regions with low conformational restrictions, suggesting that many of the viral genes of this population are highly purified over its evolution. At the fine-scale resolution (24 h time series), combining digital PCR and metagenomics, we identified two peaks of cellular infection for the targeted vSAG 37-F6 viral strain (up to approximately 10[3] copies/ng of prokaryotic DNA), one before sunrise and the second shortly after midday. Considering the high number of co-occurring strains of this microdiverse virus, the abundance values at the species or genus level could be orders of magnitudes higher. These findings represent a significant advancement in understanding the dynamics of the potentially most abundant oceanic virus, providing valuable insights into ecologically relevant marine viruses.}, }
@article {pmid39599719, year = {2024}, author = {Senaprom, S and Namjud, N and Ondee, T and Bumrungpert, A and Pongpirul, K}, title = {Sugar Composition of Thai Desserts and Their Impact on the Gut Microbiome in Healthy Volunteers: A Randomized Controlled Trial.}, journal = {Nutrients}, volume = {16}, number = {22}, pages = {}, pmid = {39599719}, issn = {2072-6643}, support = {FOODF67300006//Thailand Science Research and Innovation Fund Chulalongkorn University/ ; //The 90th Anniversary of Chulalongkorn University, Ratchadaphisek Somphot Fund/ ; //The Second Century Fund (C2F) for PhD Scholarship, Chulalongkorn University/ ; }, mesh = {Adolescent ; Adult ; Female ; Humans ; Male ; Middle Aged ; Young Adult ; Bacteria/classification/genetics ; *Dietary Sugars ; *Feces/microbiology ; *Gastrointestinal Microbiome ; Healthy Volunteers ; RNA, Ribosomal, 16S/genetics ; Thailand ; }, abstract = {BACKGROUND: The relationship between consuming Thai desserts-predominantly composed of carbohydrates-and gut microbiome profiles remains unclear. This study aimed to evaluate the effects of consuming various Thai desserts with different GI values on the gut microbiomes of healthy volunteers.
METHODS: This open-label, parallel randomized clinical trial involved 30 healthy individuals aged 18 to 45 years. Participants were randomly assigned to one of three groups: Phetchaburi's Custard Cake (192 g, low-GI group, n = 10), Saraburi's Curry Puff (98 g, medium-GI group, n = 10), and Lampang's Crispy Rice Cracker (68 g, high-GI group, n = 10), each consumed alongside their standard breakfast. Fecal samples were collected at baseline and 24 h post-intervention for metagenomic analysis of gut microbiome profiles using 16S rRNA gene sequencing.
RESULTS: After 24 h, distinct trends in the relative abundance of various gut microbiota were observed among the dessert groups. In the high-GI dessert group, the abundance of Collinsella and Bifidobacterium decreased compared to the low- and medium-GI groups, while Roseburia and Ruminococcus showed slight increases. Correlation analysis revealed a significant negative relationship between sugar intake and Lactobacillus abundance in the medium- and high-GI groups, but not in the low-GI group. Additionally, a moderately negative association was observed between Akkermansia abundance and sugar intake in the high-GI group. These bacteria are implicated in energy metabolism and insulin regulation. LEfSe analysis identified Porphyromonadaceae and Porphyromonas as core microbiota in the low-GI group, whereas Klebsiella was enriched in the high-GI group, with no predominant bacteria identified in the medium-GI group.
CONCLUSIONS: The findings suggest that Thai desserts with varying GI levels can influence specific gut bacteria, though these effects may be temporary.}, }
@article {pmid39598209, year = {2024}, author = {Al-Awthan, YS and Mir, R and Alharbi, BM and Alatawi, AS and Almutairi, FM and Khafaga, T and Shohdi, WM and Fakhry, AM and Alatawi, MM}, title = {Metagenomic Analysis of Sediment Bacterial Diversity and Composition in Natural Lakes and Artificial Waterpoints of Tabuk Region in King Salman Bin Abdulaziz Royal Natural Reserve, Saudi Arabia.}, journal = {Life (Basel, Switzerland)}, volume = {14}, number = {11}, pages = {}, pmid = {39598209}, issn = {2075-1729}, abstract = {The Tabuk region is located in the northern part of Saudi Arabia, and it has an area of 117,000 km[2] between longitudes 26° N and 29° N and latitudes 34° E and 38° E. King Salman Bin Abdulaziz Royal Natural Reserve (KSRNR) is the largest natural reserve in Saudi Arabia and covers about 130,700 km[2]. It represents a new tourist attraction area in the Tabuk region. Human activities around the lake may lead to changes in water quality, with subsequent changes in microenvironment components, including microbial diversity. The current study was designed to assess possible changes in bacterial communities of the water sediment at some natural lakes and artificial waterpoints of KSRNR. Water samples were collected from ten different locations within KSRNR: W1, W2, W3 (at the border of the royal reserve); W4, W5, W6, W7 (at the middle); and W8, W9, and W10 (artificial waterpoints). The total DNA of the samples was extracted and subjected to 16S rRNA sequencing and metagenomic analysis; also, the environmental parameters (temperature and humidity) were recorded for all locations. Metagenomic sequencing yielded a total of 24,696 operational taxonomic units (OTUs), which were subsequently annotated to 193 phyla, 215 classes, 445 orders, 947 families, and 3960 genera. At the phylum level, Pseudomonadota dominated the microbial communities across all samples. At the class level, Gammaproteobacteria, Clostridia, Alphaproteobacteria, Bacilli, and Betaproteobacteria were the most prevalent. The dominant families included Enterobacteriaceae, Pseudomonadaceae, Clostridiaceae, Comamonadaceae, and Moraxellaceae. At the genus level, Pseudomonas, Clostridium, Acinetobacter, Paenibacillus, and Acidovorax exhibited the highest relative abundances. The most abundant species were Hungatella xylanolytica, Pseudescherichia vulneris, Pseudorhizobium tarimense, Paenibacillus sp. Yn15, and Enterobacter sp. Sa187. The observed species richness revealed substantial heterogeneity across samples using species richness estimators, Chao1 and ACE, indicating particularly high diversity in samples W3, W5, and W6. Current study results help in recognizing the structure of bacterial communities at the Tubaiq area in relation to their surroundings for planning for environmental protection and future restoration of affected ecosystems. The findings highlight the dominance of various bacterial phyla, classes, families, and genera, with remarkable species richness in some areas. These results underscore the influence of human activities on microbial diversity, as well as the significance of monitoring and conserving the reserve's natural ecosystems.}, }
@article {pmid39597714, year = {2024}, author = {Yang, T and He, Y and Yang, M and Gao, Z and Zhou, J and Wang, Y}, title = {Community Structure and Biodiversity of Active Microbes in the Deep South China Sea.}, journal = {Microorganisms}, volume = {12}, number = {11}, pages = {}, pmid = {39597714}, issn = {2076-2607}, support = {42376149//National Natural Science Foundation of China/ ; }, abstract = {The deep ocean harbors a group of highly diversified microbes, while our understanding of the active microbes that are real contributors to the nutrient cycle remains limited. In this study, we report eukaryotic and prokaryotic communities in ~590 m and 1130 m depths using 16S and 18S rRNA Illumina reads (miTags) extracted from 15 metagenomes (MG) and 14 metatranscriptomes (MT). The metagenomic 16S miTags revealed the dominance of Gammaproteobacteria, Alphaproteobacteria, and Nitrososphaeria, while the metatranscriptomic 16S miTags were highly occupied by Gammaproteobacteria, Acidimicrobiia, and SAR324. The consistency of the active taxa between the two depths suggests the homogeneity of the functional microbial groups across the two depths. The eukaryotic microbial communities revealed by the 18S miTags of the metagenomic data are dominated by Polycystinea; however, they were almost all absent in the 18S metatranscriptomic miTags. The active eukaryotes were represented by the Arthropoda class (at 590 m depth), Dinophyceae, and Ciliophora classes. Consistent eukaryotic communities were also exhibited by the 18S miTags of the metatranscriptomic data of the two depths. In terms of biodiversity, the ACE and Shannon indices of the 590 m depth calculated using the 18S metatranscriptomic miTags were much higher than those of the 1130 m depth, while a reverse trend was shown for the indices based on the metagenomic data. Our study reports the active microbiomes functioning in the nutrient utilization and carbon cycle in the deep-sea zone, casting light on the quantification of the ecological processes occurring in the deep ocean.}, }
@article {pmid39597627, year = {2024}, author = {Vilo, C and Fábrega, F and Campos, VL and Gómez-Silva, B}, title = {Microbial Biodiversity in Sediment from the Amuyo Ponds: Three Andean Hydrothermal Lagoons in Northern Chile.}, journal = {Microorganisms}, volume = {12}, number = {11}, pages = {}, pmid = {39597627}, issn = {2076-2607}, support = {FB 0001//ANID, Chile/ ; }, abstract = {The Amuyo Ponds (APs) are a group of three brackish hydrothermal lagoons located at 3700 m above sea level in a pre-Andean setting in the Atacama Desert. Each pond shows a conspicuous green (GP), red (RP), or yellow (YP) coloration, and discharges water rich in arsenic and boron into the Caritaya River (Camarones Basin, northern Chile). Microorganisms are subjected to harsh environmental conditions in these ponds, and the microbial composition and diversity in the Amuyo Ponds' sediments are unknown. The microbial life colonizing AP sediments was explored by metagenomics analyses, showing a diverse microbial life dominated by members of the bacterial domain, with nearly 800 bacterial genome sequences, and sequences associated with Archaea, Eukarya, and viruses. The genus Pseudomonas was more abundant in GP and YP sediments, while the genera Pseudomonas, Aeromonas, and Shewanella were enriched in RP sediments. Archaeal composition was similar in all sediments, and enriched with methanogens sequences from the Archaeoglobi and Halobacteria classes. Abundant fungi sequences were detected in all sediments from the phyla Blastocladiomycota and Ascomycota. We also report putative functional capabilities related to virulence and defense genes, the biosynthesis of secondary metabolites, and tolerance to arsenic. Thirteen bacterial and fourteen viral metagenome-assembled genomes were reconstructed and informed here. This work expands our knowledge on the richness of the microorganisms in the APs and open further studies on the ecology and genomics of this striking Andean geosite.}, }
@article {pmid39596262, year = {2024}, author = {Mang, Q and Gao, J and Li, Q and Sun, Y and Xu, G and Xu, P}, title = {Probiotics Enhance Coilia nasus Growth Performance and Nutritional Value by Regulating Glucolipid Metabolism via the Gut-Liver Axis.}, journal = {International journal of molecular sciences}, volume = {25}, number = {22}, pages = {}, pmid = {39596262}, issn = {1422-0067}, support = {32302976//National Natural Science Foundation of China/ ; BK20230179//Natural Science Foundation of Jiangsu Province/ ; 2022YFD2400904//National Key Research and development Program of China/ ; JSGS[2021]134//Jiangsu Province seed industry revitalization "revealing-list" project/ ; }, mesh = {*Probiotics/pharmacology ; Animals ; *Gastrointestinal Microbiome/drug effects ; *Liver/metabolism ; Nutritive Value ; Lipid Metabolism ; Fishes/metabolism/growth & development ; Animal Feed ; Glycolipids/metabolism ; }, abstract = {Large-scale intensive feeding triggered reduced growth performance and nutritional value. Exogenous probiotics can promote the growth performance and nutritional value of fish through improving the intestinal microbiota. However, detailed research on the correlation between the intestinal microbiota, growth performance, and nutritional value remains to be elucidated. Therefore, we performed metagenomic and metabolomic analysis to investigate the effects of probiotic addition to basal diet (1.0 × 10[8] CFU/g) (PF) and water (1.0 × 10[8] CFU/g) (PW) on the growth performance, muscle nutritional value, intestinal microbiota and their metabolites, and glucolipid metabolism in Coilia nasus. The results showed that FBW, BL, and SGR were enhanced in PF and PW groups. The concentrations of EAAs, TAAs, SFAs, MUFAs, and PUFAs were increased in PF and PW groups. Metagenomic and metabolic analyses revealed that bacterial community structure and metabolism were changed in the PF and PW groups. Moreover, adding probiotics to diet and water increased SCFAs and bile acids in the intestine. The gene expression associated with lipolysis and oxidation (hsl, pparα, cpt1, and acadm) and glycolysis (gck and pfk) was upregulated, while the gene expression associated with lipid synthesis (srebp1, acc, dgat, and elovl6) and gluconeogenesis (g6pca1, g6pca2, and pck) was downregulated in the liver. Correlation analysis displayed that hepatic glucolipid metabolism was regulated through the microbiota-gut-liver axis. Mantel test analysis showed that growth performance and muscle nutritional value were improved by the gut-liver axis. Our findings offered novel insights into the mechanisms that underlie the enhancement of growth performance and nutritional value in C. nasus and other fish by adding probiotics.}, }
@article {pmid39593380, year = {2024}, author = {Cardinali, F and Rampanti, G and Paderni, G and Milanović, V and Ferrocino, I and Reale, A and Boscaino, F and Raicevic, N and Ilincic, M and Osimani, A and Aquilanti, L and Martinovic, A and Garofalo, C}, title = {A comprehensive study on the autochthonous microbiota, volatilome, physico-chemical, and morpho-textural features of Montenegrin Njeguški cheese.}, journal = {Food research international (Ottawa, Ont.)}, volume = {197}, number = {Pt 1}, pages = {115169}, doi = {10.1016/j.foodres.2024.115169}, pmid = {39593380}, issn = {1873-7145}, mesh = {*Cheese/microbiology/analysis ; *Food Microbiology ; *Microbiota ; *Volatile Organic Compounds/analysis ; *Biogenic Amines/analysis ; Montenegro ; Bacteria/classification ; Odorants/analysis ; }, abstract = {The present study aims to deepen the knowledge of the microbiota, gross composition, physico-chemical and morpho-textural features, biogenic amines content and volatilome of Njeguški cheese, one of the most popular indigenous cheeses produced in Montenegro. Cheese samples were collected in duplicate from three different batches produced by three Montenegrin artisan producers. For the first time, the microbiota of Njeguški cheese was investigated using both culture-dependent techniques and metagenomic analysis. Coagulase positive staphylococci viable counts were below the detection limit of the analysis (<1 log cfu g[-1]). Salmonella spp., Listeria monocytogenes and staphylococcal enterotoxins were absent. However, relatively high viable counts of Enterobacteriaceae, Escherichia coli, Pseudomonadaceae and eumycetes were detected. Metataxonomic analysis revealed a core microbiome composed of Lactococcus lactis, Streptococcus thermophilus, Debaryomyces hansenii, and Kluyveromyces marxianus. Furthermore, the detection of opportunistic pathogenic yeasts such as Magnusiomyces capitatus and Wickerhamiella pararugosa, along with the variable content of biogenic amines, suggests the need for increased attention to hygienic conditions during Njeguški cheese production. Significant variability was observed in humidity (ranging from 38.37 to 45.58 %), salt content (ranging from 0.70 to 1.78 %), proteins content (ranging from 21.42 to 25.08 %), ash content (ranging from 2.97 to 4.05 %), hardness, springiness, and color among samples from different producers. Gas chromatography-mass spectrometry analysis showed a well-defined and complex volatilome profile of the Njeguški cheese, with alcohols (ethanol, isoamyl alcohol, phenetyl alcol), esters and acetates (ethyl acetate, ethyl butanoate, isoamyl acetate), ketones (acetoin, 2-butanone), and acids (acetic, butanoic, hexanoic acids) being the main chemical groups involved in aroma formation. This research will provide new insights into the still poorly explored identity of Njeguški cheese, thus serving as a first baseline for future studies aimed at protecting its tradition.}, }
@article {pmid39593354, year = {2024}, author = {Peng, Q and Zheng, H and Zhou, H and Chen, J and Xu, Y and Wang, Z and Xie, G}, title = {Elucidating core microbiota in yellow wine (Huangjiu) through flavor-oriented synthesis and construction of microbial communities.}, journal = {Food research international (Ottawa, Ont.)}, volume = {197}, number = {Pt 1}, pages = {115139}, doi = {10.1016/j.foodres.2024.115139}, pmid = {39593354}, issn = {1873-7145}, mesh = {*Volatile Organic Compounds/analysis ; *Fermentation ; *Microbiota ; *Wine/analysis/microbiology ; *Taste ; Humans ; Gas Chromatography-Mass Spectrometry ; Solid Phase Microextraction ; Pentanols/metabolism/analysis ; Odorants/analysis ; Flavoring Agents/analysis ; China ; Male ; Saccharomyces cerevisiae/metabolism ; Food Microbiology ; Female ; Phenylethyl Alcohol/metabolism/analysis ; Adult ; Butanols ; }, abstract = {Huangjiu, a traditional Chinese alcoholic beverage with a history spanning thousands of years, holds significant cultural and economic value in China. Despite its importance, the complexity of Huangjiu fermentation and the intricate interactions within its microbial community remain underexplored. This study addresses this gap by identifying the core volatile organic compounds (VOCs) and key microorganisms that define the flavor profile of Huangjiu. We employed HS-SPME-GC-MS along with aroma reconstitution and omission experiments to identify core VOCs, including Isobutanol, Isoamyl alcohol, β-Phenylethanol, and others. Metagenomic sequencing combined with QPCR was used to analyze microbial communities, revealing the temporal and spatial dynamics during fermentation. A synthetic microbial community model was constructed using the core microbes identified: Saccharomyces cerevisiae, Lactobacillus brevis, Saccharopolyspora rectivirgula, Bacillus subtilis, Leuconostoc citreum, Lactobacillus plantarum, Lactobacillus curvatus, Lactobacillus casei, and Aspergillus oryzae. This model successfully replicated Huangjiu's core VOCs and sensory characteristics, increased alcohol content, and reduced acidity. Our study contributes valuable insights into the microbial influences on Huangjiu quality, paving the way for its enhanced production and providing a foundation for future research in fermented beverages.}, }
@article {pmid39593339, year = {2024}, author = {Scarano, L and Peruzy, MF and Fallico, V and Blaiotta, G and Aponte, M and Anastasio, A and Murru, N}, title = {Provolone del Monaco PDO cheese: Lactic microflora, biogenic amines and volatilome characterization.}, journal = {Food research international (Ottawa, Ont.)}, volume = {197}, number = {Pt 1}, pages = {115257}, doi = {10.1016/j.foodres.2024.115257}, pmid = {39593339}, issn = {1873-7145}, mesh = {*Cheese/analysis/microbiology ; *Biogenic Amines/analysis ; *Lactobacillales/classification/genetics/isolation & purification ; *Volatile Organic Compounds/analysis ; Metagenome/genetics ; RNA, Ribosomal, 16S ; Microbiota/genetics ; Bacterial Load ; *Food Microbiology ; }, abstract = {One commercial production run of Provolone del Monaco - a long-ripened pasta filata cheese - was followed up to the end of ripening for a total of 20 samples. 371 LAB isolates were subject to genetic characterization followed by 16S rRNA gene sequencing. The dominant species were Lacticaseibacillus casei/paracasei (19.4 %), Streptococcus macedonicus (19.1 %) and Enterococcus faecalis (13.2 %). Strains were screened for features of technological interest or safety relevance. Tyramine-producing cultures were quite common, above all within enterococci. By MALDI TOF Mass Spectrometry, one Lactococcus lactis and one Enterococcus faecium strain proved to be bacteriocin producers. Four further cheese wheels from the same production run at 623 days of ripening were evaluated for volatile organic compounds, biogenic amines, and bacterial community by metagenomic sequencing. Three individual wheel samples shared a rather similar microbiome with Lactobacillus delbrueckii and Streptococcus thermophilus as the most represented species, while the fourth wheel appeared wholly different being dominated by Lentilactobacillus buchneri and St. infantarius. Additionally, this sample had the greatest content of biogenic amines and a different VOCs composition. Given the variance seen among cheese wheels processed and ripened under the same conditions, the search for adjunct cultures in the production of this cheese seems to be of utmost importance.}, }
@article {pmid39593310, year = {2024}, author = {Li, X and Du, C and Zhao, Y and Li, J and Hu, Y and Dong, W and Peng, N and Zhao, S}, title = {Differences in microbial communities among different types of zaopei and their effects on quality and flavor of baijiu.}, journal = {Food research international (Ottawa, Ont.)}, volume = {197}, number = {Pt 1}, pages = {115224}, doi = {10.1016/j.foodres.2024.115224}, pmid = {39593310}, issn = {1873-7145}, mesh = {*Fermentation ; *Microbiota ; *Food Microbiology ; *Taste ; Ethanol/metabolism ; Fermented Foods/microbiology ; Lactobacillales/genetics/metabolism/classification ; Lactic Acid/metabolism/analysis ; Fungi/classification/genetics ; Acetic Acid/metabolism/analysis ; Oryza/microbiology ; Bacteria/classification/genetics/metabolism ; Flavoring Agents/analysis ; }, abstract = {Three types of zaopei (fermented grain) of xiaoqu light-flavor baijiu (XQZP), daqu light-flavor baijiu (DQZP), and strong-flavor baijiu (SFZP) at the end of fermentation and their dominant lactic acid bacteria were systematically compared and analyzed in this study. The results showed that these three types of zaopei differed significantly in acidity, reducing sugar content, and ethanol content, and that the main factors influencing their microbial community were acidity and lactic acid. The diversity and contents of flavor substances were significantly higher in SFZP than in DQZP and XQZP. Additionally, there was a strong correlation between dominant lactic acid bacteria and flavor substances in all three zaopei, but the correlation between fungi and flavor substances was higher than that between bacteria and flavor substances. Differential gene analysis revealed that the microbial activities followed the order of SFZP > DQZP > XQZP. The KEGG enrichment analysis indicated that the differential genes from different zaopei were enriched in different metabolic pathways. Furthermore, various microorganisms in 3 types of zaopei contained different functional genes, of which fungi mainly contained genes responsible for the synthesis of ethanol and acetic acid, while lactic acid bacteria mainly contained genes responsible for the synthesis of lactic acid. In XQZP, L. helveticus was dominant lactic acid bacteria prominent in acetic acid tolerance and lactic acid production; in DQZP, L. acetotolerans was remarkable in its tolerance to lactic acid, acetic acid, ethanol and lactic acid production; and in SFZP, A. jinshanensis was superior in acetic acid tolerance and production. Taken together, this study reveals the mechanism underlying flavor differences among three types of baijiu and provides valuable references for the development and utilization of baijiu microbial resources.}, }
@article {pmid39592704, year = {2024}, author = {Hai, C and Hao, Z and Bu, L and Lei, J and Liu, X and Zhao, Y and Bai, C and Su, G and Yang, L and Li, G}, title = {Increased rumen Prevotella enhances BCAA synthesis, leading to synergistically increased skeletal muscle in myostatin-knockout cattle.}, journal = {Communications biology}, volume = {7}, number = {1}, pages = {1575}, pmid = {39592704}, issn = {2399-3642}, support = {32360837, 32341052//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {Animals ; Cattle ; *Myostatin/genetics/metabolism ; *Amino Acids, Branched-Chain/metabolism/biosynthesis ; *Prevotella/genetics/metabolism ; *Muscle, Skeletal/metabolism ; *Rumen/microbiology/metabolism ; Gene Knockout Techniques ; Gastrointestinal Microbiome/genetics ; }, abstract = {Myostatin (MSTN) is a negative regulator of muscle growth, and its relationship with the gut microbiota is not well understood. In this study, we observed increase muscle area and branched-chain amino acids (BCAAs), an energy source of muscle, in myostatin knockout (MSTN-KO) cattle. To explore the link between increased BCAAs and rumen microbiota, we performed metagenomic sequencing, metabolome analysis of rumen fluid, and muscle transcriptomics. MSTN-KO cattle showed a significant increase in the phylum Bacteroidota (formerly Bacteroidetes), particularly the genus Prevotella (P = 3.12e-04). Within this genus, Prevotella_sp._CAG:732, Prevotella_sp._MSX73, and Prevotella_sp._MA2016 showed significant upregulation of genes related to BCAA synthesis. Functional enrichment analysis indicated enrichment of BCAA synthesis-related pathways in both rumen metagenomes and metabolomes. Additionally, muscle transcriptomics indicated enrichment in muscle fiber and amino acid metabolism, with upregulation of solute carrier family genes, enhancing BCAA transport. These findings suggest that elevated rumen Prevotella in MSTN-KO cattle, combined with MSTN deletion, synergistically improves muscle growth through enhanced BCAA synthesis and transport.}, }
@article {pmid39591974, year = {2024}, author = {Peng, Y and Zhu, J and Wang, S and Liu, Y and Liu, X and DeLeon, O and Zhu, W and Xu, Z and Zhang, X and Zhao, S and Liang, S and Li, H and Ho, B and Ching, JY and Cheung, CP and Leung, TF and Tam, WH and Leung, TY and Chang, EB and Chan, FKL and Zhang, L and Ng, SC and Tun, HM}, title = {A metagenome-assembled genome inventory for children reveals early-life gut bacteriome and virome dynamics.}, journal = {Cell host & microbe}, volume = {32}, number = {12}, pages = {2212-2230.e8}, doi = {10.1016/j.chom.2024.10.017}, pmid = {39591974}, issn = {1934-6069}, mesh = {*Gastrointestinal Microbiome/genetics ; Infant ; Humans ; *Virome/genetics ; *Metagenome/genetics ; Child, Preschool ; Infant, Newborn ; Child ; Bacteriophages/genetics/isolation & purification ; Bacteria/genetics/virology/classification ; Genome, Viral/genetics ; Feces/microbiology/virology ; Metagenomics/methods ; Female ; Bifidobacterium/genetics/isolation & purification/classification ; Phylogeny ; Male ; Genome, Bacterial ; }, abstract = {Existing microbiota databases are biased toward adult samples, hampering accurate profiling of the infant gut microbiome. Here, we generated a metagenome-assembled genome inventory for children (MAGIC) from a large collection of bulk and viral-like particle-enriched metagenomes from 0 to 7 years of age, encompassing 3,299 prokaryotic and 139,624 viral species-level genomes, 8.5% and 63.9% of which are unique to MAGIC. MAGIC improves early-life microbiome profiling, with the greatest improvement in read mapping observed in Africans. We then identified 54 candidate keystone species, including several Bifidobacterium spp. and four phages, forming guilds that fluctuated in abundance with time. Their abundances were reduced in preterm infants and were associated with childhood allergies. By analyzing the B. longum pangenome, we found evidence of phage-mediated evolution and quorum sensing-related ecological adaptation. Together, the MAGIC database recovers genomes that enable characterization of the dynamics of early-life microbiomes, identification of candidate keystone species, and strain-level study of target species.}, }
@article {pmid39591453, year = {2024}, author = {Wang, L and Liu, Y and Ni, H and Zuo, W and Shi, H and Liao, W and Liu, H and Chen, J and Bai, Y and Yue, H and Huang, A and Friedman, J and Si, T and Liu, Y and Chen, M and Dai, L}, title = {Systematic characterization of plant-associated bacteria that can degrade indole-3-acetic acid.}, journal = {PLoS biology}, volume = {22}, number = {11}, pages = {e3002921}, pmid = {39591453}, issn = {1545-7885}, mesh = {*Indoleacetic Acids/metabolism ; *Oryza/microbiology/metabolism ; *Arabidopsis/microbiology/metabolism ; *Plant Roots/microbiology/metabolism ; *Bacteria/metabolism/genetics ; Plant Growth Regulators/metabolism ; Rhizosphere ; Soil Microbiology ; Phylogeny ; Operon/genetics ; Microbiota/physiology ; Seedlings/microbiology/metabolism ; }, abstract = {Plant-associated microbiota affect pant growth and development by regulating plant hormones homeostasis. Indole-3-acetic acid (IAA), a well-known plant hormone, can be produced by various plant-associated bacteria. However, the prevalence of bacteria with the capacity to degrade IAA in the rhizosphere has not been systematically studied. In this study, we analyzed the IAA degradation capabilities of bacterial isolates from the roots of Arabidopsis and rice. Using genomics analysis and in vitro assays, we found that 21 out of 183 taxonomically diverse bacterial isolates possess the ability to degrade IAA. Through comparative genomics and transcriptomic assays, we identified iac-like or iad-like operon in the genomes of these IAA degraders. Additionally, the putative regulator of the operon was found to be highly conserved among these strains through protein structure similarity analysis. Some of the IAA degraders could utilize IAA as their carbon and energy source. In planta, most of the IAA degrading strains mitigated Arabidopsis and rice seedling root growth inhibition (RGI) triggered by exogenous IAA. Moreover, RGI caused by complex synthetic bacterial community can be alleviated by introducing IAA degraders. Importantly, we observed increased colonization preference of IAA degraders from soil to root according to the frequency of the biomarker genes in metagenome-assembled genomes (MAGs) collected from different habitats, suggesting that there is a close association between IAA degraders and IAA producers. In summary, our findings further the understanding of the functional diversity and potential biological roles of plant-associated bacteria in host plant root morphogenesis.}, }
@article {pmid39589660, year = {2024}, author = {Xue, X and Zhao, Z and Zhao, LB and Gao, YH and Xu, WH and Cai, WM and Chen, SH and Li, TJ and Nie, TY and Rui, D and Ma, Y and Qian, XS and Lin, JL and Liu, L}, title = {Gut microbiota changes in healthy individuals, obstructive sleep apnea patients, and patients treated using continuous positive airway pressure: a whole-genome metagenomic analysis.}, journal = {Sleep & breathing = Schlaf & Atmung}, volume = {29}, number = {1}, pages = {11}, pmid = {39589660}, issn = {1522-1709}, support = {22BJZ52//Military Health Care Project/ ; 23BJZ27//Military Health Care Project/ ; SYDW_KY[2021]04//Military experimental animal special research project/ ; }, mesh = {Humans ; *Continuous Positive Airway Pressure ; *Sleep Apnea, Obstructive/therapy/microbiology ; *Gastrointestinal Microbiome/physiology/genetics ; Male ; Middle Aged ; Female ; Adult ; *Metagenomics ; Polysomnography ; }, abstract = {PURPOSE: This study investigated variations in gut microbiota among severe obstructive sleep apnea (OSA) patients and changes in gut microbiota after continuous positive airway pressure (CPAP) treatment.
METHOD: From November 2020 to August 2021, laboratory-based polysomnography (PSG) was used to measure sleep parameters in healthy controls, severe OSA patients, and severe OSA patients treated with CPAP for three months. A fully automated biochemical analyzer was used to evaluate routine blood tests and biochemical indicators. Whole-genome metagenomic analysis was used to determine the microbial composition of gut samples from all participants. The relationships between gut microbiota and hypertension were examined using correlation analysis.
RESULT: The relative abundances of Bacteroides, Firmicutes, and Parabacteroides were significantly lower at the species level. Enterobacterales and Turicibacter were significantly higher in participants with severe OSA than healthy controls. Negative correlations were identified between Bacteroides coprocola and systolic blood pressure (SBP) (r = - 0.710, P = 0.003) and diastolic blood pressure (DBP) (r = - 0.615, P = 0.015). Conversely, a positive correlation was found between Escherichia coli and SBP (r = 0.568, P = 0.027).
CONCLUSION: The metabolic pathways and gut microbiota differed significantly between the control group and individuals with severe OSA. Additionally, CPAP therapy substantially changed the metabolic pathways and gut microbial composition among patients diagnosed with severe OSA. Correlation analysis further revealed a strong association between Escherichia coli, Bacteroides coprocola, and blood pressure levels.}, }
@article {pmid39589588, year = {2024}, author = {Wanna, W and Aucharean, C and Jaeram, N}, title = {Analysis of Gut Microbiota Associated with WSSV Resistance in Litopenaeus vannamei.}, journal = {Marine biotechnology (New York, N.Y.)}, volume = {27}, number = {1}, pages = {10}, pmid = {39589588}, issn = {1436-2236}, support = {SCI6601054S//The National Science, Research and Innovation Fund (NSRF) and Prince of Songkla University/ ; SCI6601054S//The National Science, Research and Innovation Fund (NSRF) and Prince of Songkla University/ ; PSU_PHD2565-004//The Graduate School, Prince of Songkla University/ ; }, mesh = {Animals ; *Penaeidae/microbiology/virology ; *White spot syndrome virus 1/genetics ; *Gastrointestinal Microbiome/genetics ; *RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification ; Disease Resistance/genetics ; Metagenome ; }, abstract = {Microorganisms in the digestive tract regulate the metabolism of host cells as well as stimulate the immune system of the host. If the microbiota is in good balance, it will promote the good health of the host. In this study, using 16S rRNA sequencing, we analyzed the microbiota of three groups of shrimp: a group of normal shrimp (control group), shrimp that were killed by infection with the white spot syndrome virus (WSSV) (susceptible group), and shrimp that survived WSSV infection (resistant group). The results showed that although the alpha diversity of the microbiota was barely affected by the WSSV, the bacterial communities in the three groups had different prevalences. The resistant group harbored significantly more bacteria than both the other groups. Remarkably, the resistant group had the greatest prevalence of the phylum Bacterioidetes, the families Rhodobacteraceae and Flavobacteriaceae, and the genus Nautella, suggesting their potential as biomarkers for shrimp resistance to WSSV infection. In addition, analysis of functional diversity in bacterial communities showed that the abundance of bacterial metagenomes in two groups infected with WSSV was mostly linked to metabolism and cellular processes. The susceptible WSSV group exhibited a significant reduction in amino acid metabolism. This result suggested that metabolism was the principal factor affecting the alteration in the microbiota after WSSV infection. This overview of the gut microbiota of shrimp infected with the WSSV offers crucial insights for aquaculture management and simplifies the use of control strategies in the future.}, }
@article {pmid39589125, year = {2024}, author = {Zhang, Z and Tong, M and Ding, W and Liu, S and Jong, M-C and Radwan, AA and Cai, Z and Zhou, J}, title = {Changes in the diversity and functionality of viruses that can bleach healthy coral.}, journal = {mSphere}, volume = {9}, number = {12}, pages = {e0081624}, pmid = {39589125}, issn = {2379-5042}, mesh = {*Anthozoa/virology/microbiology ; Animals ; *Microbiota/genetics ; *Viruses/genetics/classification ; *Metagenomics ; Bacteria/genetics/classification/virology/isolation & purification ; Symbiosis ; Bacteriophages/genetics/physiology/classification/isolation & purification ; }, abstract = {UNLABELLED: Coral microbiomes play a crucial role in maintaining the health and functionality of holobionts. Disruption in the equilibrium of holobionts, including bacteria, fungi, and archaea, can result in the bleaching of coral. However, little is known about the viruses that can infect holobionts in coral, especially bacteriophages. Here, we employed a combination of amplicon and metagenomic analyses on Acropora muricata and Galaxea astreata to investigate the diversity and functionality of viruses in healthy and bleached corals. Analysis showed that the alpha diversity of holobionts (bacteria, eukaryotes, zooxanthellae, and lysogenic and lytic viruses) was higher in bleached corals than that in healthy corals. Meanwhile, bleached corals exhibited a relatively higher abundance of specific viral classes, including Revtraviricetes, Arfiviricetes, Faserviricetes, Caudoviricetes, Herviviricetes, and Tectiliviricetes; moreover, we found that the expression levels of functional genes involved in carbon and sulfur metabolism were enriched. An increase in Vibrio abundance has been reported as a notable factor in coral bleaching; our analysis also revealed an increased abundance of Vibrio in bleached coral. Finally, bleached corals contained a higher abundance of Vibrio phages and encoded more virulence factor genes to increase the competitiveness of Vibrio after coral bleaching. In conclusion, we attempted to understand the causes of coral bleaching from the perspective of phage-bacteria-coral tripartite interaction.
IMPORTANCE: Viruses, especially bacteriophages, outnumber other microorganisms by approximately 10-fold and represent the most abundant members of coral holobionts. Corals represent a model system for the study of symbiosis, the influence of viruses on organisms inhabiting healthy coral reef, the role of rapid horizontal gene transfer, and the expression of auxiliary metabolic genes. However, the least studied component of coral holobiont are viruses. Therefore, there is a critical need to investigate the viral community of viruses, and their functionality, in healthy and bleached coral. Here, we compared the composition and functionality of viruses in healthy and bleached corals and found that viruses may participate in the induction of coral bleaching by enhancing the expression of virulence genes and other auxiliary metabolic functions.}, }
@article {pmid39588334, year = {2024}, author = {Zhang, J and Wu, L and Zhang, Z and Li, D and Han, R and Ye, L and Zhang, Y and Hong, J and Gu, W}, title = {Gut microbiota and metabolic profiles in adults with unclassified diabetes: a cross-sectional study.}, journal = {Frontiers in endocrinology}, volume = {15}, number = {}, pages = {1440984}, pmid = {39588334}, issn = {1664-2392}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Female ; Male ; Adult ; Case-Control Studies ; Cross-Sectional Studies ; *Diabetes Mellitus, Type 2/microbiology/metabolism/blood ; *Metabolome ; Diabetes Mellitus, Type 1/microbiology/metabolism/blood ; Biomarkers/blood ; Young Adult ; }, abstract = {AIMS: Our study, employing a multi-omics approach, aimed to delineate the distinct gut microbiota and metabolic characteristics in individuals under 30 with unclassified diabetes, thus shedding light on the underlying pathophysiological mechanisms.
METHODS: This age- and sex-matched case-control study involved 18 patients with unclassified diabetes, 18 patients with classic type 1 diabetes, 13 patients with type 2 diabetes, and 18 healthy individuals. Metagenomics facilitated the profiling of the gut microbiota, while untargeted liquid chromatography-mass spectrometry was used to quantify the serum lipids and metabolites.
RESULTS: Our findings revealed a unique gut microbiota composition in unclassified diabetes patients, marked by a depletion of Butyrivibrio proteoclasticus and Clostridium and an increase in Ruminococcus torques and Lachnospiraceae bacterium 8_1_57FAA. Comparative analysis identified the combined marker panel of five bacterial species, seven serum biomarkers, and three clinical parameters could differentiate patients with UDM from HCs with an AUC of 0.94 (95% CI 0.85-1). Notably, the gut microbiota structure of patients with unclassified diabetes resembled that of type 2 diabetes patients, especially regarding disrupted lipid and branched-chain amino acid metabolism.
CONCLUSIONS: Despite sharing certain metabolic features with type 2 diabetes, unclassified diabetes presents unique features. The distinct microbiota and metabolites in unclassified diabetes patients suggest a significant role in modulating glucose, lipid, and amino acid metabolism, potentially influencing disease progression. Further longitudinal studies are essential to explore therapeutic strategies targeting the gut microbiota and metabolites to modify the disease trajectory.}, }
@article {pmid39587811, year = {2024}, author = {Xu, N and Chen, B and Wang, Y and Lei, C and Zhang, Z and Ye, Y and Jin, M and Zhang, Q and Lu, T and Dong, H and Shou, J and Penuelas, J and Zhu, YG and Qian, H}, title = {Integrating Anthropogenic-Pesticide Interactions Into a Soil Health-Mic