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RJR: Recommended Bibliography 19 Feb 2025 at 01:32 Created:
Metagenomics
While genomics is the study of DNA extracted from individuals — individual cells, tissues, or organisms — metagenomics is a more recent refinement that analyzes samples of pooled DNA taken from the environment, not from an individual. Like genomics, metagenomic methods have great potential in many areas of biology, but none so much as in providing access to the hitherto invisible world of unculturable microbes, often estimated to comprise 90% or more of bacterial species and, in some ecosystems, the bulk of the biomass. A recent describes how this new science of metagenomics is beginning to reveal the secrets of our microbial world: The opportunity that stands before microbiologists today is akin to a reinvention of the microscope in the expanse of research questions it opens to investigation. Metagenomics provides a new way of examining the microbial world that not only will transform modern microbiology but has the potential to revolutionize understanding of the entire living world. In metagenomics, the power of genomic analysis is applied to entire communities of microbes, bypassing the need to isolate and culture individual bacterial community members.
Created with PubMed® Query: ( metagenomic OR metagenomics OR metagenome ) NOT pmcbook NOT ispreviousversion
Citations The Papers (from PubMed®)
RevDate: 2025-02-18
Metagenomic analysis reveal the phytoremediation effects of monocropping and intercropping of halophytes Halogeton glomeratus and Suaeda glauca in saline soil of Northwestern China.
BMC plant biology, 25(1):213.
AIMS: Planting halophytes is a widely used method of phytoremediation for saline soils. The succulent halophytes Halogeton glomeratus and Suaeda glauca are widely used for remediation of saline soil in the arid region of Northwestern China. However, whether intercropping of H. glomeratus and S. glauca can increase the improvement effect for saline soil is yet to be proved.
MATERIALS AND METHODS: Therefore, this study analyzed three phytoremediation planting modes: monocropping of H. glomeratus (Hg), monocropping of S. glauca (Sg), and H. glomeratus and S. glauca intercropping (Hg||Sg). These were applied in field experiments, with biomass and soil physicochemical properties measured for each treatment, and the mechanism was analyzed using macrogenomics.
RESULTS: After harvesting the halophytes after one season, the Hg treatment had the highest dry biomass and soil total dissolved salt content was reduced; correspondingly, soil pH were decreased and soil organic matter content were increased. The results showed that Actinobacteria, Acidobacteria and Proteobacteria were the dominant phylum under the four treatments. This suggests that Hg treatment was more capable of producing microorganisms favorable to saline soil remediation.
CONCLUSIONS: Thus, H. glomeratus monocropping is a more effective phytoremediation strategy for saline soil in the dry zone of Northwestern China.
Additional Links: PMID-39966722
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@article {pmid39966722,
year = {2025},
author = {Wang, J and Song, M and Yao, L and Li, P and Si, E and Li, B and Meng, Y and Ma, X and Yang, K and Zhang, H and Shang, X and Wang, H},
title = {Metagenomic analysis reveal the phytoremediation effects of monocropping and intercropping of halophytes Halogeton glomeratus and Suaeda glauca in saline soil of Northwestern China.},
journal = {BMC plant biology},
volume = {25},
number = {1},
pages = {213},
pmid = {39966722},
issn = {1471-2229},
support = {32001514//National Natural Science Foundation of China/ ; 31960072//National Natural Science Foundation of China/ ; 20JR10RA507//Key Projects of Natural Science Foundation of Gansu Province/ ; 22JR5RA880//Key Projects of Natural Science Foundation of Gansu Province/ ; Ganfx-03Y06//Fuxi Talent Project of Gansu Agricultural University/ ; GAUfx-04Y011//Fuxi Talent Project of Gansu Agricultural University/ ; 2021CYZC-12//Industrial Support Project of Colleges and Universities in Gansu Province/ ; Grant CARS-05-04B-2//China Agriculture Research System/ ; },
abstract = {AIMS: Planting halophytes is a widely used method of phytoremediation for saline soils. The succulent halophytes Halogeton glomeratus and Suaeda glauca are widely used for remediation of saline soil in the arid region of Northwestern China. However, whether intercropping of H. glomeratus and S. glauca can increase the improvement effect for saline soil is yet to be proved.
MATERIALS AND METHODS: Therefore, this study analyzed three phytoremediation planting modes: monocropping of H. glomeratus (Hg), monocropping of S. glauca (Sg), and H. glomeratus and S. glauca intercropping (Hg||Sg). These were applied in field experiments, with biomass and soil physicochemical properties measured for each treatment, and the mechanism was analyzed using macrogenomics.
RESULTS: After harvesting the halophytes after one season, the Hg treatment had the highest dry biomass and soil total dissolved salt content was reduced; correspondingly, soil pH were decreased and soil organic matter content were increased. The results showed that Actinobacteria, Acidobacteria and Proteobacteria were the dominant phylum under the four treatments. This suggests that Hg treatment was more capable of producing microorganisms favorable to saline soil remediation.
CONCLUSIONS: Thus, H. glomeratus monocropping is a more effective phytoremediation strategy for saline soil in the dry zone of Northwestern China.},
}
RevDate: 2025-02-18
CmpDate: 2025-02-18
Species-resolved profiling of antibiotic resistance genes in complex metagenomes through long-read overlapping with Argo.
Nature communications, 16(1):1744.
Environmental surveillance of antibiotic resistance genes (ARGs) is critical for understanding and mitigating the spread of antimicrobial resistance. Current short-read-based ARG profiling methods are limited in their ability to provide detailed host information, which is indispensable for tracking the transmission and assessing the risk of ARGs. Here, we present Argo, a novel approach that leverages long-read overlapping to rapidly identify and quantify ARGs in complex environmental metagenomes at the species level. Argo significantly enhances the resolution of ARG detection by assigning taxonomic labels collectively to clusters of reads, rather than to individual reads. By benchmarking the performance in host identification using simulation, we confirm the advantage of long-read overlapping over existing metagenomic profiling strategies in terms of accuracy. Using sequenced mock communities with varying quality scores and read lengths, along with a global fecal dataset comprising 329 human and non-human primate samples, we demonstrate Argo's capability to deliver comprehensive and species-resolved ARG profiles in real settings.
Additional Links: PMID-39966439
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@article {pmid39966439,
year = {2025},
author = {Chen, X and Yin, X and Xu, X and Zhang, T},
title = {Species-resolved profiling of antibiotic resistance genes in complex metagenomes through long-read overlapping with Argo.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {1744},
pmid = {39966439},
issn = {2041-1723},
support = {T21-705/20-N//University Grants Committee (UGC)/ ; },
mesh = {*Metagenome/genetics ; Humans ; Animals ; *Metagenomics/methods ; *Drug Resistance, Microbial/genetics ; *Feces/microbiology ; Anti-Bacterial Agents/pharmacology ; Primates/genetics ; Genes, Bacterial/genetics ; Drug Resistance, Bacterial/genetics ; },
abstract = {Environmental surveillance of antibiotic resistance genes (ARGs) is critical for understanding and mitigating the spread of antimicrobial resistance. Current short-read-based ARG profiling methods are limited in their ability to provide detailed host information, which is indispensable for tracking the transmission and assessing the risk of ARGs. Here, we present Argo, a novel approach that leverages long-read overlapping to rapidly identify and quantify ARGs in complex environmental metagenomes at the species level. Argo significantly enhances the resolution of ARG detection by assigning taxonomic labels collectively to clusters of reads, rather than to individual reads. By benchmarking the performance in host identification using simulation, we confirm the advantage of long-read overlapping over existing metagenomic profiling strategies in terms of accuracy. Using sequenced mock communities with varying quality scores and read lengths, along with a global fecal dataset comprising 329 human and non-human primate samples, we demonstrate Argo's capability to deliver comprehensive and species-resolved ARG profiles in real settings.},
}
MeSH Terms:
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*Metagenome/genetics
Humans
Animals
*Metagenomics/methods
*Drug Resistance, Microbial/genetics
*Feces/microbiology
Anti-Bacterial Agents/pharmacology
Primates/genetics
Genes, Bacterial/genetics
Drug Resistance, Bacterial/genetics
RevDate: 2025-02-18
Ammonia-oxidizing activity and microbial structure of ammonia-oxidizing bacteria, ammonia-oxidizing archaea and complete ammonia oxidizers in biofilm systems with different salinities.
Bioresource technology pii:S0960-8524(25)00214-7 [Epub ahead of print].
Ammonia-oxidizing activity of different ammonia-oxidizing microorganisms (AOMs), such as ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA), and complete ammonia oxidizers (comammoxs), were investigated by adding the inhibitors such as 2-phenyl-4,4,5,5-tetramethylimidazoline-1-oxyl 3-oxide, octyne, and KCLO3 in biofilm systems with different salinities. It was found that the ammonia-oxidizing activity of all AOMs gradually decreased with increasing salinity. The ammonia-oxidizing activity of AOB was consistently higher than those of AOA and comammox at different salinities. Moreover, nitrite-oxidizing bacteria (NOB) were more sensitive to changes in salinity than AOMs. Metagenomic analysis revealed that nitrifiers were detected at high level, with the AOB Nitrosomonas sp. comprising 24.9 % and the NOB Nitrospira sp. comprising 47.2% of all nitrifiers. The main functional genes involved in the nitrification reaction were amoABC, hao, and nxrAB. This study demonstrates that higher abundance of functional microorganisms and genes is related to the ammonia-oxidizing activity and ammonia removal contribution rate.
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@article {pmid39965710,
year = {2025},
author = {Qiu, H and Zhao, W and Qin, Y and Wang, Y and Bai, M and Su, S and Wang, C and Zhao, Z},
title = {Ammonia-oxidizing activity and microbial structure of ammonia-oxidizing bacteria, ammonia-oxidizing archaea and complete ammonia oxidizers in biofilm systems with different salinities.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {132248},
doi = {10.1016/j.biortech.2025.132248},
pmid = {39965710},
issn = {1873-2976},
abstract = {Ammonia-oxidizing activity of different ammonia-oxidizing microorganisms (AOMs), such as ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA), and complete ammonia oxidizers (comammoxs), were investigated by adding the inhibitors such as 2-phenyl-4,4,5,5-tetramethylimidazoline-1-oxyl 3-oxide, octyne, and KCLO3 in biofilm systems with different salinities. It was found that the ammonia-oxidizing activity of all AOMs gradually decreased with increasing salinity. The ammonia-oxidizing activity of AOB was consistently higher than those of AOA and comammox at different salinities. Moreover, nitrite-oxidizing bacteria (NOB) were more sensitive to changes in salinity than AOMs. Metagenomic analysis revealed that nitrifiers were detected at high level, with the AOB Nitrosomonas sp. comprising 24.9 % and the NOB Nitrospira sp. comprising 47.2% of all nitrifiers. The main functional genes involved in the nitrification reaction were amoABC, hao, and nxrAB. This study demonstrates that higher abundance of functional microorganisms and genes is related to the ammonia-oxidizing activity and ammonia removal contribution rate.},
}
RevDate: 2025-02-18
Enrichment of the nutritional value of pea flour milling fractions through fermentation.
Food chemistry, 476:143303 pii:S0308-8146(25)00554-0 [Epub ahead of print].
In this work, pea flour and two milling fractions obtained by industrial-scale air classification were characterized and fermented by Lactiplantibacillus plantarum to increase their nutritional value. Scanning electron microscopy and chemical analysis revealed major differences in the morphology and composition of the flours. Protein-rich (43.7 %) fraction exhibits a few-fold higher mineral, spermidine (290 μg/g), but also a higher phytate (20.4 mg/g) content compared to starch-rich fraction. Flour type and inoculum majorly influenced the composition of the fermented product. In spontaneously fermented flours, biogenic amines accumulated up to 6.6 mg/g, which was the main drawback besides the large variations between batches, as confirmed by metagenomic analysis. Higher contents of lactic acid, free amino groups formed by proteolysis and gamma-aminobutyric acid were determined in inoculated fermentations of protein rich fraction, whereas a higher relative bioavailability of minerals was found in the inoculated starch-rich fraction, as the phytate content was reduced by 42 %.
Additional Links: PMID-39965343
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@article {pmid39965343,
year = {2025},
author = {Šaula, T and Cigić, B and Jamnik, P and Kralj Cigić, I and Poklar Ulrih, N and Požrl, T and Marolt, G},
title = {Enrichment of the nutritional value of pea flour milling fractions through fermentation.},
journal = {Food chemistry},
volume = {476},
number = {},
pages = {143303},
doi = {10.1016/j.foodchem.2025.143303},
pmid = {39965343},
issn = {1873-7072},
abstract = {In this work, pea flour and two milling fractions obtained by industrial-scale air classification were characterized and fermented by Lactiplantibacillus plantarum to increase their nutritional value. Scanning electron microscopy and chemical analysis revealed major differences in the morphology and composition of the flours. Protein-rich (43.7 %) fraction exhibits a few-fold higher mineral, spermidine (290 μg/g), but also a higher phytate (20.4 mg/g) content compared to starch-rich fraction. Flour type and inoculum majorly influenced the composition of the fermented product. In spontaneously fermented flours, biogenic amines accumulated up to 6.6 mg/g, which was the main drawback besides the large variations between batches, as confirmed by metagenomic analysis. Higher contents of lactic acid, free amino groups formed by proteolysis and gamma-aminobutyric acid were determined in inoculated fermentations of protein rich fraction, whereas a higher relative bioavailability of minerals was found in the inoculated starch-rich fraction, as the phytate content was reduced by 42 %.},
}
RevDate: 2025-02-18
Effect of prenatal antibiotics on breast milk and neonatal IgA and microbiome: a case-control translational study protocol.
Pediatric research [Epub ahead of print].
BACKGROUND: Up to 25-35% of women receive antibiotics (ABX) during pregnancy, but little is known about the consequences on a key mucosal interface such as the mammary gland, and on the development of the neonatal gut's microbiota and IgA. We hypothesize that prenatal ABX negatively affect the immune functionality of mammary gland, the composition of breast milk microbiota, the development of neonatal fecal microbiota and the abundance of neonatal fecal IgA.
METHODS: Case-control translational cohort study on women and neonates in the presence or absence (N = 41 + 41 pairs) of exposure to prenatal ABX for at least 7 consecutive days after 32 weeks of gestation.
RESULTS: We will evaluate IgA concentration in breast milk and in neonatal feces up to one year after delivery. We will also evaluate clinical parameters, neurodevelopment and the composition of the IgA-coated and uncoated fractions of breast milk and fecal microbiota by means of magnetic-activated cell sorting (MACS) coupled with shotgun metagenomics. Finally, we will measure the concentration of the chemokine CCL28 on maternal serum and breast milk, as a marker of activity of the entero-mammary pathway.
CONCLUSIONS: Our results might support a data-driven evaluation of breast milk immune function in women exposed to prenatal ABX.
IMPACT: Breast milk IgA and microbiota are critical to determine the positive effects of breastfeeding in infants. This research protocol will investigate breast milk IgA, microbiota, and the IgA[+] / IgA[-] fractions of neonatal fecal microbiota upon exposure to prenatal antibiotics. Fecal IgA and microbiota in infants exposed or not exposed to prenatal antibiotics will be analyzed up to 1 year after birth. This research will clarify the impact of prenatal antibiotics on the immune function of breast milk. This, in turn, might support the selective evaluation of breast milk IgA/microbiota in mothers exposed to prenatal antibiotics, or in donor human milk.
Additional Links: PMID-39966546
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@article {pmid39966546,
year = {2025},
author = {Pietrasanta, C and Ronchi, A and Carlosama, C and Lizier, M and Silvestri, A and Fornasa, G and Melacarne, A and D'Ambrosi, F and Lutterotti, M and Carbone, E and Cetin, I and Fumagalli, M and Ferrazzi, E and Penna, G and Mosca, F and Pugni, L and Rescigno, M},
title = {Effect of prenatal antibiotics on breast milk and neonatal IgA and microbiome: a case-control translational study protocol.},
journal = {Pediatric research},
volume = {},
number = {},
pages = {},
pmid = {39966546},
issn = {1530-0447},
abstract = {BACKGROUND: Up to 25-35% of women receive antibiotics (ABX) during pregnancy, but little is known about the consequences on a key mucosal interface such as the mammary gland, and on the development of the neonatal gut's microbiota and IgA. We hypothesize that prenatal ABX negatively affect the immune functionality of mammary gland, the composition of breast milk microbiota, the development of neonatal fecal microbiota and the abundance of neonatal fecal IgA.
METHODS: Case-control translational cohort study on women and neonates in the presence or absence (N = 41 + 41 pairs) of exposure to prenatal ABX for at least 7 consecutive days after 32 weeks of gestation.
RESULTS: We will evaluate IgA concentration in breast milk and in neonatal feces up to one year after delivery. We will also evaluate clinical parameters, neurodevelopment and the composition of the IgA-coated and uncoated fractions of breast milk and fecal microbiota by means of magnetic-activated cell sorting (MACS) coupled with shotgun metagenomics. Finally, we will measure the concentration of the chemokine CCL28 on maternal serum and breast milk, as a marker of activity of the entero-mammary pathway.
CONCLUSIONS: Our results might support a data-driven evaluation of breast milk immune function in women exposed to prenatal ABX.
IMPACT: Breast milk IgA and microbiota are critical to determine the positive effects of breastfeeding in infants. This research protocol will investigate breast milk IgA, microbiota, and the IgA[+] / IgA[-] fractions of neonatal fecal microbiota upon exposure to prenatal antibiotics. Fecal IgA and microbiota in infants exposed or not exposed to prenatal antibiotics will be analyzed up to 1 year after birth. This research will clarify the impact of prenatal antibiotics on the immune function of breast milk. This, in turn, might support the selective evaluation of breast milk IgA/microbiota in mothers exposed to prenatal antibiotics, or in donor human milk.},
}
RevDate: 2025-02-18
Metagenomic estimation of dietary intake from human stool.
Nature metabolism [Epub ahead of print].
Dietary intake is tightly coupled to gut microbiota composition, human metabolism and the incidence of virtually all major chronic diseases. Dietary and nutrient intake are usually assessed using self-reporting methods, including dietary questionnaires and food records, which suffer from reporting biases and require strong compliance from study participants. Here, we present Metagenomic Estimation of Dietary Intake (MEDI): a method for quantifying food-derived DNA in human faecal metagenomes. We show that DNA-containing food components can be reliably detected in stool-derived metagenomic data, even when present at low abundances (more than ten reads). We show how MEDI dietary intake profiles can be converted into detailed metabolic representations of nutrient intake. MEDI identifies the onset of solid food consumption in infants, shows significant agreement with food frequency questionnaire responses in an adult population and shows agreement with food and nutrient intake in two controlled-feeding studies. Finally, we identify specific dietary features associated with metabolic syndrome in a large clinical cohort without dietary records, providing a proof-of-concept for detailed tracking of individual-specific, health-relevant dietary patterns without the need for questionnaires.
Additional Links: PMID-39966520
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@article {pmid39966520,
year = {2025},
author = {Diener, C and Holscher, HD and Filek, K and Corbin, KD and Moissl-Eichinger, C and Gibbons, SM},
title = {Metagenomic estimation of dietary intake from human stool.},
journal = {Nature metabolism},
volume = {},
number = {},
pages = {},
pmid = {39966520},
issn = {2522-5812},
support = {R01DK133468//U.S. Department of Health & Human Services | NIH | Office of Extramural Research, National Institutes of Health (OER)/ ; Cluster of Excellence COE7//Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung)/ ; Cluster of Excellence COE7//Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung)/ ; },
abstract = {Dietary intake is tightly coupled to gut microbiota composition, human metabolism and the incidence of virtually all major chronic diseases. Dietary and nutrient intake are usually assessed using self-reporting methods, including dietary questionnaires and food records, which suffer from reporting biases and require strong compliance from study participants. Here, we present Metagenomic Estimation of Dietary Intake (MEDI): a method for quantifying food-derived DNA in human faecal metagenomes. We show that DNA-containing food components can be reliably detected in stool-derived metagenomic data, even when present at low abundances (more than ten reads). We show how MEDI dietary intake profiles can be converted into detailed metabolic representations of nutrient intake. MEDI identifies the onset of solid food consumption in infants, shows significant agreement with food frequency questionnaire responses in an adult population and shows agreement with food and nutrient intake in two controlled-feeding studies. Finally, we identify specific dietary features associated with metabolic syndrome in a large clinical cohort without dietary records, providing a proof-of-concept for detailed tracking of individual-specific, health-relevant dietary patterns without the need for questionnaires.},
}
RevDate: 2025-02-18
Newly identified species from the dog dental plaque microbiome highlight little overlap with humans.
NPJ biofilms and microbiomes, 11(1):30.
Understudied pet-associated microbiomes represent a rich source for the discovery of microbial taxa important for pet and human health. From a cohort of 23 dogs, we sampled and metagenomically sequenced 64 dental plaque microbiomes, generating 1945 metagenome-assembled genomes spanning 347 microbial species, including 277 undercharacterized species without cultivated representatives. Integration with human microbiome data revealed the dog plaque microbiome is more diverse than - and shows little overlap (5.9% species in common) with - the human plaque microbiome, even though some shared periodontal pathobionts arise as a potential concern.
Additional Links: PMID-39966419
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@article {pmid39966419,
year = {2025},
author = {Heidrich, V and Fackelmann, G and Malesevic, M and Armanini, F and Dey, H and Mengoni, C and Stanisavljevic, N and Vukotic, G and Segata, N},
title = {Newly identified species from the dog dental plaque microbiome highlight little overlap with humans.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {30},
pmid = {39966419},
issn = {2055-5008},
abstract = {Understudied pet-associated microbiomes represent a rich source for the discovery of microbial taxa important for pet and human health. From a cohort of 23 dogs, we sampled and metagenomically sequenced 64 dental plaque microbiomes, generating 1945 metagenome-assembled genomes spanning 347 microbial species, including 277 undercharacterized species without cultivated representatives. Integration with human microbiome data revealed the dog plaque microbiome is more diverse than - and shows little overlap (5.9% species in common) with - the human plaque microbiome, even though some shared periodontal pathobionts arise as a potential concern.},
}
RevDate: 2025-02-18
Impacts of successive Chinese fir plantations on soil carbon and nitrogen dynamics: Conclusive insights from metagenomic analysis.
Journal of environmental management, 376:124510 pii:S0301-4797(25)00486-4 [Epub ahead of print].
Chinese fir forests play a significant role both economically and ecologically, contributing to soil and water conservation while also serving as an efficient timber-producing species that brings economic benefits. However, the issue of soil degradation due to continuous Chinese fir planting cannot be overlooked. Continuous planting leads to a decrease in soil nutrients, a reduction in microbial diversity, and changes in microbial community composition, which in turn affect the abundance of carbon and nitrogen cycle functional genes in Chinese fir forest soils. We utilized metagenomic sequencing technology to investigate the dynamics of microbial community composition and carbon and nitrogen-related functional genes in the soils of Chinese fir forests across different plantation generations, exploring their relationship with soil carbon and nitrogen nutrients. We found that the relative abundance of bacterial communities is dominant in both phylum and genus levels within microbial communities. The partial least squares path models (PLS-PM) indicated that planting generations had a negative effect on dissolved organic carbon (DOC), nitrate nitrogen (NO3[-]-N), and microbial biomass nitrogen (MBN), with a significant negative impact on microbial residual carbon (MRC). Easily utilizable carbon nutrient (DOC) in Chinese fir forest soil showed a significant positive effect on the abundance of carbon fixation functional genes (direct effect = 0.91, p < 0.01), and on the abundance of methane metabolism functional genes (direct effect = 1.27, p < 0.01). Nitrogen nutrients (NO3[-]-N, MBN) in the soil also had a significant positive effect on the abundance of carbon fixation functional genes (direct effect = 0.90, p < 0.01). Bacterial communities (Acidobacteria and Verrucomicrobia) had significant negative effects on carbon and nitrogen cycling processes. The abundance of nasA and nirA genes generally showed a decreasing trend with increasing plantation generations. The decrease in available nitrogen nutrients with increased plantation generations was influenced by Assimilatory nitrogen reduction to ammonia (ANRA), an energy-consuming process. In summary, the continuous planting of Chinese fir had significant impacts on the carbon and nitrogen nutrient cycling processes, and it influenced the composition of microbial communities and the spatial distribution of functional genes. Clarifying the changes in carbon and nitrogen nutrient cycling processes in Chinese fir continuous planting provides a reference for maintaining the productivity of Chinese fir plantations.
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@article {pmid39965493,
year = {2025},
author = {Zhang, H and Pan, F and Wen, Z and Chen, W and Zhou, C},
title = {Impacts of successive Chinese fir plantations on soil carbon and nitrogen dynamics: Conclusive insights from metagenomic analysis.},
journal = {Journal of environmental management},
volume = {376},
number = {},
pages = {124510},
doi = {10.1016/j.jenvman.2025.124510},
pmid = {39965493},
issn = {1095-8630},
abstract = {Chinese fir forests play a significant role both economically and ecologically, contributing to soil and water conservation while also serving as an efficient timber-producing species that brings economic benefits. However, the issue of soil degradation due to continuous Chinese fir planting cannot be overlooked. Continuous planting leads to a decrease in soil nutrients, a reduction in microbial diversity, and changes in microbial community composition, which in turn affect the abundance of carbon and nitrogen cycle functional genes in Chinese fir forest soils. We utilized metagenomic sequencing technology to investigate the dynamics of microbial community composition and carbon and nitrogen-related functional genes in the soils of Chinese fir forests across different plantation generations, exploring their relationship with soil carbon and nitrogen nutrients. We found that the relative abundance of bacterial communities is dominant in both phylum and genus levels within microbial communities. The partial least squares path models (PLS-PM) indicated that planting generations had a negative effect on dissolved organic carbon (DOC), nitrate nitrogen (NO3[-]-N), and microbial biomass nitrogen (MBN), with a significant negative impact on microbial residual carbon (MRC). Easily utilizable carbon nutrient (DOC) in Chinese fir forest soil showed a significant positive effect on the abundance of carbon fixation functional genes (direct effect = 0.91, p < 0.01), and on the abundance of methane metabolism functional genes (direct effect = 1.27, p < 0.01). Nitrogen nutrients (NO3[-]-N, MBN) in the soil also had a significant positive effect on the abundance of carbon fixation functional genes (direct effect = 0.90, p < 0.01). Bacterial communities (Acidobacteria and Verrucomicrobia) had significant negative effects on carbon and nitrogen cycling processes. The abundance of nasA and nirA genes generally showed a decreasing trend with increasing plantation generations. The decrease in available nitrogen nutrients with increased plantation generations was influenced by Assimilatory nitrogen reduction to ammonia (ANRA), an energy-consuming process. In summary, the continuous planting of Chinese fir had significant impacts on the carbon and nitrogen nutrient cycling processes, and it influenced the composition of microbial communities and the spatial distribution of functional genes. Clarifying the changes in carbon and nitrogen nutrient cycling processes in Chinese fir continuous planting provides a reference for maintaining the productivity of Chinese fir plantations.},
}
RevDate: 2025-02-18
Waterlogging alone and combined with other abiotic stresses provides unique metabolic signatures at the plant-rhizosphere interface: A multi-omics perspective on root metabolome, root exudation and rhizomicrobiome.
Plant physiology and biochemistry : PPB, 221:109646 pii:S0981-9428(25)00174-3 [Epub ahead of print].
Despite the growing evidence on unique and unpredictable impact of stress combination over plants, waterlogging-combined stresses effects are still underexplored. Under those conditions, besides the impairment of plant aerial parts, the root system is particularly vulnerable, leading to consequences on plant survival. Here, we report on the short-term exposure of soil-grown Arabidopsis thaliana L. to waterlogging alone and combined with cold, heat, and salinity to inspect their antagonistic, additive or synergistic effects in the rhizosphere. To this aim, root metabolic changes, exudation profiles, and microbial diversity were investigated using a combination of metabolomics and metagenomics, and their interaction was analysed through multi-omics data integration. In roots, waterlogging strongly affected metabolism compared to other single stresses, causing a down-accumulation of targeted classes of compounds including, phenylpropanoids, sterols, terpenoids, and alkaloids. Additive and synergistic effects were reported in roots under waterlogging combined with heat and cold stresses, respectively. Regarding root exudates, flavonoids, terpenoids, and alkaloids were the main classes of compounds affected. Waterlogging caused a down-accumulation of all classes except for coumarins, and mixed trends were observed in waterlogging-combined stresses, with waterlogging-salinity stresses resulting in an ameliorating effect. Even though microbial communities' alpha- and beta-diversity remained stable, suggesting their resilience under short-term exposure, specific taxa modulation was recorded under each condition. Overall, these results contribute to understanding the hierarchical impact of waterlogging on root metabolism and exudation, influencing rhizosphere interactions. This multi-omics approach advances our understanding of plant stress responses and microbial dynamics, paving the way for future studies on adaptive mechanisms.
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@article {pmid39965412,
year = {2025},
author = {Secomandi, E and De Gregorio, MA and Garcia-Perez, P and Vaccari, F and Puglisi, E and Lucini, L},
title = {Waterlogging alone and combined with other abiotic stresses provides unique metabolic signatures at the plant-rhizosphere interface: A multi-omics perspective on root metabolome, root exudation and rhizomicrobiome.},
journal = {Plant physiology and biochemistry : PPB},
volume = {221},
number = {},
pages = {109646},
doi = {10.1016/j.plaphy.2025.109646},
pmid = {39965412},
issn = {1873-2690},
abstract = {Despite the growing evidence on unique and unpredictable impact of stress combination over plants, waterlogging-combined stresses effects are still underexplored. Under those conditions, besides the impairment of plant aerial parts, the root system is particularly vulnerable, leading to consequences on plant survival. Here, we report on the short-term exposure of soil-grown Arabidopsis thaliana L. to waterlogging alone and combined with cold, heat, and salinity to inspect their antagonistic, additive or synergistic effects in the rhizosphere. To this aim, root metabolic changes, exudation profiles, and microbial diversity were investigated using a combination of metabolomics and metagenomics, and their interaction was analysed through multi-omics data integration. In roots, waterlogging strongly affected metabolism compared to other single stresses, causing a down-accumulation of targeted classes of compounds including, phenylpropanoids, sterols, terpenoids, and alkaloids. Additive and synergistic effects were reported in roots under waterlogging combined with heat and cold stresses, respectively. Regarding root exudates, flavonoids, terpenoids, and alkaloids were the main classes of compounds affected. Waterlogging caused a down-accumulation of all classes except for coumarins, and mixed trends were observed in waterlogging-combined stresses, with waterlogging-salinity stresses resulting in an ameliorating effect. Even though microbial communities' alpha- and beta-diversity remained stable, suggesting their resilience under short-term exposure, specific taxa modulation was recorded under each condition. Overall, these results contribute to understanding the hierarchical impact of waterlogging on root metabolism and exudation, influencing rhizosphere interactions. This multi-omics approach advances our understanding of plant stress responses and microbial dynamics, paving the way for future studies on adaptive mechanisms.},
}
RevDate: 2025-02-18
Co-occurrence and co-expression of antibiotic, biocide, and metal resistance genes with mobile genetic elements in microbial communities subjected to long-term antibiotic pressure: Novel insights from metagenomics and metatranscriptomics.
Journal of hazardous materials, 489:137559 pii:S0304-3894(25)00473-X [Epub ahead of print].
The burgeoning of antibiotic resistance has emerged as a pressing global challenge. To gain a deeper understanding of the interactions between antibiotic resistance genes (ARGs), biocide and metal resistance genes (BRGs&MRGs), and mobile genetic elements (MGEs), this study utilized metagenomics and metatranscriptomics to investigate their co-occurrence and co-expression in two consortia subjected to long-term exposure to chloramphenicol and lincomycin. Long-term exposure to these antibiotics resulted in significant disparities in resistance profiles: ConsortiumCAP harbored 130 ARGs and 150 BRGs&MRGs, while ConsortiumLIN contained 57 ARGs and 32 BRGs&MRGs. Horizontal gene transfer (HGT) events were predicted at 125 and 300 instances in ConsortiumCAP and ConsortiumLIN, respectively, facilitating the emergence of multidrug-resistant bacteria, such as Caballeronia (10 ARGs, 2 BRGs&MRGs), Cupriavidus (2 ARGs, 10 BRGs&MRGs), and Bacillus (14 ARGs, 21 BRGs&MRGs). Chloramphenicol exposure significantly enriched genes linked to phenicol resistance (floR, capO) and co-expressed ARGs and BRGs&MRGs, while lincomycin exerted narrower effects on resistance genes. Additionally, both antibiotics modulated the expression of degradation genes and virulence factors, highlighting their role in altering bacterial substrate utilization and pathogenic traits. This study provides quantitative insights into the impact of antibiotics on microbial resistance profiles and functions at both DNA and RNA levels, highlighting the importance of reducing antibiotic pollution and limiting the spread of resistance genes in the environment.
Additional Links: PMID-39965334
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@article {pmid39965334,
year = {2025},
author = {Zhang, J and Lei, H and Huang, J and Wong, JWC and Li, B},
title = {Co-occurrence and co-expression of antibiotic, biocide, and metal resistance genes with mobile genetic elements in microbial communities subjected to long-term antibiotic pressure: Novel insights from metagenomics and metatranscriptomics.},
journal = {Journal of hazardous materials},
volume = {489},
number = {},
pages = {137559},
doi = {10.1016/j.jhazmat.2025.137559},
pmid = {39965334},
issn = {1873-3336},
abstract = {The burgeoning of antibiotic resistance has emerged as a pressing global challenge. To gain a deeper understanding of the interactions between antibiotic resistance genes (ARGs), biocide and metal resistance genes (BRGs&MRGs), and mobile genetic elements (MGEs), this study utilized metagenomics and metatranscriptomics to investigate their co-occurrence and co-expression in two consortia subjected to long-term exposure to chloramphenicol and lincomycin. Long-term exposure to these antibiotics resulted in significant disparities in resistance profiles: ConsortiumCAP harbored 130 ARGs and 150 BRGs&MRGs, while ConsortiumLIN contained 57 ARGs and 32 BRGs&MRGs. Horizontal gene transfer (HGT) events were predicted at 125 and 300 instances in ConsortiumCAP and ConsortiumLIN, respectively, facilitating the emergence of multidrug-resistant bacteria, such as Caballeronia (10 ARGs, 2 BRGs&MRGs), Cupriavidus (2 ARGs, 10 BRGs&MRGs), and Bacillus (14 ARGs, 21 BRGs&MRGs). Chloramphenicol exposure significantly enriched genes linked to phenicol resistance (floR, capO) and co-expressed ARGs and BRGs&MRGs, while lincomycin exerted narrower effects on resistance genes. Additionally, both antibiotics modulated the expression of degradation genes and virulence factors, highlighting their role in altering bacterial substrate utilization and pathogenic traits. This study provides quantitative insights into the impact of antibiotics on microbial resistance profiles and functions at both DNA and RNA levels, highlighting the importance of reducing antibiotic pollution and limiting the spread of resistance genes in the environment.},
}
RevDate: 2025-02-18
Biodiversity of strains belonging to the freshwater genus Aquirufa in a riparian forest restoration area in Salzburg, Austria, with a focus on the description of Aquirufa salirivi sp. nov. and Aquirufa novilacunae sp. nov.
International microbiology : the official journal of the Spanish Society for Microbiology [Epub ahead of print].
During a citizen science project, four freshwater habitats in a riparian forest restoration area in Salzburg, Austria, were sampled. The primary aim was to obtain bacterial strains of the genus Aquirufa, a group of typical and widespread freshwater bacteria. Numerous pure cultures of Aquirufa strains could be obtained, three of them originating from the river Salzach, a newly created pond and the lake Ausee represented new species. Strain 1-SAACH-A3[T] was characterized by a genome size of 3.2 Mbp and a G + C value of 38.4 mol% and encoded genes predicted for nitrate uptake and nitrous oxide utilization. Strains BAHN-186B[T] and 2-AUSEE-184A6 were characterized by a genome size of 2.4 Mbp and a G + C value of 42.4 and 42.2 mol%, respectively, and encoded genes predicted for the light-harvesting rhodopsin system. Calculated whole-genome average nucleotide identity values with Aquirufa type strains resulted in a maximum value of 93.65% for comparison of strain 1-SAACH[T] with the type strain of Aquirufa ecclesiirivi, which is slightly under the proposed threshold of species demarcation. The calculated gANI value comparing strains BAHN-186B[T] and 2-AUSEE-184A6 revealed 95.76%, thus a value slightly above the threshold. Further analyses revealed that the three new strains represent two new species, proposed here as Aquirufa salirivi sp. nov. with type strain 1-SAACH-A3[T] (= DSM 117800[ T] = JCM 37097[ T]) and Aquirufa novilacunae sp. nov. with type strain BAHN-186B[T] (= DSM 118143[ T] = JCM 37099[ T]). Analyses of 123 publicly available metagenomes and a metagenome of the lake Ausee resulted in no detection of A. salirivi sp. nov. In contrast, A. novilacunae sp. nov. could be detected in 15 water samples of rivers, mainly from Asia, but also from North America and Australia. The analyses suggested that the species occurs in most of these samples in low relative abundance, detections derived from metagenomes of water samples from the river Yangtze in the subtropical zone could be interpreted as occurrence in higher abundances.
Additional Links: PMID-39964655
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@article {pmid39964655,
year = {2025},
author = {Pitt, A and Lienbacher, S and Schmidt, J and Neumann-Schaal, M and Wolf, J and Wenng, H and Oren, A and Huber, Z and Hahn, MW},
title = {Biodiversity of strains belonging to the freshwater genus Aquirufa in a riparian forest restoration area in Salzburg, Austria, with a focus on the description of Aquirufa salirivi sp. nov. and Aquirufa novilacunae sp. nov.},
journal = {International microbiology : the official journal of the Spanish Society for Microbiology},
volume = {},
number = {},
pages = {},
pmid = {39964655},
issn = {1618-1905},
abstract = {During a citizen science project, four freshwater habitats in a riparian forest restoration area in Salzburg, Austria, were sampled. The primary aim was to obtain bacterial strains of the genus Aquirufa, a group of typical and widespread freshwater bacteria. Numerous pure cultures of Aquirufa strains could be obtained, three of them originating from the river Salzach, a newly created pond and the lake Ausee represented new species. Strain 1-SAACH-A3[T] was characterized by a genome size of 3.2 Mbp and a G + C value of 38.4 mol% and encoded genes predicted for nitrate uptake and nitrous oxide utilization. Strains BAHN-186B[T] and 2-AUSEE-184A6 were characterized by a genome size of 2.4 Mbp and a G + C value of 42.4 and 42.2 mol%, respectively, and encoded genes predicted for the light-harvesting rhodopsin system. Calculated whole-genome average nucleotide identity values with Aquirufa type strains resulted in a maximum value of 93.65% for comparison of strain 1-SAACH[T] with the type strain of Aquirufa ecclesiirivi, which is slightly under the proposed threshold of species demarcation. The calculated gANI value comparing strains BAHN-186B[T] and 2-AUSEE-184A6 revealed 95.76%, thus a value slightly above the threshold. Further analyses revealed that the three new strains represent two new species, proposed here as Aquirufa salirivi sp. nov. with type strain 1-SAACH-A3[T] (= DSM 117800[ T] = JCM 37097[ T]) and Aquirufa novilacunae sp. nov. with type strain BAHN-186B[T] (= DSM 118143[ T] = JCM 37099[ T]). Analyses of 123 publicly available metagenomes and a metagenome of the lake Ausee resulted in no detection of A. salirivi sp. nov. In contrast, A. novilacunae sp. nov. could be detected in 15 water samples of rivers, mainly from Asia, but also from North America and Australia. The analyses suggested that the species occurs in most of these samples in low relative abundance, detections derived from metagenomes of water samples from the river Yangtze in the subtropical zone could be interpreted as occurrence in higher abundances.},
}
RevDate: 2025-02-18
Microbiome insights from a South African cultural and natural landmark cave using metagenomics next-generation sequencing.
Microbiology resource announcements [Epub ahead of print].
The microbiome study of Sterkfontein Cave (a natural and cultural cave) revealed fascinating insights into its metagenome study and functional annotation. The largely unexplored cave soil microbiota showcases intricate survival adaptations with promising potential for various human applications. Here, we report the microbial diversity and functions associated with Sterkfontein Cave soil.
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@article {pmid39964161,
year = {2025},
author = {Babalola, OO and Adedayo, AA and Akinola, SA},
title = {Microbiome insights from a South African cultural and natural landmark cave using metagenomics next-generation sequencing.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0118324},
doi = {10.1128/mra.01183-24},
pmid = {39964161},
issn = {2576-098X},
abstract = {The microbiome study of Sterkfontein Cave (a natural and cultural cave) revealed fascinating insights into its metagenome study and functional annotation. The largely unexplored cave soil microbiota showcases intricate survival adaptations with promising potential for various human applications. Here, we report the microbial diversity and functions associated with Sterkfontein Cave soil.},
}
RevDate: 2025-02-18
Wildfire impact on soil microbiome life history traits and roles in ecosystem carbon cycling.
ISME communications, 4(1):ycae108.
Wildfires, which are increasing in frequency and severity with climate change, reduce soil microbial biomass and alter microbial community composition and function. The soil microbiome plays a vital role in carbon (C) and nitrogen (N) cycling, but its complexity makes it challenging to predict post-wildfire soil microbial dynamics and resulting impacts on ecosystem biogeochemistry. The application of biogeochemically relevant conceptual trait-based frameworks to the soil microbiome can distill this complexity, enabling enhanced predictability of soil microbiome recovery following wildfire and subsequent impacts to biogeochemical cycles. Conceptual frameworks that have direct links to soil C and N cycling have been developed for the soil microbiome; the Y-A-S framework overviews soil microbiome life history strategies that have tradeoffs with one another and others have proposed frameworks specific to wildfire. Here, we aimed to delineate post-wildfire changes of bacterial traits in western US coniferous forests to inform how severe wildfire influences soil microbiome recovery and resultant biogeochemical cycling. We utilized a comprehensive metagenome-assembled genome catalog from post-wildfire soils representing 1 to 11 years following low- and high-severity burning to identify traits that enable the persistence of microbial taxa in burned soils and influence ecosystem C and N cycling. We found that high-severity wildfire initially selects for fast growers and, up to a decade post-fire, taxa that invest in genes for acquiring diverse resources from the external environment, which in combination could increase soil C losses. This work begins to disentangle how climate change-induced shifts in wildfire behavior might alter microbially mediated soil biogeochemical cycling.
Additional Links: PMID-39963501
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Citation:
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@article {pmid39963501,
year = {2024},
author = {Nelson, AR and Rhoades, CC and Fegel, TS and Roth, HK and Caiafa, MV and Glassman, SI and Borch, T and Wilkins, MJ},
title = {Wildfire impact on soil microbiome life history traits and roles in ecosystem carbon cycling.},
journal = {ISME communications},
volume = {4},
number = {1},
pages = {ycae108},
pmid = {39963501},
issn = {2730-6151},
abstract = {Wildfires, which are increasing in frequency and severity with climate change, reduce soil microbial biomass and alter microbial community composition and function. The soil microbiome plays a vital role in carbon (C) and nitrogen (N) cycling, but its complexity makes it challenging to predict post-wildfire soil microbial dynamics and resulting impacts on ecosystem biogeochemistry. The application of biogeochemically relevant conceptual trait-based frameworks to the soil microbiome can distill this complexity, enabling enhanced predictability of soil microbiome recovery following wildfire and subsequent impacts to biogeochemical cycles. Conceptual frameworks that have direct links to soil C and N cycling have been developed for the soil microbiome; the Y-A-S framework overviews soil microbiome life history strategies that have tradeoffs with one another and others have proposed frameworks specific to wildfire. Here, we aimed to delineate post-wildfire changes of bacterial traits in western US coniferous forests to inform how severe wildfire influences soil microbiome recovery and resultant biogeochemical cycling. We utilized a comprehensive metagenome-assembled genome catalog from post-wildfire soils representing 1 to 11 years following low- and high-severity burning to identify traits that enable the persistence of microbial taxa in burned soils and influence ecosystem C and N cycling. We found that high-severity wildfire initially selects for fast growers and, up to a decade post-fire, taxa that invest in genes for acquiring diverse resources from the external environment, which in combination could increase soil C losses. This work begins to disentangle how climate change-induced shifts in wildfire behavior might alter microbially mediated soil biogeochemical cycling.},
}
RevDate: 2025-02-18
Assessing the authenticity and purity of a commercial Bacillus thuringiensis bioinsecticide through whole genome sequencing and metagenomics approaches.
Frontiers in microbiology, 16:1532788.
Biopesticides, biological agents for pest control in plants, are becoming increasingly prevalent in agricultural practices. However, no established methodology currently exists to assess their quality, and there are currently no publicly available authenticity and purity evaluations of commercial products. This lack of data may represent risks because of their widespread dispersal in the environment. We evaluated the potential of whole genome sequencing (WGS) and metagenomics approaches, including nanopore long-read sequencing, to verify both authenticity (i.e., the labeled strain) and biological purity (i.e., the absence of any undesired genetic material) of commercial Bacillus thuringiensis bioinsecticides. Four commercially available bioinsecticidal products containing Bacillus thuringiensis serovar kurstaki strain HD-1 were collected from the European market as a case study. Two sequencing approaches were employed: WGS of isolates and metagenomics sequencing of all genetic material in a product. To assess authenticity, isolate WGS data were compared against the publicly available reference genome of the expected strain. Antimicrobial resistance gene content, insecticidal gene content, and single nucleotide polymorphism differences were characterized to evaluate similarity to the reference genome. To assess purity, metagenomic sequencing data were analyzed using read classification and strain differentiation methods. Additionally, long- and short-read data were used to assess potential large-scale structural variations. Our results confirmed all investigated products to be authentic and pure. With the increasing usage of biopesticides, it is crucial to have adequate quality control methods. Our proposed approach could be adapted for other biopesticides, and similar products, providing a standardized and robust approach to contribute to biopesticide safety.
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@article {pmid39963497,
year = {2025},
author = {Van Laere, Y and Fraiture, MA and Gobbo, A and De Keersmaecker, SCJ and Marchal, K and Roosens, NHC and Vanneste, K},
title = {Assessing the authenticity and purity of a commercial Bacillus thuringiensis bioinsecticide through whole genome sequencing and metagenomics approaches.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1532788},
pmid = {39963497},
issn = {1664-302X},
abstract = {Biopesticides, biological agents for pest control in plants, are becoming increasingly prevalent in agricultural practices. However, no established methodology currently exists to assess their quality, and there are currently no publicly available authenticity and purity evaluations of commercial products. This lack of data may represent risks because of their widespread dispersal in the environment. We evaluated the potential of whole genome sequencing (WGS) and metagenomics approaches, including nanopore long-read sequencing, to verify both authenticity (i.e., the labeled strain) and biological purity (i.e., the absence of any undesired genetic material) of commercial Bacillus thuringiensis bioinsecticides. Four commercially available bioinsecticidal products containing Bacillus thuringiensis serovar kurstaki strain HD-1 were collected from the European market as a case study. Two sequencing approaches were employed: WGS of isolates and metagenomics sequencing of all genetic material in a product. To assess authenticity, isolate WGS data were compared against the publicly available reference genome of the expected strain. Antimicrobial resistance gene content, insecticidal gene content, and single nucleotide polymorphism differences were characterized to evaluate similarity to the reference genome. To assess purity, metagenomic sequencing data were analyzed using read classification and strain differentiation methods. Additionally, long- and short-read data were used to assess potential large-scale structural variations. Our results confirmed all investigated products to be authentic and pure. With the increasing usage of biopesticides, it is crucial to have adequate quality control methods. Our proposed approach could be adapted for other biopesticides, and similar products, providing a standardized and robust approach to contribute to biopesticide safety.},
}
RevDate: 2025-02-18
Standardized and accessible multi-omics bioinformatics workflows through the NMDC EDGE resource.
Computational and structural biotechnology journal, 23:3575-3583.
Accessible and easy-to-use standardized bioinformatics workflows are necessary to advance microbiome research from observational studies to large-scale, data-driven approaches. Standardized multi-omics data enables comparative studies, data reuse, and applications of machine learning to model biological processes. To advance broad accessibility of standardized multi-omics bioinformatics workflows, the National Microbiome Data Collaborative (NMDC) has developed the Empowering the Development of Genomics Expertise (NMDC EDGE) resource, a user-friendly, open-source web application (https://nmdc-edge.org). Here, we describe the design and main functionality of the NMDC EDGE resource for processing metagenome, metatranscriptome, natural organic matter, and metaproteome data. The architecture relies on three main layers (web application, orchestration, and execution) to ensure flexibility and expansion to future workflows. The orchestration and execution layers leverage best practices in software containers and accommodate high-performance computing and cloud computing services. Further, we have adopted a robust user research process to collect feedback for continuous improvement of the resource. NMDC EDGE provides an accessible interface for researchers to process multi-omics microbiome data using production-quality workflows to facilitate improved data standardization and interoperability.
Additional Links: PMID-39963423
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@article {pmid39963423,
year = {2024},
author = {Kelliher, JM and Xu, Y and Flynn, MC and Babinski, M and Canon, S and Cavanna, E and Clum, A and Corilo, YE and Fujimoto, G and Giberson, C and Johnson, LYD and Li, KJ and Li, PE and Li, V and Lo, CC and Lynch, W and Piehowski, P and Prime, K and Purvine, S and Rodriguez, F and Roux, S and Shakya, M and Smith, M and Sarrafan, S and Cholia, S and McCue, LA and Mungall, C and Hu, B and Eloe-Fadrosh, EA and Chain, PSG},
title = {Standardized and accessible multi-omics bioinformatics workflows through the NMDC EDGE resource.},
journal = {Computational and structural biotechnology journal},
volume = {23},
number = {},
pages = {3575-3583},
pmid = {39963423},
issn = {2001-0370},
abstract = {Accessible and easy-to-use standardized bioinformatics workflows are necessary to advance microbiome research from observational studies to large-scale, data-driven approaches. Standardized multi-omics data enables comparative studies, data reuse, and applications of machine learning to model biological processes. To advance broad accessibility of standardized multi-omics bioinformatics workflows, the National Microbiome Data Collaborative (NMDC) has developed the Empowering the Development of Genomics Expertise (NMDC EDGE) resource, a user-friendly, open-source web application (https://nmdc-edge.org). Here, we describe the design and main functionality of the NMDC EDGE resource for processing metagenome, metatranscriptome, natural organic matter, and metaproteome data. The architecture relies on three main layers (web application, orchestration, and execution) to ensure flexibility and expansion to future workflows. The orchestration and execution layers leverage best practices in software containers and accommodate high-performance computing and cloud computing services. Further, we have adopted a robust user research process to collect feedback for continuous improvement of the resource. NMDC EDGE provides an accessible interface for researchers to process multi-omics microbiome data using production-quality workflows to facilitate improved data standardization and interoperability.},
}
RevDate: 2025-02-18
CmpDate: 2025-02-18
[Diagnosis of mucormycosis in three children following hematopoietic stem cell transplantation using metagenomic next-generation sequencing].
Zhongguo dang dai er ke za zhi = Chinese journal of contemporary pediatrics, 27(2):219-224.
This article reports the clinical characteristics and treatment processes of three cases of mucormycosis occurring after hematopoietic stem cell transplantation in children, along with a review of relevant literature. All three patients presented with chest pain as the initial symptom, and metagenomic next-generation sequencing (mNGS) confirmed the mucycete infection early in all cases. Two patients recovered after treatment, while one succumbed to disseminated infection. mNGS has facilitated early diagnosis and treatment, reducing mortality rates. Additionally, surgical intervention is an important strategy for improving the prognosis of this condition.
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@article {pmid39962786,
year = {2025},
author = {Li, Y and Zhou, XH and Wang, XD and Wang, CJ and Cao, K and Liu, SX},
title = {[Diagnosis of mucormycosis in three children following hematopoietic stem cell transplantation using metagenomic next-generation sequencing].},
journal = {Zhongguo dang dai er ke za zhi = Chinese journal of contemporary pediatrics},
volume = {27},
number = {2},
pages = {219-224},
pmid = {39962786},
issn = {1008-8830},
mesh = {Humans ; *Mucormycosis/diagnosis/etiology ; *Hematopoietic Stem Cell Transplantation/adverse effects ; Male ; *High-Throughput Nucleotide Sequencing ; Female ; Child ; Child, Preschool ; Metagenomics/methods ; },
abstract = {This article reports the clinical characteristics and treatment processes of three cases of mucormycosis occurring after hematopoietic stem cell transplantation in children, along with a review of relevant literature. All three patients presented with chest pain as the initial symptom, and metagenomic next-generation sequencing (mNGS) confirmed the mucycete infection early in all cases. Two patients recovered after treatment, while one succumbed to disseminated infection. mNGS has facilitated early diagnosis and treatment, reducing mortality rates. Additionally, surgical intervention is an important strategy for improving the prognosis of this condition.},
}
MeSH Terms:
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Humans
*Mucormycosis/diagnosis/etiology
*Hematopoietic Stem Cell Transplantation/adverse effects
Male
*High-Throughput Nucleotide Sequencing
Female
Child
Child, Preschool
Metagenomics/methods
RevDate: 2025-02-18
CmpDate: 2025-02-18
Novel Gene Clusters for Secondary Metabolite Synthesis in Mesophotic Sponge-Associated Bacteria.
Microbial biotechnology, 18(2):e70107.
Mesophotic coral ecosystems (MCEs) host a diverse array of sponge species, which represent a promising source of bioactive compounds. Increasing evidence suggests that sponge-associated bacteria may be the primary producers of these compounds. However, cultivating these bacteria under laboratory conditions remains a significant challenge. To investigate the rich resource of bioactive compounds synthesised by mesophotic sponge-associated bacteria, we retrieved 429 metagenome-assembled genomes (MAGs) from 15 mesophotic sponges, revealing a strong correlation between bacterial diversity and sponge species. Furthermore, we identified 1637 secondary metabolite biosynthetic gene clusters (BGCs) within these MAGs. Among the identified BGCs, terpenes were the most abundant (495), followed by 369 polyketide synthases (PKSs), 293 ribosomally synthesised and post-translationally modified peptides (RiPPs) and 135 nonribosomal peptide synthetases (NRPSs). The BGCs were classified into 1086 gene cluster families (GCFs) based on sequence similarity. Notably, only five GCFs included experimentally validated reference BGCs from the Minimum Information about a Biosynthetic Gene cluster database (MIBiG). Additionally, an unusual abundance of BGCs was detected in Entotheonella sp. (s191209.Bin93) from the Tectomicrobia phylum. In contrast, members of Proteobacteria and Acidobacteriota harboured fewer BGCs (6-7 on average), yet their high abundance in MCE sponges suggests a potentially rich reservoir of BGCs. Analysis of the BGC distribution patterns revealed that a subset of BGCs, including terpene GCFs (FAM_00447 and FAM_01046), PKS GCF (FAM_00235), and RiPPs GCF (FAM_01143), were widespread across mesophotic sponges. Furthermore, 32 GCFs were consistently present in the same MAGs across different sponges, highlighting their potential key biological roles and capacity to yield novel bioactive compounds. This study not only underscores the untapped potential of mesophotic sponge-associated bacteria as a source of bioactive compounds but also provides valuable insights into the intricate interactions between sponges and their symbiotic microbial communities.
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@article {pmid39962733,
year = {2025},
author = {Chen, N and Liu, L and Wang, J and Mao, D and Lu, H and Shishido, TK and Zhi, S and Chen, H and He, S},
title = {Novel Gene Clusters for Secondary Metabolite Synthesis in Mesophotic Sponge-Associated Bacteria.},
journal = {Microbial biotechnology},
volume = {18},
number = {2},
pages = {e70107},
doi = {10.1111/1751-7915.70107},
pmid = {39962733},
issn = {1751-7915},
support = {422010882//Startup Foundation of Ningbo University/ ; 422110473//Startup Foundation of Ningbo University/ ; 422207513//Startup Foundation of Ningbo University/ ; 31600016//National Natural Science Foundation of China/ ; 41776168//National Natural Science Foundation of China/ ; 2021Z04//Ningbo Natural Science Foundation/ ; D16013//National 111 Project of China/ ; NNF22OC0080109//Novo Nordisk Fonden/ ; },
mesh = {*Multigene Family ; *Porifera/microbiology ; *Secondary Metabolism/genetics ; *Bacteria/genetics/metabolism/classification ; Animals ; Polyketide Synthases/genetics/metabolism ; Biosynthetic Pathways/genetics ; Metagenome ; Peptide Synthases/genetics/metabolism ; Terpenes/metabolism ; Phylogeny ; },
abstract = {Mesophotic coral ecosystems (MCEs) host a diverse array of sponge species, which represent a promising source of bioactive compounds. Increasing evidence suggests that sponge-associated bacteria may be the primary producers of these compounds. However, cultivating these bacteria under laboratory conditions remains a significant challenge. To investigate the rich resource of bioactive compounds synthesised by mesophotic sponge-associated bacteria, we retrieved 429 metagenome-assembled genomes (MAGs) from 15 mesophotic sponges, revealing a strong correlation between bacterial diversity and sponge species. Furthermore, we identified 1637 secondary metabolite biosynthetic gene clusters (BGCs) within these MAGs. Among the identified BGCs, terpenes were the most abundant (495), followed by 369 polyketide synthases (PKSs), 293 ribosomally synthesised and post-translationally modified peptides (RiPPs) and 135 nonribosomal peptide synthetases (NRPSs). The BGCs were classified into 1086 gene cluster families (GCFs) based on sequence similarity. Notably, only five GCFs included experimentally validated reference BGCs from the Minimum Information about a Biosynthetic Gene cluster database (MIBiG). Additionally, an unusual abundance of BGCs was detected in Entotheonella sp. (s191209.Bin93) from the Tectomicrobia phylum. In contrast, members of Proteobacteria and Acidobacteriota harboured fewer BGCs (6-7 on average), yet their high abundance in MCE sponges suggests a potentially rich reservoir of BGCs. Analysis of the BGC distribution patterns revealed that a subset of BGCs, including terpene GCFs (FAM_00447 and FAM_01046), PKS GCF (FAM_00235), and RiPPs GCF (FAM_01143), were widespread across mesophotic sponges. Furthermore, 32 GCFs were consistently present in the same MAGs across different sponges, highlighting their potential key biological roles and capacity to yield novel bioactive compounds. This study not only underscores the untapped potential of mesophotic sponge-associated bacteria as a source of bioactive compounds but also provides valuable insights into the intricate interactions between sponges and their symbiotic microbial communities.},
}
MeSH Terms:
show MeSH Terms
hide MeSH Terms
*Multigene Family
*Porifera/microbiology
*Secondary Metabolism/genetics
*Bacteria/genetics/metabolism/classification
Animals
Polyketide Synthases/genetics/metabolism
Biosynthetic Pathways/genetics
Metagenome
Peptide Synthases/genetics/metabolism
Terpenes/metabolism
Phylogeny
RevDate: 2025-02-18
CmpDate: 2025-02-18
[Microbial Community Structure and Functional Genes of Phosphorus Cycling in Cotton Field Soil Under Long-term Saline Drip Irrigation].
Huan jing ke xue= Huanjing kexue, 46(2):1225-1235.
Freshwater resources are scarce in arid regions, and the rational use of brackish water resources can alleviate local freshwater shortages, but long-term brackish drip irrigation increases the risk of soil salinization, which in turn affects soil nutrient transformation and microbial diversity. Soil phosphorus availability is critical for crop growth, yet it is unclear how long-term brackish drip irrigation will affect soil phosphorus transformation. Therefore, to investigate the effects of long-term brackish drip irrigation on soil phosphorus-transforming microorganisms and their functional genes in cotton fields, the experiment was set up with two irrigation water salinities, freshwater (0.35 dS·m[-1], FW) and brackish water (8.04 dS·m[-1], SW). The results showed that long-term brackish drip irrigation significantly decreased cotton dry matter weight, phosphorus uptake, yield, soil pH, and Ca2-P and Ca10-P contents but significantly increased cotton phosphorus content and soil water content; electrical conductivity; quick phosphorus; and Ca8-P, Al-P, Fe-P, and O-P contents. The dominant species in each treatment at the phylum level were Ascomycetes, Actinobacteria, Acidobacteria, Bacillus, and Greenscapes; and at the phylum level, the dominant species were α-Ascomycetes, Actinobacteria, β-Ascomycetes, Oleococcus thermophilus, and γ-Ascomycetes. including Proteobacteria, Actinobacteria, Acidobacteria, Gemmatimonadetes, and Chloroflexi. Select dominant species at the class level included Alphaproteobacteria, Actinomycetia, Betaproteobacteria, Thermoleophilia, and Gammaproteobacteria. Long-term saline drip irrigation significantly reduced the relative abundance of Actinobacteria, Acidobacteria, and Nitrospirae but significantly increased the relative abundance of Proteobacteria, Gemmatimonadetes, and Bacteroidetes and significantly reduced the expression levels of the organic phosphorus mineralization gene phnA, transport gene pit, and polyphosphate synthesis gene ppaC. Moreover, it significantly increased the expression levels of the polyphosphate degradation gene HDDC3; organic phosphorus mineralization genes phnG, phoA, phnH, phnL, phnM, phnN, phnP, and phnW; transport genes phnK, phnE, phnC, and phnD; and the regulatory gene phoB. Correlation analysis showed that soil phosphorus-cycling microorganisms and functional genes were closely related to soil physicochemical properties and soil inorganic phosphorus content. Therefore, long-term saline drip irrigation changes the composition of soil phosphorus-cycling microorganisms by affecting soil physical and chemical properties and inorganic phosphorus content, which in turn drives the expression of phosphorus-cycling-related functional genes to regulate and adapt to salt stress.
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@article {pmid39962698,
year = {2025},
author = {Ye, Y and Guo, XW and Yang, MQ and Min, W and Guo, HJ},
title = {[Microbial Community Structure and Functional Genes of Phosphorus Cycling in Cotton Field Soil Under Long-term Saline Drip Irrigation].},
journal = {Huan jing ke xue= Huanjing kexue},
volume = {46},
number = {2},
pages = {1225-1235},
doi = {10.13227/j.hjkx.202402036},
pmid = {39962698},
issn = {0250-3301},
mesh = {*Phosphorus/metabolism ; *Gossypium/growth & development/genetics ; *Agricultural Irrigation/methods ; *Soil Microbiology ; *Soil/chemistry ; Microbiota ; Salinity ; Saline Waters ; Bacteria/genetics/classification/metabolism/growth & development ; },
abstract = {Freshwater resources are scarce in arid regions, and the rational use of brackish water resources can alleviate local freshwater shortages, but long-term brackish drip irrigation increases the risk of soil salinization, which in turn affects soil nutrient transformation and microbial diversity. Soil phosphorus availability is critical for crop growth, yet it is unclear how long-term brackish drip irrigation will affect soil phosphorus transformation. Therefore, to investigate the effects of long-term brackish drip irrigation on soil phosphorus-transforming microorganisms and their functional genes in cotton fields, the experiment was set up with two irrigation water salinities, freshwater (0.35 dS·m[-1], FW) and brackish water (8.04 dS·m[-1], SW). The results showed that long-term brackish drip irrigation significantly decreased cotton dry matter weight, phosphorus uptake, yield, soil pH, and Ca2-P and Ca10-P contents but significantly increased cotton phosphorus content and soil water content; electrical conductivity; quick phosphorus; and Ca8-P, Al-P, Fe-P, and O-P contents. The dominant species in each treatment at the phylum level were Ascomycetes, Actinobacteria, Acidobacteria, Bacillus, and Greenscapes; and at the phylum level, the dominant species were α-Ascomycetes, Actinobacteria, β-Ascomycetes, Oleococcus thermophilus, and γ-Ascomycetes. including Proteobacteria, Actinobacteria, Acidobacteria, Gemmatimonadetes, and Chloroflexi. Select dominant species at the class level included Alphaproteobacteria, Actinomycetia, Betaproteobacteria, Thermoleophilia, and Gammaproteobacteria. Long-term saline drip irrigation significantly reduced the relative abundance of Actinobacteria, Acidobacteria, and Nitrospirae but significantly increased the relative abundance of Proteobacteria, Gemmatimonadetes, and Bacteroidetes and significantly reduced the expression levels of the organic phosphorus mineralization gene phnA, transport gene pit, and polyphosphate synthesis gene ppaC. Moreover, it significantly increased the expression levels of the polyphosphate degradation gene HDDC3; organic phosphorus mineralization genes phnG, phoA, phnH, phnL, phnM, phnN, phnP, and phnW; transport genes phnK, phnE, phnC, and phnD; and the regulatory gene phoB. Correlation analysis showed that soil phosphorus-cycling microorganisms and functional genes were closely related to soil physicochemical properties and soil inorganic phosphorus content. Therefore, long-term saline drip irrigation changes the composition of soil phosphorus-cycling microorganisms by affecting soil physical and chemical properties and inorganic phosphorus content, which in turn drives the expression of phosphorus-cycling-related functional genes to regulate and adapt to salt stress.},
}
MeSH Terms:
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*Phosphorus/metabolism
*Gossypium/growth & development/genetics
*Agricultural Irrigation/methods
*Soil Microbiology
*Soil/chemistry
Microbiota
Salinity
Saline Waters
Bacteria/genetics/classification/metabolism/growth & development
RevDate: 2025-02-18
A summer in the greater Paris: trophic status of peri-urban lakes shapes prokaryotic community structure and functional potential.
Environmental microbiome, 20(1):24.
With more than 12 million inhabitants, the Greater Paris offers a "natural laboratory" to explore the effects of eutrophication on freshwater lake's microbiomes within a relative restricted area (~ 70 km radius). Here, a 4-months survey was carried out during summertime to monitor planktonic microbial communities of nine lakes located around Paris (Île-de-France, France) of comparable morphologies, yet distinct trophic statuses from mesotrophic to hypereutrophic. By thus minimizing the confounding factors, we investigated how trophic status could influence prokaryotic community structures (16S rRNA gene sequencing) and functions (shotgun metagenomics). These freshwater lakes harbored highly distinct and diverse prokaryotic communities, and their trophic status appears as the main driver explaining both differences in community structure and functional potential. Although their gene pool was quite stable and shared among lakes, taxonomical and functional changes were correlated. According to trophic status, differences in phosphorus metabolism-related genes were highlighted among the relevant functions involved in the biogeochemical cycles. Overall, hypereutrophic lakes microbiomes displayed the highest contrast and heterogeneity over time, suggesting a specific microbial regime shift compared to eutrophic and mesotrophic lakes.
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@article {pmid39962619,
year = {2025},
author = {Foucault, P and Halary, S and Duval, C and Goto, M and Marie, B and Hamlaoui, S and Jardillier, L and Lamy, D and Lance, E and Raimbault, E and Allouti, F and Troussellier, M and Bernard, C and Leloup, J and Duperron, S},
title = {A summer in the greater Paris: trophic status of peri-urban lakes shapes prokaryotic community structure and functional potential.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {24},
pmid = {39962619},
issn = {2524-6372},
support = {COM2LIFE (ANR-20-CE32-0006)//Agence Nationale de la Recherche/ ; COM2LIFE (ANR-20-CE32-0006)//Agence Nationale de la Recherche/ ; },
abstract = {With more than 12 million inhabitants, the Greater Paris offers a "natural laboratory" to explore the effects of eutrophication on freshwater lake's microbiomes within a relative restricted area (~ 70 km radius). Here, a 4-months survey was carried out during summertime to monitor planktonic microbial communities of nine lakes located around Paris (Île-de-France, France) of comparable morphologies, yet distinct trophic statuses from mesotrophic to hypereutrophic. By thus minimizing the confounding factors, we investigated how trophic status could influence prokaryotic community structures (16S rRNA gene sequencing) and functions (shotgun metagenomics). These freshwater lakes harbored highly distinct and diverse prokaryotic communities, and their trophic status appears as the main driver explaining both differences in community structure and functional potential. Although their gene pool was quite stable and shared among lakes, taxonomical and functional changes were correlated. According to trophic status, differences in phosphorus metabolism-related genes were highlighted among the relevant functions involved in the biogeochemical cycles. Overall, hypereutrophic lakes microbiomes displayed the highest contrast and heterogeneity over time, suggesting a specific microbial regime shift compared to eutrophic and mesotrophic lakes.},
}
RevDate: 2025-02-18
CmpDate: 2025-02-18
Host DNA depletion assisted metagenomic sequencing of bronchoalveolar lavage fluids for diagnosis of pulmonary tuberculosis.
Annals of clinical microbiology and antimicrobials, 24(1):13.
Metagenomic next-generation sequencing (mNGS) has greatly improved our understanding of pathogens in infectious diseases such as pulmonary tuberculosis (PTB). However, high human DNA background (> 95%) impedes the detection sensitivity of mNGS in identifying intracellular Mycobacterium tuberculosis (MTB), posing a pressing challenge for MTB diagnosis. Therefore, there is an urgent need to improve MTB diagnosis performance in PTB patients. In this study, we optimized mNGS method for diagnosis of PTB. This led to the development of the host DNA depletion assisted mNGS (HDA-mNGS) technique, which we compared with conventional mNGS and the host DNA depletion-assisted Nanopore sequencing (HDA-Nanopore) in diagnostic performance. We collected 105 bronchoalveolar lavage fluid (BALF) samples from suspected PTB patients across three medical centers to assess the clinical performance of these methods. The results of our study showed that HDA-mNGS had the highest sensitivity (72.0%) and accuracy (74.5%) in PTB detection. This was significantly higher compared to mNGS (51.2%, 58.2%) and HDA-Nanopore (58.5%, 62.2%). Furthermore, HDA-mNGS provided an increased coverage of the MTB genome by up to 16-fold. Antibiotic resistance gene analysis indicated that HDA-mNGS could provide increased depth to the detection of Antimicrobial resistance (AMR) locus more effectively. These findings indicate that HDA-mNGS can significantly improve the clinical performance of PTB diagnosis for BALF samples, offering great potential in managing antibiotic resistance in PTB patients.
Additional Links: PMID-39962548
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@article {pmid39962548,
year = {2025},
author = {Yuan, J and Ma, L and Du, J and Sun, H and Li, S and Zhou, G and Rao, G and Sun, F and Chen, W and Miao, H and Tian, D and Cheng, C and Wang, Y and Li, L and Li, L and Pang, Y},
title = {Host DNA depletion assisted metagenomic sequencing of bronchoalveolar lavage fluids for diagnosis of pulmonary tuberculosis.},
journal = {Annals of clinical microbiology and antimicrobials},
volume = {24},
number = {1},
pages = {13},
pmid = {39962548},
issn = {1476-0711},
support = {2024-4-1042//Capital's Funds for Health Improvement and Research/ ; 2024-1-1041//Capital's Funds for Health Improvement and Research/ ; },
mesh = {Humans ; *Bronchoalveolar Lavage Fluid/microbiology ; *Tuberculosis, Pulmonary/diagnosis/microbiology ; *Mycobacterium tuberculosis/genetics/isolation & purification ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; Sensitivity and Specificity ; DNA, Bacterial/genetics ; Male ; Female ; Adult ; Middle Aged ; Nanopore Sequencing/methods ; Genome, Bacterial ; },
abstract = {Metagenomic next-generation sequencing (mNGS) has greatly improved our understanding of pathogens in infectious diseases such as pulmonary tuberculosis (PTB). However, high human DNA background (> 95%) impedes the detection sensitivity of mNGS in identifying intracellular Mycobacterium tuberculosis (MTB), posing a pressing challenge for MTB diagnosis. Therefore, there is an urgent need to improve MTB diagnosis performance in PTB patients. In this study, we optimized mNGS method for diagnosis of PTB. This led to the development of the host DNA depletion assisted mNGS (HDA-mNGS) technique, which we compared with conventional mNGS and the host DNA depletion-assisted Nanopore sequencing (HDA-Nanopore) in diagnostic performance. We collected 105 bronchoalveolar lavage fluid (BALF) samples from suspected PTB patients across three medical centers to assess the clinical performance of these methods. The results of our study showed that HDA-mNGS had the highest sensitivity (72.0%) and accuracy (74.5%) in PTB detection. This was significantly higher compared to mNGS (51.2%, 58.2%) and HDA-Nanopore (58.5%, 62.2%). Furthermore, HDA-mNGS provided an increased coverage of the MTB genome by up to 16-fold. Antibiotic resistance gene analysis indicated that HDA-mNGS could provide increased depth to the detection of Antimicrobial resistance (AMR) locus more effectively. These findings indicate that HDA-mNGS can significantly improve the clinical performance of PTB diagnosis for BALF samples, offering great potential in managing antibiotic resistance in PTB patients.},
}
MeSH Terms:
show MeSH Terms
hide MeSH Terms
Humans
*Bronchoalveolar Lavage Fluid/microbiology
*Tuberculosis, Pulmonary/diagnosis/microbiology
*Mycobacterium tuberculosis/genetics/isolation & purification
*High-Throughput Nucleotide Sequencing/methods
*Metagenomics/methods
Sensitivity and Specificity
DNA, Bacterial/genetics
Male
Female
Adult
Middle Aged
Nanopore Sequencing/methods
Genome, Bacterial
RevDate: 2025-02-17
The relationship between the gastric cancer microbiome and clinicopathological factors: a metagenomic investigation from the 100,000 genomes project and The Cancer Genome Atlas.
Gastric cancer : official journal of the International Gastric Cancer Association and the Japanese Gastric Cancer Association [Epub ahead of print].
BACKGROUND: Findings from previous gastric cancer microbiome studies have been conflicting, potentially due to patient and/or tumor heterogeneity. The intratumoral gastric cancer microbiome and its relationship with clinicopathological variables have not yet been characterized in detail. We hypothesized that variation in gastric cancer microbial abundance, alpha diversity, and composition is related to clinicopathological characteristics.
METHODS: Metagenomic analysis of 529 GC samples was performed, including whole exome sequencing data from The Cancer Genome Atlas (TCGA) and whole genome sequencing data from the 100,000 Genomes Project. Microbial abundance, alpha diversity, and composition were compared across patient age, sex, tumor location, geographic origin, pathological depth of invasion, pathological lymph node status, histological phenotype, microsatellite instability status, and TCGA molecular subtype.
RESULTS: Gastric cancer microbiomes resembled previous results, with Prevotella, Selenomonas, Stomatobaculum, Streptococcus, Lactobacillus, and Lachnospiraceae commonly seen across both cohorts. Within the TCGA cohort, microbial abundance and alpha diversity were greater in gastric cancers with microsatellite instability, lower pathological depth of invasion, intestinal-type histology, and those originating from Asia. Microsatellite instability status was associated with microbiome composition in both cohorts. Sex and pathological depth of invasion were associated with microbiome composition in the TCGA cohort.
CONCLUSION: The intratumoral gastric cancer microbiome appears to differ according to clinicopathological factors. Certain clinicopathological factors associated with favourable outcomes in gastric cancer were observed to be associated with greater microbial abundance and diversity. This highlights the need for further work to understand the underlying biological mechanisms behind the observed microbiome differences and their potential clinical and therapeutic impact.
Additional Links: PMID-39961991
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@article {pmid39961991,
year = {2025},
author = {Booth, ME and Wood, HM and Travis, MA and , and Quirke, P and Grabsch, HI},
title = {The relationship between the gastric cancer microbiome and clinicopathological factors: a metagenomic investigation from the 100,000 genomes project and The Cancer Genome Atlas.},
journal = {Gastric cancer : official journal of the International Gastric Cancer Association and the Japanese Gastric Cancer Association},
volume = {},
number = {},
pages = {},
pmid = {39961991},
issn = {1436-3305},
abstract = {BACKGROUND: Findings from previous gastric cancer microbiome studies have been conflicting, potentially due to patient and/or tumor heterogeneity. The intratumoral gastric cancer microbiome and its relationship with clinicopathological variables have not yet been characterized in detail. We hypothesized that variation in gastric cancer microbial abundance, alpha diversity, and composition is related to clinicopathological characteristics.
METHODS: Metagenomic analysis of 529 GC samples was performed, including whole exome sequencing data from The Cancer Genome Atlas (TCGA) and whole genome sequencing data from the 100,000 Genomes Project. Microbial abundance, alpha diversity, and composition were compared across patient age, sex, tumor location, geographic origin, pathological depth of invasion, pathological lymph node status, histological phenotype, microsatellite instability status, and TCGA molecular subtype.
RESULTS: Gastric cancer microbiomes resembled previous results, with Prevotella, Selenomonas, Stomatobaculum, Streptococcus, Lactobacillus, and Lachnospiraceae commonly seen across both cohorts. Within the TCGA cohort, microbial abundance and alpha diversity were greater in gastric cancers with microsatellite instability, lower pathological depth of invasion, intestinal-type histology, and those originating from Asia. Microsatellite instability status was associated with microbiome composition in both cohorts. Sex and pathological depth of invasion were associated with microbiome composition in the TCGA cohort.
CONCLUSION: The intratumoral gastric cancer microbiome appears to differ according to clinicopathological factors. Certain clinicopathological factors associated with favourable outcomes in gastric cancer were observed to be associated with greater microbial abundance and diversity. This highlights the need for further work to understand the underlying biological mechanisms behind the observed microbiome differences and their potential clinical and therapeutic impact.},
}
RevDate: 2025-02-17
Metagenomic Analysis of Microbial Community Associated with Food Waste Composting.
Applied biochemistry and biotechnology [Epub ahead of print].
Food waste is an increasing cause of concern in India. Its management through composting plays a vital role in managing the biodegradable fraction of municipal solid waste. However, the existing composting process has many challenges, such as the lack of optimum microenvironment and microbiome knowledge, which limits efficient outcomes. Therefore, the present study aims to bridge the gap by applying metagenomics to study microbial community dynamicity during different stages of composting. The bacterial community analysis showed that genus Marionobacter (9.4%) and Halomonas (7.4%) were prevalent during the mesophilic stage, whereas the Bacillus (12.2%) and Cellulomonas (0.1%) were prevalent during the thermophilic and maturation stage of composting. The functional profiling of metagenome indicated the abundance of genes involved in degradation of polymeric compounds such as carbohydrates, lipids, and proteins. The relative abundance of arginine and proline metabolisms increased during the thermophilic stage. Whereas the relative abundance of genes involved in fatty acid, tryptophan, galactose, and propanoate metabolisms declined. Similarly, the CAZyme tool predicted that the genes encoding for glycoside hydrolase (GH) families were higher during the mesophilic and thermophilic stages of composting. These enzymes play an important role in degradation of complex polysaccharides such as cellulose and hemicellulose. The data obtained from the present study could be utilized for the optimization and improving the composting process.
Additional Links: PMID-39961944
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@article {pmid39961944,
year = {2025},
author = {Andraskar, J and Khan, D and Yadav, S and Kapley, A},
title = {Metagenomic Analysis of Microbial Community Associated with Food Waste Composting.},
journal = {Applied biochemistry and biotechnology},
volume = {},
number = {},
pages = {},
pmid = {39961944},
issn = {1559-0291},
support = {DBT/JRF/BET-18/1/2018/AL/23//Department of Biotechnology, Ministry of Science and Technology, India/ ; },
abstract = {Food waste is an increasing cause of concern in India. Its management through composting plays a vital role in managing the biodegradable fraction of municipal solid waste. However, the existing composting process has many challenges, such as the lack of optimum microenvironment and microbiome knowledge, which limits efficient outcomes. Therefore, the present study aims to bridge the gap by applying metagenomics to study microbial community dynamicity during different stages of composting. The bacterial community analysis showed that genus Marionobacter (9.4%) and Halomonas (7.4%) were prevalent during the mesophilic stage, whereas the Bacillus (12.2%) and Cellulomonas (0.1%) were prevalent during the thermophilic and maturation stage of composting. The functional profiling of metagenome indicated the abundance of genes involved in degradation of polymeric compounds such as carbohydrates, lipids, and proteins. The relative abundance of arginine and proline metabolisms increased during the thermophilic stage. Whereas the relative abundance of genes involved in fatty acid, tryptophan, galactose, and propanoate metabolisms declined. Similarly, the CAZyme tool predicted that the genes encoding for glycoside hydrolase (GH) families were higher during the mesophilic and thermophilic stages of composting. These enzymes play an important role in degradation of complex polysaccharides such as cellulose and hemicellulose. The data obtained from the present study could be utilized for the optimization and improving the composting process.},
}
RevDate: 2025-02-17
Microbial ecology of Serpentinite-hosted ecosystems.
The ISME journal pii:8019724 [Epub ahead of print].
Serpentinization, the collective set of geochemical reactions initiated by the hydration of ultramafic rock, has occurred throughout Earth history and is inferred to occur on several planets and moons in our solar system. These reactions generate highly reducing conditions that can drive organic synthesis reactions potentially conducive to the emergence of life, while concomitantly generating fluids that challenge life owing to hyperalkalinity and limited inorganic carbon (and oxidant) availability. Consequently, the serpentinite-hosted biosphere offers insights into the earliest life, the habitable limits for life, and the potential for life on other planets. However, the support of abundant microbial communities by serpentinites was only recognized ~20 years ago with the discovery of deep-sea hydrothermal vents emanating serpentinized fluids. Here, we review the microbial ecology of both marine and continental serpentinization-influenced ecosystems in conjunction with a comparison of publicly available metagenomic sequence data from these communities to provide a global perspective of serpentinite microbial ecology. Synthesis of observations across global systems reveal consistent themes in the diversity, ecology, and functioning of communities. Nevertheless, individual systems exhibit nuances due to local geology, hydrology, and input of oxidized, near-surface/seawater fluids. Further, several new (and old) questions remain including the provenance of carbon to support biomass synthesis, the physical and chemical limits of life in serpentinites, the mode and tempo of in situ evolution, and the extent that modern serpentinites serve as analogs for those on early Earth. These topics are explored from a microbial perspective to outline key knowledge-gaps for future research.
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@article {pmid39961017,
year = {2025},
author = {Colman, DR and Templeton, AS and Spear, JR and Boyd, ES},
title = {Microbial ecology of Serpentinite-hosted ecosystems.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf029},
pmid = {39961017},
issn = {1751-7370},
abstract = {Serpentinization, the collective set of geochemical reactions initiated by the hydration of ultramafic rock, has occurred throughout Earth history and is inferred to occur on several planets and moons in our solar system. These reactions generate highly reducing conditions that can drive organic synthesis reactions potentially conducive to the emergence of life, while concomitantly generating fluids that challenge life owing to hyperalkalinity and limited inorganic carbon (and oxidant) availability. Consequently, the serpentinite-hosted biosphere offers insights into the earliest life, the habitable limits for life, and the potential for life on other planets. However, the support of abundant microbial communities by serpentinites was only recognized ~20 years ago with the discovery of deep-sea hydrothermal vents emanating serpentinized fluids. Here, we review the microbial ecology of both marine and continental serpentinization-influenced ecosystems in conjunction with a comparison of publicly available metagenomic sequence data from these communities to provide a global perspective of serpentinite microbial ecology. Synthesis of observations across global systems reveal consistent themes in the diversity, ecology, and functioning of communities. Nevertheless, individual systems exhibit nuances due to local geology, hydrology, and input of oxidized, near-surface/seawater fluids. Further, several new (and old) questions remain including the provenance of carbon to support biomass synthesis, the physical and chemical limits of life in serpentinites, the mode and tempo of in situ evolution, and the extent that modern serpentinites serve as analogs for those on early Earth. These topics are explored from a microbial perspective to outline key knowledge-gaps for future research.},
}
RevDate: 2025-02-17
CmpDate: 2025-02-17
Diagnosis of early neurobrucellosis using metagenomic next-generation sequencing of the cerebrospinal fluid in nonepidemic zone: Case report and lecture review.
Medicine, 104(7):e41481.
RATIONALE: Brucella neuropathy is a rare clinical condition, particularly in nonendemic areas, where it often presents with nonspecific symptoms such as fever and headaches, leading to frequent misdiagnoses. In these regions, Brucella antibodies are not routinely tested, and the positive rate of blood cultures is relatively low during the early stage of the disease. In addition, the low culture-positive rate of cerebrospinal fluid (CSF) means that many neurobrucellosis diagnoses rely on peripheral blood cultures or Brucella antibodies, which is not rigorous. This is problematic because the treatment of central nervous system brucellosis differs significantly from that of other types of brucellosis. The purpose of this study is to provide a method for the early diagnosis of Brucella neuropathy in nonendemic areas. We present a case of early-stage neurobrucellosis diagnosed using metagenomic next-generation sequencing (mNGS) of CSF. This approach helps avoid delaying diagnosis in the early stage in nonepidemic areas, potentially reducing the duration before diagnosis, which is of great significance for timely and appropriate treatment.
PATIENT CONCERNS: The patient had fever, mild headache, and a slight increase in CSF leukocytes.
DIAGNOSES: CSF mNGS detected Brucella, which was later confirmed by serum Brucella antibody testing.
INTERVENTIONS: The patient was treated with rifampicin, doxycycline, and ceftriaxone.
OUTCOMES: The patient experienced significant relief from the headache, and the fever did not recur. Subsequent examinations revealed no abnormalities in the CSF leukocytes or mNGS results.
LESSONS: We reviewed 10 articles on brucellosis diagnosed using mNGS, including 7 articles on neurobrucellosis (10 cases). Our review highlights the sensitivity of mNGS as a powerful tool for early detection of neurobrucellosis in the CSF. The common symptoms include fever and headache, with brain magnetic resonance imaging detecting lesions in most cases. CSF mNGS results varied, with only a few positive Brucella cultures or antibody tests.
Additional Links: PMID-39960952
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@article {pmid39960952,
year = {2025},
author = {Liu, H and Li, Q and Ouyang, X and Li, Q and Min, Y and Dai, L},
title = {Diagnosis of early neurobrucellosis using metagenomic next-generation sequencing of the cerebrospinal fluid in nonepidemic zone: Case report and lecture review.},
journal = {Medicine},
volume = {104},
number = {7},
pages = {e41481},
doi = {10.1097/MD.0000000000041481},
pmid = {39960952},
issn = {1536-5964},
mesh = {Humans ; *Brucellosis/diagnosis/cerebrospinal fluid/drug therapy ; *High-Throughput Nucleotide Sequencing/methods ; Metagenomics/methods ; Anti-Bacterial Agents/therapeutic use ; Female ; Central Nervous System Bacterial Infections/diagnosis/cerebrospinal fluid/drug therapy/microbiology ; Doxycycline/therapeutic use ; Male ; Early Diagnosis ; Brucella/isolation & purification ; Adult ; },
abstract = {RATIONALE: Brucella neuropathy is a rare clinical condition, particularly in nonendemic areas, where it often presents with nonspecific symptoms such as fever and headaches, leading to frequent misdiagnoses. In these regions, Brucella antibodies are not routinely tested, and the positive rate of blood cultures is relatively low during the early stage of the disease. In addition, the low culture-positive rate of cerebrospinal fluid (CSF) means that many neurobrucellosis diagnoses rely on peripheral blood cultures or Brucella antibodies, which is not rigorous. This is problematic because the treatment of central nervous system brucellosis differs significantly from that of other types of brucellosis. The purpose of this study is to provide a method for the early diagnosis of Brucella neuropathy in nonendemic areas. We present a case of early-stage neurobrucellosis diagnosed using metagenomic next-generation sequencing (mNGS) of CSF. This approach helps avoid delaying diagnosis in the early stage in nonepidemic areas, potentially reducing the duration before diagnosis, which is of great significance for timely and appropriate treatment.
PATIENT CONCERNS: The patient had fever, mild headache, and a slight increase in CSF leukocytes.
DIAGNOSES: CSF mNGS detected Brucella, which was later confirmed by serum Brucella antibody testing.
INTERVENTIONS: The patient was treated with rifampicin, doxycycline, and ceftriaxone.
OUTCOMES: The patient experienced significant relief from the headache, and the fever did not recur. Subsequent examinations revealed no abnormalities in the CSF leukocytes or mNGS results.
LESSONS: We reviewed 10 articles on brucellosis diagnosed using mNGS, including 7 articles on neurobrucellosis (10 cases). Our review highlights the sensitivity of mNGS as a powerful tool for early detection of neurobrucellosis in the CSF. The common symptoms include fever and headache, with brain magnetic resonance imaging detecting lesions in most cases. CSF mNGS results varied, with only a few positive Brucella cultures or antibody tests.},
}
MeSH Terms:
show MeSH Terms
hide MeSH Terms
Humans
*Brucellosis/diagnosis/cerebrospinal fluid/drug therapy
*High-Throughput Nucleotide Sequencing/methods
Metagenomics/methods
Anti-Bacterial Agents/therapeutic use
Female
Central Nervous System Bacterial Infections/diagnosis/cerebrospinal fluid/drug therapy/microbiology
Doxycycline/therapeutic use
Male
Early Diagnosis
Brucella/isolation & purification
Adult
RevDate: 2025-02-17
CmpDate: 2025-02-17
First case report of long-term latent infection paracoccidioidomycosis in China.
Medicine, 104(7):e41409.
RATIONALE: Although paracoccidioidomycosis is one of the most prevalent endemic mycoses in Latin American countries, where at least 10 million people are infected, the prevalence of paracoccidioidomycosis in China remains unknown because no related case has been reported, and its diagnosis is extremely challenging for local clinicians because of the complexity of disease progression and lack of specific evidence.
PATIENT CONCERNS: Here, we report the first case of PCM in a male patient with a long-term latent infection in China.
DIAGNOSIS: The results of special staining, immunohistochemistry, lymph node biopsy pathology, and metagenomic second-generation sequencing indicated that the patient was infected with Paracoccidioides brasiliensis.
INTERVENTIONS: In this case, the patient was administered voriconazole 200 mg twice daily.
OUTCOMES: After continuous treatment for 6 months, the patient's symptoms improved significantly, and the medication was discontinued. The outpatient follow-up revealed no discomfort.
LESSONS: This case is of great value for the early diagnosis, treatment, and prevention of the spread of this emerging infectious disease in China.
Additional Links: PMID-39960906
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PubMed:
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@article {pmid39960906,
year = {2025},
author = {Dong, H and Feng, J and Wu, S and Liang, F and Li, H and Liang, X and Liao, W and Pan, Y and Tang, G and Li, D and Zhou, W and Cao, Z and Wang, W and Hu, J},
title = {First case report of long-term latent infection paracoccidioidomycosis in China.},
journal = {Medicine},
volume = {104},
number = {7},
pages = {e41409},
doi = {10.1097/MD.0000000000041409},
pmid = {39960906},
issn = {1536-5964},
support = {2021-2023//Guangzhou Medical Key Discipline/ ; 202002030152, 202201010744 and 2023A03J0539//Science and Technology Program of Guangzhou/ ; 2023A03J0539//Science and Technology Program of Guangzhou/ ; B2021038//Medical Science Research Foundation of Guangdong Province/ ; },
mesh = {Humans ; *Paracoccidioidomycosis/diagnosis/drug therapy/epidemiology ; Male ; China/epidemiology ; *Antifungal Agents/therapeutic use ; *Paracoccidioides/isolation & purification ; *Latent Infection/diagnosis/drug therapy ; Voriconazole/therapeutic use/administration & dosage ; Middle Aged ; },
abstract = {RATIONALE: Although paracoccidioidomycosis is one of the most prevalent endemic mycoses in Latin American countries, where at least 10 million people are infected, the prevalence of paracoccidioidomycosis in China remains unknown because no related case has been reported, and its diagnosis is extremely challenging for local clinicians because of the complexity of disease progression and lack of specific evidence.
PATIENT CONCERNS: Here, we report the first case of PCM in a male patient with a long-term latent infection in China.
DIAGNOSIS: The results of special staining, immunohistochemistry, lymph node biopsy pathology, and metagenomic second-generation sequencing indicated that the patient was infected with Paracoccidioides brasiliensis.
INTERVENTIONS: In this case, the patient was administered voriconazole 200 mg twice daily.
OUTCOMES: After continuous treatment for 6 months, the patient's symptoms improved significantly, and the medication was discontinued. The outpatient follow-up revealed no discomfort.
LESSONS: This case is of great value for the early diagnosis, treatment, and prevention of the spread of this emerging infectious disease in China.},
}
MeSH Terms:
show MeSH Terms
hide MeSH Terms
Humans
*Paracoccidioidomycosis/diagnosis/drug therapy/epidemiology
Male
China/epidemiology
*Antifungal Agents/therapeutic use
*Paracoccidioides/isolation & purification
*Latent Infection/diagnosis/drug therapy
Voriconazole/therapeutic use/administration & dosage
Middle Aged
RevDate: 2025-02-17
What every neuropathologist needs to know: Update on neuro infectious disease workups and consultation resources.
Journal of neuropathology and experimental neurology pii:8019573 [Epub ahead of print].
Efficient histopathological diagnosis of central nervous system infections can be challenging but is critical for therapeutic decision making in cases for which less invasive blood or cerebrospinal fluid testing has been unrevealing. A wide variety of bacteria, fungi, viruses, and parasites can cause infections, particularly in immunocompromised individuals. Histological findings may be nonspecific or overlap with noninfectious inflammatory conditions. To minimize wasted tissue and time, a systematic approach is recommended in which: (1) relevant patient history (eg, comorbidities, travel and other exposures, and immune status) and radiological findings are reviewed, (2) a preliminary differential diagnosis based on this information and on inflammatory patterns and visualization of potential microorganisms on hematoxylin and eosin stains is generated, (3) special stains, immunohistochemistry, in situ hybridization, or molecular testing (pathogen-specific or broad-spectrum) are used for confirmation and further classification, and (4) correlation with culture results and other laboratory testing is performed to arrive at a final integrated diagnosis. Discrepancies between molecular and histological findings are often due to contamination and require careful evaluation to avoid treatment of false positives. Consultation with infectious disease pathologists or public health reference laboratories may be needed to confirm diagnoses of unusual organisms or when specialized testing is required.
Additional Links: PMID-39960726
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PubMed:
Citation:
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@article {pmid39960726,
year = {2025},
author = {Kenyon, AL and Solomon, IH},
title = {What every neuropathologist needs to know: Update on neuro infectious disease workups and consultation resources.},
journal = {Journal of neuropathology and experimental neurology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jnen/nlaf009},
pmid = {39960726},
issn = {1554-6578},
abstract = {Efficient histopathological diagnosis of central nervous system infections can be challenging but is critical for therapeutic decision making in cases for which less invasive blood or cerebrospinal fluid testing has been unrevealing. A wide variety of bacteria, fungi, viruses, and parasites can cause infections, particularly in immunocompromised individuals. Histological findings may be nonspecific or overlap with noninfectious inflammatory conditions. To minimize wasted tissue and time, a systematic approach is recommended in which: (1) relevant patient history (eg, comorbidities, travel and other exposures, and immune status) and radiological findings are reviewed, (2) a preliminary differential diagnosis based on this information and on inflammatory patterns and visualization of potential microorganisms on hematoxylin and eosin stains is generated, (3) special stains, immunohistochemistry, in situ hybridization, or molecular testing (pathogen-specific or broad-spectrum) are used for confirmation and further classification, and (4) correlation with culture results and other laboratory testing is performed to arrive at a final integrated diagnosis. Discrepancies between molecular and histological findings are often due to contamination and require careful evaluation to avoid treatment of false positives. Consultation with infectious disease pathologists or public health reference laboratories may be needed to confirm diagnoses of unusual organisms or when specialized testing is required.},
}
RevDate: 2025-02-17
Acute Necrotizing Fasciitis Caused by Rhizopus Infection in a Patient with Diabetes and Pulmonary Tuberculosis: A Case Report.
Infection and drug resistance, 18:775-782.
BACKGROUND: Zygomycosis, also termed mucormycosis, is a rare yet highly fatal fungal infection caused by Mucorales species, notably Rhizopus spp.
CASE PRESENTATION: This case study details a 72-year-old man with diabetes, pulmonary tuberculosis, and nephrotic syndrome who developed acute necrotizing fasciitis attributable to R. oryzae. Despite initial empirical antibiotic therapy, the infection progressed rapidly. Metagenomic next-generation sequencing (mNGS) facilitated a swift diagnosis, identifying R. oryzae in blood and drainage samples. The treatment included amphotericin B and isavuconazole, along with aggressive surgical debridement. The patient exhibited substantial improvement, and he was discharged after stabilization.
CONCLUSION: This case highlights the critical role of early diagnosis through mNGS and the need for a multidisciplinary approach to manage severe mucormycosis in immunocompromised patients.
Additional Links: PMID-39958980
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Citation:
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@article {pmid39958980,
year = {2025},
author = {Huang, X and Qiu, J and Pan, L and Wang, C and Tang, C},
title = {Acute Necrotizing Fasciitis Caused by Rhizopus Infection in a Patient with Diabetes and Pulmonary Tuberculosis: A Case Report.},
journal = {Infection and drug resistance},
volume = {18},
number = {},
pages = {775-782},
pmid = {39958980},
issn = {1178-6973},
abstract = {BACKGROUND: Zygomycosis, also termed mucormycosis, is a rare yet highly fatal fungal infection caused by Mucorales species, notably Rhizopus spp.
CASE PRESENTATION: This case study details a 72-year-old man with diabetes, pulmonary tuberculosis, and nephrotic syndrome who developed acute necrotizing fasciitis attributable to R. oryzae. Despite initial empirical antibiotic therapy, the infection progressed rapidly. Metagenomic next-generation sequencing (mNGS) facilitated a swift diagnosis, identifying R. oryzae in blood and drainage samples. The treatment included amphotericin B and isavuconazole, along with aggressive surgical debridement. The patient exhibited substantial improvement, and he was discharged after stabilization.
CONCLUSION: This case highlights the critical role of early diagnosis through mNGS and the need for a multidisciplinary approach to manage severe mucormycosis in immunocompromised patients.},
}
RevDate: 2025-02-17
CmpDate: 2025-02-17
A comprehensive analysis of the uterine microbiome in endometrial cancer patients - identification of Anaerococcus as a potential biomarker and carcinogenic cofactor.
Frontiers in cellular and infection microbiology, 15:1511625.
INTRODUCTION: Endometrial cancer (EC) is a significant gynecological malignancy with increasing incidence worldwide. Emerging evidence highlights the role of the uterine microbiome in the pathogenesis of EC. This study aims to characterize the uterine microbiome in EC patients and identify potential microbial biomarkers, with a focus on Anaerococcus as a differentiating taxon.
METHODS: The endocervical canal swabs from patients with EC (n=16) and non-cancerous patients (EM, n=13) were collected. The V3-V4 region of the 16S rRNA gene was sequenced using the Illumina platform. Bioinformatic analyses were performed with QIIME2, and statistical comparisons were conducted to assess differences in microbial composition and diversity. In vitro experiments were conducted to assess the functional impact of Anaerococcus on human uterine fibroblasts, including its ability to adhere to the human cells and induce oxidative stress.
RESULTS: The α-diversity metrics, including Shannon entropy and observed amplicon sequence variants (ASVs), revealed significantly higher microbial diversity in EC samples compared to EM. Anaerococcus was identified as a key taxon differentiating EC from EM groups, showing a higher relative abundance in EC samples. Functional predictions and in vitro assays indicated that Anaerococcus may contribute to carcinogenesis by inducing reactive oxygen species (ROS) production, and has the high ability to adhere to the human endometrial fibroblasts.
DISCUSSION: The study provides evidence of distinct microbial signatures in EC, with Anaerococcus emerging as a potential biomarker. The in vitro findings suggest its role in endometrial carcinogenesis, underscoring its potential as a target for future diagnostic and therapeutic applications.
Additional Links: PMID-39958933
PubMed:
Citation:
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@article {pmid39958933,
year = {2025},
author = {Kuźmycz, O and Kowalczyk, A and Bolanowska, A and Drozdzowska, A and Lach, J and Wierzbińska, W and Kluz, T and Stączek, P},
title = {A comprehensive analysis of the uterine microbiome in endometrial cancer patients - identification of Anaerococcus as a potential biomarker and carcinogenic cofactor.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1511625},
pmid = {39958933},
issn = {2235-2988},
mesh = {Humans ; Female ; *Endometrial Neoplasms/microbiology/genetics ; *Microbiota/genetics ; *RNA, Ribosomal, 16S/genetics ; Uterus/microbiology ; Middle Aged ; Phylogeny ; Biomarkers ; Adult ; Aged ; Reactive Oxygen Species/metabolism ; Carcinogenesis ; Fibroblasts/microbiology ; Biomarkers, Tumor/genetics ; Computational Biology/methods ; Oxidative Stress ; },
abstract = {INTRODUCTION: Endometrial cancer (EC) is a significant gynecological malignancy with increasing incidence worldwide. Emerging evidence highlights the role of the uterine microbiome in the pathogenesis of EC. This study aims to characterize the uterine microbiome in EC patients and identify potential microbial biomarkers, with a focus on Anaerococcus as a differentiating taxon.
METHODS: The endocervical canal swabs from patients with EC (n=16) and non-cancerous patients (EM, n=13) were collected. The V3-V4 region of the 16S rRNA gene was sequenced using the Illumina platform. Bioinformatic analyses were performed with QIIME2, and statistical comparisons were conducted to assess differences in microbial composition and diversity. In vitro experiments were conducted to assess the functional impact of Anaerococcus on human uterine fibroblasts, including its ability to adhere to the human cells and induce oxidative stress.
RESULTS: The α-diversity metrics, including Shannon entropy and observed amplicon sequence variants (ASVs), revealed significantly higher microbial diversity in EC samples compared to EM. Anaerococcus was identified as a key taxon differentiating EC from EM groups, showing a higher relative abundance in EC samples. Functional predictions and in vitro assays indicated that Anaerococcus may contribute to carcinogenesis by inducing reactive oxygen species (ROS) production, and has the high ability to adhere to the human endometrial fibroblasts.
DISCUSSION: The study provides evidence of distinct microbial signatures in EC, with Anaerococcus emerging as a potential biomarker. The in vitro findings suggest its role in endometrial carcinogenesis, underscoring its potential as a target for future diagnostic and therapeutic applications.},
}
MeSH Terms:
show MeSH Terms
hide MeSH Terms
Humans
Female
*Endometrial Neoplasms/microbiology/genetics
*Microbiota/genetics
*RNA, Ribosomal, 16S/genetics
Uterus/microbiology
Middle Aged
Phylogeny
Biomarkers
Adult
Aged
Reactive Oxygen Species/metabolism
Carcinogenesis
Fibroblasts/microbiology
Biomarkers, Tumor/genetics
Computational Biology/methods
Oxidative Stress
RevDate: 2025-02-17
Brewers' spent grain as fish feed ingredient: Evaluation of bio-safety and analysis of its impact on gut bacteria of Cirrhinus reba by 16S Metagenomic sequencing.
Current research in microbial sciences, 7:100286.
A comprehensive eight week feeding trial was conducted to investigate the potential of brewers' spent grain (BSG) as a sustainable fish feed ingredient. The study assessed both the biosafety of BSG and its impact on the gut microbiome of Cirrhinus reba, utilizing advanced 16S metagenomic sequencing techniques to analyze the composition and diversity of gut bacteria. A total of 90 healthy C. reba juveniles (average weight: 12 ± 1 g) were divided into two dietary groups [for control (C), for BSG meal (tB)] in triplicates. Feed prepared with conventional ingredients was used to feed the control group (C). The group tB was fed with BSG meal. After the feeding trial, the fish in tB group showed significantly higher (p < 0.05) growth parameters as compared to the control group. The results of bio-safety assessment indicated the absence of any pathological symptoms in the BSG meal fed carps. The fish in tB group didn't show any histopathological abnormality. Fish fed the Brewers' Spent Grain exhibited significantly elevated serum biochemical parameters, including alanine transaminase (ALT) and aspartate transaminase (AST), compared to the control group (p < 0.05). 16S Metagenomic sequencing of the fish gut microbiota provides insights into how BSG inclusion affects microbial diversity and composition within the digestive tract of C. reba. The analysis revealed the existence of 240 and 250 diverse bacterial genera in the gastrointestinal tract (GIT) of C. reba in dietary groups C and tB respectively. Importantly, the study found the gut of fish in tB group to be dominated by different beneficial genus including Bacillus, Lactobacillus, Bifidobacterium, Paenibacillus, and Lysinibacillus. Feeding C. reba with BSG meal significantly increased the alpha diversity of the gastrointestinal microbiota, as evidenced by elevated Chao 1 estimator and Shannon index values compared to the control diet (p < 0.05). This study provides comprehensive evidence for the bio-safety of BSG as a sustainable feed ingredient in aquaculture, demonstrating its potential to support healthy fish growth and development. Moreover, the prebiotic potential of BSG in fish has also been highlighted.
Additional Links: PMID-39957783
PubMed:
Citation:
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@article {pmid39957783,
year = {2024},
author = {Chattaraj, S and Mitra, D and Chattaraj, M and Ganguly, A and Thatoi, H and Mohapatra, PKD},
title = {Brewers' spent grain as fish feed ingredient: Evaluation of bio-safety and analysis of its impact on gut bacteria of Cirrhinus reba by 16S Metagenomic sequencing.},
journal = {Current research in microbial sciences},
volume = {7},
number = {},
pages = {100286},
pmid = {39957783},
issn = {2666-5174},
abstract = {A comprehensive eight week feeding trial was conducted to investigate the potential of brewers' spent grain (BSG) as a sustainable fish feed ingredient. The study assessed both the biosafety of BSG and its impact on the gut microbiome of Cirrhinus reba, utilizing advanced 16S metagenomic sequencing techniques to analyze the composition and diversity of gut bacteria. A total of 90 healthy C. reba juveniles (average weight: 12 ± 1 g) were divided into two dietary groups [for control (C), for BSG meal (tB)] in triplicates. Feed prepared with conventional ingredients was used to feed the control group (C). The group tB was fed with BSG meal. After the feeding trial, the fish in tB group showed significantly higher (p < 0.05) growth parameters as compared to the control group. The results of bio-safety assessment indicated the absence of any pathological symptoms in the BSG meal fed carps. The fish in tB group didn't show any histopathological abnormality. Fish fed the Brewers' Spent Grain exhibited significantly elevated serum biochemical parameters, including alanine transaminase (ALT) and aspartate transaminase (AST), compared to the control group (p < 0.05). 16S Metagenomic sequencing of the fish gut microbiota provides insights into how BSG inclusion affects microbial diversity and composition within the digestive tract of C. reba. The analysis revealed the existence of 240 and 250 diverse bacterial genera in the gastrointestinal tract (GIT) of C. reba in dietary groups C and tB respectively. Importantly, the study found the gut of fish in tB group to be dominated by different beneficial genus including Bacillus, Lactobacillus, Bifidobacterium, Paenibacillus, and Lysinibacillus. Feeding C. reba with BSG meal significantly increased the alpha diversity of the gastrointestinal microbiota, as evidenced by elevated Chao 1 estimator and Shannon index values compared to the control diet (p < 0.05). This study provides comprehensive evidence for the bio-safety of BSG as a sustainable feed ingredient in aquaculture, demonstrating its potential to support healthy fish growth and development. Moreover, the prebiotic potential of BSG in fish has also been highlighted.},
}
RevDate: 2025-02-16
CmpDate: 2025-02-16
Contrasting Methane, Sulfide and Nitrogen-Loading Regimes in Bioreactors Shape Microbial Communities Originating From Methane-Rich Coastal Sediment of the Stockholm Archipelago.
Environmental microbiology, 27(2):e70056.
Coastal ecosystems are increasingly exposed to high nutrient loads and salinity intrusions due to rising seawater levels. Microbial communities, key drivers of elemental cycles in these ecosystems, consequently, experience fluctuations. This study investigates how the methane-rich coastal sediment microbiome from the Stockholm Archipelago copes with high and low nitrogen and sulfide loading by simulating coastal conditions in two methane-saturated anoxic brackish bioreactors. Over a year, the bioreactors were subjected to the same ratio of nitrate, ammonium and sulfide (2:1:1) under eutrophic or oligotrophic conditions and monitored using 16S rRNA gene amplicon and metagenomic sequencing. Sulfide was depleted in both conditions. Sulfide-dependent denitrification was the predominant process in eutrophic conditions, whereas dissimilatory nitrate reduction to ammonium dominated under oligotrophic conditions. Methane oxidation was driven by Methylobacter and Methylomonas in eutrophic conditions, whereas a more diverse methane-oxidising microbial community developed under oligotrophic conditions, which likely competed for nitrate with anaerobic methanotrophic archaea and the gammaproteobacterial MBAE14. Novel putative copper-dependent membrane-bound monooxygenases (Cu-MMOs) were identified in MBAE14 and co-enriched Rugosibacter genomes, suggesting the need for further physiological and genetic characterisation. This study highlights the importance of understanding coastal anoxic microbiomes under fluctuating conditions, revealing complex interactions and novel pathways crucial for ecosystem functioning.
Additional Links: PMID-39956110
Publisher:
PubMed:
Citation:
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@article {pmid39956110,
year = {2025},
author = {Echeveste Medrano, MJ and Smith, GJ and Sánchez-Andrea, I and Jetten, MSM and Welte, CU},
title = {Contrasting Methane, Sulfide and Nitrogen-Loading Regimes in Bioreactors Shape Microbial Communities Originating From Methane-Rich Coastal Sediment of the Stockholm Archipelago.},
journal = {Environmental microbiology},
volume = {27},
number = {2},
pages = {e70056},
doi = {10.1111/1462-2920.70056},
pmid = {39956110},
issn = {1462-2920},
support = {854088//European Commission/ ; 024.002.002//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; VI.Vidi.223.012//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; },
mesh = {*Methane/metabolism ; *Geologic Sediments/microbiology ; *Bioreactors/microbiology ; *Sulfides/metabolism ; Sweden ; *Nitrogen/metabolism ; *Microbiota ; *RNA, Ribosomal, 16S/genetics ; *Archaea/metabolism/genetics/classification ; Seawater/microbiology ; Bacteria/classification/genetics/metabolism ; Oxidation-Reduction ; Denitrification ; Nitrates/metabolism ; Phylogeny ; Ecosystem ; },
abstract = {Coastal ecosystems are increasingly exposed to high nutrient loads and salinity intrusions due to rising seawater levels. Microbial communities, key drivers of elemental cycles in these ecosystems, consequently, experience fluctuations. This study investigates how the methane-rich coastal sediment microbiome from the Stockholm Archipelago copes with high and low nitrogen and sulfide loading by simulating coastal conditions in two methane-saturated anoxic brackish bioreactors. Over a year, the bioreactors were subjected to the same ratio of nitrate, ammonium and sulfide (2:1:1) under eutrophic or oligotrophic conditions and monitored using 16S rRNA gene amplicon and metagenomic sequencing. Sulfide was depleted in both conditions. Sulfide-dependent denitrification was the predominant process in eutrophic conditions, whereas dissimilatory nitrate reduction to ammonium dominated under oligotrophic conditions. Methane oxidation was driven by Methylobacter and Methylomonas in eutrophic conditions, whereas a more diverse methane-oxidising microbial community developed under oligotrophic conditions, which likely competed for nitrate with anaerobic methanotrophic archaea and the gammaproteobacterial MBAE14. Novel putative copper-dependent membrane-bound monooxygenases (Cu-MMOs) were identified in MBAE14 and co-enriched Rugosibacter genomes, suggesting the need for further physiological and genetic characterisation. This study highlights the importance of understanding coastal anoxic microbiomes under fluctuating conditions, revealing complex interactions and novel pathways crucial for ecosystem functioning.},
}
MeSH Terms:
show MeSH Terms
hide MeSH Terms
*Methane/metabolism
*Geologic Sediments/microbiology
*Bioreactors/microbiology
*Sulfides/metabolism
Sweden
*Nitrogen/metabolism
*Microbiota
*RNA, Ribosomal, 16S/genetics
*Archaea/metabolism/genetics/classification
Seawater/microbiology
Bacteria/classification/genetics/metabolism
Oxidation-Reduction
Denitrification
Nitrates/metabolism
Phylogeny
Ecosystem
RevDate: 2025-02-16
Gastrointestinal anaerobes and Enterococcus faecalis promote Candida glabrata gastrointestinal colonization and organ dissemination.
Journal of infection and chemotherapy : official journal of the Japan Society of Chemotherapy pii:S1341-321X(25)00055-8 [Epub ahead of print].
BACKGROUND: Candida glabrata is a common causative pathogen of endogenous candidiasis. It is assumed that the gastrointestinal flora affects C. glabrata gastrointestinal colonization and organ dissemination in the gastrointestinal tract (GIT). However, no reports have yet described the relationships between C. glabrata and bacteria in the GIT. This study aimed to clarify these relationships using a mouse endogenous candidiasis model with cortisone acetate immunosuppression.
METHODS: Dysbiosis was induced in the GIT by several antibiotic combinations, and then C. glabrata gastrointestinal colonization and organ dissemination were evaluated. Next, metagenomic sequencing analysis of the gastrointestinal flora was performed to identify bacteria associated with C. glabrata organ dissemination. Finally, coinfection experiments were performed using bacteria isolated from the mouse GIT.
RESULTS: C. glabrata organ dissemination was significantly promoted using specific antibiotics regardless of the amount of colonization in the GIT. Metagenomic sequencing analysis of the gastrointestinal flora showed that Enterococcus species and anaerobes were significantly associated with enhanced organ dissemination, whereas Enterobacterales, such as Escherichia species and Klebsiella species, were associated with the suppression of organ dissemination. In coinfection experiments, Enterococcus faecalis and Faecalibaculum rodentium inoculation, but not either of them, increased C. glabrata organ dissemination without affecting gastrointestinal colonization.
CONCLUSIONS: Coinfection with gastrointestinal bacteria promoted C. glabrata organ dissemination, which would indicate that gastrointestinal flora could affect C. glabrata dissemination. Therefore, the gastrointestinal flora could be a target for intervention or treatment in clinical settings. Insights from this study would lead to better control of endogenous candidiasis focusing on the gastrointestinal flora.
Additional Links: PMID-39956369
Publisher:
PubMed:
Citation:
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@article {pmid39956369,
year = {2025},
author = {Abe, M and Sekizuka, T and Miyazaki, Y},
title = {Gastrointestinal anaerobes and Enterococcus faecalis promote Candida glabrata gastrointestinal colonization and organ dissemination.},
journal = {Journal of infection and chemotherapy : official journal of the Japan Society of Chemotherapy},
volume = {},
number = {},
pages = {102658},
doi = {10.1016/j.jiac.2025.102658},
pmid = {39956369},
issn = {1437-7780},
abstract = {BACKGROUND: Candida glabrata is a common causative pathogen of endogenous candidiasis. It is assumed that the gastrointestinal flora affects C. glabrata gastrointestinal colonization and organ dissemination in the gastrointestinal tract (GIT). However, no reports have yet described the relationships between C. glabrata and bacteria in the GIT. This study aimed to clarify these relationships using a mouse endogenous candidiasis model with cortisone acetate immunosuppression.
METHODS: Dysbiosis was induced in the GIT by several antibiotic combinations, and then C. glabrata gastrointestinal colonization and organ dissemination were evaluated. Next, metagenomic sequencing analysis of the gastrointestinal flora was performed to identify bacteria associated with C. glabrata organ dissemination. Finally, coinfection experiments were performed using bacteria isolated from the mouse GIT.
RESULTS: C. glabrata organ dissemination was significantly promoted using specific antibiotics regardless of the amount of colonization in the GIT. Metagenomic sequencing analysis of the gastrointestinal flora showed that Enterococcus species and anaerobes were significantly associated with enhanced organ dissemination, whereas Enterobacterales, such as Escherichia species and Klebsiella species, were associated with the suppression of organ dissemination. In coinfection experiments, Enterococcus faecalis and Faecalibaculum rodentium inoculation, but not either of them, increased C. glabrata organ dissemination without affecting gastrointestinal colonization.
CONCLUSIONS: Coinfection with gastrointestinal bacteria promoted C. glabrata organ dissemination, which would indicate that gastrointestinal flora could affect C. glabrata dissemination. Therefore, the gastrointestinal flora could be a target for intervention or treatment in clinical settings. Insights from this study would lead to better control of endogenous candidiasis focusing on the gastrointestinal flora.},
}
RevDate: 2025-02-15
CmpDate: 2025-02-15
Temporal stability and lack of variance in microbiome composition and functionality in fit recreational athletes.
Scientific reports, 15(1):5619.
Human gut microbiome composition and function is influenced by environmental and lifestyle factors, including exercise and fitness. We studied the composition and functionality of the faecal microbiome of recreational (non-elite) runners (n = 62) with serial shotgun metagenomics, at 4 time points over a 7-week period. Gut microbiome composition and function was stable over time. Grouping of samples on the basis of their fitness level (fair, good, excellent, and superior) or habitual training (low (4-6 h/week), medium (7-9 h/week), high (10-12 h/week), and extreme (13 + hours/week)) revealed no significant microbiome-related differences. Overall, the species Faecalibacterium prausnitzii, Blautia wexlerae, and Prevotella copri were the most abundant members of the gut microbiome. Analysis of co-abundance groups (CAGs) revealed no significant relationship between CAGs and fitness levels or training subgroups. Functional pathways were similar across all samples and timepoints with no clustering based on associated metadata. The most abundant genes identified within samples corresponded to pathways for nucleoside and nucleotide biosynthesis, amino acid biosynthesis, and cell wall biosynthesis. Collectively, these results describe the microbiome of active recreational runners and note temporal stability amongst participants.
Additional Links: PMID-39955324
PubMed:
Citation:
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@article {pmid39955324,
year = {2025},
author = {O' Donovan, CM and Nori, SRC and Shanahan, F and Celentano, G and Murphy, TB and Cotter, PD and Sullivan, OO},
title = {Temporal stability and lack of variance in microbiome composition and functionality in fit recreational athletes.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {5619},
pmid = {39955324},
issn = {2045-2322},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Male ; Adult ; *Athletes ; Female ; *Feces/microbiology ; Metagenomics/methods ; Prevotella/genetics/isolation & purification ; Young Adult ; Running ; Faecalibacterium prausnitzii/genetics ; },
abstract = {Human gut microbiome composition and function is influenced by environmental and lifestyle factors, including exercise and fitness. We studied the composition and functionality of the faecal microbiome of recreational (non-elite) runners (n = 62) with serial shotgun metagenomics, at 4 time points over a 7-week period. Gut microbiome composition and function was stable over time. Grouping of samples on the basis of their fitness level (fair, good, excellent, and superior) or habitual training (low (4-6 h/week), medium (7-9 h/week), high (10-12 h/week), and extreme (13 + hours/week)) revealed no significant microbiome-related differences. Overall, the species Faecalibacterium prausnitzii, Blautia wexlerae, and Prevotella copri were the most abundant members of the gut microbiome. Analysis of co-abundance groups (CAGs) revealed no significant relationship between CAGs and fitness levels or training subgroups. Functional pathways were similar across all samples and timepoints with no clustering based on associated metadata. The most abundant genes identified within samples corresponded to pathways for nucleoside and nucleotide biosynthesis, amino acid biosynthesis, and cell wall biosynthesis. Collectively, these results describe the microbiome of active recreational runners and note temporal stability amongst participants.},
}
MeSH Terms:
show MeSH Terms
hide MeSH Terms
Humans
*Gastrointestinal Microbiome/genetics
Male
Adult
*Athletes
Female
*Feces/microbiology
Metagenomics/methods
Prevotella/genetics/isolation & purification
Young Adult
Running
Faecalibacterium prausnitzii/genetics
RevDate: 2025-02-15
Methodological aspects of investigating the resistome in pig farm environments.
Journal of microbiological methods pii:S0167-7012(25)00019-3 [Epub ahead of print].
A typical One Health issue, antimicrobial resistance (AMR) development and its spread among people, animals, and the environment attracts significant research attention. The animal sector is one of the major contributors to the development and dissemination of AMR and accounts for more than 50 % of global antibiotics usage. The use of antibiotics exerts a selective pressure for resistant bacteria in the exposed microbiome, but many questions about the epidemiology of AMR in farm environments remain unanswered. This is connected to several methodological challenges and limitations, such as inconsistent sampling methods, complexity of farm environment samples and the lack of standardized protocols for sample collection, processing and bioinformatical analysis. In this project, we combined metagenomics and bioinformatics to optimise the methodology for reproducible research on the resistome in complex samples from the indoor farm environment. The work included optimizing sample collection, transportation, and storage, as well as DNA extraction, sequencing, and bioinformatic analysis, such as metagenome assembly and antibiotic resistance gene (ARG) detection. Our studies suggest that the current most optimal and cost-effective pipeline for ARG search should be based on Illumina sequencing of sock sample material at high depth (at least 25 M 250 bp PE for AMR gene families and 43 M for gene variants). We present a computational analysis utilizing MEGAHIT assembly to balance the identification of bacteria carrying ARGs with the potential loss of diversity and abundance of resistance genes. Our findings indicate that searching against multiple ARG databases is essential for detecting the highest diversity of ARGs.
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@article {pmid39954816,
year = {2025},
author = {Ladyhina, V and Rajala, E and Sternberg-Lewerin, S and Nazirzadeh, L and Bongcam-Rudloff, E and Dicksved, J},
title = {Methodological aspects of investigating the resistome in pig farm environments.},
journal = {Journal of microbiological methods},
volume = {},
number = {},
pages = {107103},
doi = {10.1016/j.mimet.2025.107103},
pmid = {39954816},
issn = {1872-8359},
abstract = {A typical One Health issue, antimicrobial resistance (AMR) development and its spread among people, animals, and the environment attracts significant research attention. The animal sector is one of the major contributors to the development and dissemination of AMR and accounts for more than 50 % of global antibiotics usage. The use of antibiotics exerts a selective pressure for resistant bacteria in the exposed microbiome, but many questions about the epidemiology of AMR in farm environments remain unanswered. This is connected to several methodological challenges and limitations, such as inconsistent sampling methods, complexity of farm environment samples and the lack of standardized protocols for sample collection, processing and bioinformatical analysis. In this project, we combined metagenomics and bioinformatics to optimise the methodology for reproducible research on the resistome in complex samples from the indoor farm environment. The work included optimizing sample collection, transportation, and storage, as well as DNA extraction, sequencing, and bioinformatic analysis, such as metagenome assembly and antibiotic resistance gene (ARG) detection. Our studies suggest that the current most optimal and cost-effective pipeline for ARG search should be based on Illumina sequencing of sock sample material at high depth (at least 25 M 250 bp PE for AMR gene families and 43 M for gene variants). We present a computational analysis utilizing MEGAHIT assembly to balance the identification of bacteria carrying ARGs with the potential loss of diversity and abundance of resistance genes. Our findings indicate that searching against multiple ARG databases is essential for detecting the highest diversity of ARGs.},
}
RevDate: 2025-02-15
Dynamics of nitrogen-transforming microbial populations in wastewater treatment during recirculation of hydrothermal liquefaction process-water.
Water research, 276:123254 pii:S0043-1354(25)00168-X [Epub ahead of print].
The global reliance on non-renewable fossil fuels highlights the urgent need for sustainable alternative energy sources. Hydrothermal liquefaction (HTL) offers a promising solution by converting biomass, such as sewage sludge, into biocrude oil. However, the integration of excess HTL-process water (HTL-PW), a by-product of this process, into conventional wastewater treatment requires careful evaluation. This study investigates the effects of recirculating HTL-PW in sequencing batch reactors (SBRs) using synthetic wastewater. Two SBRs were operated in parallel: one fed 0.15 % (v/v) HTL-PW and the other with only synthetic feed. The reactor receiving HTL-PW demonstrated superior stability, effective nitrification, and consistent denitrification with no adverse effects on nitrogen species turnover. A comprehensive approach combining 16S rRNA gene amplicon sequencing for relative abundance and metagenomic analysis, for enhanced resolution of nitrogen-transforming populations, revealed the genetic repertoire and potential of 58±4 % and 65±4 % of the genus-level annotations from the HTL-PW and control reactors, respectively. The HTL-PW-fed reactor maintained robust performance, with microbial community analysis revealing a strong association between nitrogen transformations and specific microbial taxa, thereby explaining the observed reactor stability and efficiency in nitrogen conversion. These findings demonstrate the feasibility of integrating HTL-PW into wastewater treatment systems, showing that recirculating HTL-PW at the tested concentrations does not adversely affect nitrogen transformations, supports stable nitrification and denitrification, ensures complete ammonium utilisation, and promotes diverse and dynamic microbial communities similar to those in full-scale wastewater treatment plants.
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@article {pmid39954461,
year = {2025},
author = {Schacksen, PS and Macêdo, WV and Rellegadla, S and Vergeynst, L and Nielsen, JL},
title = {Dynamics of nitrogen-transforming microbial populations in wastewater treatment during recirculation of hydrothermal liquefaction process-water.},
journal = {Water research},
volume = {276},
number = {},
pages = {123254},
doi = {10.1016/j.watres.2025.123254},
pmid = {39954461},
issn = {1879-2448},
abstract = {The global reliance on non-renewable fossil fuels highlights the urgent need for sustainable alternative energy sources. Hydrothermal liquefaction (HTL) offers a promising solution by converting biomass, such as sewage sludge, into biocrude oil. However, the integration of excess HTL-process water (HTL-PW), a by-product of this process, into conventional wastewater treatment requires careful evaluation. This study investigates the effects of recirculating HTL-PW in sequencing batch reactors (SBRs) using synthetic wastewater. Two SBRs were operated in parallel: one fed 0.15 % (v/v) HTL-PW and the other with only synthetic feed. The reactor receiving HTL-PW demonstrated superior stability, effective nitrification, and consistent denitrification with no adverse effects on nitrogen species turnover. A comprehensive approach combining 16S rRNA gene amplicon sequencing for relative abundance and metagenomic analysis, for enhanced resolution of nitrogen-transforming populations, revealed the genetic repertoire and potential of 58±4 % and 65±4 % of the genus-level annotations from the HTL-PW and control reactors, respectively. The HTL-PW-fed reactor maintained robust performance, with microbial community analysis revealing a strong association between nitrogen transformations and specific microbial taxa, thereby explaining the observed reactor stability and efficiency in nitrogen conversion. These findings demonstrate the feasibility of integrating HTL-PW into wastewater treatment systems, showing that recirculating HTL-PW at the tested concentrations does not adversely affect nitrogen transformations, supports stable nitrification and denitrification, ensures complete ammonium utilisation, and promotes diverse and dynamic microbial communities similar to those in full-scale wastewater treatment plants.},
}
RevDate: 2025-02-15
Metagenomic next-generation sequencing of bronchoalveolar lavage fluid samples offers diagnostic utility in bacteriologically negative pulmonary tuberculosis.
Diagnostic microbiology and infectious disease, 111(4):116725 pii:S0732-8893(25)00048-3 [Epub ahead of print].
Rapid diagnosing Mycobacterium tuberculosis (M. tb) in patients with pulmonary tuberculosis (PTB) cases is critical, particularly in cases without bacteriologically confirmed disease, as it enables timely treatment initiation and can thus interrupt further disease transmission. In this study, the utility of metagenomic next-generation sequencing (mNGS) as a diagnostic tool was evaluated using samples of bronchoalveolar lavage fluid (BALF) samples from 300 bacteriologically negative PTB (BN-PTB) patients hospitalized from January 2020 through December 2023. The diagnostic performance of mNGS was compared to that of acid-fast staining (AFS), conventional Roche culture, and the Xpert method among these BN-PTB patients, using clinical diagnosis as the gold standard. The final analyses enrolled 112 PTB patients and 188 non-PTB cases. These analyses revealed that mNGS-based M. tb detection yields a sensitivity of 94.64 % (106/112), a specificity of 98.94 % (186/188), a positive predictive value (PPV) of 98.15 % (106/108), and a negative predictive value (NPV) of 96.88 % (186/192). This mNGS approach outperformed the AFS, Roche culture, and Xpert methods in terms of sensitivity, specificity, PPV, and NPV (p < 0.05). The superior diagnostic performance of this approach was further supported by its area under the curve and corresponding confidence intervals. Together, these data demonstrate that mNGS can improve the detection of M. tb in BALF samples from BN-PTB patients with high levels of speed, sensitivity, and specificity. This mNGS approach may thus be a valuable diagnostic tool for the rapid detection of M. tb in BN-PTB, providing a foundation for the precision diagnosis and treatment of PTB in the future.
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@article {pmid39954395,
year = {2025},
author = {Xiao, H and Zhou, C and Xiao, Z and Cai, F and Zhang, S and Sheng, S and Jin, C and Fu, Y},
title = {Metagenomic next-generation sequencing of bronchoalveolar lavage fluid samples offers diagnostic utility in bacteriologically negative pulmonary tuberculosis.},
journal = {Diagnostic microbiology and infectious disease},
volume = {111},
number = {4},
pages = {116725},
doi = {10.1016/j.diagmicrobio.2025.116725},
pmid = {39954395},
issn = {1879-0070},
abstract = {Rapid diagnosing Mycobacterium tuberculosis (M. tb) in patients with pulmonary tuberculosis (PTB) cases is critical, particularly in cases without bacteriologically confirmed disease, as it enables timely treatment initiation and can thus interrupt further disease transmission. In this study, the utility of metagenomic next-generation sequencing (mNGS) as a diagnostic tool was evaluated using samples of bronchoalveolar lavage fluid (BALF) samples from 300 bacteriologically negative PTB (BN-PTB) patients hospitalized from January 2020 through December 2023. The diagnostic performance of mNGS was compared to that of acid-fast staining (AFS), conventional Roche culture, and the Xpert method among these BN-PTB patients, using clinical diagnosis as the gold standard. The final analyses enrolled 112 PTB patients and 188 non-PTB cases. These analyses revealed that mNGS-based M. tb detection yields a sensitivity of 94.64 % (106/112), a specificity of 98.94 % (186/188), a positive predictive value (PPV) of 98.15 % (106/108), and a negative predictive value (NPV) of 96.88 % (186/192). This mNGS approach outperformed the AFS, Roche culture, and Xpert methods in terms of sensitivity, specificity, PPV, and NPV (p < 0.05). The superior diagnostic performance of this approach was further supported by its area under the curve and corresponding confidence intervals. Together, these data demonstrate that mNGS can improve the detection of M. tb in BALF samples from BN-PTB patients with high levels of speed, sensitivity, and specificity. This mNGS approach may thus be a valuable diagnostic tool for the rapid detection of M. tb in BN-PTB, providing a foundation for the precision diagnosis and treatment of PTB in the future.},
}
RevDate: 2025-02-15
High risk of Vibrio pathogen and antibiotic resistance transfer in live seafood wet markets of Shantou, China.
International journal of food microbiology, 432:111098 pii:S0168-1605(25)00043-1 [Epub ahead of print].
The global demand for seafood necessitates robust food safety practices, particularly within traditional wet markets. This study investigated the microbiomes of live Japanese mantis shrimp (JMS) and their associated environments (water and biofilm) in local wet markets to assess the risk of pathogen and antibiotic resistance gene (ARG) transfer. Metagenomic analysis showed a significant link between microbiome composition and the type of sample (shrimp, biofilm, and water). While several known human pathogens were associated with shrimp samples, water and biofilm samples exhibited higher abundances of ARGs, suggesting a high risk of pathogen and ARG transfer from the market environment. Notably, this study focused on the diversity and characterization of poorly understood Vibrio species associated with JMS. The prevalence of β-lactam resistance genes in Vibrio isolates, combined with a comparative genomic analysis of several species, highlights this concern. Our study emphasizes the need to improve hygiene practices in wet markets to reduce foodborne illness risks and address antibiotic resistance. This work represents, to our knowledge, the first comparative genomic analysis of Vibrio species in the context of JMS and wet market seafood safety.
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@article {pmid39954350,
year = {2025},
author = {Dong, Y and Liu, H and Habimana, O},
title = {High risk of Vibrio pathogen and antibiotic resistance transfer in live seafood wet markets of Shantou, China.},
journal = {International journal of food microbiology},
volume = {432},
number = {},
pages = {111098},
doi = {10.1016/j.ijfoodmicro.2025.111098},
pmid = {39954350},
issn = {1879-3460},
abstract = {The global demand for seafood necessitates robust food safety practices, particularly within traditional wet markets. This study investigated the microbiomes of live Japanese mantis shrimp (JMS) and their associated environments (water and biofilm) in local wet markets to assess the risk of pathogen and antibiotic resistance gene (ARG) transfer. Metagenomic analysis showed a significant link between microbiome composition and the type of sample (shrimp, biofilm, and water). While several known human pathogens were associated with shrimp samples, water and biofilm samples exhibited higher abundances of ARGs, suggesting a high risk of pathogen and ARG transfer from the market environment. Notably, this study focused on the diversity and characterization of poorly understood Vibrio species associated with JMS. The prevalence of β-lactam resistance genes in Vibrio isolates, combined with a comparative genomic analysis of several species, highlights this concern. Our study emphasizes the need to improve hygiene practices in wet markets to reduce foodborne illness risks and address antibiotic resistance. This work represents, to our knowledge, the first comparative genomic analysis of Vibrio species in the context of JMS and wet market seafood safety.},
}
RevDate: 2025-02-15
CmpDate: 2025-02-15
Functional and structural insights into α-L-Rhamnosidase: cloning, characterization, and decoding evolutionary constraints through structural motif.
Archives of microbiology, 207(3):61.
α-L-rhamnosidase [E.C. 3.2.1.40] is important in various industrial and biotechnological applications. However, limited knowledge of the structural features of its active site residues and their local geometric arrangements during substrate interaction hinders further application development. In this study, we examined functionally characterized microbial α-L-rhamnosidases. Despite considerable differences in their global structures, the local structures of the substrate-binding sites and key residues were highly conserved. Using the local structural motif, we characterized α-L-rhamnosidase genes from metagenomic samples of traditional fermentation starters. To comprehensively understand the distribution of α-L-rhamnosidases with this motif in the AlphaFold database, we screened 26,858 α-L-rhamnosidase structures. Our findings showed that only 5678 out of 26,858 structures contain the specific conserved motifs, emphasizing their potential significance in mining enzyme function. Moreover, the analysis of structural diversity among representative enzymes demonstrated variation in the number and types of domains within this enzyme family. Further investigation of representative α-L-rhamnosidase sequences with this structural motif confirmed the evolutionary constraints of 15 key residues, indicating strong selective pressures to maintain these elements essential for enzyme functionality. These residues were consistently present across ancestral sequences, underscoring their importance throughout the enzyme's evolutionary history. This study suggests that structure-guided approaches are valuable for discovering functional enzymes. Identifying conserved motif across diverse microbial taxa not only aids in predicting enzyme functionality but also offers opportunities for enzyme engineering and biotechnological applications.
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@article {pmid39954080,
year = {2025},
author = {Liang, Y and Zhao, Y and Yin, Z and Zeng, X and Han, X and Wen, M},
title = {Functional and structural insights into α-L-Rhamnosidase: cloning, characterization, and decoding evolutionary constraints through structural motif.},
journal = {Archives of microbiology},
volume = {207},
number = {3},
pages = {61},
pmid = {39954080},
issn = {1432-072X},
support = {2023KF005//Yunnan University/ ; 2023KF005//Yunnan University/ ; },
mesh = {*Glycoside Hydrolases/genetics/chemistry/metabolism ; *Cloning, Molecular ; Catalytic Domain ; Substrate Specificity ; Amino Acid Sequence ; Amino Acid Motifs ; Evolution, Molecular ; Bacterial Proteins/genetics/chemistry/metabolism ; Binding Sites ; Phylogeny ; Models, Molecular ; Bacteria/enzymology/genetics ; },
abstract = {α-L-rhamnosidase [E.C. 3.2.1.40] is important in various industrial and biotechnological applications. However, limited knowledge of the structural features of its active site residues and their local geometric arrangements during substrate interaction hinders further application development. In this study, we examined functionally characterized microbial α-L-rhamnosidases. Despite considerable differences in their global structures, the local structures of the substrate-binding sites and key residues were highly conserved. Using the local structural motif, we characterized α-L-rhamnosidase genes from metagenomic samples of traditional fermentation starters. To comprehensively understand the distribution of α-L-rhamnosidases with this motif in the AlphaFold database, we screened 26,858 α-L-rhamnosidase structures. Our findings showed that only 5678 out of 26,858 structures contain the specific conserved motifs, emphasizing their potential significance in mining enzyme function. Moreover, the analysis of structural diversity among representative enzymes demonstrated variation in the number and types of domains within this enzyme family. Further investigation of representative α-L-rhamnosidase sequences with this structural motif confirmed the evolutionary constraints of 15 key residues, indicating strong selective pressures to maintain these elements essential for enzyme functionality. These residues were consistently present across ancestral sequences, underscoring their importance throughout the enzyme's evolutionary history. This study suggests that structure-guided approaches are valuable for discovering functional enzymes. Identifying conserved motif across diverse microbial taxa not only aids in predicting enzyme functionality but also offers opportunities for enzyme engineering and biotechnological applications.},
}
MeSH Terms:
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*Glycoside Hydrolases/genetics/chemistry/metabolism
*Cloning, Molecular
Catalytic Domain
Substrate Specificity
Amino Acid Sequence
Amino Acid Motifs
Evolution, Molecular
Bacterial Proteins/genetics/chemistry/metabolism
Binding Sites
Phylogeny
Models, Molecular
Bacteria/enzymology/genetics
RevDate: 2025-02-15
Contrasting recovery of metagenome‑assembled genomes and derived bacterial communities and functional profiles from lizard fecal and cloacal samples.
Animal microbiome, 7(1):15.
Genome-resolved metagenomics, based on shotgun sequencing, has become a powerful strategy for investigating animal-associated bacterial communities, due its heightened capability for delivering detailed taxonomic, phylogenetic, and functional insights compared to amplicon sequencing-based approaches. While genome-resolved metagenomics holds promise across various non-lethal sample types, their effectiveness in yielding high-quality metagenome-assembled genomes remains largely unexplored. Our investigation of fecal and cloacal microbiota of the mesquite lizards (Sceloporus grammicus) using genome-resolved metagenomics revealed that fecal samples contributed 97% of the 127 reconstructed bacterial genomes, whereas only 3% were recovered from cloacal swabs, which were largely enriched with host DNA. Taxonomic, phylogenetic and functional alpha bacterial diversity was greater in fecal samples than in cloacal swabs. We also observed significant differences in bacterial community composition between sampling methods, and higher inter-individual variation in cloacal swabs. Bacteroides, Phocaeicola and Parabacteroides (all Bacteroidota) were more abundant in the feces, whereas Hafnia and Salmonella (both Pseudomonadota) increased in the cloaca. Functional analyses showed that metabolic capacities of the microbiota to degrade polysaccharides, sugars and nitrogen compounds were enriched in fecal samples, likely reflecting the role of intestinal bacteria in nutrient metabolism. Overall, our results indicate that fecal samples outperform cloacal swabs in characterizing bacterial assemblages within lizards using genome-resolved metagenomics.
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@article {pmid39955557,
year = {2025},
author = {Hernández, M and Langa, J and Aizpurua, O and Navarro-Noya, YE and Alberdi, A},
title = {Contrasting recovery of metagenome‑assembled genomes and derived bacterial communities and functional profiles from lizard fecal and cloacal samples.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {15},
pmid = {39955557},
issn = {2524-4671},
support = {POS_2022_1_0011//Hezkuntza, Hizkuntza Politika Eta Kultura Saila, Eusko Jaurlaritza/ ; DNRF143//Danmarks Grundforskningsfond/ ; },
abstract = {Genome-resolved metagenomics, based on shotgun sequencing, has become a powerful strategy for investigating animal-associated bacterial communities, due its heightened capability for delivering detailed taxonomic, phylogenetic, and functional insights compared to amplicon sequencing-based approaches. While genome-resolved metagenomics holds promise across various non-lethal sample types, their effectiveness in yielding high-quality metagenome-assembled genomes remains largely unexplored. Our investigation of fecal and cloacal microbiota of the mesquite lizards (Sceloporus grammicus) using genome-resolved metagenomics revealed that fecal samples contributed 97% of the 127 reconstructed bacterial genomes, whereas only 3% were recovered from cloacal swabs, which were largely enriched with host DNA. Taxonomic, phylogenetic and functional alpha bacterial diversity was greater in fecal samples than in cloacal swabs. We also observed significant differences in bacterial community composition between sampling methods, and higher inter-individual variation in cloacal swabs. Bacteroides, Phocaeicola and Parabacteroides (all Bacteroidota) were more abundant in the feces, whereas Hafnia and Salmonella (both Pseudomonadota) increased in the cloaca. Functional analyses showed that metabolic capacities of the microbiota to degrade polysaccharides, sugars and nitrogen compounds were enriched in fecal samples, likely reflecting the role of intestinal bacteria in nutrient metabolism. Overall, our results indicate that fecal samples outperform cloacal swabs in characterizing bacterial assemblages within lizards using genome-resolved metagenomics.},
}
RevDate: 2025-02-15
Taxonomic description and genome sequence of Anaerorudis cellulosivorans gen. Nov. sp. nov., a novel cellulose- and Xylan-degrading bacterium of the Bacteroidota phylum isolated from a lab-scale methanogenic landfill bioreactor digesting municipal solid waste.
Systematic and applied microbiology, 48(2):126590 pii:S0723-2020(25)00012-8 [Epub ahead of print].
Bacteria responsible for the anaerobic decomposition of lignocellulosic waste biomass play key roles in the global carbon cycle and possess enzymes with potential industrial application. Here, a novel anaerobic, thermophilic, non-spore-forming bacterium, strain m5[T], was isolated from methanogenic enrichment cultures obtained from a lab-scale methanogenic landfill bioreactor digesting anaerobic municipal solid waste. Cells were Gram-stain-negative, catalase-negative, oxidase-negative, rod-shaped, and non-motile. The genomic DNA G + C content was 40.92 mol%. The optimal NaCl concentration, temperature and pH for growth were 0.5-1 g.L[-1], 45 °C, and at pH 7.0, respectively. The major fatty acids were C14:0, C16:0, C18:0, C18:1ω9c, and anteisoC15:0. Strain m5[T] was able to grow in the absence of yeast extract on glucose, fructose, arabinose, cellobiose, galactose, maltose, raffinose, sucrose, lactose, and pyruvate. In the presence of 0.2 % yeast extract, strain m5[T] grew on wide range of carbohydrates and amino acids, and was able to use complex substrates such cellulose and xylan. Major end products from cellulose and xylan degradation were valerate and propionate. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the new isolate was most closely related to Seramator thermalis SYSU GA16112[T] (94.42 % 16S rRNA gene sequence identity). Genome-based relatedness as well as both Average Nucleotide Identity (ANI), and Average Amino Acid Identity (AAI) strongly supported that strain m5[T] belongs to the Dysgonomonadaceae family. Metagenomic analysis of the landfill bioreactor community revealed that the Dysgonomonadaceae family was the most abundant in the constructed bioreactors. Based on its unique genomic features, strain m5[T] is considered to represent a novel genus, for which the name Anaerorudis is proposed. Moreover, several phenotypic, biochemical, and physiological properties differentiated the novel bacterial strain from related species, indicating that the strain represents a new species for which the name Anaerorudis cellulosivorans sp. nov. is proposed, with strain m5[T] (= DSM 112743[T] = ATCC TSD-267[T]) being the type of strain. This study highlights the biotechnological potential of strain m5[T], specifically in the bioconversion of cellulose and xylan, a recalcitrant substrate within lignocellulosic plant biomass, to enhance biogas production.
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@article {pmid39954481,
year = {2025},
author = {El Houari, A and Carpenter, M and Chaplin, D and Golyshin, P and McDonald, JE},
title = {Taxonomic description and genome sequence of Anaerorudis cellulosivorans gen. Nov. sp. nov., a novel cellulose- and Xylan-degrading bacterium of the Bacteroidota phylum isolated from a lab-scale methanogenic landfill bioreactor digesting municipal solid waste.},
journal = {Systematic and applied microbiology},
volume = {48},
number = {2},
pages = {126590},
doi = {10.1016/j.syapm.2025.126590},
pmid = {39954481},
issn = {1618-0984},
abstract = {Bacteria responsible for the anaerobic decomposition of lignocellulosic waste biomass play key roles in the global carbon cycle and possess enzymes with potential industrial application. Here, a novel anaerobic, thermophilic, non-spore-forming bacterium, strain m5[T], was isolated from methanogenic enrichment cultures obtained from a lab-scale methanogenic landfill bioreactor digesting anaerobic municipal solid waste. Cells were Gram-stain-negative, catalase-negative, oxidase-negative, rod-shaped, and non-motile. The genomic DNA G + C content was 40.92 mol%. The optimal NaCl concentration, temperature and pH for growth were 0.5-1 g.L[-1], 45 °C, and at pH 7.0, respectively. The major fatty acids were C14:0, C16:0, C18:0, C18:1ω9c, and anteisoC15:0. Strain m5[T] was able to grow in the absence of yeast extract on glucose, fructose, arabinose, cellobiose, galactose, maltose, raffinose, sucrose, lactose, and pyruvate. In the presence of 0.2 % yeast extract, strain m5[T] grew on wide range of carbohydrates and amino acids, and was able to use complex substrates such cellulose and xylan. Major end products from cellulose and xylan degradation were valerate and propionate. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the new isolate was most closely related to Seramator thermalis SYSU GA16112[T] (94.42 % 16S rRNA gene sequence identity). Genome-based relatedness as well as both Average Nucleotide Identity (ANI), and Average Amino Acid Identity (AAI) strongly supported that strain m5[T] belongs to the Dysgonomonadaceae family. Metagenomic analysis of the landfill bioreactor community revealed that the Dysgonomonadaceae family was the most abundant in the constructed bioreactors. Based on its unique genomic features, strain m5[T] is considered to represent a novel genus, for which the name Anaerorudis is proposed. Moreover, several phenotypic, biochemical, and physiological properties differentiated the novel bacterial strain from related species, indicating that the strain represents a new species for which the name Anaerorudis cellulosivorans sp. nov. is proposed, with strain m5[T] (= DSM 112743[T] = ATCC TSD-267[T]) being the type of strain. This study highlights the biotechnological potential of strain m5[T], specifically in the bioconversion of cellulose and xylan, a recalcitrant substrate within lignocellulosic plant biomass, to enhance biogas production.},
}
RevDate: 2025-02-15
Elevated salinity decreases microbial communities complexity and carbon, nitrogen and phosphorus metabolism in the Songnen Plain wetlands of China.
Water research, 276:123285 pii:S0043-1354(25)00199-X [Epub ahead of print].
Salinity can induce changes in the structure and function of soil microbial communities, which plays an important role in soil carbon (C), nitrogen (N) and phosphorus (P) cycling. However, there are few studies on the relationship between microbial communities and functional properties of wetland soil under elevated salinity. In this study, soil samples from Zhalong, Momoge, Niuxintaobao, and Xianghai wetlands in the Songnen Plain of China were cultured with different salinity and analyzed by metagenomic sequencing to assess the overall impact of salinity on microorganisms. The results showed that increasing soil salinity decreased soil microbial diversity and significantly changed its composition. Elevated salinity led to the replacement of core species (Sphingomonas) by halophilic species (Halomonadaceae, Halomohas campaniensis), reducing the stability of microbial ecological networks. C fixation, denitrification and purine metabolism were the key ways for the maintenance of C, N and P functions in Songnen plain wetlands, and these processes were significantly reduced with increasing salinity. Key genes involved in C, N and P metabolism include EC1.1.1.42, EC4.1.1.31, EC6.4.1.1, nosZ, nirK, purB, purC, adk, purM, and purQ. They were all effectively suppressed due to increased salinity. In summary, elevated salinity reduced the complexity of microorganisms and inhibited the related functions of C, N and P cycling, and affected the stability of wetland ecosystems. Wetland protection should be strengthened to prevent the aggravation of salinization. This study provides a new scientific framework for the restoration and management of salinized wetland ecosystems in the face of upcoming global changes.
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@article {pmid39954460,
year = {2025},
author = {Luo, S and Yuan, J and Song, Y and Ren, J and Qi, J and Zhu, M and Feng, Y and Li, M and Wang, B and Li, X and Song, C},
title = {Elevated salinity decreases microbial communities complexity and carbon, nitrogen and phosphorus metabolism in the Songnen Plain wetlands of China.},
journal = {Water research},
volume = {276},
number = {},
pages = {123285},
doi = {10.1016/j.watres.2025.123285},
pmid = {39954460},
issn = {1879-2448},
abstract = {Salinity can induce changes in the structure and function of soil microbial communities, which plays an important role in soil carbon (C), nitrogen (N) and phosphorus (P) cycling. However, there are few studies on the relationship between microbial communities and functional properties of wetland soil under elevated salinity. In this study, soil samples from Zhalong, Momoge, Niuxintaobao, and Xianghai wetlands in the Songnen Plain of China were cultured with different salinity and analyzed by metagenomic sequencing to assess the overall impact of salinity on microorganisms. The results showed that increasing soil salinity decreased soil microbial diversity and significantly changed its composition. Elevated salinity led to the replacement of core species (Sphingomonas) by halophilic species (Halomonadaceae, Halomohas campaniensis), reducing the stability of microbial ecological networks. C fixation, denitrification and purine metabolism were the key ways for the maintenance of C, N and P functions in Songnen plain wetlands, and these processes were significantly reduced with increasing salinity. Key genes involved in C, N and P metabolism include EC1.1.1.42, EC4.1.1.31, EC6.4.1.1, nosZ, nirK, purB, purC, adk, purM, and purQ. They were all effectively suppressed due to increased salinity. In summary, elevated salinity reduced the complexity of microorganisms and inhibited the related functions of C, N and P cycling, and affected the stability of wetland ecosystems. Wetland protection should be strengthened to prevent the aggravation of salinization. This study provides a new scientific framework for the restoration and management of salinized wetland ecosystems in the face of upcoming global changes.},
}
RevDate: 2025-02-15
Evaluating Nanopore Sequencing as a Respiratory Virus Diagnostic Tool for the Prehospital Setting.
Military medicine pii:8015940 [Epub ahead of print].
INTRODUCTION: Upper respiratory tract infections are a strain on military that results in lost duty days and an overall reduced readiness of the force. Improved diagnostic testing would enable better force health protection measures and earlier treatment of illness. Lightweight portable devices are preferred for diagnostic testing in austere environments where they are sometimes needed during military deployment. Current diagnostic testing is targeted to specific pathogens despite multiple pathogens that present with similar symptoms. In practice the pathogens that cause upper respiratory tract infections often go unidentified, which could be improved using agnostic or semi-agnostic diagnostic testing. Here, we performed an evaluation of shotgun metagenomic sequencing using the Oxford Nanopore Technologies (ONT) Rapid Sequencing Kit as a method for diagnostic testing of upper respiratory tract infections. This sequencing library preparation kit was chosen because of its ease of use and compatibility with the ONT MinION, a lightweight portable sequencer.
MATERIALS AND METHODS: Samples from patients with symptoms of upper respiratory tract infections were collected at Wilford Hall Ambulatory Surgical Center under an approved IRB protocol. Nasal rinse samples from 59 study participants were tested using the BioFire FilmArray Respiratory 2.1 Panel as well as shotgun metagenomic sequencing using ONT Rapid Sequencing Kit and ONT R9.4.1 flow cells.
RESULTS: A mixture of various viral pathogens was present among the 59 samples used in this study. We observed high specificity and modest sensitivity to detect the identified pathogens using shotgun metagenomic sequencing. Shotgun metagenomic sequencing detected additional pathogens that were missed by the BioFire FilmArray Respiratory 2.1 Panel, which are discussed. Lastly, we observe modest evidence of nonuniformity of the proportion of reads belonging to the pathogen during the duration of sequencing runs, which has implications for improving sensitivity by increasing the amount of sequencing performed.
CONCLUSIONS: Overall, ONT Rapid Sequencing Kit combined with alignment to a known panel of pathogens has shown great potential utility in our hands for quickly and accurately identifying viral respiratory pathogens. This, combined with its ease of use and portability, makes it a great candidate for further research and development toward a deployable agnostic diagnostic testing platform.
Additional Links: PMID-39953827
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@article {pmid39953827,
year = {2025},
author = {Reed, GM and Strickland, AK and Mutchler, CT and Ochoa, AR and Asin, SN and Blackburn, AN},
title = {Evaluating Nanopore Sequencing as a Respiratory Virus Diagnostic Tool for the Prehospital Setting.},
journal = {Military medicine},
volume = {},
number = {},
pages = {},
doi = {10.1093/milmed/usaf046},
pmid = {39953827},
issn = {1930-613X},
support = {DS21RES11//Defense Health Agency/ ; DS21RES11//Defense Health Agency/ ; },
abstract = {INTRODUCTION: Upper respiratory tract infections are a strain on military that results in lost duty days and an overall reduced readiness of the force. Improved diagnostic testing would enable better force health protection measures and earlier treatment of illness. Lightweight portable devices are preferred for diagnostic testing in austere environments where they are sometimes needed during military deployment. Current diagnostic testing is targeted to specific pathogens despite multiple pathogens that present with similar symptoms. In practice the pathogens that cause upper respiratory tract infections often go unidentified, which could be improved using agnostic or semi-agnostic diagnostic testing. Here, we performed an evaluation of shotgun metagenomic sequencing using the Oxford Nanopore Technologies (ONT) Rapid Sequencing Kit as a method for diagnostic testing of upper respiratory tract infections. This sequencing library preparation kit was chosen because of its ease of use and compatibility with the ONT MinION, a lightweight portable sequencer.
MATERIALS AND METHODS: Samples from patients with symptoms of upper respiratory tract infections were collected at Wilford Hall Ambulatory Surgical Center under an approved IRB protocol. Nasal rinse samples from 59 study participants were tested using the BioFire FilmArray Respiratory 2.1 Panel as well as shotgun metagenomic sequencing using ONT Rapid Sequencing Kit and ONT R9.4.1 flow cells.
RESULTS: A mixture of various viral pathogens was present among the 59 samples used in this study. We observed high specificity and modest sensitivity to detect the identified pathogens using shotgun metagenomic sequencing. Shotgun metagenomic sequencing detected additional pathogens that were missed by the BioFire FilmArray Respiratory 2.1 Panel, which are discussed. Lastly, we observe modest evidence of nonuniformity of the proportion of reads belonging to the pathogen during the duration of sequencing runs, which has implications for improving sensitivity by increasing the amount of sequencing performed.
CONCLUSIONS: Overall, ONT Rapid Sequencing Kit combined with alignment to a known panel of pathogens has shown great potential utility in our hands for quickly and accurately identifying viral respiratory pathogens. This, combined with its ease of use and portability, makes it a great candidate for further research and development toward a deployable agnostic diagnostic testing platform.},
}
RevDate: 2025-02-15
Functional Insights Into the Effect of Feralisation on the Gut Microbiota of Cats Worldwide.
Molecular ecology [Epub ahead of print].
Successfully adapting to a feral lifestyle with different access to food, shelter and other resources requires rapid physiological and behavioural changes, which could potentially be facilitated by gut microbiota plasticity. To investigate whether alterations in gut microbiota support this transition to a feral lifestyle, we analysed the gut microbiomes of domestic and feral cats from six geographically diverse locations using genome-resolved metagenomics. By reconstructing 229 non-redundant metagenome-assembled genomes from 92 cats, we identified a typical carnivore microbiome structure, with notable diversity and taxonomic differences across regions. While overall diversity metrics did not differ significantly between domestic and feral cats, hierarchical modelling of species communities, accounting for geographic and sex covariates, revealed significantly larger microbial functional capacities among feral cats. The increased capacity for amino acid and lipid degradation corresponds to feral cats' dietary reliance on crude protein and fat. A second modelling analysis, using behavioural phenotype as the main predictor, unveiled a positive association between microbial production of short-chain fatty acids, neurotransmitters and vitamins and cat aggressiveness, suggesting that gut microbes might contribute to heightened aggression and elusiveness observed in feral cats. Functional microbiome shifts may therefore play a significant role in the development of physiological and behavioural traits advantageous for a feral lifestyle, a hypothesis that warrants validation through microbiota manipulation experiments.
Additional Links: PMID-39953749
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@article {pmid39953749,
year = {2025},
author = {Aizpurua, O and Botnen, AB and Eisenhofer, R and Odriozola, I and Santos-Bay, L and Bjørnsen, MB and Gilbert, MTP and Alberdi, A},
title = {Functional Insights Into the Effect of Feralisation on the Gut Microbiota of Cats Worldwide.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {e17695},
doi = {10.1111/mec.17695},
pmid = {39953749},
issn = {1365-294X},
support = {CF20-0460//Carlsbergfondet/ ; 17417//Villum Fonden/ ; DNRF143//Danmarks Grundforskningsfond/ ; },
abstract = {Successfully adapting to a feral lifestyle with different access to food, shelter and other resources requires rapid physiological and behavioural changes, which could potentially be facilitated by gut microbiota plasticity. To investigate whether alterations in gut microbiota support this transition to a feral lifestyle, we analysed the gut microbiomes of domestic and feral cats from six geographically diverse locations using genome-resolved metagenomics. By reconstructing 229 non-redundant metagenome-assembled genomes from 92 cats, we identified a typical carnivore microbiome structure, with notable diversity and taxonomic differences across regions. While overall diversity metrics did not differ significantly between domestic and feral cats, hierarchical modelling of species communities, accounting for geographic and sex covariates, revealed significantly larger microbial functional capacities among feral cats. The increased capacity for amino acid and lipid degradation corresponds to feral cats' dietary reliance on crude protein and fat. A second modelling analysis, using behavioural phenotype as the main predictor, unveiled a positive association between microbial production of short-chain fatty acids, neurotransmitters and vitamins and cat aggressiveness, suggesting that gut microbes might contribute to heightened aggression and elusiveness observed in feral cats. Functional microbiome shifts may therefore play a significant role in the development of physiological and behavioural traits advantageous for a feral lifestyle, a hypothesis that warrants validation through microbiota manipulation experiments.},
}
RevDate: 2025-02-14
CmpDate: 2025-02-14
Distinctive circulating microbial metagenomic signatures in the plasma of patients with lung cancer and their potential value as molecular biomarkers.
Journal of translational medicine, 23(1):186.
Lung cancer (LC) remains the leading cause of cancer death globally. Recent reports have suggested that circulating microbial nucleic acids have potential as promising biomarkers for cancer liquid biopsies. However, circulating microbial profiles and their potential clinical value in LC patients remained unexplored. In this study, plasma samples from 76 LC patients, 9 liver cancer patients, 11 pancreatic cancer patients, and 53 healthy controls (HCs) were collected and underwent metagenomic analyses by whole genome sequencing. The composition and relative abundance of the microbial profiles were significantly different between the LC patients and HCs. A distinct plasma-based microbial profile was observed in LC patients. By differential analysis using MaAslin, 40 significant species between LC patients and HCs were identified. Five species were selected as optimal circulating microbial biomarkers for LC. The constructed classifier based on these five species showed an AUC of 0.9592, 0.9131, and 0.8077 in the discovery, validation, and additional validation cohorts, respectively. Furthermore, metagenomic profiles of 25 lung tumor tissue and plasma paired samples were analyzed and compared. The microbial diversity was significantly increased in plasma compared with the tumor tissue. Among the 13 shared core microbial species, 10 had no difference between the tumor tissue and paired plasma. In conclusion, circulating microbial nucleic acids in the plasma have potential as biomarkers for LC liquid biopsies. The microbiome in the tumor tissue was one of the possible sources of circulating microbial nucleic acids.
Additional Links: PMID-39953591
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@article {pmid39953591,
year = {2025},
author = {Chen, H and Yao, X and Yang, C and Zhang, Y and Dong, H and Zhai, J and Fan, D and Zhou, Q},
title = {Distinctive circulating microbial metagenomic signatures in the plasma of patients with lung cancer and their potential value as molecular biomarkers.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {186},
pmid = {39953591},
issn = {1479-5876},
support = {YCZYPT [2018]06//National Human Genetic Resource Sharing Service Platform/ ; },
mesh = {Humans ; *Lung Neoplasms/blood/microbiology/genetics ; *Metagenomics/methods ; *Biomarkers, Tumor/blood ; Female ; Male ; Middle Aged ; Metagenome/genetics ; Aged ; Case-Control Studies ; ROC Curve ; },
abstract = {Lung cancer (LC) remains the leading cause of cancer death globally. Recent reports have suggested that circulating microbial nucleic acids have potential as promising biomarkers for cancer liquid biopsies. However, circulating microbial profiles and their potential clinical value in LC patients remained unexplored. In this study, plasma samples from 76 LC patients, 9 liver cancer patients, 11 pancreatic cancer patients, and 53 healthy controls (HCs) were collected and underwent metagenomic analyses by whole genome sequencing. The composition and relative abundance of the microbial profiles were significantly different between the LC patients and HCs. A distinct plasma-based microbial profile was observed in LC patients. By differential analysis using MaAslin, 40 significant species between LC patients and HCs were identified. Five species were selected as optimal circulating microbial biomarkers for LC. The constructed classifier based on these five species showed an AUC of 0.9592, 0.9131, and 0.8077 in the discovery, validation, and additional validation cohorts, respectively. Furthermore, metagenomic profiles of 25 lung tumor tissue and plasma paired samples were analyzed and compared. The microbial diversity was significantly increased in plasma compared with the tumor tissue. Among the 13 shared core microbial species, 10 had no difference between the tumor tissue and paired plasma. In conclusion, circulating microbial nucleic acids in the plasma have potential as biomarkers for LC liquid biopsies. The microbiome in the tumor tissue was one of the possible sources of circulating microbial nucleic acids.},
}
MeSH Terms:
show MeSH Terms
hide MeSH Terms
Humans
*Lung Neoplasms/blood/microbiology/genetics
*Metagenomics/methods
*Biomarkers, Tumor/blood
Female
Male
Middle Aged
Metagenome/genetics
Aged
Case-Control Studies
ROC Curve
RevDate: 2025-02-14
CmpDate: 2025-02-15
A case of explosive community-acquired pneumonia and septic shock caused by Acinetobacter pittii.
BMC pulmonary medicine, 25(1):80 pii:10.1186/s12890-024-03457-0.
BACKGROUND: Acinetobacter pittii, belongs to the genus Acinetobacter, has a special pathogenesis and is commonly known as nosocomial pathogen; community infections are rare.
OBJECTIVE: To present a case study of community-acquired pneumonia and septic shock resulting from infection with Acinetobacter pittii and to investigate the diagnosis, clinical features and treatment of Acinetobacter pittii infection.
METHODS: The clinical features and prognosis of patients with Acinetobacter pittii, infection were analyzed retrospectively.
RESULTS: The sepsis caused by Acinetobacter pittii, was improved after treatment.
DISCUSSION AND CONCLUSION: Pneumonia caused by fully sensitive hypervirulent Acinetobacter pittii is rare, usually with acute course, severe illness and high mortality. It is necessary to identify the infectious agent as soon as possible, and early treatment can improve the success rate of treatment.
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@article {pmid39953490,
year = {2025},
author = {Zhan, X and Tian, X and Zhang, C and Ye, J},
title = {A case of explosive community-acquired pneumonia and septic shock caused by Acinetobacter pittii.},
journal = {BMC pulmonary medicine},
volume = {25},
number = {1},
pages = {80},
doi = {10.1186/s12890-024-03457-0},
pmid = {39953490},
issn = {1471-2466},
mesh = {Humans ; *Shock, Septic/microbiology ; *Community-Acquired Infections/microbiology ; *Acinetobacter Infections/diagnosis/drug therapy/microbiology/complications ; *Acinetobacter/isolation & purification ; *Anti-Bacterial Agents/therapeutic use ; Male ; Pneumonia, Bacterial/microbiology/complications/diagnosis ; Middle Aged ; Female ; Aged ; Retrospective Studies ; },
abstract = {BACKGROUND: Acinetobacter pittii, belongs to the genus Acinetobacter, has a special pathogenesis and is commonly known as nosocomial pathogen; community infections are rare.
OBJECTIVE: To present a case study of community-acquired pneumonia and septic shock resulting from infection with Acinetobacter pittii and to investigate the diagnosis, clinical features and treatment of Acinetobacter pittii infection.
METHODS: The clinical features and prognosis of patients with Acinetobacter pittii, infection were analyzed retrospectively.
RESULTS: The sepsis caused by Acinetobacter pittii, was improved after treatment.
DISCUSSION AND CONCLUSION: Pneumonia caused by fully sensitive hypervirulent Acinetobacter pittii is rare, usually with acute course, severe illness and high mortality. It is necessary to identify the infectious agent as soon as possible, and early treatment can improve the success rate of treatment.},
}
MeSH Terms:
show MeSH Terms
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Humans
*Shock, Septic/microbiology
*Community-Acquired Infections/microbiology
*Acinetobacter Infections/diagnosis/drug therapy/microbiology/complications
*Acinetobacter/isolation & purification
*Anti-Bacterial Agents/therapeutic use
Male
Pneumonia, Bacterial/microbiology/complications/diagnosis
Middle Aged
Female
Aged
Retrospective Studies
RevDate: 2025-02-14
CmpDate: 2025-02-14
Cold seeps are potential hotspots of deep-sea nitrogen loss driven by microorganisms across 21 phyla.
Nature communications, 16(1):1646.
Nitrogen bioavailability, governed by fixation and loss processes, is crucial for oceanic productivity and global biogeochemical cycles. The key nitrogen loss organisms-denitrifiers and anaerobic ammonium-oxidizing (anammox) bacteria-remain poorly understood in deep-sea cold seeps. This study combined geochemical measurements, [15]N stable isotope tracer analysis, metagenomics, metatranscriptomics, and three-dimensional protein structural simulations to explore cold-seeps nitrogen loss processes. Geochemical evidence from 359 sediment samples shows significantly higher nitrogen loss rates in cold seeps compared to typical deep-sea sediments, with nitrogen loss flux from surface sediments estimated at 4.96-7.63 Tg N yr[-1] (1.65-2.54% of global marine sediment). Examination of 147 million non-redundant genes indicates a high prevalence of nitrogen loss genes, including nitrous-oxide reductase (NosZ; 6.88 genes per million reads, GPM), nitric oxide dismutase (Nod; 1.29 GPM), and hydrazine synthase (HzsA; 3.35 GPM) in surface sediments. Analysis of 3,164 metagenome-assembled genomes expands the nitrous-oxide reducers by three phyla, nitric oxide-dismutating organisms by one phylum and two orders, and anammox bacteria by ten phyla going beyond Planctomycetota. These microbes exhibit structural adaptations and complex gene cluster enabling survival in cold seeps. Cold seeps likely are previously underestimated nitrogen loss hotspots, potentially contributing notably to the global nitrogen cycle.
Additional Links: PMID-39952920
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@article {pmid39952920,
year = {2025},
author = {Jiang, Q and Cao, L and Han, Y and Li, S and Zhao, R and Zhang, X and Ruff, SE and Zhao, Z and Peng, J and Liao, J and Zhu, B and Wang, M and Lin, X and Dong, X},
title = {Cold seeps are potential hotspots of deep-sea nitrogen loss driven by microorganisms across 21 phyla.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {1646},
pmid = {39952920},
issn = {2041-1723},
mesh = {*Geologic Sediments/microbiology ; *Nitrogen/metabolism ; *Bacteria/genetics/metabolism/classification ; Seawater/microbiology ; Cold Temperature ; Metagenomics/methods ; Nitrogen Cycle/genetics ; Metagenome/genetics ; Ammonium Compounds/metabolism ; Phylogeny ; Oceans and Seas ; },
abstract = {Nitrogen bioavailability, governed by fixation and loss processes, is crucial for oceanic productivity and global biogeochemical cycles. The key nitrogen loss organisms-denitrifiers and anaerobic ammonium-oxidizing (anammox) bacteria-remain poorly understood in deep-sea cold seeps. This study combined geochemical measurements, [15]N stable isotope tracer analysis, metagenomics, metatranscriptomics, and three-dimensional protein structural simulations to explore cold-seeps nitrogen loss processes. Geochemical evidence from 359 sediment samples shows significantly higher nitrogen loss rates in cold seeps compared to typical deep-sea sediments, with nitrogen loss flux from surface sediments estimated at 4.96-7.63 Tg N yr[-1] (1.65-2.54% of global marine sediment). Examination of 147 million non-redundant genes indicates a high prevalence of nitrogen loss genes, including nitrous-oxide reductase (NosZ; 6.88 genes per million reads, GPM), nitric oxide dismutase (Nod; 1.29 GPM), and hydrazine synthase (HzsA; 3.35 GPM) in surface sediments. Analysis of 3,164 metagenome-assembled genomes expands the nitrous-oxide reducers by three phyla, nitric oxide-dismutating organisms by one phylum and two orders, and anammox bacteria by ten phyla going beyond Planctomycetota. These microbes exhibit structural adaptations and complex gene cluster enabling survival in cold seeps. Cold seeps likely are previously underestimated nitrogen loss hotspots, potentially contributing notably to the global nitrogen cycle.},
}
MeSH Terms:
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*Geologic Sediments/microbiology
*Nitrogen/metabolism
*Bacteria/genetics/metabolism/classification
Seawater/microbiology
Cold Temperature
Metagenomics/methods
Nitrogen Cycle/genetics
Metagenome/genetics
Ammonium Compounds/metabolism
Phylogeny
Oceans and Seas
RevDate: 2025-02-14
CmpDate: 2025-02-14
Exploring viral diversity in fermented vegetables through viral metagenomics.
Food microbiology, 128:104733.
Fermented vegetables are traditionally produced using the endogenous microorganisms present in raw ingredients. While the diversity of bacteria and fungi in fermented vegetables has been relatively well studied, phage communities remain largely unexplored. In this study, we collected twelve samples of fermented cabbage, carrot, and turnip after fermentation and analyzed the microbial and viral communities using shotgun and viral metagenomic approaches. Assessment of the viral diversity also benefited from epifluorescence microscopy to estimate viral load. The viral metagenomics approach targeted dsDNA, ssDNA, and RNA viruses. The microbiome of fermented vegetables was dominated by lactic acid bacteria and varied according to the type of vegetable used as raw material. The analysis of metagenome-assembled-genomes allowed the detection of 22 prophages of which 8 were present as free particles and therefore detected in the metaviromes. The viral community, estimated to range from 5.28 to 7.57 log virus-like particles per gram of fermented vegetables depending on the sample, was mainly composed of dsDNA viruses, although ssDNA and non-bacterial RNA viruses, possibly originating from the phyllosphere, were also detected. The dsDNA viral community, primarily comprising bacteriophages, varied depending on the type of vegetable used for fermentation. The bacterial hosts predicted for these phages mainly belonged to Lactobacillaceae and Enterobacteriaceae families. These results highlighted the complex microbial and viral composition of fermented vegetables, which varied depending on the three types of vegetables used as raw material. Further research is needed to deepen our understanding of the impact of these viruses on the microbial ecology of fermented vegetables and on the quality of the final products.
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@article {pmid39952771,
year = {2025},
author = {Cantuti Gendre, J and Le Marrec, C and Chaillou, S and Omhover-Fougy, L and Landaud, S and Dugat-Bony, E},
title = {Exploring viral diversity in fermented vegetables through viral metagenomics.},
journal = {Food microbiology},
volume = {128},
number = {},
pages = {104733},
doi = {10.1016/j.fm.2025.104733},
pmid = {39952771},
issn = {1095-9998},
mesh = {*Metagenomics ; *Vegetables/virology/microbiology ; *Fermentation ; *Bacteriophages/genetics/isolation & purification/classification ; Microbiota ; Brassica/microbiology/virology ; Fermented Foods/microbiology/virology ; Bacteria/genetics/classification/isolation & purification/virology ; Biodiversity ; Daucus carota/microbiology/virology ; Food Microbiology ; Viruses/isolation & purification/classification/genetics ; Enterobacteriaceae/isolation & purification/genetics/virology/classification ; Metagenome ; Lactobacillaceae/isolation & purification/genetics/classification ; },
abstract = {Fermented vegetables are traditionally produced using the endogenous microorganisms present in raw ingredients. While the diversity of bacteria and fungi in fermented vegetables has been relatively well studied, phage communities remain largely unexplored. In this study, we collected twelve samples of fermented cabbage, carrot, and turnip after fermentation and analyzed the microbial and viral communities using shotgun and viral metagenomic approaches. Assessment of the viral diversity also benefited from epifluorescence microscopy to estimate viral load. The viral metagenomics approach targeted dsDNA, ssDNA, and RNA viruses. The microbiome of fermented vegetables was dominated by lactic acid bacteria and varied according to the type of vegetable used as raw material. The analysis of metagenome-assembled-genomes allowed the detection of 22 prophages of which 8 were present as free particles and therefore detected in the metaviromes. The viral community, estimated to range from 5.28 to 7.57 log virus-like particles per gram of fermented vegetables depending on the sample, was mainly composed of dsDNA viruses, although ssDNA and non-bacterial RNA viruses, possibly originating from the phyllosphere, were also detected. The dsDNA viral community, primarily comprising bacteriophages, varied depending on the type of vegetable used for fermentation. The bacterial hosts predicted for these phages mainly belonged to Lactobacillaceae and Enterobacteriaceae families. These results highlighted the complex microbial and viral composition of fermented vegetables, which varied depending on the three types of vegetables used as raw material. Further research is needed to deepen our understanding of the impact of these viruses on the microbial ecology of fermented vegetables and on the quality of the final products.},
}
MeSH Terms:
show MeSH Terms
hide MeSH Terms
*Metagenomics
*Vegetables/virology/microbiology
*Fermentation
*Bacteriophages/genetics/isolation & purification/classification
Microbiota
Brassica/microbiology/virology
Fermented Foods/microbiology/virology
Bacteria/genetics/classification/isolation & purification/virology
Biodiversity
Daucus carota/microbiology/virology
Food Microbiology
Viruses/isolation & purification/classification/genetics
Enterobacteriaceae/isolation & purification/genetics/virology/classification
Metagenome
Lactobacillaceae/isolation & purification/genetics/classification
RevDate: 2025-02-14
CmpDate: 2025-02-14
Analyzing fungal community succession and its correlation to flavor compounds in the Cupei fermentation process of Sichuan shai vinegar.
Food microbiology, 128:104718.
Sichuan Shai vinegar, a distinctive condiment from Southwest China, is produced through open-air solid-state fermentation, employing a unique Chinese herbal medicine mixture (Yaoqu) as the fermentation starter. Despite its culinary significance, the dynamics and roles of fungal communities within the Cupei fermentation phase remain understudied. This study employed high-performance liquid chromatography (HPLC) to quantify 11 organic acids and 17 amino acids, revealing a significant increase in organic acid content from 2.56 g/100 g-17.47 g/100 g dry weight and a gradual elevation in free amino acid content from 0.53 g/100 g-5.59 g/100 g throughout the fermentation process. Headspace solid-phase microextraction coupled with gas chromatography-mass spectrometry (HS-SPME/GC-MS) identified 85 volatile flavor compounds, predominantly consisting of 2 alcohols, 10 acids, 29 esters, 4 ketones, 6 aldehydes, and 14 other types. High-throughput sequencing facilitated the identification of key microorganisms, with Lichtheimia, Brettanomyces, Pichia, Saccharomyces, Kazachstania, and Syncephalastrum emerging as the most abundant fungal genera. Correlation analysis revealed significant positive correlations between 20 fungi and 11 organic acids, 24 fungi and 16 amino acids, and 50 fungi and 76 volatile flavor compounds. Notably, Lichtheimia, Pichia, and Brettanomyces were identified as the most influential in flavor metabolism. These findings elucidate the microbial metabolic mechanisms during Sichuan Shai vinegar fermentation, laying a foundation for further research and potential applications in vinegar production.
Additional Links: PMID-39952762
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@article {pmid39952762,
year = {2025},
author = {Li, Z and Liao, Y and Huang, C and Liu, J and Kong, X and Li, L and Li, Z and Gui, Y},
title = {Analyzing fungal community succession and its correlation to flavor compounds in the Cupei fermentation process of Sichuan shai vinegar.},
journal = {Food microbiology},
volume = {128},
number = {},
pages = {104718},
doi = {10.1016/j.fm.2024.104718},
pmid = {39952762},
issn = {1095-9998},
mesh = {*Fermentation ; *Acetic Acid/metabolism/analysis ; *Volatile Organic Compounds/metabolism/analysis/chemistry ; *Flavoring Agents/metabolism/chemistry ; *Fungi/classification/metabolism/genetics/isolation & purification ; China ; Gas Chromatography-Mass Spectrometry ; Amino Acids/metabolism/analysis ; Solid Phase Microextraction ; Food Microbiology ; Mycobiome ; Chromatography, High Pressure Liquid ; Condiments/microbiology/analysis ; },
abstract = {Sichuan Shai vinegar, a distinctive condiment from Southwest China, is produced through open-air solid-state fermentation, employing a unique Chinese herbal medicine mixture (Yaoqu) as the fermentation starter. Despite its culinary significance, the dynamics and roles of fungal communities within the Cupei fermentation phase remain understudied. This study employed high-performance liquid chromatography (HPLC) to quantify 11 organic acids and 17 amino acids, revealing a significant increase in organic acid content from 2.56 g/100 g-17.47 g/100 g dry weight and a gradual elevation in free amino acid content from 0.53 g/100 g-5.59 g/100 g throughout the fermentation process. Headspace solid-phase microextraction coupled with gas chromatography-mass spectrometry (HS-SPME/GC-MS) identified 85 volatile flavor compounds, predominantly consisting of 2 alcohols, 10 acids, 29 esters, 4 ketones, 6 aldehydes, and 14 other types. High-throughput sequencing facilitated the identification of key microorganisms, with Lichtheimia, Brettanomyces, Pichia, Saccharomyces, Kazachstania, and Syncephalastrum emerging as the most abundant fungal genera. Correlation analysis revealed significant positive correlations between 20 fungi and 11 organic acids, 24 fungi and 16 amino acids, and 50 fungi and 76 volatile flavor compounds. Notably, Lichtheimia, Pichia, and Brettanomyces were identified as the most influential in flavor metabolism. These findings elucidate the microbial metabolic mechanisms during Sichuan Shai vinegar fermentation, laying a foundation for further research and potential applications in vinegar production.},
}
MeSH Terms:
show MeSH Terms
hide MeSH Terms
*Fermentation
*Acetic Acid/metabolism/analysis
*Volatile Organic Compounds/metabolism/analysis/chemistry
*Flavoring Agents/metabolism/chemistry
*Fungi/classification/metabolism/genetics/isolation & purification
China
Gas Chromatography-Mass Spectrometry
Amino Acids/metabolism/analysis
Solid Phase Microextraction
Food Microbiology
Mycobiome
Chromatography, High Pressure Liquid
Condiments/microbiology/analysis
RevDate: 2025-02-14
CmpDate: 2025-02-14
Environmental microbiome mapping in poultry processing chain and assessment of microbial dynamics in response to different storage conditions.
Food microbiology, 128:104734.
Poultry production chain comprises a complex network involving various stages from rearing to the final distribution of poultry products. This study explores the intricate dynamics within this chain, using shotgun metagenomics, particularly focusing on taxonomic and functional composition of the microbiome, antibiotic resistance and virulence potential. Moreover, the study of the impact of different packaging and storage conditions provides insights into how diverse packaging strategies and storage temperature can impact the shelf-life of chicken meat. Microbiome mapping in poultry processing facility revealed the dominance of Brochothrix thermosphacta, Pseudomonas fragi and Psychrobacter immobilis on poultry-based products and industrial surfaces. Indeed, surfaces of equipment and tools have a significant impact on the microbial composition of the final food products. Furthermore, the study of the microbiome dynamics in chicken meat stored in different packaging (air, modified atmosphere, under vacuum) and temperatures (0, 4 and 10 °C) revealed temperature-dependent microbiota shifts in chicken meat, highlighting specific spoilage organisms (SSOs) in the different packaging methods. Additionally, our results showed that poultry-based products and industrial surfaces belonging to carcasses processing area hosted elevated levels of Antibiotic Resistance Genes, mainly associated with resistance to aminoglycosides, β-lactams, MLSPs (which includes macrolides, lincosamides, streptogramins and pleuromutilins) amphenicols and tetracyclines classes and several Virulence-associated genes related to adherence, biofilm, effector delivery system, motility, nutritional/metabolic factors and regulation. Finally, our findings underscored a notably mobile resistome, showing multiple AR class correlated with mobile elements. This poses a considerable risk, emphasizing the urgent need for proactive measures in addressing potential antibiotic resistance genes dissemination in the poultry chain.
Additional Links: PMID-39952751
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@article {pmid39952751,
year = {2025},
author = {Sequino, G and Cobo-Diaz, JF and Valentino, V and Tassou, C and Volpe, S and Torrieri, E and Nychas, GJ and Álvarez Ordóñez, A and Ercolini, D and De Filippis, F},
title = {Environmental microbiome mapping in poultry processing chain and assessment of microbial dynamics in response to different storage conditions.},
journal = {Food microbiology},
volume = {128},
number = {},
pages = {104734},
doi = {10.1016/j.fm.2025.104734},
pmid = {39952751},
issn = {1095-9998},
mesh = {Animals ; *Microbiota ; *Bacteria/genetics/classification/isolation & purification ; *Chickens/microbiology ; *Food Storage ; Poultry Products/microbiology ; Food Packaging/methods ; Food Microbiology ; Poultry/microbiology ; Drug Resistance, Bacterial ; Temperature ; Meat/microbiology ; Brochothrix/genetics/isolation & purification ; Anti-Bacterial Agents/pharmacology ; Environmental Microbiology ; Metagenomics ; },
abstract = {Poultry production chain comprises a complex network involving various stages from rearing to the final distribution of poultry products. This study explores the intricate dynamics within this chain, using shotgun metagenomics, particularly focusing on taxonomic and functional composition of the microbiome, antibiotic resistance and virulence potential. Moreover, the study of the impact of different packaging and storage conditions provides insights into how diverse packaging strategies and storage temperature can impact the shelf-life of chicken meat. Microbiome mapping in poultry processing facility revealed the dominance of Brochothrix thermosphacta, Pseudomonas fragi and Psychrobacter immobilis on poultry-based products and industrial surfaces. Indeed, surfaces of equipment and tools have a significant impact on the microbial composition of the final food products. Furthermore, the study of the microbiome dynamics in chicken meat stored in different packaging (air, modified atmosphere, under vacuum) and temperatures (0, 4 and 10 °C) revealed temperature-dependent microbiota shifts in chicken meat, highlighting specific spoilage organisms (SSOs) in the different packaging methods. Additionally, our results showed that poultry-based products and industrial surfaces belonging to carcasses processing area hosted elevated levels of Antibiotic Resistance Genes, mainly associated with resistance to aminoglycosides, β-lactams, MLSPs (which includes macrolides, lincosamides, streptogramins and pleuromutilins) amphenicols and tetracyclines classes and several Virulence-associated genes related to adherence, biofilm, effector delivery system, motility, nutritional/metabolic factors and regulation. Finally, our findings underscored a notably mobile resistome, showing multiple AR class correlated with mobile elements. This poses a considerable risk, emphasizing the urgent need for proactive measures in addressing potential antibiotic resistance genes dissemination in the poultry chain.},
}
MeSH Terms:
show MeSH Terms
hide MeSH Terms
Animals
*Microbiota
*Bacteria/genetics/classification/isolation & purification
*Chickens/microbiology
*Food Storage
Poultry Products/microbiology
Food Packaging/methods
Food Microbiology
Poultry/microbiology
Drug Resistance, Bacterial
Temperature
Meat/microbiology
Brochothrix/genetics/isolation & purification
Anti-Bacterial Agents/pharmacology
Environmental Microbiology
Metagenomics
RevDate: 2025-02-14
Novel insights into the effect of arbuscular mycorrhizal fungi inoculation in soils under long-term biosolids application: emphasis on antibiotic and metal resistance genes, and mobile genetic elements.
Environmental pollution (Barking, Essex : 1987) pii:S0269-7491(25)00219-2 [Epub ahead of print].
The application of biosolids can improve soil fertility and crop productivity but also accompanies risks of heavy metals and antibiotics introduction. In the presence of heavy metals contamination, using arbuscular mycorrhizal fungi (AMF) is a promising strategy to enhance soil microbial community stability and plant tolerance resistance to heavy metals, and to reduce the spread of antibiotic resistance genes (ARGs). The present study investigated the impacts of AMF inoculation on soil and plant heavy metal contents, and soil microbial communities by pot experiments. The results showed that AMF inoculation significantly enhanced plant biomass, and reduced soil and plant heavy metals contents. While AMF inoculation did not alter bacterial and fungal community compositions, it increased bacterial diversity at higher biosolids concentrations. Notably, AMF inoculation enhanced microbial network complexity and increased keystone taxa abundance. Furthermore, several beneficial microorganisms with high resistance to heavy metals were enriched in AMF-inoculated soils. Metagenomic analysis revealed a reduction in the mobile genetic element (MGE) gene IS91 in AMF-inoculated soils and an increase in heavy metal resistance genes compared to soils without AMF. The possibility of reduction in MGE-mediated spread of ARGs is one of the key findings of this study. As a caution, this study also detected enrichment of few ARGs in high biosolids-amended soils with AMF inoculation. Overall, AMF inoculation could be a valuable strategy in agriculture for mitigating the environmental risks associated with biosolids, heavy metals and antibiotic resistance, thereby promoting sustainable soil management and health.
Additional Links: PMID-39952592
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@article {pmid39952592,
year = {2025},
author = {Sun, T and Delaplace, P and Li, G and James, A and Pan, J and Zhang, J},
title = {Novel insights into the effect of arbuscular mycorrhizal fungi inoculation in soils under long-term biosolids application: emphasis on antibiotic and metal resistance genes, and mobile genetic elements.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {125846},
doi = {10.1016/j.envpol.2025.125846},
pmid = {39952592},
issn = {1873-6424},
abstract = {The application of biosolids can improve soil fertility and crop productivity but also accompanies risks of heavy metals and antibiotics introduction. In the presence of heavy metals contamination, using arbuscular mycorrhizal fungi (AMF) is a promising strategy to enhance soil microbial community stability and plant tolerance resistance to heavy metals, and to reduce the spread of antibiotic resistance genes (ARGs). The present study investigated the impacts of AMF inoculation on soil and plant heavy metal contents, and soil microbial communities by pot experiments. The results showed that AMF inoculation significantly enhanced plant biomass, and reduced soil and plant heavy metals contents. While AMF inoculation did not alter bacterial and fungal community compositions, it increased bacterial diversity at higher biosolids concentrations. Notably, AMF inoculation enhanced microbial network complexity and increased keystone taxa abundance. Furthermore, several beneficial microorganisms with high resistance to heavy metals were enriched in AMF-inoculated soils. Metagenomic analysis revealed a reduction in the mobile genetic element (MGE) gene IS91 in AMF-inoculated soils and an increase in heavy metal resistance genes compared to soils without AMF. The possibility of reduction in MGE-mediated spread of ARGs is one of the key findings of this study. As a caution, this study also detected enrichment of few ARGs in high biosolids-amended soils with AMF inoculation. Overall, AMF inoculation could be a valuable strategy in agriculture for mitigating the environmental risks associated with biosolids, heavy metals and antibiotic resistance, thereby promoting sustainable soil management and health.},
}
RevDate: 2025-02-14
CmpDate: 2025-02-14
Integrated metagenomic and metabolomic analyses of the effects of total flavonoids of Rhizoma Drynariae on reducing ovariectomized-induced osteoporosis by regulating gut microbiota and related metabolites.
PloS one, 20(2):e0317832 pii:PONE-D-24-42978.
TFRD has been widely used in China to treat osteoporosis (OP). However, the specific molecular mechanism of TFRD against OP has not been fully clarified. Our previous studies have also proved that TFRD could attenuate OP and the clinical equivalent dose of 67.5mg/kg/d is the effective dose for TFRD treating OP. Therefore, this study used 67.5mg/kg as the dosage of TFRD in combination with multi omics to investigate the mechanism of action of TFRD in the treatment of OP. The aim of this study was to further elucidate molecular mechanism of TFRD for treating OP based on metagenomic and metabolomic analyses. In this study, hematoxylin-eosin (H&E) staining, micro computed tomography (micro-CT) and bone mineral density (BMD) analysis were used to observe pharmacological effects of TFRD against ovariectomized (OVX)-induced OP. Subsequently, multiomics analysis including metagenomics, untargeted and short chain fatty acids (SCFAs) metabolomics were carried out to identify whether the anti-osteoporosis mechanism of TFRD correlated with gut microbiota and related metabolites. Our results indicate that TFRD could improve the microstructure and density of trabecular bone in OVX rats. 17 differential species, which mainly from Akkermansia, Bacteroides, and Phascolarctobacterium genus, 14 related differential metabolites and acetic acid in SCFAs were significantly altered by OVX and reversed by TFRD. Furthermore, according to results of untargeted metabolomics analysis, it was found that several metabolic pathways such as phenylalanine metabolism, phenylalanine, tyrosine and tryptophan biosynthesis and so on might play an important role in TFRD against OP. In order to further study the relationship between gut microbiota and related metabolites, spearman correlation analysis was used, and showed that gut microbiota such as Akkermansia muciniphila might be closely related to several metabolites and metabolic pathways. These findings suggest that TFRD treatment could reduce the effects of OVX-induced OP by altering community composition and abundance of gut microbiota, regulating metabolites and SCFAs. It was speculated that the gut microbiota especially Akkermansia muciniphila and related metabolites might play an important role in TFRD against OP, and deserve further study by follow-up experiment. This conclusion provides new theoretical support for mechanism research of TFRD against OP.
Additional Links: PMID-39951448
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PubMed:
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@article {pmid39951448,
year = {2025},
author = {Li, Q and Wu, X and Niu, X and Yu, Z and Fang, S and Chu, X and Zhu, J and Song, Q and Hou, C and Wei, X},
title = {Integrated metagenomic and metabolomic analyses of the effects of total flavonoids of Rhizoma Drynariae on reducing ovariectomized-induced osteoporosis by regulating gut microbiota and related metabolites.},
journal = {PloS one},
volume = {20},
number = {2},
pages = {e0317832},
doi = {10.1371/journal.pone.0317832},
pmid = {39951448},
issn = {1932-6203},
mesh = {*Gastrointestinal Microbiome/drug effects ; Animals ; Female ; *Ovariectomy ; *Osteoporosis/drug therapy/metabolism ; *Metabolomics ; Rats ; *Flavonoids/pharmacology ; *Bone Density/drug effects ; *Polypodiaceae ; Metagenomics ; Rats, Sprague-Dawley ; Drugs, Chinese Herbal/pharmacology ; Rhizome ; },
abstract = {TFRD has been widely used in China to treat osteoporosis (OP). However, the specific molecular mechanism of TFRD against OP has not been fully clarified. Our previous studies have also proved that TFRD could attenuate OP and the clinical equivalent dose of 67.5mg/kg/d is the effective dose for TFRD treating OP. Therefore, this study used 67.5mg/kg as the dosage of TFRD in combination with multi omics to investigate the mechanism of action of TFRD in the treatment of OP. The aim of this study was to further elucidate molecular mechanism of TFRD for treating OP based on metagenomic and metabolomic analyses. In this study, hematoxylin-eosin (H&E) staining, micro computed tomography (micro-CT) and bone mineral density (BMD) analysis were used to observe pharmacological effects of TFRD against ovariectomized (OVX)-induced OP. Subsequently, multiomics analysis including metagenomics, untargeted and short chain fatty acids (SCFAs) metabolomics were carried out to identify whether the anti-osteoporosis mechanism of TFRD correlated with gut microbiota and related metabolites. Our results indicate that TFRD could improve the microstructure and density of trabecular bone in OVX rats. 17 differential species, which mainly from Akkermansia, Bacteroides, and Phascolarctobacterium genus, 14 related differential metabolites and acetic acid in SCFAs were significantly altered by OVX and reversed by TFRD. Furthermore, according to results of untargeted metabolomics analysis, it was found that several metabolic pathways such as phenylalanine metabolism, phenylalanine, tyrosine and tryptophan biosynthesis and so on might play an important role in TFRD against OP. In order to further study the relationship between gut microbiota and related metabolites, spearman correlation analysis was used, and showed that gut microbiota such as Akkermansia muciniphila might be closely related to several metabolites and metabolic pathways. These findings suggest that TFRD treatment could reduce the effects of OVX-induced OP by altering community composition and abundance of gut microbiota, regulating metabolites and SCFAs. It was speculated that the gut microbiota especially Akkermansia muciniphila and related metabolites might play an important role in TFRD against OP, and deserve further study by follow-up experiment. This conclusion provides new theoretical support for mechanism research of TFRD against OP.},
}
MeSH Terms:
show MeSH Terms
hide MeSH Terms
*Gastrointestinal Microbiome/drug effects
Animals
Female
*Ovariectomy
*Osteoporosis/drug therapy/metabolism
*Metabolomics
Rats
*Flavonoids/pharmacology
*Bone Density/drug effects
*Polypodiaceae
Metagenomics
Rats, Sprague-Dawley
Drugs, Chinese Herbal/pharmacology
Rhizome
RevDate: 2025-02-14
CmpDate: 2025-02-14
Whole metagenome sequencing and 16S rRNA gene amplicon analyses reveal the complex microbiome responsible for the success of enhanced in-situ reductive dechlorination (ERD) of a tetrachloroethene-contaminated Superfund site.
PloS one, 20(2):e0306503 pii:PONE-D-24-24820.
The North Railroad Avenue Plume (NRAP) Superfund site in New Mexico, USA exemplifies successful chlorinated solvent bioremediation. NRAP was the result of leakage from a dry-cleaning that operated for 37 years. The presence of tetrachloroethene biodegradation byproducts, organohalide respiring genera (OHRG), and reductive dehalogenase (rdh) genes detected in groundwater samples indicated that enhanced reductive dechlorination (ERD) was the remedy of choice. This was achieved through biostimulation by mixing emulsified vegetable oil into the contaminated aquifer. This report combines metagenomic techniques with site monitoring metadata to reveal new details of ERD. DNA extracts from groundwater samples collected prior to and at four, 23 and 39 months after remedy implementation were subjected to whole metagenome sequencing (WMS) and 16S rRNA gene amplicon (16S) analyses. The response of the indigenous NRAP microbiome to ERD protocols is consistent with results obtained from microcosms, dechlorinating consortia, and observations at other contaminated sites. WMS detects three times as many phyla and six times as many genera as 16S. Both techniques reveal abundance changes in Dehalococcoides and Dehalobacter that reflect organohalide form and availability. Methane was not detected before biostimulation but appeared afterwards, corresponding to an increase in methanogenic Archaea. Assembly of WMS reads produced scaffolds containing rdh genes from Dehalococcoides, Dehalobacter, Dehalogenimonas, Desulfocarbo, and Desulfobacula. Anaerobic and aerobic cometabolic organohalide degrading microbes that increase in abundance include methanogenic Archaea, methanotrophs, Dechloromonas, and Xanthobacter, some of which contain hydrolytic dehalogenase genes. Aerobic cometabolism may be supported by oxygen gradients existing in aquifer microenvironments or by microbes that produce O2 via microbial dismutation. The NRAP model for successful ERD is consistent with the established pathway and identifies new taxa and processes that support this syntrophic process. This project explores the potential of metagenomic tools (MGT) as the next advancement in bioremediation.
Additional Links: PMID-39951402
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PubMed:
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@article {pmid39951402,
year = {2025},
author = {Reiss, RA and Guerra, PA and Makhnin, O and Kellom, M},
title = {Whole metagenome sequencing and 16S rRNA gene amplicon analyses reveal the complex microbiome responsible for the success of enhanced in-situ reductive dechlorination (ERD) of a tetrachloroethene-contaminated Superfund site.},
journal = {PloS one},
volume = {20},
number = {2},
pages = {e0306503},
doi = {10.1371/journal.pone.0306503},
pmid = {39951402},
issn = {1932-6203},
mesh = {*RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; *Biodegradation, Environmental ; *Groundwater/microbiology ; *Metagenome ; *Tetrachloroethylene/metabolism ; Water Pollutants, Chemical/metabolism ; Halogenation ; Metagenomics/methods ; Bacteria/genetics/metabolism/classification ; New Mexico ; },
abstract = {The North Railroad Avenue Plume (NRAP) Superfund site in New Mexico, USA exemplifies successful chlorinated solvent bioremediation. NRAP was the result of leakage from a dry-cleaning that operated for 37 years. The presence of tetrachloroethene biodegradation byproducts, organohalide respiring genera (OHRG), and reductive dehalogenase (rdh) genes detected in groundwater samples indicated that enhanced reductive dechlorination (ERD) was the remedy of choice. This was achieved through biostimulation by mixing emulsified vegetable oil into the contaminated aquifer. This report combines metagenomic techniques with site monitoring metadata to reveal new details of ERD. DNA extracts from groundwater samples collected prior to and at four, 23 and 39 months after remedy implementation were subjected to whole metagenome sequencing (WMS) and 16S rRNA gene amplicon (16S) analyses. The response of the indigenous NRAP microbiome to ERD protocols is consistent with results obtained from microcosms, dechlorinating consortia, and observations at other contaminated sites. WMS detects three times as many phyla and six times as many genera as 16S. Both techniques reveal abundance changes in Dehalococcoides and Dehalobacter that reflect organohalide form and availability. Methane was not detected before biostimulation but appeared afterwards, corresponding to an increase in methanogenic Archaea. Assembly of WMS reads produced scaffolds containing rdh genes from Dehalococcoides, Dehalobacter, Dehalogenimonas, Desulfocarbo, and Desulfobacula. Anaerobic and aerobic cometabolic organohalide degrading microbes that increase in abundance include methanogenic Archaea, methanotrophs, Dechloromonas, and Xanthobacter, some of which contain hydrolytic dehalogenase genes. Aerobic cometabolism may be supported by oxygen gradients existing in aquifer microenvironments or by microbes that produce O2 via microbial dismutation. The NRAP model for successful ERD is consistent with the established pathway and identifies new taxa and processes that support this syntrophic process. This project explores the potential of metagenomic tools (MGT) as the next advancement in bioremediation.},
}
MeSH Terms:
show MeSH Terms
hide MeSH Terms
*RNA, Ribosomal, 16S/genetics
*Microbiota/genetics
*Biodegradation, Environmental
*Groundwater/microbiology
*Metagenome
*Tetrachloroethylene/metabolism
Water Pollutants, Chemical/metabolism
Halogenation
Metagenomics/methods
Bacteria/genetics/metabolism/classification
New Mexico
RevDate: 2025-02-14
CmpDate: 2025-02-14
Time-restricted feeding promotes glucagon-like peptide-1 secretion and regulates appetite via tryptophan metabolism of gut Lactobacillus in pigs.
Gut microbes, 17(1):2467185.
Previous clinical trials have shown that time-restricted feeding can be involved in regulating the metabolic health of humans and animals. However, the underlying mechanism has not been fully explored. In this study, the pig model was employed to simulate four prevalent human eating habits, with the aim of investigating the impact of gut microbiota and microbial metabolites on gut hormone secretion and appetite regulation. Compared to the ad libitum feeding (ALF) pattern, three time-restricted feeding patterns reduced total food intake and eating time. Meanwhile, three time-restricted feeding patterns induced elevated levels of serum and hypothalamic glucagon-like peptide-1 (GLP-1), while suppressing reward-related circuits in the hypothalamus. It is noteworthy that the early time-restricted feeding (eTRF) pattern increased the number of intestinal enteroendocrine cells (EECs) compared to ALF. Metagenomic and metabonomic analyses revealed that three time-restricted feeding patterns induced colonization of Lactobacillus and significantly increased the levels of its metabolite, indole-3-lactic acid (ILA). Dietary supplementation with ILA exhibited an increasing trend in fasting serum GLP-1 level of piglets. In vitro studies with pig intestinal organoids showed the Lactobacillus metabolite ILA enhanced GLP-1 secretion through the promotion of intestinal stem cell differentiation into EECs, rather than activating the ability of EECs to secrete GLP-1. Overall, time-restricted feeding promoted GLP-1 secretion and affected long-term appetite regulation by promoting the colonization of Lactobacillus and modulating microbial tryptophan metabolism.
Additional Links: PMID-39951352
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PubMed:
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@article {pmid39951352,
year = {2025},
author = {Li, Q and Tan, D and Xiong, S and Yu, K and Su, Y and Zhu, W},
title = {Time-restricted feeding promotes glucagon-like peptide-1 secretion and regulates appetite via tryptophan metabolism of gut Lactobacillus in pigs.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2467185},
doi = {10.1080/19490976.2025.2467185},
pmid = {39951352},
issn = {1949-0984},
mesh = {Animals ; *Glucagon-Like Peptide 1/metabolism/blood ; *Gastrointestinal Microbiome ; Swine ; *Tryptophan/metabolism ; *Lactobacillus/metabolism ; *Appetite/physiology ; Enteroendocrine Cells/metabolism ; Feeding Behavior ; Hypothalamus/metabolism ; },
abstract = {Previous clinical trials have shown that time-restricted feeding can be involved in regulating the metabolic health of humans and animals. However, the underlying mechanism has not been fully explored. In this study, the pig model was employed to simulate four prevalent human eating habits, with the aim of investigating the impact of gut microbiota and microbial metabolites on gut hormone secretion and appetite regulation. Compared to the ad libitum feeding (ALF) pattern, three time-restricted feeding patterns reduced total food intake and eating time. Meanwhile, three time-restricted feeding patterns induced elevated levels of serum and hypothalamic glucagon-like peptide-1 (GLP-1), while suppressing reward-related circuits in the hypothalamus. It is noteworthy that the early time-restricted feeding (eTRF) pattern increased the number of intestinal enteroendocrine cells (EECs) compared to ALF. Metagenomic and metabonomic analyses revealed that three time-restricted feeding patterns induced colonization of Lactobacillus and significantly increased the levels of its metabolite, indole-3-lactic acid (ILA). Dietary supplementation with ILA exhibited an increasing trend in fasting serum GLP-1 level of piglets. In vitro studies with pig intestinal organoids showed the Lactobacillus metabolite ILA enhanced GLP-1 secretion through the promotion of intestinal stem cell differentiation into EECs, rather than activating the ability of EECs to secrete GLP-1. Overall, time-restricted feeding promoted GLP-1 secretion and affected long-term appetite regulation by promoting the colonization of Lactobacillus and modulating microbial tryptophan metabolism.},
}
MeSH Terms:
show MeSH Terms
hide MeSH Terms
Animals
*Glucagon-Like Peptide 1/metabolism/blood
*Gastrointestinal Microbiome
Swine
*Tryptophan/metabolism
*Lactobacillus/metabolism
*Appetite/physiology
Enteroendocrine Cells/metabolism
Feeding Behavior
Hypothalamus/metabolism
RevDate: 2025-02-14
Short-term antiretroviral therapy may not correct the dysregulations of plasma virome and cytokines induced by HIV-1 infection.
Virulence [Epub ahead of print].
An expansion of plasma anelloviruses and dysregulation of inflammation was associated with HIV-1 infection. However, how antiretroviral therapy (ART) affects the dynamics of plasma virome and cytokine profile remains largely unknown. To characterize the dynamics of plasma virome and cytokines in HIV-1-infected individuals before and during the first year of ART, a cohort of 26 HIV-1-infected individuals and 19 healthy controls was recruited. Blood samples were collected and subjected to metagenomic analysis and the measurement of 27 cytokines. Metagenomic analysis revealed an increased abundance and prevalence of human pegivirus type 1 (HPgV-1) and a slightly decreased diversity and abundance of anellovirus in plasma of HIV-1-infected individuals after ART. No obvious impact was observed on other plasma commensal viruses. Increased abundance and prevalence of HPgV-1 were further confirmed by RT-qPCR assay in a larger cohort of 114 HIV-1-infected individuals. Notably, most dysregulated cytokines were not fully restored by ART, with extremely abnormal levels of IL-10, GM-CSF, VEGF, and eotaxin, and a significantly increased level of plasma I-FABP. Anelloviruses showed significantly negative correlations with other commensal viruses except HPgV-1, but had positive corrections with several anti-inflammatory and Th1 cytokines. These results suggest that short-term ART may not significantly correct the virome and cytokine dysregulations induced by HIV-1 infection. The results highlight a need for further investigation into the long-term effect of ART on virome and cytokine profile in HIV-1-infected individuals.
Additional Links: PMID-39950859
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PubMed:
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@article {pmid39950859,
year = {2025},
author = {Ma, Y and Zhang, M and Wang, Z and Cao, L and Li, Y and Wan, Z and Kane, Y and Wang, G and Li, X and Zhang, C},
title = {Short-term antiretroviral therapy may not correct the dysregulations of plasma virome and cytokines induced by HIV-1 infection.},
journal = {Virulence},
volume = {},
number = {},
pages = {2467168},
doi = {10.1080/21505594.2025.2467168},
pmid = {39950859},
issn = {2150-5608},
abstract = {An expansion of plasma anelloviruses and dysregulation of inflammation was associated with HIV-1 infection. However, how antiretroviral therapy (ART) affects the dynamics of plasma virome and cytokine profile remains largely unknown. To characterize the dynamics of plasma virome and cytokines in HIV-1-infected individuals before and during the first year of ART, a cohort of 26 HIV-1-infected individuals and 19 healthy controls was recruited. Blood samples were collected and subjected to metagenomic analysis and the measurement of 27 cytokines. Metagenomic analysis revealed an increased abundance and prevalence of human pegivirus type 1 (HPgV-1) and a slightly decreased diversity and abundance of anellovirus in plasma of HIV-1-infected individuals after ART. No obvious impact was observed on other plasma commensal viruses. Increased abundance and prevalence of HPgV-1 were further confirmed by RT-qPCR assay in a larger cohort of 114 HIV-1-infected individuals. Notably, most dysregulated cytokines were not fully restored by ART, with extremely abnormal levels of IL-10, GM-CSF, VEGF, and eotaxin, and a significantly increased level of plasma I-FABP. Anelloviruses showed significantly negative correlations with other commensal viruses except HPgV-1, but had positive corrections with several anti-inflammatory and Th1 cytokines. These results suggest that short-term ART may not significantly correct the virome and cytokine dysregulations induced by HIV-1 infection. The results highlight a need for further investigation into the long-term effect of ART on virome and cytokine profile in HIV-1-infected individuals.},
}
RevDate: 2025-02-14
CmpDate: 2025-02-14
Gut Microbiota Predicts Treatment Response to Empagliflozin Among MASLD Patients Without Diabetes Mellitus.
Liver international : official journal of the International Association for the Study of the Liver, 45(3):e70023.
BACKGROUND AND AIM: We aimed to investigate whether gut microbiota could predict the treatment response to pharmacological agents among metabolic dysfunction-associated steatotic liver disease (MASLD) patients without diabetes mellitus (DM), as data are lacking.
METHODS: We prospectively followed up non-diabetic MASLD patients who used empagliflozin. Clinical, anthropometric, laboratory assessments and magnetic resonance imaging-proton density fat fraction (MRI-PDFF) were performed from baseline to week 52 (EOT). Baseline stool samples were collected, and shotgun DNA metagenomic sequencing was performed to profile microbiome. The primary outcome was treatment response to empagliflozin at EOT, defined as MRI-PDFF decline ≥ 30% at EOT from baseline. Linear discriminant analysis [LDA] effect size was used to identify putative bacterial species. Multivariable logistic regression was used to derive adjusted odds ratio (aOR) of outcome with bacterial species by adjusting for clinical factors.
RESULTS: Twenty-two (48.9%) of 45 patients (median age: 56.9 years [IQR: 51.0-63.2]; male: 23 [51.1%]) achieved treatment response at EOT. There was difference in alpha diversity (Shannon index: p < 0.001; Simpson index: p = 0.001) and beta diversity (p = 0.048) in baseline microbiome between treatment response and non-response groups. Faecalibacterium prausnitzii (log10LDAscore = 4.27), Lachnospira pectinoschiza (log10LDAscore = 3.99), Anaerostipes hadrus (log10LDAscore = 3.98), Roseburia faecis (log10LDAscore = 3.97), Roseburia inulinivorans (log10LDAscore = 3.58) and Agathobaculum butyriciproducens (log10LDAscore = 2.77) were enriched in the treatment response group. L. pectinoschiza (aOR: 34.1; p = 0.015), A. hadrus (aOR:35.0; p = 0.032) and A. butyriciproducens (aOR:22.3; p = 0.023) independently predicted treatment response but not clinical factors. These three species collectively predicted treatment response with AUROC of 0.89 (95% CI: 0.80-0.99).
CONCLUSIONS: Certain gut bacterial species, particularly the combination of A. hadrus, L. pectinoschiza and A. butyriciproducens, may predict treatment response to empagliflozin in MAFLD patients without DM.
Additional Links: PMID-39950834
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@article {pmid39950834,
year = {2025},
author = {Ng, HY and Zhang, L and Tan, JT and Hui, RWH and Yuen, MF and Seto, WK and Leung, WK and Cheung, KS},
title = {Gut Microbiota Predicts Treatment Response to Empagliflozin Among MASLD Patients Without Diabetes Mellitus.},
journal = {Liver international : official journal of the International Association for the Study of the Liver},
volume = {45},
number = {3},
pages = {e70023},
doi = {10.1111/liv.70023},
pmid = {39950834},
issn = {1478-3231},
support = {//General Research Fund, Research Grant Council, The Government of the Hong Kong Special Administrative Region/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; Male ; Female ; *Glucosides/therapeutic use ; Middle Aged ; Prospective Studies ; *Benzhydryl Compounds/therapeutic use ; Non-alcoholic Fatty Liver Disease/drug therapy/microbiology ; Treatment Outcome ; Magnetic Resonance Imaging ; Feces/microbiology ; Sodium-Glucose Transporter 2 Inhibitors/therapeutic use ; Logistic Models ; },
abstract = {BACKGROUND AND AIM: We aimed to investigate whether gut microbiota could predict the treatment response to pharmacological agents among metabolic dysfunction-associated steatotic liver disease (MASLD) patients without diabetes mellitus (DM), as data are lacking.
METHODS: We prospectively followed up non-diabetic MASLD patients who used empagliflozin. Clinical, anthropometric, laboratory assessments and magnetic resonance imaging-proton density fat fraction (MRI-PDFF) were performed from baseline to week 52 (EOT). Baseline stool samples were collected, and shotgun DNA metagenomic sequencing was performed to profile microbiome. The primary outcome was treatment response to empagliflozin at EOT, defined as MRI-PDFF decline ≥ 30% at EOT from baseline. Linear discriminant analysis [LDA] effect size was used to identify putative bacterial species. Multivariable logistic regression was used to derive adjusted odds ratio (aOR) of outcome with bacterial species by adjusting for clinical factors.
RESULTS: Twenty-two (48.9%) of 45 patients (median age: 56.9 years [IQR: 51.0-63.2]; male: 23 [51.1%]) achieved treatment response at EOT. There was difference in alpha diversity (Shannon index: p < 0.001; Simpson index: p = 0.001) and beta diversity (p = 0.048) in baseline microbiome between treatment response and non-response groups. Faecalibacterium prausnitzii (log10LDAscore = 4.27), Lachnospira pectinoschiza (log10LDAscore = 3.99), Anaerostipes hadrus (log10LDAscore = 3.98), Roseburia faecis (log10LDAscore = 3.97), Roseburia inulinivorans (log10LDAscore = 3.58) and Agathobaculum butyriciproducens (log10LDAscore = 2.77) were enriched in the treatment response group. L. pectinoschiza (aOR: 34.1; p = 0.015), A. hadrus (aOR:35.0; p = 0.032) and A. butyriciproducens (aOR:22.3; p = 0.023) independently predicted treatment response but not clinical factors. These three species collectively predicted treatment response with AUROC of 0.89 (95% CI: 0.80-0.99).
CONCLUSIONS: Certain gut bacterial species, particularly the combination of A. hadrus, L. pectinoschiza and A. butyriciproducens, may predict treatment response to empagliflozin in MAFLD patients without DM.},
}
MeSH Terms:
show MeSH Terms
hide MeSH Terms
Humans
*Gastrointestinal Microbiome/drug effects
Male
Female
*Glucosides/therapeutic use
Middle Aged
Prospective Studies
*Benzhydryl Compounds/therapeutic use
Non-alcoholic Fatty Liver Disease/drug therapy/microbiology
Treatment Outcome
Magnetic Resonance Imaging
Feces/microbiology
Sodium-Glucose Transporter 2 Inhibitors/therapeutic use
Logistic Models
RevDate: 2025-02-14
Diversity and abundance of filamentous and non-filamentous "Leptothrix" in global wastewater treatment plants.
Applied and environmental microbiology [Epub ahead of print].
Species belonging to the genus Leptothrix are widely distributed in the environment and in activated sludge (AS) wastewater treatment plants (WWTPs). They are commonly found in iron-rich environments and reported to cause filamentous bulking in WWTPs. In this study, the diversity, distribution, and metabolic potential of the most prevalent Leptothrix spp. found in AS worldwide were studied. Our 16S rRNA amplicon survey showed that Leptothrix belongs to the general core community of AS worldwide, comprising 32 species with four species being most commonly found. Their taxonomic classification was re-evaluated based on both 16S rRNA gene and genome-based phylogenetic analysis showing that three of the most abundant "Leptothrix" species represented species in three other genera, Rubrivivax, Ideonella, and the novel genus, Ca. Intricatilinea. New fluorescence in situ hybridization (FISH) probes revealed rod-shaped morphology for the novel Ca. Rubrivivax defluviihabitans and Ca. Ideonella esbjergensis, while filamentous morphology was found only for Ca. Intricatilinea gracilis. Analysis of high-quality metagenome-assembled genomes revealed metabolic potential for aerobic growth, fermentation, storage of intracellular polymers, partial denitrification, photosynthesis, and iron reduction. FISH in combination with Raman microspectroscopy confirmed the in situ presence of chlorophyll and carotenoids in Ca. Rubrivivax defluviihabitans and Ca. Intricatilinea gracilis. This study resolves the taxonomy of abundant but poorly classified "Leptothrix" species, providing important insights into their diversity, morphology, and function in global AS wastewater treatment systems.IMPORTANCEThe genus Leptothrix has been extensively studied and described since the 1880s, with six species currently described but with the majority uncultured and undescribed. Some species are assumed to have a filamentous morphology and can cause settling problems in wastewater treatment plants (WWTPs). Here, we revised the classification of the most abundant Leptothrix spp. present in WWTPs across the world, showing that most belong to other genera, such as Rubrivivax and Ideonella. Furthermore, most do not have a filamentous morphology and are not problematic in WWTPs as previously believed. Metabolic reconstruction, including some traits validated in situ by the application of new fluorescence in situ hybridization probes and Raman microspectroscopy, provided additional insights into their metabolism. The study has contributed to a better understanding of the diversity, morphology, and function of "Leptothrix," which belong to the abundant core community across global activated sludge WWTPs.
Additional Links: PMID-39950813
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PubMed:
Citation:
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@article {pmid39950813,
year = {2025},
author = {Seguel Suazo, K and Nierychlo, M and Kondrotaite, Z and Petriglieri, F and Peces, M and Singleton, C and Dries, J and Nielsen, PH},
title = {Diversity and abundance of filamentous and non-filamentous "Leptothrix" in global wastewater treatment plants.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0148524},
doi = {10.1128/aem.01485-24},
pmid = {39950813},
issn = {1098-5336},
abstract = {Species belonging to the genus Leptothrix are widely distributed in the environment and in activated sludge (AS) wastewater treatment plants (WWTPs). They are commonly found in iron-rich environments and reported to cause filamentous bulking in WWTPs. In this study, the diversity, distribution, and metabolic potential of the most prevalent Leptothrix spp. found in AS worldwide were studied. Our 16S rRNA amplicon survey showed that Leptothrix belongs to the general core community of AS worldwide, comprising 32 species with four species being most commonly found. Their taxonomic classification was re-evaluated based on both 16S rRNA gene and genome-based phylogenetic analysis showing that three of the most abundant "Leptothrix" species represented species in three other genera, Rubrivivax, Ideonella, and the novel genus, Ca. Intricatilinea. New fluorescence in situ hybridization (FISH) probes revealed rod-shaped morphology for the novel Ca. Rubrivivax defluviihabitans and Ca. Ideonella esbjergensis, while filamentous morphology was found only for Ca. Intricatilinea gracilis. Analysis of high-quality metagenome-assembled genomes revealed metabolic potential for aerobic growth, fermentation, storage of intracellular polymers, partial denitrification, photosynthesis, and iron reduction. FISH in combination with Raman microspectroscopy confirmed the in situ presence of chlorophyll and carotenoids in Ca. Rubrivivax defluviihabitans and Ca. Intricatilinea gracilis. This study resolves the taxonomy of abundant but poorly classified "Leptothrix" species, providing important insights into their diversity, morphology, and function in global AS wastewater treatment systems.IMPORTANCEThe genus Leptothrix has been extensively studied and described since the 1880s, with six species currently described but with the majority uncultured and undescribed. Some species are assumed to have a filamentous morphology and can cause settling problems in wastewater treatment plants (WWTPs). Here, we revised the classification of the most abundant Leptothrix spp. present in WWTPs across the world, showing that most belong to other genera, such as Rubrivivax and Ideonella. Furthermore, most do not have a filamentous morphology and are not problematic in WWTPs as previously believed. Metabolic reconstruction, including some traits validated in situ by the application of new fluorescence in situ hybridization probes and Raman microspectroscopy, provided additional insights into their metabolism. The study has contributed to a better understanding of the diversity, morphology, and function of "Leptothrix," which belong to the abundant core community across global activated sludge WWTPs.},
}
RevDate: 2025-02-14
Prospective comparison of the digestive tract resistome and microbiota in cattle raised in grass-fed versus grain-fed production systems.
mSphere [Epub ahead of print].
Most antimicrobials sold in the United States are used in food animals. Farm management practices contribute to antibacterial resistance (AR). Controversially, grass-fed diets have been recommended over grain-fed diets to reduce AR in beef cattle. Ionophore feed additives (non-therapeutic antibiotics that enhance feed efficiency) may contribute to AR development. We used shotgun metagenomic sequencing of fecal swabs to prospectively compare the cattle gastrointestinal resistome and microbiota in two different production systems over five periods from pre-weaning to pre-harvest. Cattle were grass-fed and pasture-raised (system A, n = 33) or grain-fed with ionophore additives in feedlots (system B, n = 34). System A cattle averaged 639 lb and 22.8 months of age, and system B cattle averaged 1,173 lb and 12.4 months of age preharvest. In total, 367 antibiotic resistance genes (ARGs) and 329 bacterial species were identified. The resistome of system A cattle had higher alpha diversity than system B cattle over their lifespan (P = 0.008). Beta-diversity estimates indicated overlap in the pre-weaning resistome and microbiota in both systems, which diverged post-weaning, with increases in several medically important ARGs when system B cattle transitioned to a grain diet. Analysis of compositions of microbiomes with bias correction indicated that levels of tetracycline, macrolide, aminoglycoside, beta-lactam, and bacitracin ARGs were significantly higher in system B cattle pre-harvest. Resistome changes were highly correlated with bacterial community changes (Procrustes, M[2] = 0.958; P = 0.001). Potentially modifiable farm management strategies, including diet and ionophores, may influence abundance and diversity of ARGs in fecal samples from cattle.IMPORTANCEAntibiotic resistance is a One Health threat. More antibiotics are used in agriculture than in human medicine. We compared the relative abundance of antibiotic resistance genes (ARGs) and bacterial species in cattle raised in two different cattle production systems (grass- and grain-fed). Fecal swab samples were collected at five time points spanning pre-weaning and prior to harvest. The antibiotic resistance gene and bacterial communities were relatively similar in the pre-weaning period when cattle in both systems were milking and on pasture. Resistance genes and bacterial communities diverged post-weaning when system B cattle were given a grain diet with feed additives for growth promotion containing non-medically important antibiotics (i.e., ionophores). The levels of medically important ARGs (e.g., macrolides) increased in system B grain-fed cattle post-weaning and were higher than in system A just prior to slaughter. These data provide additional evidence that farm management strategies impact the level of antibiotic resistance.
Additional Links: PMID-39950811
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PubMed:
Citation:
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@article {pmid39950811,
year = {2025},
author = {Kwon, J and Tanner, W and Kong, Y and Wade, M and Bitler, C and Chiavegato, MB and Pettigrew, MM},
title = {Prospective comparison of the digestive tract resistome and microbiota in cattle raised in grass-fed versus grain-fed production systems.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0073824},
doi = {10.1128/msphere.00738-24},
pmid = {39950811},
issn = {2379-5042},
abstract = {Most antimicrobials sold in the United States are used in food animals. Farm management practices contribute to antibacterial resistance (AR). Controversially, grass-fed diets have been recommended over grain-fed diets to reduce AR in beef cattle. Ionophore feed additives (non-therapeutic antibiotics that enhance feed efficiency) may contribute to AR development. We used shotgun metagenomic sequencing of fecal swabs to prospectively compare the cattle gastrointestinal resistome and microbiota in two different production systems over five periods from pre-weaning to pre-harvest. Cattle were grass-fed and pasture-raised (system A, n = 33) or grain-fed with ionophore additives in feedlots (system B, n = 34). System A cattle averaged 639 lb and 22.8 months of age, and system B cattle averaged 1,173 lb and 12.4 months of age preharvest. In total, 367 antibiotic resistance genes (ARGs) and 329 bacterial species were identified. The resistome of system A cattle had higher alpha diversity than system B cattle over their lifespan (P = 0.008). Beta-diversity estimates indicated overlap in the pre-weaning resistome and microbiota in both systems, which diverged post-weaning, with increases in several medically important ARGs when system B cattle transitioned to a grain diet. Analysis of compositions of microbiomes with bias correction indicated that levels of tetracycline, macrolide, aminoglycoside, beta-lactam, and bacitracin ARGs were significantly higher in system B cattle pre-harvest. Resistome changes were highly correlated with bacterial community changes (Procrustes, M[2] = 0.958; P = 0.001). Potentially modifiable farm management strategies, including diet and ionophores, may influence abundance and diversity of ARGs in fecal samples from cattle.IMPORTANCEAntibiotic resistance is a One Health threat. More antibiotics are used in agriculture than in human medicine. We compared the relative abundance of antibiotic resistance genes (ARGs) and bacterial species in cattle raised in two different cattle production systems (grass- and grain-fed). Fecal swab samples were collected at five time points spanning pre-weaning and prior to harvest. The antibiotic resistance gene and bacterial communities were relatively similar in the pre-weaning period when cattle in both systems were milking and on pasture. Resistance genes and bacterial communities diverged post-weaning when system B cattle were given a grain diet with feed additives for growth promotion containing non-medically important antibiotics (i.e., ionophores). The levels of medically important ARGs (e.g., macrolides) increased in system B grain-fed cattle post-weaning and were higher than in system A just prior to slaughter. These data provide additional evidence that farm management strategies impact the level of antibiotic resistance.},
}
RevDate: 2025-02-14
CmpDate: 2025-02-14
Investigation of Tilapia (Oreochromis niloticus) Mortality Events Targeting Tilapia Lake Virus Disease (TiLVD) in Bangladesh.
Veterinary medicine and science, 11(2):e70262.
BACKGROUND: Tilapia lake virus (TiLV) is an emerging threat to the global tilapia industry. In early 2017, FAO declared that Bangladesh was in a high-risk zone of TiLV disease (TiLVD) spread.
OBJECTIVES: Considering the current scenario, the present work was designed to investigate the occurrence of TiLV in cultured Nile tilapia (Oreochromis niloticus) causing TiLVD in Bangladesh.
METHODS: In this study, several unusual tilapia mortality incidences were investigated. A total of 102 pooled organ samples of 102 tilapia fish were collected from 34 ponds of 25 farms in the regions of 12 Upazilas in Bangladesh from May to October 2019. As a part of the classical approach, histopathological analysis was performed. For molecular identification, both conventional and real-time PCR were used as diagnostic tools to identify TiLV in farm-raised Nile tilapia.
RESULTS: A total of 12 representative organ samples did not show any pathognomonic lesions related to TiLV infection in histopathological analysis. Conventional and real-time PCR assays yielded negative results for TiLV.
CONCLUSIONS: In our investigation, no trace of TiLV was detected in the studied samples. A large-scale study involving a broader range of samples collected across Bangladesh, along with the application of a viral metagenomics approach, could provide valuable insights into the unusual mortalities of tilapia in the country.
Additional Links: PMID-39950541
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PubMed:
Citation:
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@article {pmid39950541,
year = {2025},
author = {Akter, MS and Punom, NJ and Eshik, MME and Ahmmed, S and Rabbane, MG and Rahman, MS},
title = {Investigation of Tilapia (Oreochromis niloticus) Mortality Events Targeting Tilapia Lake Virus Disease (TiLVD) in Bangladesh.},
journal = {Veterinary medicine and science},
volume = {11},
number = {2},
pages = {e70262},
doi = {10.1002/vms3.70262},
pmid = {39950541},
issn = {2053-1095},
support = {//Grant for Advanced Research in Education (GARE)/ ; //Ministry of Education/ ; 37.20.0000.004.033.020.2016.673//Government of the People's Republic of Bangladesh/ ; },
mesh = {Animals ; Bangladesh/epidemiology ; *Fish Diseases/virology/mortality/epidemiology ; *Cichlids ; DNA Virus Infections/veterinary/virology/mortality/epidemiology ; Aquaculture ; },
abstract = {BACKGROUND: Tilapia lake virus (TiLV) is an emerging threat to the global tilapia industry. In early 2017, FAO declared that Bangladesh was in a high-risk zone of TiLV disease (TiLVD) spread.
OBJECTIVES: Considering the current scenario, the present work was designed to investigate the occurrence of TiLV in cultured Nile tilapia (Oreochromis niloticus) causing TiLVD in Bangladesh.
METHODS: In this study, several unusual tilapia mortality incidences were investigated. A total of 102 pooled organ samples of 102 tilapia fish were collected from 34 ponds of 25 farms in the regions of 12 Upazilas in Bangladesh from May to October 2019. As a part of the classical approach, histopathological analysis was performed. For molecular identification, both conventional and real-time PCR were used as diagnostic tools to identify TiLV in farm-raised Nile tilapia.
RESULTS: A total of 12 representative organ samples did not show any pathognomonic lesions related to TiLV infection in histopathological analysis. Conventional and real-time PCR assays yielded negative results for TiLV.
CONCLUSIONS: In our investigation, no trace of TiLV was detected in the studied samples. A large-scale study involving a broader range of samples collected across Bangladesh, along with the application of a viral metagenomics approach, could provide valuable insights into the unusual mortalities of tilapia in the country.},
}
MeSH Terms:
show MeSH Terms
hide MeSH Terms
Animals
Bangladesh/epidemiology
*Fish Diseases/virology/mortality/epidemiology
*Cichlids
DNA Virus Infections/veterinary/virology/mortality/epidemiology
Aquaculture
RevDate: 2025-02-14
CmpDate: 2025-02-14
Retrospective analysis of 300 microbial cell-free DNA sequencing results in routine blood stream infection diagnostics.
Frontiers in cellular and infection microbiology, 15:1504262.
INTRODUCTION: Bloodstream infections are a critical challenge worldwide due to the slow turnaround time of conventional microbiological tests for detecting bacteremia in septic patients. Noscendo GmbH (Duisburg, Germany) has developed the CE/IVD pipeline DISQVER for clinical metagenomics testing based on cell-free DNA (cfDNA) from blood samples to address this issue.
METHODS: We conducted a retrospective study to evaluate the diagnostic utility of this methodological setup in improving treatment decisions since it was introduced into our clinical setting. Between January 2021 and June 2022, the first 300 cases in which DISQVER was applied at our university hospital were collected and analyzed. The results were compared with routine microbiology test results, clinical picture, associated treatment decisions, and clinical course.
RESULTS: Our findings demonstrate that DISQVER results where no pathogen was reported effectively ruled out bacterial bloodstream infections, whereas positive results varied in their usefulness. While the metagenomic approach proved highly valuable for detecting non-culturable and rare pathogens, its utility was limited in cases where detected microorganisms were commonly associated with the microbiota.
DISCUSSION: Performing on-site analysis might mitigate delays resulting from logistical challenges and might help optimizing antibiotic stewardship. Once prompt results can be obtained, the relevance of incorporating molecular resistograms will become more pronounced. Further, the specific patient subgroups that most benefit from this analysis must be worked out. Guiding clinicians in identifying the infection focus based on the detected bacteria would significantly improve patient care. Lastly, evidence of filamentous fungi must be diligently followed up.
Additional Links: PMID-39949721
PubMed:
Citation:
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@article {pmid39949721,
year = {2025},
author = {Neidhöfer, C and Klein, N and Yürüktümen, A and Hattenhauer, T and Mispelbaum, R and Bode, C and Holderried, TAW and Hoerauf, A and Parčina, M},
title = {Retrospective analysis of 300 microbial cell-free DNA sequencing results in routine blood stream infection diagnostics.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1504262},
pmid = {39949721},
issn = {2235-2988},
mesh = {Humans ; Retrospective Studies ; *Bacteremia/diagnosis/microbiology ; Male ; Female ; *Cell-Free Nucleic Acids/blood ; *Metagenomics/methods ; Middle Aged ; Aged ; Adult ; Bacteria/genetics/isolation & purification/classification ; Aged, 80 and over ; Sequence Analysis, DNA ; Young Adult ; DNA, Bacterial/genetics ; },
abstract = {INTRODUCTION: Bloodstream infections are a critical challenge worldwide due to the slow turnaround time of conventional microbiological tests for detecting bacteremia in septic patients. Noscendo GmbH (Duisburg, Germany) has developed the CE/IVD pipeline DISQVER for clinical metagenomics testing based on cell-free DNA (cfDNA) from blood samples to address this issue.
METHODS: We conducted a retrospective study to evaluate the diagnostic utility of this methodological setup in improving treatment decisions since it was introduced into our clinical setting. Between January 2021 and June 2022, the first 300 cases in which DISQVER was applied at our university hospital were collected and analyzed. The results were compared with routine microbiology test results, clinical picture, associated treatment decisions, and clinical course.
RESULTS: Our findings demonstrate that DISQVER results where no pathogen was reported effectively ruled out bacterial bloodstream infections, whereas positive results varied in their usefulness. While the metagenomic approach proved highly valuable for detecting non-culturable and rare pathogens, its utility was limited in cases where detected microorganisms were commonly associated with the microbiota.
DISCUSSION: Performing on-site analysis might mitigate delays resulting from logistical challenges and might help optimizing antibiotic stewardship. Once prompt results can be obtained, the relevance of incorporating molecular resistograms will become more pronounced. Further, the specific patient subgroups that most benefit from this analysis must be worked out. Guiding clinicians in identifying the infection focus based on the detected bacteria would significantly improve patient care. Lastly, evidence of filamentous fungi must be diligently followed up.},
}
MeSH Terms:
show MeSH Terms
hide MeSH Terms
Humans
Retrospective Studies
*Bacteremia/diagnosis/microbiology
Male
Female
*Cell-Free Nucleic Acids/blood
*Metagenomics/methods
Middle Aged
Aged
Adult
Bacteria/genetics/isolation & purification/classification
Aged, 80 and over
Sequence Analysis, DNA
Young Adult
DNA, Bacterial/genetics
RevDate: 2025-02-14
CmpDate: 2025-02-14
Insects as Natural Hosts, Vectors and Reservoirs of Botulinum Neurotoxin-Producing Clostridia and Their Non-Toxinogenic Counterparts: Preliminary Evidence.
Environmental microbiology, 27(2):e70053.
Insects play a significant role in the transmission and spread of bacterial pathogens that cause various diseases in humans and animals. The relationship among insects, bacterial pathogens and diseases is complex and depends on the specificity of the pathogens. Some clostridial species produce botulinum neurotoxin (BoNT), which is responsible for paralytic botulism. However, the ecology of these bacterial species and their non-toxinogenic phylogenetic counterparts remains unclear. This study specifically explored in silico evidence of the interconnection between BoNT-producing Clostridia and their non-toxinogenic counterparts with insects. Based on literature meta-analysis, the mining of 16S rRNA amplicon and metagenomic sequencing datasets and a pilot feeding experiment in the Glanville fritillary butterfly, Melitaea cinxia, we propose that BoNT-producing Clostridia and their non-toxinogenic phylogenetic counterparts are carried internally and/or externally in different insect orders. While previous case studies have indicated associations between Clostridia and insects, this work provides a more comprehensive view of their occurrence. It also highlights the need for further multidisciplinary investigations to characterise the natural ecology of BoNT-producing Clostridia and their non-toxinogenic counterparts in insects.
Additional Links: PMID-39948721
Publisher:
PubMed:
Citation:
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@article {pmid39948721,
year = {2025},
author = {Douillard, FP and Lanzoni, O and Duplouy, A and Lindström, M},
title = {Insects as Natural Hosts, Vectors and Reservoirs of Botulinum Neurotoxin-Producing Clostridia and Their Non-Toxinogenic Counterparts: Preliminary Evidence.},
journal = {Environmental microbiology},
volume = {27},
number = {2},
pages = {e70053},
doi = {10.1111/1462-2920.70053},
pmid = {39948721},
issn = {1462-2920},
support = {328944//Academy of Finland/ ; 340705//Academy of Finland/ ; 683099/ERC_/European Research Council/International ; },
mesh = {Animals ; *Phylogeny ; *Clostridium/genetics/metabolism/classification ; *Botulinum Toxins/genetics/metabolism ; *Botulism/microbiology ; RNA, Ribosomal, 16S/genetics ; Insecta/microbiology ; Insect Vectors/microbiology ; Butterflies/microbiology ; },
abstract = {Insects play a significant role in the transmission and spread of bacterial pathogens that cause various diseases in humans and animals. The relationship among insects, bacterial pathogens and diseases is complex and depends on the specificity of the pathogens. Some clostridial species produce botulinum neurotoxin (BoNT), which is responsible for paralytic botulism. However, the ecology of these bacterial species and their non-toxinogenic phylogenetic counterparts remains unclear. This study specifically explored in silico evidence of the interconnection between BoNT-producing Clostridia and their non-toxinogenic counterparts with insects. Based on literature meta-analysis, the mining of 16S rRNA amplicon and metagenomic sequencing datasets and a pilot feeding experiment in the Glanville fritillary butterfly, Melitaea cinxia, we propose that BoNT-producing Clostridia and their non-toxinogenic phylogenetic counterparts are carried internally and/or externally in different insect orders. While previous case studies have indicated associations between Clostridia and insects, this work provides a more comprehensive view of their occurrence. It also highlights the need for further multidisciplinary investigations to characterise the natural ecology of BoNT-producing Clostridia and their non-toxinogenic counterparts in insects.},
}
MeSH Terms:
show MeSH Terms
hide MeSH Terms
Animals
*Phylogeny
*Clostridium/genetics/metabolism/classification
*Botulinum Toxins/genetics/metabolism
*Botulism/microbiology
RNA, Ribosomal, 16S/genetics
Insecta/microbiology
Insect Vectors/microbiology
Butterflies/microbiology
RevDate: 2025-02-13
CmpDate: 2025-02-13
Structural and functional changes in the oral microbiome of patients with craniofacial microsomia.
Scientific reports, 15(1):5400.
Craniofacial microsomia (CFM) is the second most common congenital craniofacial deformity, presenting diverse clinical manifestations and treatments that may influence oral bacteria dysbiosis (OBD). However, research linking CFM to OBD is limited. Saliva samples were collected from 20 patients with CFM and 24 controls. We compared oral microflora and gene function using 16 S ribosomal RNA sequencing and metagenomics. We also evaluated the correlation between CFM clinical phenotypes and microbiota community structure. Patients with CFM demonstrated greater richness and evenness in their oral microflora. The dominant genera included several pathogenic species, such as Actinomyces, Fusobacterium, and Prevotella. Notably, the severity of CFM correlated positively with the abundance of Neisseria and Porphyromonas. Upregulated pathways were primarily linked to biotin and amino acid metabolism, such as Tryptophan metabolism and Lysine degradation, and further underscored the need for focused oral health interventions in this population. This study is the first to indicate that CFM patients exhibit unique oral bacterial dysbiosis, marked by a higher presence of opportunistic pathogens and increased pathways related to oral and systemic health. These findings highlight the importance of monitoring oral health in patients with CFM.
Additional Links: PMID-39948426
PubMed:
Citation:
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@article {pmid39948426,
year = {2025},
author = {Zang, T and Zhang, Z and Liu, W and Yin, L and Zhao, S and Liu, B and Ma, L and Li, Z and Tang, X},
title = {Structural and functional changes in the oral microbiome of patients with craniofacial microsomia.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {5400},
pmid = {39948426},
issn = {2045-2322},
support = {2021-I2M-1-068//Chinese Academy of Medical Science Innovation Fund for Medical Sciences/ ; },
mesh = {Humans ; Male ; *Microbiota ; Female ; *Mouth/microbiology ; *Saliva/microbiology/metabolism ; RNA, Ribosomal, 16S/genetics ; Child ; Goldenhar Syndrome/microbiology ; Dysbiosis/microbiology ; Adolescent ; Adult ; Bacteria/classification/genetics/isolation & purification/metabolism ; Young Adult ; Metagenomics/methods ; Child, Preschool ; Case-Control Studies ; },
abstract = {Craniofacial microsomia (CFM) is the second most common congenital craniofacial deformity, presenting diverse clinical manifestations and treatments that may influence oral bacteria dysbiosis (OBD). However, research linking CFM to OBD is limited. Saliva samples were collected from 20 patients with CFM and 24 controls. We compared oral microflora and gene function using 16 S ribosomal RNA sequencing and metagenomics. We also evaluated the correlation between CFM clinical phenotypes and microbiota community structure. Patients with CFM demonstrated greater richness and evenness in their oral microflora. The dominant genera included several pathogenic species, such as Actinomyces, Fusobacterium, and Prevotella. Notably, the severity of CFM correlated positively with the abundance of Neisseria and Porphyromonas. Upregulated pathways were primarily linked to biotin and amino acid metabolism, such as Tryptophan metabolism and Lysine degradation, and further underscored the need for focused oral health interventions in this population. This study is the first to indicate that CFM patients exhibit unique oral bacterial dysbiosis, marked by a higher presence of opportunistic pathogens and increased pathways related to oral and systemic health. These findings highlight the importance of monitoring oral health in patients with CFM.},
}
MeSH Terms:
show MeSH Terms
hide MeSH Terms
Humans
Male
*Microbiota
Female
*Mouth/microbiology
*Saliva/microbiology/metabolism
RNA, Ribosomal, 16S/genetics
Child
Goldenhar Syndrome/microbiology
Dysbiosis/microbiology
Adolescent
Adult
Bacteria/classification/genetics/isolation & purification/metabolism
Young Adult
Metagenomics/methods
Child, Preschool
Case-Control Studies
RevDate: 2025-02-13
CmpDate: 2025-02-13
Dose-dependent M2 macrophage polarization induced by Talaromyces marneffei promotes lung cancer cell growth via arginine-ornithine-cycle activation.
Medical microbiology and immunology, 214(1):11.
It is now widely accepted that lungs are colonized by diverse microbes. Dysbiosis of the lung microbiota has been found to affect the progression of lung cancer. Fungi are a major component of the lung microbiota. However, the causal links between the mycobiome or specific species and lung cancer remain unclear. To address this, we conducted a study examining the composition of lung mycobiota in Non-Small-Cell Lung Cancer (NSCLC) patients using shotgun metagenomics. The differential taxa between NSCLC patients and non-cancer controls were defined by the Wilcoxon rank-sum test. Nested PCR was used to measure the abundance of specific fungal species. Metabolomics analysis was performed to investigate the metabolic reprogramming of macrophages triggered by intracellular infection of specific fungal species. In vitro and in vivo assays were conducted to examine the effect of the specific fungus on cancer cell growth. Our findings showed that Ascomycota, Microsporidia and Mucoromycota were the dominant fungal taxa in the lungs. Talaromyces marneffei (T.marneffei) was the most significantly differential fungus between lung cancer patients and non-cancer controls, with its abundance positively correlated with lung cancer. The lung cancer animal model demonstrated that T.marneffei promotes lung cancer growth. Our study also demonstrated that T.marneffei promotes lung cancer cell growth by inducing dose-dependent M2 macrophage polarization through arginine-ornithine-cycle activation. Furthermore, inhibition of arginase can reduce M2 polarization of macrophages and the survival of T. marneffei inside macrophages. In summary, our study reveals that the increased abundance of T. marneffei in the lungs affects lung cancer cell growth by triggering arginine-induced M2 polarization of macrophages. These findings provide potential drug targets for the development of therapies aimed at targeting the survival of fungi inside macrophages in the fight against cancer.
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@article {pmid39948184,
year = {2025},
author = {Chen, A and Yu, Q and Zheng, L and Yi, J and Tang, Z and Ge, H and Ning, Y and Yin, N and Xie, Y and Chen, S and Shi, W and She, X and Xiang, J and Tang, J},
title = {Dose-dependent M2 macrophage polarization induced by Talaromyces marneffei promotes lung cancer cell growth via arginine-ornithine-cycle activation.},
journal = {Medical microbiology and immunology},
volume = {214},
number = {1},
pages = {11},
pmid = {39948184},
issn = {1432-1831},
support = {81972198, 81773147//National Natural Science Foundation of China/ ; 2019SK2253//Key Research and Development Program of Hunan Province of China/ ; ZLXD2017004//Central South University/ ; ZLXD2017004//Central South University/ ; kq2208299//National Natural Science Foundation of Changsha/ ; },
mesh = {*Talaromyces ; Humans ; Animals ; *Macrophages/microbiology/immunology ; *Lung Neoplasms/microbiology ; Mice ; *Arginine/metabolism ; *Ornithine/metabolism/analogs & derivatives/pharmacology ; Carcinoma, Non-Small-Cell Lung/microbiology/pathology ; Cell Proliferation ; Macrophage Activation ; Female ; Male ; Metagenomics ; Disease Models, Animal ; Cell Line, Tumor ; Mycobiome ; Lung/microbiology/pathology ; },
abstract = {It is now widely accepted that lungs are colonized by diverse microbes. Dysbiosis of the lung microbiota has been found to affect the progression of lung cancer. Fungi are a major component of the lung microbiota. However, the causal links between the mycobiome or specific species and lung cancer remain unclear. To address this, we conducted a study examining the composition of lung mycobiota in Non-Small-Cell Lung Cancer (NSCLC) patients using shotgun metagenomics. The differential taxa between NSCLC patients and non-cancer controls were defined by the Wilcoxon rank-sum test. Nested PCR was used to measure the abundance of specific fungal species. Metabolomics analysis was performed to investigate the metabolic reprogramming of macrophages triggered by intracellular infection of specific fungal species. In vitro and in vivo assays were conducted to examine the effect of the specific fungus on cancer cell growth. Our findings showed that Ascomycota, Microsporidia and Mucoromycota were the dominant fungal taxa in the lungs. Talaromyces marneffei (T.marneffei) was the most significantly differential fungus between lung cancer patients and non-cancer controls, with its abundance positively correlated with lung cancer. The lung cancer animal model demonstrated that T.marneffei promotes lung cancer growth. Our study also demonstrated that T.marneffei promotes lung cancer cell growth by inducing dose-dependent M2 macrophage polarization through arginine-ornithine-cycle activation. Furthermore, inhibition of arginase can reduce M2 polarization of macrophages and the survival of T. marneffei inside macrophages. In summary, our study reveals that the increased abundance of T. marneffei in the lungs affects lung cancer cell growth by triggering arginine-induced M2 polarization of macrophages. These findings provide potential drug targets for the development of therapies aimed at targeting the survival of fungi inside macrophages in the fight against cancer.},
}
MeSH Terms:
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*Talaromyces
Humans
Animals
*Macrophages/microbiology/immunology
*Lung Neoplasms/microbiology
Mice
*Arginine/metabolism
*Ornithine/metabolism/analogs & derivatives/pharmacology
Carcinoma, Non-Small-Cell Lung/microbiology/pathology
Cell Proliferation
Macrophage Activation
Female
Male
Metagenomics
Disease Models, Animal
Cell Line, Tumor
Mycobiome
Lung/microbiology/pathology
RevDate: 2025-02-13
CmpDate: 2025-02-13
Dominant Dolichospermum and microcystin production in Detroit Lake (Oregon, USA).
Harmful algae, 142:102802.
The excessive growth of harmful cyanobacteria, including Dolichospermum (formerly known as Anabaena), in freshwater bodies has become a pressing global concern. However, detailed information about the role of Dolichospermum in shaping bloom dynamics and producing cyanotoxins is limited. In this study, a bloom event dominated by Dolichospermum spp. at Detroit Lake (Oregon, USA) was examined from 2019 to 2021. In 2019, early summer cyanobacterial community succession reached up to 8.7 % of total phytoplankton abundance. Dolichospermum was the major microcystin (MC)-producing genus, with peak MC levels of 7.34 μg L[-1]. The presence of MCs was strongly correlated with the abundance of Dolichospermum (r = 0.84, p < 0.05) and MC synthetase gene, mcyE-Ana (r = 0.63, p < 0.05). Metabolic analyses further showed that the presence of nif/pst genes linked to nitrogen and phosphorus metabolism was dominated by Dolichospermum from the bloom onset until September. In addition, the abundance of Dolichospermum was significantly correlated with the abundance of nitrogen-fixing nif-Ana gene (r = 0.62, p < 0.05). As the lake experienced a longer N and P scarcity period (May to September), the N2-fixing Dolichospermum was able to dominate over other non-fixing cyanobacteria present, including Microcystis and Planktothrix. Overall, our results facilitate a better understanding of the organism and will help working toward managing/predicting future blooms.
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@article {pmid39947845,
year = {2025},
author = {Jeon, Y and Struewing, I and Clauson, K and Reetz, N and Fairchild, N and Goeres-Priest, L and Dreher, TW and Labiosa, R and Carpenter, KD and Rosen, BH and Villegas, EN and Lu, J},
title = {Dominant Dolichospermum and microcystin production in Detroit Lake (Oregon, USA).},
journal = {Harmful algae},
volume = {142},
number = {},
pages = {102802},
doi = {10.1016/j.hal.2025.102802},
pmid = {39947845},
issn = {1878-1470},
mesh = {*Lakes/microbiology/chemistry ; *Microcystins/metabolism ; Cyanobacteria/metabolism/genetics ; Harmful Algal Bloom ; },
abstract = {The excessive growth of harmful cyanobacteria, including Dolichospermum (formerly known as Anabaena), in freshwater bodies has become a pressing global concern. However, detailed information about the role of Dolichospermum in shaping bloom dynamics and producing cyanotoxins is limited. In this study, a bloom event dominated by Dolichospermum spp. at Detroit Lake (Oregon, USA) was examined from 2019 to 2021. In 2019, early summer cyanobacterial community succession reached up to 8.7 % of total phytoplankton abundance. Dolichospermum was the major microcystin (MC)-producing genus, with peak MC levels of 7.34 μg L[-1]. The presence of MCs was strongly correlated with the abundance of Dolichospermum (r = 0.84, p < 0.05) and MC synthetase gene, mcyE-Ana (r = 0.63, p < 0.05). Metabolic analyses further showed that the presence of nif/pst genes linked to nitrogen and phosphorus metabolism was dominated by Dolichospermum from the bloom onset until September. In addition, the abundance of Dolichospermum was significantly correlated with the abundance of nitrogen-fixing nif-Ana gene (r = 0.62, p < 0.05). As the lake experienced a longer N and P scarcity period (May to September), the N2-fixing Dolichospermum was able to dominate over other non-fixing cyanobacteria present, including Microcystis and Planktothrix. Overall, our results facilitate a better understanding of the organism and will help working toward managing/predicting future blooms.},
}
MeSH Terms:
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*Lakes/microbiology/chemistry
*Microcystins/metabolism
Cyanobacteria/metabolism/genetics
Harmful Algal Bloom
RevDate: 2025-02-13
Oral microbiota in colorectal cancer: Unraveling mechanisms and application potential.
Life sciences pii:S0024-3205(25)00095-5 [Epub ahead of print].
Colorectal cancer (CRC), with a rising prevalence, is the third most commonly diagnosed cancer and the third leading cause of cancer-related death. Studies have shown that a complex interplay between the development of CRC and alterations in the oral microbiome. Recent advancements in genomics and metagenomics have highlighted the significant roles of certain oral microbes, particularly Porphyromonas gingivalis (P. gingivalis) and Fusobacterium nucleatum (F. nucleatum), in the progression of CRC. However, the detailed mechanisms by which the oral microbiota influence CRC development remain unclear. This review aims to elucidate the role of oral microbiota in CRC progression, evaluate their potential as biomarkers, and explore therapeutic strategies targeting these microbes. This review offers insights into the mechanisms underlying the interaction between oral microbiota and CRC, underscoring the potential of oral microbes as diagnostic and prognostic biomarkers, as well as therapeutic targets. Future research should focus on clarifying the exact pathways and developing innovative therapeutic strategies to enhance the diagnosis and treatment.
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@article {pmid39947314,
year = {2025},
author = {Zhang, X and Chen, Y and Xia, Y and Lin, S and Zhou, X and Pang, X and Yu, J and Sun, L},
title = {Oral microbiota in colorectal cancer: Unraveling mechanisms and application potential.},
journal = {Life sciences},
volume = {},
number = {},
pages = {123462},
doi = {10.1016/j.lfs.2025.123462},
pmid = {39947314},
issn = {1879-0631},
abstract = {Colorectal cancer (CRC), with a rising prevalence, is the third most commonly diagnosed cancer and the third leading cause of cancer-related death. Studies have shown that a complex interplay between the development of CRC and alterations in the oral microbiome. Recent advancements in genomics and metagenomics have highlighted the significant roles of certain oral microbes, particularly Porphyromonas gingivalis (P. gingivalis) and Fusobacterium nucleatum (F. nucleatum), in the progression of CRC. However, the detailed mechanisms by which the oral microbiota influence CRC development remain unclear. This review aims to elucidate the role of oral microbiota in CRC progression, evaluate their potential as biomarkers, and explore therapeutic strategies targeting these microbes. This review offers insights into the mechanisms underlying the interaction between oral microbiota and CRC, underscoring the potential of oral microbes as diagnostic and prognostic biomarkers, as well as therapeutic targets. Future research should focus on clarifying the exact pathways and developing innovative therapeutic strategies to enhance the diagnosis and treatment.},
}
RevDate: 2025-02-13
CmpDate: 2025-02-13
Phylogenetic and Functional Diversity of Soluble Di-Iron Monooxygenases.
Environmental microbiology, 27(2):e70050.
Monooxygenase (MO) enzymes are responsible for the oxidation of hydrocarbons and other compounds in the carbon and nitrogen cycles, are important for the biodegradation of pollutants and can act as biocatalysts for chemical manufacture. The soluble di-iron monooxygenases (SDIMOs) are of interest due to their broad substrate range, high enantioselectivity and ability to oxidise inert substrates such as methane. Here, we re-examine the phylogeny and functions of these enzymes, using recent advances in the field and expansions in sequence diversity in databases to highlight relationships between SDIMOs and revisit their classification. We discuss the impact of horizontal gene transfer on SDIMO phylogeny, the potential of SDIMOs for the biodegradation of pollutants and the importance of heterologous expression as a tool for understanding SDIMO functions and enabling their use as biocatalysts. Our analysis highlights current knowledge gaps, most notably, the unknown substrate ranges and physiological roles of enzymes that have so far only been detected via genome or metagenome sequencing. Enhanced understanding of the diversity and functions of the SDIMO enzymes will enable better prediction and management of biogeochemical processes and also enable new applications of these enzymes for biocatalysis and bioremediation.
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@article {pmid39947201,
year = {2025},
author = {Yang, SNN and Kertesz, MA and Coleman, NV},
title = {Phylogenetic and Functional Diversity of Soluble Di-Iron Monooxygenases.},
journal = {Environmental microbiology},
volume = {27},
number = {2},
pages = {e70050},
doi = {10.1111/1462-2920.70050},
pmid = {39947201},
issn = {1462-2920},
support = {//University of Sydney/ ; },
mesh = {*Phylogeny ; *Mixed Function Oxygenases/genetics/metabolism/chemistry ; *Bacteria/enzymology/genetics/classification ; Biodegradation, Environmental ; Gene Transfer, Horizontal ; Substrate Specificity ; Oxidation-Reduction ; Oxygenases/genetics/metabolism ; Bacterial Proteins/genetics/metabolism/chemistry ; Iron/metabolism ; },
abstract = {Monooxygenase (MO) enzymes are responsible for the oxidation of hydrocarbons and other compounds in the carbon and nitrogen cycles, are important for the biodegradation of pollutants and can act as biocatalysts for chemical manufacture. The soluble di-iron monooxygenases (SDIMOs) are of interest due to their broad substrate range, high enantioselectivity and ability to oxidise inert substrates such as methane. Here, we re-examine the phylogeny and functions of these enzymes, using recent advances in the field and expansions in sequence diversity in databases to highlight relationships between SDIMOs and revisit their classification. We discuss the impact of horizontal gene transfer on SDIMO phylogeny, the potential of SDIMOs for the biodegradation of pollutants and the importance of heterologous expression as a tool for understanding SDIMO functions and enabling their use as biocatalysts. Our analysis highlights current knowledge gaps, most notably, the unknown substrate ranges and physiological roles of enzymes that have so far only been detected via genome or metagenome sequencing. Enhanced understanding of the diversity and functions of the SDIMO enzymes will enable better prediction and management of biogeochemical processes and also enable new applications of these enzymes for biocatalysis and bioremediation.},
}
MeSH Terms:
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hide MeSH Terms
*Phylogeny
*Mixed Function Oxygenases/genetics/metabolism/chemistry
*Bacteria/enzymology/genetics/classification
Biodegradation, Environmental
Gene Transfer, Horizontal
Substrate Specificity
Oxidation-Reduction
Oxygenases/genetics/metabolism
Bacterial Proteins/genetics/metabolism/chemistry
Iron/metabolism
RevDate: 2025-02-13
A genome-scale metabolic reconstruction resource of 247,092 diverse human microbes spanning multiple continents, age groups, and body sites.
Cell systems pii:S2405-4712(25)00029-8 [Epub ahead of print].
Genome-scale modeling of microbiome metabolism enables the simulation of diet-host-microbiome-disease interactions. However, current genome-scale reconstruction resources are limited in scope by computational challenges. We developed an optimized and highly parallelized reconstruction and analysis pipeline to build a resource of 247,092 microbial genome-scale metabolic reconstructions, deemed APOLLO. APOLLO spans 19 phyla, contains >60% of uncharacterized strains, and accounts for strains from 34 countries, all age groups, and multiple body sites. Using machine learning, we predicted with high accuracy the taxonomic assignment of strains based on the computed metabolic features. We then built 14,451 metagenomic sample-specific microbiome community models to systematically interrogate their community-level metabolic capabilities. We show that sample-specific metabolic pathways accurately stratify microbiomes by body site, age, and disease state. APOLLO is freely available, enables the systematic interrogation of the metabolic capabilities of largely still uncultured and unclassified species, and provides unprecedented opportunities for systems-level modeling of personalized host-microbiome co-metabolism.
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@article {pmid39947184,
year = {2025},
author = {Heinken, A and Hulshof, TO and Nap, B and Martinelli, F and Basile, A and O'Brolchain, A and O'Sullivan, NF and Gallagher, C and Magee, E and McDonagh, F and Lalor, I and Bergin, M and Evans, P and Daly, R and Farrell, R and Delaney, RM and Hill, S and McAuliffe, SR and Kilgannon, T and Fleming, RMT and Thinnes, CC and Thiele, I},
title = {A genome-scale metabolic reconstruction resource of 247,092 diverse human microbes spanning multiple continents, age groups, and body sites.},
journal = {Cell systems},
volume = {},
number = {},
pages = {101196},
doi = {10.1016/j.cels.2025.101196},
pmid = {39947184},
issn = {2405-4720},
abstract = {Genome-scale modeling of microbiome metabolism enables the simulation of diet-host-microbiome-disease interactions. However, current genome-scale reconstruction resources are limited in scope by computational challenges. We developed an optimized and highly parallelized reconstruction and analysis pipeline to build a resource of 247,092 microbial genome-scale metabolic reconstructions, deemed APOLLO. APOLLO spans 19 phyla, contains >60% of uncharacterized strains, and accounts for strains from 34 countries, all age groups, and multiple body sites. Using machine learning, we predicted with high accuracy the taxonomic assignment of strains based on the computed metabolic features. We then built 14,451 metagenomic sample-specific microbiome community models to systematically interrogate their community-level metabolic capabilities. We show that sample-specific metabolic pathways accurately stratify microbiomes by body site, age, and disease state. APOLLO is freely available, enables the systematic interrogation of the metabolic capabilities of largely still uncultured and unclassified species, and provides unprecedented opportunities for systems-level modeling of personalized host-microbiome co-metabolism.},
}
RevDate: 2025-02-13
CmpDate: 2025-02-13
A meta-analysis of the gut microbiome in inflammatory bowel disease patients identifies disease-associated small molecules.
Cell host & microbe, 33(2):218-234.e12.
Gut microbiome changes have been associated with several human diseases, but the molecular and functional details underlying these associations remain largely unknown. Here, we performed a meta-analysis of small molecule biosynthetic gene clusters (BGCs) in metagenomic samples of the gut microbiome from inflammatory bowel disease (IBD) patients and matched healthy subjects and identified two Clostridia-derived BGCs that are significantly associated with Crohn's disease (CD), a main IBD type. Using synthetic biology, we discovered and solved the structures of six fatty acid amides as the products of the CD-enriched BGCs, which we subsequently detected in fecal samples from IBD patients. Finally, we show that the discovered molecules disrupt gut permeability and exacerbate disease in chemically or genetically susceptible mouse models of colitis. These findings suggest that microbiome-derived small molecules may play a role in the etiology of IBD and represent a generalizable approach for discovering molecular mediators of disease-relevant microbiome-host interactions.
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@article {pmid39947133,
year = {2025},
author = {Elmassry, MM and Sugihara, K and Chankhamjon, P and Kim, Y and Camacho, FR and Wang, S and Sugimoto, Y and Chatterjee, S and Chen, LA and Kamada, N and Donia, MS},
title = {A meta-analysis of the gut microbiome in inflammatory bowel disease patients identifies disease-associated small molecules.},
journal = {Cell host & microbe},
volume = {33},
number = {2},
pages = {218-234.e12},
doi = {10.1016/j.chom.2025.01.002},
pmid = {39947133},
issn = {1934-6069},
mesh = {*Gastrointestinal Microbiome ; Humans ; Mice ; Animals ; *Inflammatory Bowel Diseases/microbiology ; Feces/microbiology ; Crohn Disease/microbiology ; Disease Models, Animal ; Multigene Family ; Colitis/microbiology ; Metagenomics ; Clostridium/genetics ; Mice, Inbred C57BL ; Female ; },
abstract = {Gut microbiome changes have been associated with several human diseases, but the molecular and functional details underlying these associations remain largely unknown. Here, we performed a meta-analysis of small molecule biosynthetic gene clusters (BGCs) in metagenomic samples of the gut microbiome from inflammatory bowel disease (IBD) patients and matched healthy subjects and identified two Clostridia-derived BGCs that are significantly associated with Crohn's disease (CD), a main IBD type. Using synthetic biology, we discovered and solved the structures of six fatty acid amides as the products of the CD-enriched BGCs, which we subsequently detected in fecal samples from IBD patients. Finally, we show that the discovered molecules disrupt gut permeability and exacerbate disease in chemically or genetically susceptible mouse models of colitis. These findings suggest that microbiome-derived small molecules may play a role in the etiology of IBD and represent a generalizable approach for discovering molecular mediators of disease-relevant microbiome-host interactions.},
}
MeSH Terms:
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*Gastrointestinal Microbiome
Humans
Mice
Animals
*Inflammatory Bowel Diseases/microbiology
Feces/microbiology
Crohn Disease/microbiology
Disease Models, Animal
Multigene Family
Colitis/microbiology
Metagenomics
Clostridium/genetics
Mice, Inbred C57BL
Female
RevDate: 2025-02-13
CO2 agitation combined with magnetized biochar to alleviate "ammonia inhibited steady-state": Exploring the mechanism by combining metagenomics with macroscopic indicators.
Water research, 276:123250 pii:S0043-1354(25)00164-2 [Epub ahead of print].
The "ammonia inhibited steady-state" phenomenon is frequently observed in the anaerobic digestion (AD) process of nitrogen-rich substrates. Reconfiguring microbial ecosystems has proven to be an effective strategy for mitigating ammonia inhibition. In the current study, biochars were screened and targeted for modification. CO2 agitation combined with magnetized biochar was used to aid the semi-continuous AD systems with "ammonia inhibited steady-state." The results indicated that coconut shell biochar had the best stimulating effect on AD performance. The content of oxygen-containing functional groups (OCFGs), which had a positive correlation with the electron donating capacity (EDC), was targeted to be regulated. This strategy significantly increased the CH4 yield by 31.7 % (from 344 to 278 mL/g VS) (p < 0.05). Isotope tracing and KEGG gene annotation indicated that this strategy stimulated the efficiency of the hydrogenotrophic pathway. Simultaneously, it accelerated the attachment of microorganisms, which made the DIET pathway between bacteria and archaea efficient. Under CO2 agitation, the attachment of functional microorganisms to the biochar accelerated. Biochar weakened the synthesis of bioelectronic carriers (Cyt-c and chemosensory pili), while the electroactivity of the AD system was enhanced. This means that biochar replaced bioelectronic carriers and improved the DIET efficiency. In addition, the strategy had a positive effect on the colonization of simultaneous nitrification-denitrifying bacteria (Georgenia), which led to a decrease in ammonia nitrogen concentrations. This study revealed the mechanism by which this strategy alleviates ammonia inhibition and provided a promising strategy for the efficient AD of nitrogen-rich substrates.
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@article {pmid39946947,
year = {2025},
author = {Yu, J and Usman, M and Liu, F and Schäfer, F and Shen, Y and Zheng, Z and Cai, Y},
title = {CO2 agitation combined with magnetized biochar to alleviate "ammonia inhibited steady-state": Exploring the mechanism by combining metagenomics with macroscopic indicators.},
journal = {Water research},
volume = {276},
number = {},
pages = {123250},
doi = {10.1016/j.watres.2025.123250},
pmid = {39946947},
issn = {1879-2448},
abstract = {The "ammonia inhibited steady-state" phenomenon is frequently observed in the anaerobic digestion (AD) process of nitrogen-rich substrates. Reconfiguring microbial ecosystems has proven to be an effective strategy for mitigating ammonia inhibition. In the current study, biochars were screened and targeted for modification. CO2 agitation combined with magnetized biochar was used to aid the semi-continuous AD systems with "ammonia inhibited steady-state." The results indicated that coconut shell biochar had the best stimulating effect on AD performance. The content of oxygen-containing functional groups (OCFGs), which had a positive correlation with the electron donating capacity (EDC), was targeted to be regulated. This strategy significantly increased the CH4 yield by 31.7 % (from 344 to 278 mL/g VS) (p < 0.05). Isotope tracing and KEGG gene annotation indicated that this strategy stimulated the efficiency of the hydrogenotrophic pathway. Simultaneously, it accelerated the attachment of microorganisms, which made the DIET pathway between bacteria and archaea efficient. Under CO2 agitation, the attachment of functional microorganisms to the biochar accelerated. Biochar weakened the synthesis of bioelectronic carriers (Cyt-c and chemosensory pili), while the electroactivity of the AD system was enhanced. This means that biochar replaced bioelectronic carriers and improved the DIET efficiency. In addition, the strategy had a positive effect on the colonization of simultaneous nitrification-denitrifying bacteria (Georgenia), which led to a decrease in ammonia nitrogen concentrations. This study revealed the mechanism by which this strategy alleviates ammonia inhibition and provided a promising strategy for the efficient AD of nitrogen-rich substrates.},
}
RevDate: 2025-02-13
Microplastic induces microbial nitrogen limitation further alters microbial nitrogentransformation: Insights from metagenomic analysis.
The Science of the total environment, 967:178825 pii:S0048-9697(25)00460-7 [Epub ahead of print].
Microplastic has a significant impact on soil microbial communities, which play crucial roles in soil nitrogen (N) cycles. However, there is a limited understanding of their influences on genes associated with the entire N cycling pathways. Through a 120-day soil incubation using conventional (PE and PET) and biodegradable microplastics (PLA and PBAT), coupled with 16S rRNA and metagenomic sequencing, we investigated the responses of N-cycling genes to microplastics in two contrasting soils (i.e. black soil and loess soil). We found that biodegradable microplastics strongly altered microbial N functional profiles, and enhanced the abundance of numerous key genes involved in N fixation, organic N mineralization, N reduction, and denitrification. Furthermore, biodegradable microplastics significantly decreased net N mineralization (Nm) compared to control and conventional microplastic treatments, suggesting microbial N immobilization outweighed N mineralization. Analysis of the function-taxon bipartite network showed that the Nm was well predicted for the abundances and diversity of bacteria within specific modules, with Nm decreasing, the abundances of specific taxa in a given network modules increasing. These results indicated that biodegradable microplastics act as a carbon source to select specific taxa involved in enhancing N bioavailability (e.g., N fixation and organic N mineralization) to meet microbial N demand, which in turn filtered the bacterial community (decreased diversity but increased abundances) and gradually formed specific function-taxon modules. Comparing the two soils, microbes in the less fertile alkaline loess soil were more sensitive to biodegradable microplastics than those in the nutrient-rich acid black soil. Our study indicated that increasing usage of biodegradable plastics in the future may lead to accelerated soil microbial N limitation and transformation.
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@article {pmid39946886,
year = {2025},
author = {Shi, J and Zhang, Q and Sun, Y and Peng, Y and Wang, J and Wang, X},
title = {Microplastic induces microbial nitrogen limitation further alters microbial nitrogentransformation: Insights from metagenomic analysis.},
journal = {The Science of the total environment},
volume = {967},
number = {},
pages = {178825},
doi = {10.1016/j.scitotenv.2025.178825},
pmid = {39946886},
issn = {1879-1026},
abstract = {Microplastic has a significant impact on soil microbial communities, which play crucial roles in soil nitrogen (N) cycles. However, there is a limited understanding of their influences on genes associated with the entire N cycling pathways. Through a 120-day soil incubation using conventional (PE and PET) and biodegradable microplastics (PLA and PBAT), coupled with 16S rRNA and metagenomic sequencing, we investigated the responses of N-cycling genes to microplastics in two contrasting soils (i.e. black soil and loess soil). We found that biodegradable microplastics strongly altered microbial N functional profiles, and enhanced the abundance of numerous key genes involved in N fixation, organic N mineralization, N reduction, and denitrification. Furthermore, biodegradable microplastics significantly decreased net N mineralization (Nm) compared to control and conventional microplastic treatments, suggesting microbial N immobilization outweighed N mineralization. Analysis of the function-taxon bipartite network showed that the Nm was well predicted for the abundances and diversity of bacteria within specific modules, with Nm decreasing, the abundances of specific taxa in a given network modules increasing. These results indicated that biodegradable microplastics act as a carbon source to select specific taxa involved in enhancing N bioavailability (e.g., N fixation and organic N mineralization) to meet microbial N demand, which in turn filtered the bacterial community (decreased diversity but increased abundances) and gradually formed specific function-taxon modules. Comparing the two soils, microbes in the less fertile alkaline loess soil were more sensitive to biodegradable microplastics than those in the nutrient-rich acid black soil. Our study indicated that increasing usage of biodegradable plastics in the future may lead to accelerated soil microbial N limitation and transformation.},
}
RevDate: 2025-02-13
Effect of microcystin-LR on intestinal microbiota, metabolism, and health of zebrafish (Danio rerio).
The Science of the total environment, 967:178838 pii:S0048-9697(25)00473-5 [Epub ahead of print].
Microcystin-LR (MC-LR) is typically produced along with the occurrence of cyanobacterial blooms, potentially exerting deleterious effects on intestinal microbiota and health in aquatic animals. To date, the underlying mechanism by which MC-LR affects intestinal health remains elusive. In this study, adult male zebrafish were exposed to MC-LR to assess its impact on the microbiome and metabolome. Histopathological and biochemical results indicated that MC-LR damaged intestinal villi and epithelial cells, induced intestinal barrier injury and inflammatory response. Metabolomics results revealed that MC-LR induced amino acid, carbohydrate, lipid, energy metabolisms dysbiosis, and specifically promoted glycine, serine and threonine metabolism. Metagenomics results demonstrated that MC-LR altered the composition of intestinal microbiota, and microbial function prediction suggested that MC-LR promoted the functions associated with amino acid, lipid, carbohydrate and energy metabolisms. Multiomics and Metorigin analyses jointly confirmed that glycine, serine and threonine metabolism was predominantly regulated by dominant Proteobacteria, Firmicutes, Fusobacteriota and Bacteroidota under MC-LR stress. This study offers a comprehensive perspective on the toxicity of microbiota and microbiota-derived metabolism in fish intestines induced by MC-LR and deepens our comprehension of the disruptive influence of MC-LR on intestinal homeostasis in organisms.
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@article {pmid39946873,
year = {2025},
author = {Feng, Y and Li, L and Ma, Q and Liu, S and Wang, P and Li, X and Ma, J},
title = {Effect of microcystin-LR on intestinal microbiota, metabolism, and health of zebrafish (Danio rerio).},
journal = {The Science of the total environment},
volume = {967},
number = {},
pages = {178838},
doi = {10.1016/j.scitotenv.2025.178838},
pmid = {39946873},
issn = {1879-1026},
abstract = {Microcystin-LR (MC-LR) is typically produced along with the occurrence of cyanobacterial blooms, potentially exerting deleterious effects on intestinal microbiota and health in aquatic animals. To date, the underlying mechanism by which MC-LR affects intestinal health remains elusive. In this study, adult male zebrafish were exposed to MC-LR to assess its impact on the microbiome and metabolome. Histopathological and biochemical results indicated that MC-LR damaged intestinal villi and epithelial cells, induced intestinal barrier injury and inflammatory response. Metabolomics results revealed that MC-LR induced amino acid, carbohydrate, lipid, energy metabolisms dysbiosis, and specifically promoted glycine, serine and threonine metabolism. Metagenomics results demonstrated that MC-LR altered the composition of intestinal microbiota, and microbial function prediction suggested that MC-LR promoted the functions associated with amino acid, lipid, carbohydrate and energy metabolisms. Multiomics and Metorigin analyses jointly confirmed that glycine, serine and threonine metabolism was predominantly regulated by dominant Proteobacteria, Firmicutes, Fusobacteriota and Bacteroidota under MC-LR stress. This study offers a comprehensive perspective on the toxicity of microbiota and microbiota-derived metabolism in fish intestines induced by MC-LR and deepens our comprehension of the disruptive influence of MC-LR on intestinal homeostasis in organisms.},
}
RevDate: 2025-02-13
Detection of multiple novel viruses in argasid and ixodid ticks in Mexico.
Ticks and tick-borne diseases, 16(2):102455 pii:S1877-959X(25)00019-6 [Epub ahead of print].
We examined ticks from Mexico using viral metagenomics to increase our understanding of the composition and diversity of the tick virome. The analysis was performed using 3,127 ticks of four Ixodidae spp. and one Argasidae spp. collected in 2019 to 2021 from domestic animals in four states of Mexico (Chiapas, Chihuahua, Guerrero, and Michoacán). All ticks were homogenized and tested for viruses using two approaches. In the first approach, an aliquot of each homogenate underwent two blind passages in Ixodes scapularis (ISE6) cells. Supernatants from all second passage cultures were subjected to polyethylene glycol (PEG) precipitation to enrich for virions then RNAs were extracted from the precipitates and analyzed by unbiased high-throughput sequencing (UHTS). In the second approach, an aliquot of every homogenate was subjected to PEG precipitation then RNAs were extracted and analyzed by UHTS, allowing for the detection of viruses unable to replicate in ISE6 cells. We identified seven novel species of viruses from multiple taxonomic groups (Bunyavirales, Flaviviridae, Nodaviridae, Nyamivirdae, Rhabdoviridae, Solemoviridae, and Totiviridae), some of which are highly divergent from all classified viruses and cannot be assigned to any established genus. Twelve recognized species of viruses were also identified. In summary, multiple novel and recognized viruses were detected in ticks from Mexico, highlighting the remarkable diversity of the tick virome.
Additional Links: PMID-39946816
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PubMed:
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@article {pmid39946816,
year = {2025},
author = {Laredo-Tiscareño, SV and Garza-Hernandez, JA and Tangudu, CS and Dankaona, W and Rodríguez-Alarcón, CA and Gonzalez-Peña, R and Adame-Gallegos, JR and Beristain-Ruiz, DM and Barajas-López, IN and Hargett, AM and Munderloh, UG and Blitvich, BJ},
title = {Detection of multiple novel viruses in argasid and ixodid ticks in Mexico.},
journal = {Ticks and tick-borne diseases},
volume = {16},
number = {2},
pages = {102455},
doi = {10.1016/j.ttbdis.2025.102455},
pmid = {39946816},
issn = {1877-9603},
abstract = {We examined ticks from Mexico using viral metagenomics to increase our understanding of the composition and diversity of the tick virome. The analysis was performed using 3,127 ticks of four Ixodidae spp. and one Argasidae spp. collected in 2019 to 2021 from domestic animals in four states of Mexico (Chiapas, Chihuahua, Guerrero, and Michoacán). All ticks were homogenized and tested for viruses using two approaches. In the first approach, an aliquot of each homogenate underwent two blind passages in Ixodes scapularis (ISE6) cells. Supernatants from all second passage cultures were subjected to polyethylene glycol (PEG) precipitation to enrich for virions then RNAs were extracted from the precipitates and analyzed by unbiased high-throughput sequencing (UHTS). In the second approach, an aliquot of every homogenate was subjected to PEG precipitation then RNAs were extracted and analyzed by UHTS, allowing for the detection of viruses unable to replicate in ISE6 cells. We identified seven novel species of viruses from multiple taxonomic groups (Bunyavirales, Flaviviridae, Nodaviridae, Nyamivirdae, Rhabdoviridae, Solemoviridae, and Totiviridae), some of which are highly divergent from all classified viruses and cannot be assigned to any established genus. Twelve recognized species of viruses were also identified. In summary, multiple novel and recognized viruses were detected in ticks from Mexico, highlighting the remarkable diversity of the tick virome.},
}
RevDate: 2025-02-13
CmpDate: 2025-02-13
Sample Size Impact (SaSii): An R script for estimating optimal sample sizes in population genetics and population genomics studies.
PloS one, 20(2):e0316634 pii:PONE-D-24-30924.
Obtaining large sample sizes for genetic studies can be challenging, time-consuming, and expensive, and small sample sizes may generate biased or imprecise results. Many studies have suggested the minimum sample size necessary to obtain robust and reliable results, but it is not possible to define one ideal minimum sample size that fits all studies. Here, we present SaSii (Sample Size Impact), an R script to help researchers define the minimum sample size. Based on empirical and simulated data analysis using SaSii, we present patterns and suggest minimum sample sizes for experiment design. The patterns were obtained by analyzing previously published genotype datasets with SaSii and can be used as a starting point for the sample design of population genetics and genomic studies. Our results showed that it is possible to estimate an adequate sample size that accurately represents the real population without requiring the scientist to write any program code, extract and sequence samples, or use population genetics programs, thus simplifying the process. We also confirmed that the minimum sample sizes for SNP (single-nucleotide polymorphism) analysis are usually smaller than for SSR (simple sequence repeat) analysis and discussed other patterns observed from empirical plant and animal datasets.
Additional Links: PMID-39946360
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@article {pmid39946360,
year = {2025},
author = {Scaketti, M and Sujii, PS and Alves-Pereira, A and Schwarcz, KD and Francisconi, AF and Moro, MS and Moreno Martins, KK and de Jesus, TA and de Souza, GBF and Zucchi, MI},
title = {Sample Size Impact (SaSii): An R script for estimating optimal sample sizes in population genetics and population genomics studies.},
journal = {PloS one},
volume = {20},
number = {2},
pages = {e0316634},
doi = {10.1371/journal.pone.0316634},
pmid = {39946360},
issn = {1932-6203},
mesh = {Sample Size ; *Genetics, Population ; *Polymorphism, Single Nucleotide ; Humans ; Genomics/methods ; Software ; Microsatellite Repeats/genetics ; Genotype ; Animals ; Metagenomics/methods ; },
abstract = {Obtaining large sample sizes for genetic studies can be challenging, time-consuming, and expensive, and small sample sizes may generate biased or imprecise results. Many studies have suggested the minimum sample size necessary to obtain robust and reliable results, but it is not possible to define one ideal minimum sample size that fits all studies. Here, we present SaSii (Sample Size Impact), an R script to help researchers define the minimum sample size. Based on empirical and simulated data analysis using SaSii, we present patterns and suggest minimum sample sizes for experiment design. The patterns were obtained by analyzing previously published genotype datasets with SaSii and can be used as a starting point for the sample design of population genetics and genomic studies. Our results showed that it is possible to estimate an adequate sample size that accurately represents the real population without requiring the scientist to write any program code, extract and sequence samples, or use population genetics programs, thus simplifying the process. We also confirmed that the minimum sample sizes for SNP (single-nucleotide polymorphism) analysis are usually smaller than for SSR (simple sequence repeat) analysis and discussed other patterns observed from empirical plant and animal datasets.},
}
MeSH Terms:
show MeSH Terms
hide MeSH Terms
Sample Size
*Genetics, Population
*Polymorphism, Single Nucleotide
Humans
Genomics/methods
Software
Microsatellite Repeats/genetics
Genotype
Animals
Metagenomics/methods
RevDate: 2025-02-13
CmpDate: 2025-02-13
Structure and diversity of intestinal methanogens in black carp (Mylopharyngodon piceus), grass carp (Ctenopharyngodon idella) and water samples.
PloS one, 20(2):e0316456 pii:PONE-D-24-40975.
The present research investigation aims to examine the community features of methanogens in the intestinal tract of black and grass carp, as well as their association with methanogens in water samples. Samples of black carp, grass carp and water in a pond were gathered in Spring 2021. Using the Illumina HiSeq 2500 high-throughput sequencing platform, the metagenomic mcrA gene sequences of black carp, grass carp and cultured water specimens were determined and analyzed. The outcomes indicate that the richness and diversity of methanogens in the intestinal tract of black and carp grass carp were highly correlated with the cultured water. Five bacterial genera were found in the three sets of samples, Methanosarcina, Methanocorpusculum, Methanospirillum, Methanobacterium and Methanofollis, in which Methanosarcina and Methanocorpusculum were the dominant genera. In addition, Methanosarcina had the greatest amount in grass carp and Methanocorpusculum had the greatest quantity in black carp. In conclusion, Methanosarcina and Methanocorpusculum were the main methanogens in the digestive tract of black and grass carp and culture water, and hydrolytic fermentative bacteria were its main metabolic substrate, hydrotrophic was its main metabolic pathway. The results will provide a reference for the relationship between intestinal methanogens and aquaculture and the greenhouse effect.
Additional Links: PMID-39946339
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@article {pmid39946339,
year = {2025},
author = {Long, C and Wang, P and Wu, J and Liu, J and Tan, Z and Li, W},
title = {Structure and diversity of intestinal methanogens in black carp (Mylopharyngodon piceus), grass carp (Ctenopharyngodon idella) and water samples.},
journal = {PloS one},
volume = {20},
number = {2},
pages = {e0316456},
doi = {10.1371/journal.pone.0316456},
pmid = {39946339},
issn = {1932-6203},
mesh = {*Carps/microbiology ; Animals ; *Gastrointestinal Microbiome/genetics ; Methane/metabolism ; Intestines/microbiology ; Bacteria/genetics/classification/isolation & purification ; Water Microbiology ; Methanosarcina/genetics/metabolism ; },
abstract = {The present research investigation aims to examine the community features of methanogens in the intestinal tract of black and grass carp, as well as their association with methanogens in water samples. Samples of black carp, grass carp and water in a pond were gathered in Spring 2021. Using the Illumina HiSeq 2500 high-throughput sequencing platform, the metagenomic mcrA gene sequences of black carp, grass carp and cultured water specimens were determined and analyzed. The outcomes indicate that the richness and diversity of methanogens in the intestinal tract of black and carp grass carp were highly correlated with the cultured water. Five bacterial genera were found in the three sets of samples, Methanosarcina, Methanocorpusculum, Methanospirillum, Methanobacterium and Methanofollis, in which Methanosarcina and Methanocorpusculum were the dominant genera. In addition, Methanosarcina had the greatest amount in grass carp and Methanocorpusculum had the greatest quantity in black carp. In conclusion, Methanosarcina and Methanocorpusculum were the main methanogens in the digestive tract of black and grass carp and culture water, and hydrolytic fermentative bacteria were its main metabolic substrate, hydrotrophic was its main metabolic pathway. The results will provide a reference for the relationship between intestinal methanogens and aquaculture and the greenhouse effect.},
}
MeSH Terms:
show MeSH Terms
hide MeSH Terms
*Carps/microbiology
Animals
*Gastrointestinal Microbiome/genetics
Methane/metabolism
Intestines/microbiology
Bacteria/genetics/classification/isolation & purification
Water Microbiology
Methanosarcina/genetics/metabolism
RevDate: 2025-02-13
Novel human coronavirus in an infant patient with pneumonia, Republic of Korea.
Emerging microbes & infections [Epub ahead of print].
Coronaviruses (CoVs) pose a significant threat to public health, causing a wide spectrum of clinical manifestations and outcomes. Beyond precipitating global outbreaks, Human CoVs (HCoVs) are frequently found among patients with respiratory infections. To date, limited attention has been directed towards alphacoronaviruses due to their low prevalence and fatality rates. Nasal swab and serum samples were collected from a paediatric patient, and an epidemiological survey was conducted. Retrospective surveillance investigated the molecular prevalence of CoV in 880 rodents collected in the Republic of Korea (ROK) from 2018 to 2022. Next-generation sequencing (NGS) and phylogenetic analyses characterised the novel HCoV and closely related CoVs harboured by Apodemus spp. On 15 December 2022, a 103-day-old infant was admitted with fever, cough, sputum production, and rhinorrhea, diagnosed with human parainfluenza virus 1 (HPIV-1) and rhinovirus co-infection. Elevated AST/ALT levels indicated transient liver dysfunction on the fourth day of hospitalisation. Metagenomic NGS (mNGS) identified a novel HCoV in nasal swab and serum samples. Retrospective rodent surveillance and phylogenetic analyses showed the novel HCoV was closely related to alphacoronaviruses carried by Apodemus spp. in the ROK and China. This case highlights the potential of mNGS to identify emerging pathogens and raises awareness of possible extra-respiratory manifestations, such as transient liver dysfunction, associated with novel HCoVs. While the liver injury in this case may be attributable to the novel HCoV, further research is necessary to elucidate its clinical significance, epidemiological prevalence, and zoonotic origins.
Additional Links: PMID-39945663
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PubMed:
Citation:
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@article {pmid39945663,
year = {2025},
author = {Park, K and Shin, M and Natasha, A and Kim, J and Noh, J and Kim, SG and Kim, B and Park, J and Seo, YR and Cho, HK and Byun, KS and Kim, JH and Lee, YS and Shim, JO and Kim, WK and Song, JW},
title = {Novel human coronavirus in an infant patient with pneumonia, Republic of Korea.},
journal = {Emerging microbes & infections},
volume = {},
number = {},
pages = {2466705},
doi = {10.1080/22221751.2025.2466705},
pmid = {39945663},
issn = {2222-1751},
abstract = {Coronaviruses (CoVs) pose a significant threat to public health, causing a wide spectrum of clinical manifestations and outcomes. Beyond precipitating global outbreaks, Human CoVs (HCoVs) are frequently found among patients with respiratory infections. To date, limited attention has been directed towards alphacoronaviruses due to their low prevalence and fatality rates. Nasal swab and serum samples were collected from a paediatric patient, and an epidemiological survey was conducted. Retrospective surveillance investigated the molecular prevalence of CoV in 880 rodents collected in the Republic of Korea (ROK) from 2018 to 2022. Next-generation sequencing (NGS) and phylogenetic analyses characterised the novel HCoV and closely related CoVs harboured by Apodemus spp. On 15 December 2022, a 103-day-old infant was admitted with fever, cough, sputum production, and rhinorrhea, diagnosed with human parainfluenza virus 1 (HPIV-1) and rhinovirus co-infection. Elevated AST/ALT levels indicated transient liver dysfunction on the fourth day of hospitalisation. Metagenomic NGS (mNGS) identified a novel HCoV in nasal swab and serum samples. Retrospective rodent surveillance and phylogenetic analyses showed the novel HCoV was closely related to alphacoronaviruses carried by Apodemus spp. in the ROK and China. This case highlights the potential of mNGS to identify emerging pathogens and raises awareness of possible extra-respiratory manifestations, such as transient liver dysfunction, associated with novel HCoVs. While the liver injury in this case may be attributable to the novel HCoV, further research is necessary to elucidate its clinical significance, epidemiological prevalence, and zoonotic origins.},
}
RevDate: 2025-02-13
Persistent delay in maturation of the developing gut microbiota in infants with cystic fibrosis.
mBio [Epub ahead of print].
The healthy human infant gut microbiome undergoes stereotypical changes in taxonomic composition between birth and maturation to an adult-like stable state. During this time, extensive communication between microbiota and the host immune system contributes to health status later in life. Although there are many reported associations between microbiota compositional alterations and disease in adults, less is known about how microbiome development is altered in pediatric diseases. One pediatric disease linked to altered gut microbiota composition is cystic fibrosis (CF), a multi-organ genetic disease involving impaired chloride secretion across epithelia and heightened inflammation both in the gut and at other body sites. Here, we use shotgun metagenomics to profile the strain-level composition and developmental dynamics of the infant fecal microbiota from several CF and non-CF longitudinal cohorts spanning from birth to greater than 36 months of life. We identify a set of keystone species that define microbiota development in early life in non-CF infants but are missing or decreased in relative abundance in infants with CF, resulting in a delayed pattern of microbiota maturation, persistent entrenchment in a transitional developmental phase, and subsequent failure to attain an adult-like stable microbiota. Delayed maturation is strongly associated with cumulative antibiotic treatments, and we also detect the increased relative abundance of oral-derived bacteria and higher levels of fungi in infants with CF, features that are associated with decreased gut bacterial density. These findings suggest the potential for future directed therapies targeted at overcoming developmental delays in microbiota maturation for infants with CF.IMPORTANCEThe human gastrointestinal tract harbors a diversity of microbes that colonize upon birth and collectively contribute to host health throughout life. Infants with the disease cystic fibrosis (CF) harbor altered gut microbiota compared to non-CF counterparts, with lower levels of beneficial bacteria. How this altered population is established in infants with CF and how it develops over the first years of life is not well understood. By leveraging multiple large non-CF infant fecal metagenomic data sets and samples from a CF cohort collected prior to highly effective modulator therapy, we define microbiome maturation in infants up to 3 years of age. Our findings identify conserved age-diagnostic species in the non-CF infant microbiome that are diminished in abundance in CF counterparts that instead exhibit an enrichment of oral-derived bacteria and fungi associated with antibiotic exposure. Together, our study builds toward microbiota-targeted therapy to restore healthy microbiota dynamics in infants with CF.
Additional Links: PMID-39945545
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PubMed:
Citation:
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@article {pmid39945545,
year = {2025},
author = {Verster, AJ and Salerno, P and Valls, R and Barrack, K and Price, CE and McClure, EA and Madan, JC and O'Toole, GA and Sanville, JL and Ross, BD},
title = {Persistent delay in maturation of the developing gut microbiota in infants with cystic fibrosis.},
journal = {mBio},
volume = {},
number = {},
pages = {e0342024},
doi = {10.1128/mbio.03420-24},
pmid = {39945545},
issn = {2150-7511},
abstract = {The healthy human infant gut microbiome undergoes stereotypical changes in taxonomic composition between birth and maturation to an adult-like stable state. During this time, extensive communication between microbiota and the host immune system contributes to health status later in life. Although there are many reported associations between microbiota compositional alterations and disease in adults, less is known about how microbiome development is altered in pediatric diseases. One pediatric disease linked to altered gut microbiota composition is cystic fibrosis (CF), a multi-organ genetic disease involving impaired chloride secretion across epithelia and heightened inflammation both in the gut and at other body sites. Here, we use shotgun metagenomics to profile the strain-level composition and developmental dynamics of the infant fecal microbiota from several CF and non-CF longitudinal cohorts spanning from birth to greater than 36 months of life. We identify a set of keystone species that define microbiota development in early life in non-CF infants but are missing or decreased in relative abundance in infants with CF, resulting in a delayed pattern of microbiota maturation, persistent entrenchment in a transitional developmental phase, and subsequent failure to attain an adult-like stable microbiota. Delayed maturation is strongly associated with cumulative antibiotic treatments, and we also detect the increased relative abundance of oral-derived bacteria and higher levels of fungi in infants with CF, features that are associated with decreased gut bacterial density. These findings suggest the potential for future directed therapies targeted at overcoming developmental delays in microbiota maturation for infants with CF.IMPORTANCEThe human gastrointestinal tract harbors a diversity of microbes that colonize upon birth and collectively contribute to host health throughout life. Infants with the disease cystic fibrosis (CF) harbor altered gut microbiota compared to non-CF counterparts, with lower levels of beneficial bacteria. How this altered population is established in infants with CF and how it develops over the first years of life is not well understood. By leveraging multiple large non-CF infant fecal metagenomic data sets and samples from a CF cohort collected prior to highly effective modulator therapy, we define microbiome maturation in infants up to 3 years of age. Our findings identify conserved age-diagnostic species in the non-CF infant microbiome that are diminished in abundance in CF counterparts that instead exhibit an enrichment of oral-derived bacteria and fungi associated with antibiotic exposure. Together, our study builds toward microbiota-targeted therapy to restore healthy microbiota dynamics in infants with CF.},
}
RevDate: 2025-02-13
Abundance of clinically relevant antimicrobial resistance genes in the golden jackal (Canis aureus) gut.
mSphere [Epub ahead of print].
UNLABELLED: The spread of antimicrobial resistance (AMR) is a critical One Health issue. Wildlife could act as reservoirs or vehicles of AMR bacteria (ARBs) and AMR genes (ARGs) but are relatively understudied. We sought to investigate clinically relevant ARGs in golden jackals (Canis aureus) thriving near human settlements in Israel. Fecal samples were collected from 111 jackals across four regions over a 10-month period. Various animal and spatio-temporal metadata were collected. Samples were analyzed by quantitative PCR (qPCR) for beta-lactamases (blaTEM, blaCTX-M15, and blaSHV), qnrS and int1. A subset of samples was subject to shotgun metagenomic sequencing followed by resistome and microbiome analyses. qPCR detected a high prevalence of ARGs, including beta-lactamases (blaTEM-1, 96.4%; blaCTX-M-15, 51.4%, blaSHV, 15.3%), fluoroquinolone resistance (qnrS, 87.4%), and class 1 integrons (Int1, 94.6%). The blaTEM-1 gene was found to be more prevalent in adult jackals compared to younger ones. Metagenomic analysis of a subset of samples revealed a diverse gut microbiome harboring a rich resistome with tetracycline resistance genes being the most prevalent. Metagenome-assembled genome analysis further identified several ARGs associated with clinically relevant bacteria. These findings highlight the potential role of golden jackals as reservoirs for AMR and emphasize the need for ongoing surveillance to better understand AMR transmission dynamics at the wildlife-human interface.
IMPORTANCE: The research highlights the potential role of the golden jackals as reservoirs for antimicrobial resistance (AMR). The high prevalence of clinically relevant AMR genes in these jackals emphasizes the need for ongoing surveillance and monitoring to better understand AMR transmission dynamics at the wildlife-human interface.
Additional Links: PMID-39945541
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PubMed:
Citation:
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@article {pmid39945541,
year = {2025},
author = {Lapid, R and Motro, Y and Craddock, H and Salah, I and King, R and Winner, K and Kahila Bar-Gal, G and Moran-Gilad, J},
title = {Abundance of clinically relevant antimicrobial resistance genes in the golden jackal (Canis aureus) gut.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0081924},
doi = {10.1128/msphere.00819-24},
pmid = {39945541},
issn = {2379-5042},
abstract = {UNLABELLED: The spread of antimicrobial resistance (AMR) is a critical One Health issue. Wildlife could act as reservoirs or vehicles of AMR bacteria (ARBs) and AMR genes (ARGs) but are relatively understudied. We sought to investigate clinically relevant ARGs in golden jackals (Canis aureus) thriving near human settlements in Israel. Fecal samples were collected from 111 jackals across four regions over a 10-month period. Various animal and spatio-temporal metadata were collected. Samples were analyzed by quantitative PCR (qPCR) for beta-lactamases (blaTEM, blaCTX-M15, and blaSHV), qnrS and int1. A subset of samples was subject to shotgun metagenomic sequencing followed by resistome and microbiome analyses. qPCR detected a high prevalence of ARGs, including beta-lactamases (blaTEM-1, 96.4%; blaCTX-M-15, 51.4%, blaSHV, 15.3%), fluoroquinolone resistance (qnrS, 87.4%), and class 1 integrons (Int1, 94.6%). The blaTEM-1 gene was found to be more prevalent in adult jackals compared to younger ones. Metagenomic analysis of a subset of samples revealed a diverse gut microbiome harboring a rich resistome with tetracycline resistance genes being the most prevalent. Metagenome-assembled genome analysis further identified several ARGs associated with clinically relevant bacteria. These findings highlight the potential role of golden jackals as reservoirs for AMR and emphasize the need for ongoing surveillance to better understand AMR transmission dynamics at the wildlife-human interface.
IMPORTANCE: The research highlights the potential role of the golden jackals as reservoirs for antimicrobial resistance (AMR). The high prevalence of clinically relevant AMR genes in these jackals emphasizes the need for ongoing surveillance and monitoring to better understand AMR transmission dynamics at the wildlife-human interface.},
}
RevDate: 2025-02-13
Induction of conidial traps in the nematode-trapping fungus Drechslerella dactyloides by soil microbes.
mSystems [Epub ahead of print].
UNLABELLED: Nematode-trapping fungi, renowned for their specialized predatory structures that ensnare nematodes, offer a promising biological approach to managing plant-parasitic nematodes. However, the efficacy of these fungi is frequently hampered by biotic and abiotic factors within the soil, which can significantly impede fungal germination (fungistasis). To counteract these environmental challenges, certain nematode-trapping fungi have evolved to produce traps from their conidia, referred to as conidial traps. This adaptation allows them to bypass the inhibitory effects of their surroundings, enhancing their predatory capabilities. In this study, we explored how soil affects conidial trap formation in Drechslerella dactyloides. Our findings revealed that Acinetobacter spp. and Pantoea spp. present in soil extracts play pivotal roles in triggering the development of these traps. Using metagenomic sequencing, we mapped the shifts in bacterial communities and their relative abundances before and after incubation for up to 24 hours to optimize soil induction effects. This analysis highlighted the enrichment of specific functional genes in soil microbes and provided insights into the mechanisms driving conidial trap formation, based on changes in soil characteristics. Furthermore, through bacterial isolation procedures, we successfully cultured and characterized the bacteria responsible for this phenomenon, confirming their potent ability to stimulate the production of conidial traps in nematode-trapping fungi. This study not only underscores the critical role of bacterial diversity in modulating the life cycle transitions of nematode-trapping fungi but also sets the stage for the development of more effective and sustainable strategies to harness these fungi in the battle against pathogenic nematodes.
IMPORTANCE: Predatory nematode-trapping fungi are important microbial antagonists of nematodes and can be developed into biocontrol agents. However, microbial biocontrol agents often suffer from inconsistent efficacy, primarily due to biotic and abiotic stresses in the rhizosphere soil. Drechslerella dactyloides, a nematode-trapping fungus, produces conidial traps in soil, serving as a survival strategy to overcome these stresses. In this study, we optimized soil suspensions to efficiently induce the formation of conidial traps. We found that bacteria in the soil directly trigger this formation. Metagenomic sequencing revealed bacterial enrichment during optimization, and we isolated and purified these bacteria with inducible activity. Our research deepens the understanding of this survival strategy of nematode-trapping fungi in nature, laying the foundation for enhancing the effectiveness of nematode biocontrol using this mechanism.
Additional Links: PMID-39945538
Publisher:
PubMed:
Citation:
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@article {pmid39945538,
year = {2025},
author = {Zhang, L and Zhang, T and Xu, Y-R and Sun, J-M and Pan, X-R and Gu, K-Z and Zhang, K-Q and Zhang, Z-G and Liang, L-M},
title = {Induction of conidial traps in the nematode-trapping fungus Drechslerella dactyloides by soil microbes.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0129124},
doi = {10.1128/msystems.01291-24},
pmid = {39945538},
issn = {2379-5077},
abstract = {UNLABELLED: Nematode-trapping fungi, renowned for their specialized predatory structures that ensnare nematodes, offer a promising biological approach to managing plant-parasitic nematodes. However, the efficacy of these fungi is frequently hampered by biotic and abiotic factors within the soil, which can significantly impede fungal germination (fungistasis). To counteract these environmental challenges, certain nematode-trapping fungi have evolved to produce traps from their conidia, referred to as conidial traps. This adaptation allows them to bypass the inhibitory effects of their surroundings, enhancing their predatory capabilities. In this study, we explored how soil affects conidial trap formation in Drechslerella dactyloides. Our findings revealed that Acinetobacter spp. and Pantoea spp. present in soil extracts play pivotal roles in triggering the development of these traps. Using metagenomic sequencing, we mapped the shifts in bacterial communities and their relative abundances before and after incubation for up to 24 hours to optimize soil induction effects. This analysis highlighted the enrichment of specific functional genes in soil microbes and provided insights into the mechanisms driving conidial trap formation, based on changes in soil characteristics. Furthermore, through bacterial isolation procedures, we successfully cultured and characterized the bacteria responsible for this phenomenon, confirming their potent ability to stimulate the production of conidial traps in nematode-trapping fungi. This study not only underscores the critical role of bacterial diversity in modulating the life cycle transitions of nematode-trapping fungi but also sets the stage for the development of more effective and sustainable strategies to harness these fungi in the battle against pathogenic nematodes.
IMPORTANCE: Predatory nematode-trapping fungi are important microbial antagonists of nematodes and can be developed into biocontrol agents. However, microbial biocontrol agents often suffer from inconsistent efficacy, primarily due to biotic and abiotic stresses in the rhizosphere soil. Drechslerella dactyloides, a nematode-trapping fungus, produces conidial traps in soil, serving as a survival strategy to overcome these stresses. In this study, we optimized soil suspensions to efficiently induce the formation of conidial traps. We found that bacteria in the soil directly trigger this formation. Metagenomic sequencing revealed bacterial enrichment during optimization, and we isolated and purified these bacteria with inducible activity. Our research deepens the understanding of this survival strategy of nematode-trapping fungi in nature, laying the foundation for enhancing the effectiveness of nematode biocontrol using this mechanism.},
}
RevDate: 2025-02-13
CmpDate: 2025-02-13
Challenges and limitations in using bacterial metabolites as immunomodulators.
Frontiers in cellular and infection microbiology, 15:1535394.
Harnessing the immunomodulatory potential of bacterial metabolites opens up exciting possibilities for treating various immune-related disorders. However, turning this potential into a reality presents significant challenges. This review investigates these challenges, focusing on discovery, production, characterization, stability, formulation, safety, and individual variability limitations. The limited bioavailability of many metabolites, as well as potential improvements along with the potential for off-target effects and the importance of precise targeting, are emphasized. Furthermore, the complex interactions between gut bacterial metabolites and the microbiome are investigated, highlighting the importance of personalized approaches. We conclude by discussing promising advances in metagenomics, metabolomics, synthetic biology, and targeted delivery systems, which hold out hope for overcoming these limitations and paving the way for the clinical translation of bacterial metabolites as effective immunomodulators.
Additional Links: PMID-39944722
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@article {pmid39944722,
year = {2025},
author = {Saravanan, C and Gopinath, NK and Ganesan, R and Thirumurugan, D},
title = {Challenges and limitations in using bacterial metabolites as immunomodulators.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1535394},
doi = {10.3389/fcimb.2025.1535394},
pmid = {39944722},
issn = {2235-2988},
mesh = {Humans ; *Bacteria/metabolism ; *Immunologic Factors/metabolism ; *Gastrointestinal Microbiome ; Animals ; Metabolomics ; Immunomodulating Agents/metabolism ; Metagenomics ; },
abstract = {Harnessing the immunomodulatory potential of bacterial metabolites opens up exciting possibilities for treating various immune-related disorders. However, turning this potential into a reality presents significant challenges. This review investigates these challenges, focusing on discovery, production, characterization, stability, formulation, safety, and individual variability limitations. The limited bioavailability of many metabolites, as well as potential improvements along with the potential for off-target effects and the importance of precise targeting, are emphasized. Furthermore, the complex interactions between gut bacterial metabolites and the microbiome are investigated, highlighting the importance of personalized approaches. We conclude by discussing promising advances in metagenomics, metabolomics, synthetic biology, and targeted delivery systems, which hold out hope for overcoming these limitations and paving the way for the clinical translation of bacterial metabolites as effective immunomodulators.},
}
MeSH Terms:
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Humans
*Bacteria/metabolism
*Immunologic Factors/metabolism
*Gastrointestinal Microbiome
Animals
Metabolomics
Immunomodulating Agents/metabolism
Metagenomics
RevDate: 2025-02-13
Bifidobacterium animalis subsp. lactis TG11 ameliorates loperamide-induced constipation in mice by modulating gut microbiota.
Frontiers in microbiology, 16:1525887.
INTRODUCTION: Constipation is a common gastrointestinal disorder that can affect quality of life. Probiotics have garnered substantial attention for their potential to alleviate constipation. This study investigates the preventive effects of Bifidobacterium animalis subsp. lactis TG11 on loperamide-induced constipation in mice.
METHODS: Mice were randomly assigned to normal control (NC), constipation model (CM), and low, medium, and high-dose TG11 treatment groups (LG, MG, HG). From days 1-14, LG, MG, and HG groups received 10[6], 10[7], and 10[8] CFU/mouse of TG11, respectively, while NC and CM groups received saline. On day 14, all groups except NC were administered loperamide (4 mg/kg) orally to induce constipation. Fecal samples were collected for short-chain fatty acid and gut microbiota analyses. Following a 16-hour fasting period, various parameters were assessed on day 15, including intestinal motility, fecal water content, defecation status, gut peptide levels in blood, and mRNA expression levels of SCF and c-kit in colonic tissue.
RESULTS: TG11 significantly enhanced intestinal motility and maintained fecal water content. It normalized blood levels of MTL, SP, SS, ET-1, Gas, and VIP in constipated mice, promoted short-chain fatty acid production, and improved microbial metabolism. TG11 markedly upregulated mRNA expression of SCF and c-kit in colonic tissue. Metagenomic sequencing revealed that TG11 modulated gut microbiota composition, increasing the abundance of beneficial bacteria, particularly Muribaculum_sp. and uncultured_Duncaniella.
DISCUSSION: Bifidobacterium animalis subsp. lactis TG11 demonstrates efficacy in ameliorating constipation, potentially through modulation of the gut microbiota composition.
Additional Links: PMID-39944653
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@article {pmid39944653,
year = {2025},
author = {Ma, W and Zhao, Y and Liu, Y and Wang, Y and Yu, S and Huang, L},
title = {Bifidobacterium animalis subsp. lactis TG11 ameliorates loperamide-induced constipation in mice by modulating gut microbiota.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1525887},
doi = {10.3389/fmicb.2025.1525887},
pmid = {39944653},
issn = {1664-302X},
abstract = {INTRODUCTION: Constipation is a common gastrointestinal disorder that can affect quality of life. Probiotics have garnered substantial attention for their potential to alleviate constipation. This study investigates the preventive effects of Bifidobacterium animalis subsp. lactis TG11 on loperamide-induced constipation in mice.
METHODS: Mice were randomly assigned to normal control (NC), constipation model (CM), and low, medium, and high-dose TG11 treatment groups (LG, MG, HG). From days 1-14, LG, MG, and HG groups received 10[6], 10[7], and 10[8] CFU/mouse of TG11, respectively, while NC and CM groups received saline. On day 14, all groups except NC were administered loperamide (4 mg/kg) orally to induce constipation. Fecal samples were collected for short-chain fatty acid and gut microbiota analyses. Following a 16-hour fasting period, various parameters were assessed on day 15, including intestinal motility, fecal water content, defecation status, gut peptide levels in blood, and mRNA expression levels of SCF and c-kit in colonic tissue.
RESULTS: TG11 significantly enhanced intestinal motility and maintained fecal water content. It normalized blood levels of MTL, SP, SS, ET-1, Gas, and VIP in constipated mice, promoted short-chain fatty acid production, and improved microbial metabolism. TG11 markedly upregulated mRNA expression of SCF and c-kit in colonic tissue. Metagenomic sequencing revealed that TG11 modulated gut microbiota composition, increasing the abundance of beneficial bacteria, particularly Muribaculum_sp. and uncultured_Duncaniella.
DISCUSSION: Bifidobacterium animalis subsp. lactis TG11 demonstrates efficacy in ameliorating constipation, potentially through modulation of the gut microbiota composition.},
}
RevDate: 2025-02-13
Integrative analysis of intestinal flora and untargeted metabolomics in attention-deficit/hyperactivity disorder.
Frontiers in microbiology, 16:1452423.
Attention Deficit Hyperactivity Disorder (ADHD) is a clinically common neurodevelopmental disorder of the brain. In addition to genetic factors, an imbalance in gut flora may also play a role in the development of ADHD. Currently, it is critical to investigate the function of gut flora and related metabolites, which may form the fundamental basis of bidirectional cross-linking between the brain and the gut, in addition to focusing on the changed gut flora in ADHD. This study aimed to investigate the possible relationship between changes in gut flora and metabolites and ADHD by analyzing metagenome and untargeted metabolomics of fecal samples from ADHD patients. Specifically, we attempted to identify key metabolites and the metabolic pathways they are involved in, as well as analyze in detail the structure and composition of the gut flora of ADHD patients. In order to further investigate the relationship between gut flora and ADHD symptoms, some behavioral studies were conducted following the transplantation of gut flora from ADHD patients into rats. The results of the metagenome analysis revealed several distinct strains, including Bacteroides cellulosilyticus, which could be important for diagnosing ADHD. Additionally, the ADHD group showed modifications in several metabolic pathways and metabolites, including the nicotinamide and nicotinic acid metabolic pathways and the metabolite nicotinamide in this pathway. The behavioral results demonstrated that rats with ADHD gut flora transplants displayed increased locomotor activity and interest, indicating that the onset of behaviors such as ADHD could be facilitated by the flora associated with ADHD. This research verified the alterations in gut flora and metabolism observed in ADHD patients and provided a list of metabolites and flora that were significantly altered in ADHD. Simultaneously, our findings revealed that modifications to the microbiome could potentially trigger behavioral changes in animals, providing an experimental basis for comprehending the function and influence of gut flora on ADHD. These results might provide new perspectives for the development of novel treatment strategies.
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@article {pmid39944648,
year = {2025},
author = {Lu, J and Jiang, M and Chai, D and Sun, Y and Wu, L},
title = {Integrative analysis of intestinal flora and untargeted metabolomics in attention-deficit/hyperactivity disorder.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1452423},
doi = {10.3389/fmicb.2025.1452423},
pmid = {39944648},
issn = {1664-302X},
abstract = {Attention Deficit Hyperactivity Disorder (ADHD) is a clinically common neurodevelopmental disorder of the brain. In addition to genetic factors, an imbalance in gut flora may also play a role in the development of ADHD. Currently, it is critical to investigate the function of gut flora and related metabolites, which may form the fundamental basis of bidirectional cross-linking between the brain and the gut, in addition to focusing on the changed gut flora in ADHD. This study aimed to investigate the possible relationship between changes in gut flora and metabolites and ADHD by analyzing metagenome and untargeted metabolomics of fecal samples from ADHD patients. Specifically, we attempted to identify key metabolites and the metabolic pathways they are involved in, as well as analyze in detail the structure and composition of the gut flora of ADHD patients. In order to further investigate the relationship between gut flora and ADHD symptoms, some behavioral studies were conducted following the transplantation of gut flora from ADHD patients into rats. The results of the metagenome analysis revealed several distinct strains, including Bacteroides cellulosilyticus, which could be important for diagnosing ADHD. Additionally, the ADHD group showed modifications in several metabolic pathways and metabolites, including the nicotinamide and nicotinic acid metabolic pathways and the metabolite nicotinamide in this pathway. The behavioral results demonstrated that rats with ADHD gut flora transplants displayed increased locomotor activity and interest, indicating that the onset of behaviors such as ADHD could be facilitated by the flora associated with ADHD. This research verified the alterations in gut flora and metabolism observed in ADHD patients and provided a list of metabolites and flora that were significantly altered in ADHD. Simultaneously, our findings revealed that modifications to the microbiome could potentially trigger behavioral changes in animals, providing an experimental basis for comprehending the function and influence of gut flora on ADHD. These results might provide new perspectives for the development of novel treatment strategies.},
}
RevDate: 2025-02-13
Unveiling the rhizosphere microbiome of Dendrobium: mechanisms, microbial interactions, and implications for sustainable agriculture.
Frontiers in microbiology, 16:1531900.
The rhizosphere microbiome plays a critical role in plant health and productivity by fostering beneficial microbial interactions that support nutrient cycling, stress tolerance, and disease suppression. In the context of Dendrobium, understanding its interactions is essential for optimizing cultivation and promoting sustainable agricultural practices. This review explores the rhizosphere microbiome of Dendrobium, focusing on the mechanisms and microbial interactions that contribute to plant health, stress tolerance, and growth and their implications for sustainable agriculture. This study highlights the diverse composition of microbial communities in the Dendrobium rhizosphere, including key bacteria (e.g., Pseudomonas fluorescens and Bacillus subtilis), fungi (e.g., Glomus spp.), and biocontrol agents (Trichoderma spp.), and discusses their roles in nutrient cycling, disease suppression, and plant growth promotion. This review emphasizes the significance of plant-microbe signaling, such as the production of flavonoids, phytohormones, and strigolactones, in shaping the microbial environment and enhancing plant resilience. Additionally, it addresses modern techniques for analyzing microbial communities, including metagenomics and next-generation sequencing, and their applications in advancing precision agriculture. Future research should focus on bridging knowledge gaps related to genotype-microbiome interactions, exploring emerging microbial consortia and enhancing the integration of microbiome management in precision agriculture systems to improve plant health and productivity.
Additional Links: PMID-39944638
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@article {pmid39944638,
year = {2025},
author = {Sarsaiya, S and Jain, A and Singh, R and Gong, Q and Wu, Q and Chen, J and Shi, J},
title = {Unveiling the rhizosphere microbiome of Dendrobium: mechanisms, microbial interactions, and implications for sustainable agriculture.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1531900},
doi = {10.3389/fmicb.2025.1531900},
pmid = {39944638},
issn = {1664-302X},
abstract = {The rhizosphere microbiome plays a critical role in plant health and productivity by fostering beneficial microbial interactions that support nutrient cycling, stress tolerance, and disease suppression. In the context of Dendrobium, understanding its interactions is essential for optimizing cultivation and promoting sustainable agricultural practices. This review explores the rhizosphere microbiome of Dendrobium, focusing on the mechanisms and microbial interactions that contribute to plant health, stress tolerance, and growth and their implications for sustainable agriculture. This study highlights the diverse composition of microbial communities in the Dendrobium rhizosphere, including key bacteria (e.g., Pseudomonas fluorescens and Bacillus subtilis), fungi (e.g., Glomus spp.), and biocontrol agents (Trichoderma spp.), and discusses their roles in nutrient cycling, disease suppression, and plant growth promotion. This review emphasizes the significance of plant-microbe signaling, such as the production of flavonoids, phytohormones, and strigolactones, in shaping the microbial environment and enhancing plant resilience. Additionally, it addresses modern techniques for analyzing microbial communities, including metagenomics and next-generation sequencing, and their applications in advancing precision agriculture. Future research should focus on bridging knowledge gaps related to genotype-microbiome interactions, exploring emerging microbial consortia and enhancing the integration of microbiome management in precision agriculture systems to improve plant health and productivity.},
}
RevDate: 2025-02-13
Antimicrobial resistance in diverse urban microbiomes: uncovering patterns and predictive markers.
Frontiers in genetics, 16:1460508 pii:1460508.
Antimicrobial resistance (AMR) is a growing global health concern, driven by urbanization and anthropogenic activities. This study investigated AMR distribution and dynamics across microbiomes from six U.S. cities, focusing on resistomes, viromes, and mobile genetic elements (MGEs). Using metagenomic data from the CAMDA 2023 challenge, we applied tools such as AMR++, Bowtie, AMRFinderPlus, and RGI for resistome profiling, along with clustering, normalization, and machine learning techniques to identify predictive markers. AMR++ and Bowtie outperformed other tools in detecting diverse AMR markers, with binary normalization improving classification accuracy. MGEs were found to play a critical role in AMR dissemination, with 394 genes shared across all cities. Removal of MGE-associated AMR genes altered resistome profiles and reduced model performance. The findings reveal a heterogeneous AMR landscape in urban microbiomes, particularly in New York City, which showed the highest resistome diversity. These results underscore the importance of MGEs in AMR profiling and provide valuable insights for designing targeted strategies to address AMR in urban settings.
Additional Links: PMID-39944596
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@article {pmid39944596,
year = {2025},
author = {Brizola Toscan, R and Lesiński, W and Stomma, P and Subramanian, B and Łabaj, PP and Rudnicki, WR},
title = {Antimicrobial resistance in diverse urban microbiomes: uncovering patterns and predictive markers.},
journal = {Frontiers in genetics},
volume = {16},
number = {},
pages = {1460508},
doi = {10.3389/fgene.2025.1460508},
pmid = {39944596},
issn = {1664-8021},
abstract = {Antimicrobial resistance (AMR) is a growing global health concern, driven by urbanization and anthropogenic activities. This study investigated AMR distribution and dynamics across microbiomes from six U.S. cities, focusing on resistomes, viromes, and mobile genetic elements (MGEs). Using metagenomic data from the CAMDA 2023 challenge, we applied tools such as AMR++, Bowtie, AMRFinderPlus, and RGI for resistome profiling, along with clustering, normalization, and machine learning techniques to identify predictive markers. AMR++ and Bowtie outperformed other tools in detecting diverse AMR markers, with binary normalization improving classification accuracy. MGEs were found to play a critical role in AMR dissemination, with 394 genes shared across all cities. Removal of MGE-associated AMR genes altered resistome profiles and reduced model performance. The findings reveal a heterogeneous AMR landscape in urban microbiomes, particularly in New York City, which showed the highest resistome diversity. These results underscore the importance of MGEs in AMR profiling and provide valuable insights for designing targeted strategies to address AMR in urban settings.},
}
RevDate: 2025-02-13
When a sore throat turns into deadly multiple serous cavity effusions: the role of Prevotella oris in rapidly progressing infection-a case report.
Frontiers in medicine, 12:1517389.
Severe infections that develop rapidly from ordinary symptoms not only increase patient misunderstandings but also lead to excessive detection of these symptoms by physicians. This case study describes a 19-year-old male individual who initially presented with a sore throat and subsequently developed multiple serous cavity effusions that lead to septic pulmonary embolism and septic shock. After multiple cultures of the patient's sputum yielded no identifiable pathogenic bacteria, the metagenomic next-generation sequencing (mNGS) revealed Prevotella oris as the predominant pathogen present in both the patient's peripheral blood and the pericardial drainage fluid. The subsequent antibiotic treatment, guided by the mNGS results, along with surgical drainage and mediastinal irrigation, effectively controlled and ultimately cured the patient's condition. This case is unique because it is the first to show that normally colonizing Prevotella can also cause fatal multiorgan infection as an opportunistic pathogen in a previously healthy young person with no immune-related diseases. The aim of this study is to expand clinical awareness of this common symptom and its potentially fatal outcome.
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@article {pmid39944485,
year = {2025},
author = {Zhang, F and Wang, JL and Zhu, J and Si, S and Guo, H and Yue, X and Wen, W},
title = {When a sore throat turns into deadly multiple serous cavity effusions: the role of Prevotella oris in rapidly progressing infection-a case report.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1517389},
doi = {10.3389/fmed.2025.1517389},
pmid = {39944485},
issn = {2296-858X},
abstract = {Severe infections that develop rapidly from ordinary symptoms not only increase patient misunderstandings but also lead to excessive detection of these symptoms by physicians. This case study describes a 19-year-old male individual who initially presented with a sore throat and subsequently developed multiple serous cavity effusions that lead to septic pulmonary embolism and septic shock. After multiple cultures of the patient's sputum yielded no identifiable pathogenic bacteria, the metagenomic next-generation sequencing (mNGS) revealed Prevotella oris as the predominant pathogen present in both the patient's peripheral blood and the pericardial drainage fluid. The subsequent antibiotic treatment, guided by the mNGS results, along with surgical drainage and mediastinal irrigation, effectively controlled and ultimately cured the patient's condition. This case is unique because it is the first to show that normally colonizing Prevotella can also cause fatal multiorgan infection as an opportunistic pathogen in a previously healthy young person with no immune-related diseases. The aim of this study is to expand clinical awareness of this common symptom and its potentially fatal outcome.},
}
RevDate: 2025-02-13
CmpDate: 2025-02-13
Evaluating methods for genome sequencing of Chlamydia trachomatis and other sexually transmitted bacteria directly from clinical swabs.
Microbial genomics, 11(2):.
Rates of bacterial sexually transmitted infections (STIs) are rising, and accessing their genomes provides information on strain evolution, circulating strains and encoded antimicrobial resistance (AMR). Notable pathogens include Chlamydia trachomatis (CT), Neisseria gonorrhoeae (NG) and Treponema pallidum (TP), globally the most common bacterial STIs. Mycoplasmoides (formerly Mycoplasma) genitalium (MG) is also a bacterial STI that is of concern due to AMR development. These bacteria are also fastidious or hard to culture, and standard sampling methods lyse bacteria, completely preventing pathogen culture. Clinical samples contain large amounts of human and other microbiota DNA. These factors hinder the sequencing of bacterial STI genomes. We aimed to overcome these challenges in obtaining whole-genome sequences and evaluated four approaches using clinical samples from Argentina (39), and Switzerland (14), and cultured samples from Finland (2) and Argentina (1). First, direct genome sequencing from swab samples was attempted through Illumina deep metagenomic sequencing, showing extremely low levels of target DNA, with under 0.01% of the sequenced reads being from the target pathogens. Second, host DNA depletion followed by Illumina sequencing was not found to produce enrichment in these very low-load samples. Third, we tried a selective long-read approach with the new adaptive sequencing from Oxford Nanopore Technologies, which also did not improve enrichment sufficiently to provide genomic information. Finally, target enrichment using a novel pan-genome set of custom SureSelect probes targeting CT, NG, TP and MG followed by Illumina sequencing was successful. We produced whole genomes from 64% of CT-positive samples, from 36% of NG-positive samples and 60% of TP-positive samples. Additionally, we enriched MG DNA to gain partial genomes from 60% of samples. This is the first publication to date to utilize a pan-genome STI panel in target enrichment. Target enrichment, though costly, proved essential for obtaining genomic data from clinical samples. These data can be utilized to examine circulating strains and genotypic resistance and guide public health strategies.
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@article {pmid39943872,
year = {2025},
author = {Büttner, KA and Bregy, V and Wegner, F and Purushothaman, S and Imkamp, F and Roloff Handschin, T and Puolakkainen, MH and Hiltunen-Back, E and Braun, D and Kisakesen, I and Schreiber, A and Entrocassi, AC and Gallo Vaulet, ML and López Aquino, D and Svidler López, L and La Rosa, L and Egli, A and Rodríguez Fermepin, M and Seth-Smith, HM and On Behalf Of The Escmid Study Group For Mycoplasma And Chlamydia Infections Esgmac, },
title = {Evaluating methods for genome sequencing of Chlamydia trachomatis and other sexually transmitted bacteria directly from clinical swabs.},
journal = {Microbial genomics},
volume = {11},
number = {2},
pages = {},
doi = {10.1099/mgen.0.001353},
pmid = {39943872},
issn = {2057-5858},
mesh = {Humans ; *Chlamydia trachomatis/genetics/isolation & purification ; *Whole Genome Sequencing/methods ; *Genome, Bacterial ; Neisseria gonorrhoeae/genetics/isolation & purification/classification ; High-Throughput Nucleotide Sequencing ; Treponema pallidum/genetics/isolation & purification ; Sexually Transmitted Diseases, Bacterial/microbiology ; Switzerland ; DNA, Bacterial/genetics ; Mycoplasma genitalium/genetics/isolation & purification ; Chlamydia Infections/microbiology ; },
abstract = {Rates of bacterial sexually transmitted infections (STIs) are rising, and accessing their genomes provides information on strain evolution, circulating strains and encoded antimicrobial resistance (AMR). Notable pathogens include Chlamydia trachomatis (CT), Neisseria gonorrhoeae (NG) and Treponema pallidum (TP), globally the most common bacterial STIs. Mycoplasmoides (formerly Mycoplasma) genitalium (MG) is also a bacterial STI that is of concern due to AMR development. These bacteria are also fastidious or hard to culture, and standard sampling methods lyse bacteria, completely preventing pathogen culture. Clinical samples contain large amounts of human and other microbiota DNA. These factors hinder the sequencing of bacterial STI genomes. We aimed to overcome these challenges in obtaining whole-genome sequences and evaluated four approaches using clinical samples from Argentina (39), and Switzerland (14), and cultured samples from Finland (2) and Argentina (1). First, direct genome sequencing from swab samples was attempted through Illumina deep metagenomic sequencing, showing extremely low levels of target DNA, with under 0.01% of the sequenced reads being from the target pathogens. Second, host DNA depletion followed by Illumina sequencing was not found to produce enrichment in these very low-load samples. Third, we tried a selective long-read approach with the new adaptive sequencing from Oxford Nanopore Technologies, which also did not improve enrichment sufficiently to provide genomic information. Finally, target enrichment using a novel pan-genome set of custom SureSelect probes targeting CT, NG, TP and MG followed by Illumina sequencing was successful. We produced whole genomes from 64% of CT-positive samples, from 36% of NG-positive samples and 60% of TP-positive samples. Additionally, we enriched MG DNA to gain partial genomes from 60% of samples. This is the first publication to date to utilize a pan-genome STI panel in target enrichment. Target enrichment, though costly, proved essential for obtaining genomic data from clinical samples. These data can be utilized to examine circulating strains and genotypic resistance and guide public health strategies.},
}
MeSH Terms:
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Humans
*Chlamydia trachomatis/genetics/isolation & purification
*Whole Genome Sequencing/methods
*Genome, Bacterial
Neisseria gonorrhoeae/genetics/isolation & purification/classification
High-Throughput Nucleotide Sequencing
Treponema pallidum/genetics/isolation & purification
Sexually Transmitted Diseases, Bacterial/microbiology
Switzerland
DNA, Bacterial/genetics
Mycoplasma genitalium/genetics/isolation & purification
Chlamydia Infections/microbiology
RevDate: 2025-02-13
Nanopore Sequencing of Amoebophrya sp. Reveals Novel Collection of Bacteria Putatively Associated with Karlodinium veneficum.
Genome biology and evolution pii:8010893 [Epub ahead of print].
The dinoflagellate parasite Amoebophrya sp. ex Karlodinium veneficum plays a major role in controlling populations of the toxic bloom-forming dinoflagellate Karlodinium veneficum and is one of the few cultured representatives of Marine Alveolate Group II. The obligate parasitic nature of this Amoebophrya spp. precludes isolation in culture, and therefore, genomic characterization of this parasite relies on metagenomic sequencing. Whole genome sequencing of an Amoebophrya sp. ex Karlodinium veneficum-infected culture using Nanopore long reads revealed a diverse community of novel bacteria as well as several species previously reported to be associated with algae. In sum, 39 metagenome-assembled genomes (MAG) were assembled, and less than half of these required binning of multiple contigs. Seven were abundant but of unknown genera, thirteen were identifiable at the generic level by BLAST (eight of which were apparently complete single-contig genomes), and the remaining 19 comprised less abundant (individually accounting for < 2% of the total bacterial reads in the culture) and often rarer and/or novel species. Attempts to culture strains identified through sequencing revealed that only two of these bacterial isolates were readily amenable to cultivation, stressing the importance of a dual culture- and sequencing-based approach for robust community analysis. Functional annotations of MAGs are presented here to support the characterization of a microbial community associated with K. veneficum and/or Amoebophrya sp. ex K. veneficum cultured from the Chesapeake Bay and give preliminary insights into the nature of the associations these bacteria have with this parasite-host complex.
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@article {pmid39943733,
year = {2025},
author = {Tizabi, D and Hill, RT and Bachvaroff, T},
title = {Nanopore Sequencing of Amoebophrya sp. Reveals Novel Collection of Bacteria Putatively Associated with Karlodinium veneficum.},
journal = {Genome biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/gbe/evaf022},
pmid = {39943733},
issn = {1759-6653},
abstract = {The dinoflagellate parasite Amoebophrya sp. ex Karlodinium veneficum plays a major role in controlling populations of the toxic bloom-forming dinoflagellate Karlodinium veneficum and is one of the few cultured representatives of Marine Alveolate Group II. The obligate parasitic nature of this Amoebophrya spp. precludes isolation in culture, and therefore, genomic characterization of this parasite relies on metagenomic sequencing. Whole genome sequencing of an Amoebophrya sp. ex Karlodinium veneficum-infected culture using Nanopore long reads revealed a diverse community of novel bacteria as well as several species previously reported to be associated with algae. In sum, 39 metagenome-assembled genomes (MAG) were assembled, and less than half of these required binning of multiple contigs. Seven were abundant but of unknown genera, thirteen were identifiable at the generic level by BLAST (eight of which were apparently complete single-contig genomes), and the remaining 19 comprised less abundant (individually accounting for < 2% of the total bacterial reads in the culture) and often rarer and/or novel species. Attempts to culture strains identified through sequencing revealed that only two of these bacterial isolates were readily amenable to cultivation, stressing the importance of a dual culture- and sequencing-based approach for robust community analysis. Functional annotations of MAGs are presented here to support the characterization of a microbial community associated with K. veneficum and/or Amoebophrya sp. ex K. veneficum cultured from the Chesapeake Bay and give preliminary insights into the nature of the associations these bacteria have with this parasite-host complex.},
}
RevDate: 2025-02-13
Metagenomics and Metagenome-Assembled Genomes: Analysis of Cupei from Sichuan Baoning Vinegar, One of the Four Traditional Renowned Vinegars in China.
Foods (Basel, Switzerland), 14(3): pii:foods14030398.
The microbial community in vinegar has primarily been investigated by analyzing short reads to determine operational taxonomic units, but it is also crucial to identify metagenome-assembled genomes (MAGs). In this study, the microbial diversity and functionality in Sichuan Baoning vinegar were examined through deep metagenomic sequencing and metagenomic binning. Results revealed that the most prevalent phylum was Firmicutes, followed by Proteobacteria and unclassified Bacteria. The most abundant bacterial species was Acetilactobacillus jinshanensis, while Saccharomyces cerevisiae was the most prevalent fungal species. The predominant viral species were Hopescreekvirus LfeInf, Myoviridae sp., and Siphoviridae sp. A total of 1395 MAGs were reconstructed, with 660 of them annotated. The majority of MAGs resolved at the species level were attributed to Firmicutes (n = 308), with Acetilactobacillus jinshanensis being the most abundant. According to the average nucleotide identity values, 223 out of the 660 MAGs might represent novel species. The recovered MAGs exhibited biomarker genes indicative of the genetic potential to encode several important secondary metabolites. This study helps to uncover the microbial composition and functional potential of microbial genomes in Sichuan Baoning vinegar.
Additional Links: PMID-39941991
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@article {pmid39941991,
year = {2025},
author = {Wu, J and Zhao, N and Li, Q and Zhao, K and Tu, M and Li, J and Hu, K and Chen, S and Liu, S and Liu, A},
title = {Metagenomics and Metagenome-Assembled Genomes: Analysis of Cupei from Sichuan Baoning Vinegar, One of the Four Traditional Renowned Vinegars in China.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {3},
pages = {},
doi = {10.3390/foods14030398},
pmid = {39941991},
issn = {2304-8158},
abstract = {The microbial community in vinegar has primarily been investigated by analyzing short reads to determine operational taxonomic units, but it is also crucial to identify metagenome-assembled genomes (MAGs). In this study, the microbial diversity and functionality in Sichuan Baoning vinegar were examined through deep metagenomic sequencing and metagenomic binning. Results revealed that the most prevalent phylum was Firmicutes, followed by Proteobacteria and unclassified Bacteria. The most abundant bacterial species was Acetilactobacillus jinshanensis, while Saccharomyces cerevisiae was the most prevalent fungal species. The predominant viral species were Hopescreekvirus LfeInf, Myoviridae sp., and Siphoviridae sp. A total of 1395 MAGs were reconstructed, with 660 of them annotated. The majority of MAGs resolved at the species level were attributed to Firmicutes (n = 308), with Acetilactobacillus jinshanensis being the most abundant. According to the average nucleotide identity values, 223 out of the 660 MAGs might represent novel species. The recovered MAGs exhibited biomarker genes indicative of the genetic potential to encode several important secondary metabolites. This study helps to uncover the microbial composition and functional potential of microbial genomes in Sichuan Baoning vinegar.},
}
RevDate: 2025-02-13
Integrating Metagenomic and Culture-Based Techniques to Detect Foodborne Pathogens and Antimicrobial Resistance Genes in Malaysian Produce.
Foods (Basel, Switzerland), 14(3): pii:foods14030352.
Foodborne illnesses pose a significant global health threat, often caused by pathogens like Escherichia coli, Listeria monocytogenes, and Salmonella spp. The emergence of antibiotic-resistant strains further exacerbates food safety challenges. This study combines shotgun metagenomics and culture-based approaches to detect foodborne pathogens and antimicrobial resistance genes (ARGs) in Malaysian produce and meats from the Kinta Valley region. A total of 27 samples comprising vegetables, meats, and fruits were analyzed. Metagenomics provided comprehensive microbial profiles, revealing diverse bacterial communities with species-level taxonomic resolution. Culture-based methods complemented these findings by identifying viable pathogens. Key foodborne pathogens were detected, with Listeria monocytogenes identified in meats and vegetables and Shigella flexneri detected inconsistently between the methods. ARGs analysis highlighted significant resistance to cephalosporins and penams, particularly in raw chicken and vegetable samples, underscoring the potential public health risks. While deli meats and fruits exhibited a lower antimicrobial resistance prevalence, resistant genes linked to E. coli and Salmonella strains were identified. Discrepancies between the methods suggest the need for integrated approaches to improve the pathogen detection accuracy. This study demonstrates the potential of metagenomics in advancing food safety research and supports its adoption as a complementary tool alongside culture-based methods for comprehensive foodborne pathogen surveillance and ARG profiling in Malaysian food systems.
Additional Links: PMID-39941945
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PubMed:
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@article {pmid39941945,
year = {2025},
author = {Quek, JJW and Wong, JL and Tan, JL and Yeo, CC and Saw, SH},
title = {Integrating Metagenomic and Culture-Based Techniques to Detect Foodborne Pathogens and Antimicrobial Resistance Genes in Malaysian Produce.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {3},
pages = {},
doi = {10.3390/foods14030352},
pmid = {39941945},
issn = {2304-8158},
support = {FRGS/1/2022/SKK06/UTAR/02/1//Ministry of Higher Education/ ; },
abstract = {Foodborne illnesses pose a significant global health threat, often caused by pathogens like Escherichia coli, Listeria monocytogenes, and Salmonella spp. The emergence of antibiotic-resistant strains further exacerbates food safety challenges. This study combines shotgun metagenomics and culture-based approaches to detect foodborne pathogens and antimicrobial resistance genes (ARGs) in Malaysian produce and meats from the Kinta Valley region. A total of 27 samples comprising vegetables, meats, and fruits were analyzed. Metagenomics provided comprehensive microbial profiles, revealing diverse bacterial communities with species-level taxonomic resolution. Culture-based methods complemented these findings by identifying viable pathogens. Key foodborne pathogens were detected, with Listeria monocytogenes identified in meats and vegetables and Shigella flexneri detected inconsistently between the methods. ARGs analysis highlighted significant resistance to cephalosporins and penams, particularly in raw chicken and vegetable samples, underscoring the potential public health risks. While deli meats and fruits exhibited a lower antimicrobial resistance prevalence, resistant genes linked to E. coli and Salmonella strains were identified. Discrepancies between the methods suggest the need for integrated approaches to improve the pathogen detection accuracy. This study demonstrates the potential of metagenomics in advancing food safety research and supports its adoption as a complementary tool alongside culture-based methods for comprehensive foodborne pathogen surveillance and ARG profiling in Malaysian food systems.},
}
RevDate: 2025-02-13
Unveiling the Resistome Landscape in Peri-Implant Health and Disease.
Journal of clinical medicine, 14(3): pii:jcm14030931.
Background: The human oral microbiome is a critical reservoir for antibiotic resistance; however, subgingival peri-implant biofilms remain underexplored in this context. We aimed to explore the prevalence and distribution of antibiotic resistance genes (ARGs) in metagenomes derived from saliva and subgingival peri-implant biofilms. Methods: A total of 100 metagenome datasets from 40 individuals were retrieved from the Sequence Read Archive (SRA) database. Of these, 20 individuals had exclusively healthy implants and 20 had both healthy and affected implants with peri-implantitis. ARGs and their taxonomic assignments were identified using the ABRicate tool, and plasmid detection was performed with PlasmidFinder. Results: Four plasmid replicons were identified in 72 metagenomes, and 55 distinct ARGs from 13 antibiotic classes were detected in 89 metagenomes. ARGs conferring resistance to macrolides-lincosamides-streptogramins, tetracyclines, beta-lactams, and fluoroquinolones were the most prevalent. The msr(D) and mef(A) genes showed the highest prevalence, except in saliva samples from individuals with healthy implants, where mef(A) ranked fourth. A pairwise PERMANOVA of principal coordinate analysis based on Jaccard distances revealed that saliva samples exhibited significantly greater ARG diversity than subgingival biofilm samples (p < 0.05). However, no significant differences were observed between healthy and peri-implantitis-affected subgingival biofilm groups (p > 0.05). The taxonomic origins of ARGs were also analyzed to understand their distribution and potential impact on oral microbial communities. Conclusions: Resistome profiles associated with both peri-implant health and disease showed no significant differences and higher salivary abundance of ARGs compared to subgingival biofilm samples.
Additional Links: PMID-39941602
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PubMed:
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@article {pmid39941602,
year = {2025},
author = {Bessa, LJ and Egas, C and Botelho, J and Machado, V and Alcoforado, G and Mendes, JJ and Alves, R},
title = {Unveiling the Resistome Landscape in Peri-Implant Health and Disease.},
journal = {Journal of clinical medicine},
volume = {14},
number = {3},
pages = {},
doi = {10.3390/jcm14030931},
pmid = {39941602},
issn = {2077-0383},
support = {2022.01430.PTDC//Fundação para a Ciência e Tecnologia/ ; },
abstract = {Background: The human oral microbiome is a critical reservoir for antibiotic resistance; however, subgingival peri-implant biofilms remain underexplored in this context. We aimed to explore the prevalence and distribution of antibiotic resistance genes (ARGs) in metagenomes derived from saliva and subgingival peri-implant biofilms. Methods: A total of 100 metagenome datasets from 40 individuals were retrieved from the Sequence Read Archive (SRA) database. Of these, 20 individuals had exclusively healthy implants and 20 had both healthy and affected implants with peri-implantitis. ARGs and their taxonomic assignments were identified using the ABRicate tool, and plasmid detection was performed with PlasmidFinder. Results: Four plasmid replicons were identified in 72 metagenomes, and 55 distinct ARGs from 13 antibiotic classes were detected in 89 metagenomes. ARGs conferring resistance to macrolides-lincosamides-streptogramins, tetracyclines, beta-lactams, and fluoroquinolones were the most prevalent. The msr(D) and mef(A) genes showed the highest prevalence, except in saliva samples from individuals with healthy implants, where mef(A) ranked fourth. A pairwise PERMANOVA of principal coordinate analysis based on Jaccard distances revealed that saliva samples exhibited significantly greater ARG diversity than subgingival biofilm samples (p < 0.05). However, no significant differences were observed between healthy and peri-implantitis-affected subgingival biofilm groups (p > 0.05). The taxonomic origins of ARGs were also analyzed to understand their distribution and potential impact on oral microbial communities. Conclusions: Resistome profiles associated with both peri-implant health and disease showed no significant differences and higher salivary abundance of ARGs compared to subgingival biofilm samples.},
}
RevDate: 2025-02-13
Transforming Microbiological Diagnostics in Nosocomial Lower Respiratory Tract Infections: Innovations Shaping the Future.
Diagnostics (Basel, Switzerland), 15(3): pii:diagnostics15030265.
Introduction: Nosocomial lower respiratory tract infections (nLRTIs), including hospital-acquired pneumonia (HAP) and ventilator-associated pneumonia (VAP), remain significant challenges due to high mortality, morbidity, and healthcare costs. Implementing accurate and timely diagnostic strategies is pivotal for guiding optimized antimicrobial therapy and addressing the growing threat of antimicrobial resistance. Areas Covered: This review examines emerging microbiological diagnostic methods for nLRTIs. Although widely utilized, traditional culture-based techniques are hindered by prolonged processing times, limiting their clinical utility in timely decision-making. Advanced molecular tools, such as real-time PCR and multiplex PCR, allow rapid pathogen identification but are constrained by predefined panels. Metagenomic next-generation sequencing (mNGS) provides comprehensive pathogen detection and resistance profiling yet faces cost, complexity, and interpretation challenges. Non-invasive methods, including exhaled breath analysis using electronic nose (e-nose) technology, gene expression profiling, and biomarker detection, hold promise for rapid and bedside diagnostics but require further validation to establish clinical applicability. Expert Opinion: Integrating molecular, metagenomic, biomarker-associated, and traditional diagnostics is essential for overcoming limitations. Continued technological refinements and cost reductions will enable broader clinical implementation. These innovations promise to enhance diagnostic accuracy, facilitate targeted therapy, and improve patient outcomes while contributing to global efforts to mitigate antimicrobial resistance.
Additional Links: PMID-39941194
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PubMed:
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@article {pmid39941194,
year = {2025},
author = {Bustos, IG and Martinez-Lemus, LF and Reyes, LF and Martin-Loeches, I},
title = {Transforming Microbiological Diagnostics in Nosocomial Lower Respiratory Tract Infections: Innovations Shaping the Future.},
journal = {Diagnostics (Basel, Switzerland)},
volume = {15},
number = {3},
pages = {},
doi = {10.3390/diagnostics15030265},
pmid = {39941194},
issn = {2075-4418},
abstract = {Introduction: Nosocomial lower respiratory tract infections (nLRTIs), including hospital-acquired pneumonia (HAP) and ventilator-associated pneumonia (VAP), remain significant challenges due to high mortality, morbidity, and healthcare costs. Implementing accurate and timely diagnostic strategies is pivotal for guiding optimized antimicrobial therapy and addressing the growing threat of antimicrobial resistance. Areas Covered: This review examines emerging microbiological diagnostic methods for nLRTIs. Although widely utilized, traditional culture-based techniques are hindered by prolonged processing times, limiting their clinical utility in timely decision-making. Advanced molecular tools, such as real-time PCR and multiplex PCR, allow rapid pathogen identification but are constrained by predefined panels. Metagenomic next-generation sequencing (mNGS) provides comprehensive pathogen detection and resistance profiling yet faces cost, complexity, and interpretation challenges. Non-invasive methods, including exhaled breath analysis using electronic nose (e-nose) technology, gene expression profiling, and biomarker detection, hold promise for rapid and bedside diagnostics but require further validation to establish clinical applicability. Expert Opinion: Integrating molecular, metagenomic, biomarker-associated, and traditional diagnostics is essential for overcoming limitations. Continued technological refinements and cost reductions will enable broader clinical implementation. These innovations promise to enhance diagnostic accuracy, facilitate targeted therapy, and improve patient outcomes while contributing to global efforts to mitigate antimicrobial resistance.},
}
RevDate: 2025-02-13
CmpDate: 2025-02-13
Quercetin and Silybin Decrease Intracellular Replication of Piscirickettsia salmonis in SHK-1 Cell.
International journal of molecular sciences, 26(3): pii:ijms26031184.
Piscirickettsia salmonis is the pathogen that has most affected the Chilean salmon industry for over 30 years. Considering the problems of excessive use of antibiotics, it is necessary to find new strategies to control this pathogen. Antivirulence therapy is an alternative to reduce the virulence of pathogens without affecting their growth. Polyphenolic compounds have been studied for their antiviral capacity. In this study, the capacity of quercetin and silybin to reduce the intracellular replication of P. salmonis in SHK-1 cells was evaluated. For this, three different infection protocols in Salmon Head Kidney-1(SHK-1) cells were used: co-incubation for 24 h, pre-incubation for 24 h prior to infection, and post-incubation for 24 h after infection. In addition, the effect of co-incubation in rainbow trout intestinal epithelial cells (RTgutGC) and the effect on the phagocytic capacity of SHK-1 cells were evaluated. The results obtained showed that quercetin and silybin decreased the intracellular replication of P. salmonis in SHK-1 cells when they were co-incubated for 24 h; however, they did not have the same effect in RTgutGC cells. On the other hand, both compounds decreased the phagocytosis of SHK-1 cells during co-incubation. These results are promising for the study of new treatments against P. salmonis.
Additional Links: PMID-39940952
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@article {pmid39940952,
year = {2025},
author = {Parra, M and Izquierdo, K and Rubio, M and de la Fuente, A and Tello, M and Modak, B},
title = {Quercetin and Silybin Decrease Intracellular Replication of Piscirickettsia salmonis in SHK-1 Cell.},
journal = {International journal of molecular sciences},
volume = {26},
number = {3},
pages = {},
doi = {10.3390/ijms26031184},
pmid = {39940952},
issn = {1422-0067},
support = {21212170//ANID/ ; 022341MC//DICYT/ ; },
mesh = {Animals ; *Quercetin/pharmacology ; *Silybin/pharmacology ; *Piscirickettsia/drug effects ; Cell Line ; Salmon/microbiology ; Fish Diseases/microbiology ; Oncorhynchus mykiss/microbiology ; Epithelial Cells/drug effects/microbiology/metabolism ; Piscirickettsiaceae Infections/microbiology ; Phagocytosis/drug effects ; Head Kidney/cytology ; },
abstract = {Piscirickettsia salmonis is the pathogen that has most affected the Chilean salmon industry for over 30 years. Considering the problems of excessive use of antibiotics, it is necessary to find new strategies to control this pathogen. Antivirulence therapy is an alternative to reduce the virulence of pathogens without affecting their growth. Polyphenolic compounds have been studied for their antiviral capacity. In this study, the capacity of quercetin and silybin to reduce the intracellular replication of P. salmonis in SHK-1 cells was evaluated. For this, three different infection protocols in Salmon Head Kidney-1(SHK-1) cells were used: co-incubation for 24 h, pre-incubation for 24 h prior to infection, and post-incubation for 24 h after infection. In addition, the effect of co-incubation in rainbow trout intestinal epithelial cells (RTgutGC) and the effect on the phagocytic capacity of SHK-1 cells were evaluated. The results obtained showed that quercetin and silybin decreased the intracellular replication of P. salmonis in SHK-1 cells when they were co-incubated for 24 h; however, they did not have the same effect in RTgutGC cells. On the other hand, both compounds decreased the phagocytosis of SHK-1 cells during co-incubation. These results are promising for the study of new treatments against P. salmonis.},
}
MeSH Terms:
show MeSH Terms
hide MeSH Terms
Animals
*Quercetin/pharmacology
*Silybin/pharmacology
*Piscirickettsia/drug effects
Cell Line
Salmon/microbiology
Fish Diseases/microbiology
Oncorhynchus mykiss/microbiology
Epithelial Cells/drug effects/microbiology/metabolism
Piscirickettsiaceae Infections/microbiology
Phagocytosis/drug effects
Head Kidney/cytology
RevDate: 2025-02-13
CmpDate: 2025-02-13
Dairy Consumption and the Colonic Mucosa-Associated Gut Microbiota in Humans-A Preliminary Investigation.
Nutrients, 17(3): pii:nu17030567.
BACKGROUND: Dairy consumption has been associated with various health outcomes that may be mediated by changes in gut microbiota.
METHODS: This cross-sectional study investigated the association between the colonic mucosa-associated gut microbiota and the self-reported intake of total dairy, milk, cheese, and yogurt. A total of 97 colonic mucosal biopsies collected from 34 polyp-free individuals were analyzed. Dairy consumption in the past year was assessed using a food frequency questionnaire. The 16S rRNA gene V4 region was amplified and sequenced. Operational taxonomic unit (OTU) classification was performed using the UPARSE and SILVA databases. OTU diversity and relative abundance were compared between lower vs. higher dairy consumption groups. Multivariable negative binomial regression models for panel data were used to estimate the incidence rate ratio and 95% confidence interval for bacterial counts and dairy consumption. False discovery rate-adjusted p values (q value) < 0.05 indicated statistical significance.
RESULTS: Higher total dairy and milk consumption and lower cheese consumption were associated with higher alpha microbial diversity (adjusted p values < 0.05). Higher total dairy and milk consumption was also associated with higher relative abundance of Faecalibacterium. Higher milk consumption was associated with higher relative abundance of Akkermansia. Higher total dairy and cheese consumption was associated with lower relative abundance of Bacteroides.
CONCLUSIONS: Dairy consumption may influence host health by modulating the structure and composition of the colonic adherent gut microbiota.
Additional Links: PMID-39940425
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PubMed:
Citation:
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@article {pmid39940425,
year = {2025},
author = {Chen, E and Ajami, NJ and White, DL and Liu, Y and Gurwara, S and Hoffman, K and Graham, DY and El-Serag, HB and Petrosino, JF and Jiao, L},
title = {Dairy Consumption and the Colonic Mucosa-Associated Gut Microbiota in Humans-A Preliminary Investigation.},
journal = {Nutrients},
volume = {17},
number = {3},
pages = {},
doi = {10.3390/nu17030567},
pmid = {39940425},
issn = {2072-6643},
support = {RP#140767//Cancer Prevention and Research Institute of Texas/ ; DK56338/DK/NIDDK NIH HHS/United States ; 001//Gillson Longenbaugh Foundation/ ; 001//Gillson Longenbaugh Foundation/ ; CX001430//U.S. Department of Veterans Affairs/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; Male ; Female ; Cross-Sectional Studies ; *Dairy Products/microbiology ; Middle Aged ; *Colon/microbiology ; *Intestinal Mucosa/microbiology ; Adult ; RNA, Ribosomal, 16S/genetics ; Bacteria/classification/genetics/isolation & purification ; Diet ; Aged ; Yogurt/microbiology ; },
abstract = {BACKGROUND: Dairy consumption has been associated with various health outcomes that may be mediated by changes in gut microbiota.
METHODS: This cross-sectional study investigated the association between the colonic mucosa-associated gut microbiota and the self-reported intake of total dairy, milk, cheese, and yogurt. A total of 97 colonic mucosal biopsies collected from 34 polyp-free individuals were analyzed. Dairy consumption in the past year was assessed using a food frequency questionnaire. The 16S rRNA gene V4 region was amplified and sequenced. Operational taxonomic unit (OTU) classification was performed using the UPARSE and SILVA databases. OTU diversity and relative abundance were compared between lower vs. higher dairy consumption groups. Multivariable negative binomial regression models for panel data were used to estimate the incidence rate ratio and 95% confidence interval for bacterial counts and dairy consumption. False discovery rate-adjusted p values (q value) < 0.05 indicated statistical significance.
RESULTS: Higher total dairy and milk consumption and lower cheese consumption were associated with higher alpha microbial diversity (adjusted p values < 0.05). Higher total dairy and milk consumption was also associated with higher relative abundance of Faecalibacterium. Higher milk consumption was associated with higher relative abundance of Akkermansia. Higher total dairy and cheese consumption was associated with lower relative abundance of Bacteroides.
CONCLUSIONS: Dairy consumption may influence host health by modulating the structure and composition of the colonic adherent gut microbiota.},
}
MeSH Terms:
show MeSH Terms
hide MeSH Terms
Humans
*Gastrointestinal Microbiome
Male
Female
Cross-Sectional Studies
*Dairy Products/microbiology
Middle Aged
*Colon/microbiology
*Intestinal Mucosa/microbiology
Adult
RNA, Ribosomal, 16S/genetics
Bacteria/classification/genetics/isolation & purification
Diet
Aged
Yogurt/microbiology
RevDate: 2025-02-13
CmpDate: 2025-02-13
Gut Microbiota Is Not Significantly Altered by Radioiodine Therapy.
Nutrients, 17(3): pii:nu17030395.
Purpose: Radiotherapy treatments are known to alter the gut microbiota. However, little is known regarding the effect of nuclear medicine treatments on gut microbiota, and it is established that nuclear medicine is inherently different from radiotherapy. To address this knowledge gap, we conducted a prospective study to identify changes in the gut microbiota of patients treated with [[131]I]NaI by comparing fecal samples before and after RAIT. Methods: Fecal samples of 64 patients (37 with thyroid cancer and 27 with hyperthyroidism) with indication for RAIT were collected 2 to 3 days before treatment and 8 to 10 days post-treatment. After DNA extraction, the gut microbiota's richness, diversity, and composition were analyzed by shotgun metagenomics. In addition, LEfSe was performed to compare compositional changes in specific bacteria. Results: Gut microbiome richness and diversity remained unchanged after RAIT, with few changes in its composition identified, especially in patients with hyperthyroidism. Conclusions: This study provides a conceptual and analytical basis for increasing our understanding of the effects of radiopharmaceuticals on gut microbiota. Our preliminary results indicate that RAIT, contrary to radiotherapy, does not cause major disruptions to the human gut microbiota.
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PubMed:
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@article {pmid39940254,
year = {2025},
author = {Barata, P and Oliveira, A and Soares, R and Fernandes, A},
title = {Gut Microbiota Is Not Significantly Altered by Radioiodine Therapy.},
journal = {Nutrients},
volume = {17},
number = {3},
pages = {},
doi = {10.3390/nu17030395},
pmid = {39940254},
issn = {2072-6643},
mesh = {Humans ; *Gastrointestinal Microbiome/radiation effects ; Female ; Middle Aged ; Male ; *Feces/microbiology ; *Iodine Radioisotopes ; *Hyperthyroidism/radiotherapy/microbiology ; Adult ; Prospective Studies ; Thyroid Neoplasms/radiotherapy/microbiology ; Aged ; Bacteria/classification/radiation effects/genetics/isolation & purification ; Metagenomics/methods ; },
abstract = {Purpose: Radiotherapy treatments are known to alter the gut microbiota. However, little is known regarding the effect of nuclear medicine treatments on gut microbiota, and it is established that nuclear medicine is inherently different from radiotherapy. To address this knowledge gap, we conducted a prospective study to identify changes in the gut microbiota of patients treated with [[131]I]NaI by comparing fecal samples before and after RAIT. Methods: Fecal samples of 64 patients (37 with thyroid cancer and 27 with hyperthyroidism) with indication for RAIT were collected 2 to 3 days before treatment and 8 to 10 days post-treatment. After DNA extraction, the gut microbiota's richness, diversity, and composition were analyzed by shotgun metagenomics. In addition, LEfSe was performed to compare compositional changes in specific bacteria. Results: Gut microbiome richness and diversity remained unchanged after RAIT, with few changes in its composition identified, especially in patients with hyperthyroidism. Conclusions: This study provides a conceptual and analytical basis for increasing our understanding of the effects of radiopharmaceuticals on gut microbiota. Our preliminary results indicate that RAIT, contrary to radiotherapy, does not cause major disruptions to the human gut microbiota.},
}
MeSH Terms:
show MeSH Terms
hide MeSH Terms
Humans
*Gastrointestinal Microbiome/radiation effects
Female
Middle Aged
Male
*Feces/microbiology
*Iodine Radioisotopes
*Hyperthyroidism/radiotherapy/microbiology
Adult
Prospective Studies
Thyroid Neoplasms/radiotherapy/microbiology
Aged
Bacteria/classification/radiation effects/genetics/isolation & purification
Metagenomics/methods
RevDate: 2025-02-12
CmpDate: 2025-02-13
The impact of regular sauerkraut consumption on the human gut microbiota: a crossover intervention trial.
Microbiome, 13(1):52.
BACKGROUND: Sauerkraut is a fermented food that has been suspected to have a beneficial impact on the gut microbiome, but scientific evidence is sparse. In this crossover intervention trial with 87 participants (DRKS00027007), we investigated the impact of daily consumption of fresh or pasteurized sauerkraut for 4 weeks on gut microbial composition and the metabolome in a healthy study population.
RESULTS: Using shotgun metagenomic sequencing, we observed changes in single bacterial species following fresh and pasteurized sauerkraut consumption. More pronounced changes were observed in the pasteurized sauerkraut intervention arm. Only pasteurized sauerkraut consumption increased serum short-chain fatty acids (SCFAs).
CONCLUSIONS: The gut microbiome of healthy individuals is rather resilient to short-term dietary interventions even though single species might be affected by sauerkraut consumption. Video Abstract.
Additional Links: PMID-39940045
PubMed:
Citation:
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@article {pmid39940045,
year = {2025},
author = {Schropp, N and Bauer, A and Stanislas, V and Huang, KD and Lesker, TR and Bielecka, AA and Strowig, T and Michels, KB},
title = {The impact of regular sauerkraut consumption on the human gut microbiota: a crossover intervention trial.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {52},
pmid = {39940045},
issn = {2049-2618},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Cross-Over Studies ; Male ; Female ; Adult ; *Bacteria/classification/genetics/isolation & purification ; *Fatty Acids, Volatile/metabolism ; *Fermented Foods/microbiology ; Middle Aged ; Feces/microbiology ; Metagenomics/methods ; Young Adult ; Metabolome ; Healthy Volunteers ; },
abstract = {BACKGROUND: Sauerkraut is a fermented food that has been suspected to have a beneficial impact on the gut microbiome, but scientific evidence is sparse. In this crossover intervention trial with 87 participants (DRKS00027007), we investigated the impact of daily consumption of fresh or pasteurized sauerkraut for 4 weeks on gut microbial composition and the metabolome in a healthy study population.
RESULTS: Using shotgun metagenomic sequencing, we observed changes in single bacterial species following fresh and pasteurized sauerkraut consumption. More pronounced changes were observed in the pasteurized sauerkraut intervention arm. Only pasteurized sauerkraut consumption increased serum short-chain fatty acids (SCFAs).
CONCLUSIONS: The gut microbiome of healthy individuals is rather resilient to short-term dietary interventions even though single species might be affected by sauerkraut consumption. Video Abstract.},
}
MeSH Terms:
show MeSH Terms
hide MeSH Terms
Humans
*Gastrointestinal Microbiome
*Cross-Over Studies
Male
Female
Adult
*Bacteria/classification/genetics/isolation & purification
*Fatty Acids, Volatile/metabolism
*Fermented Foods/microbiology
Middle Aged
Feces/microbiology
Metagenomics/methods
Young Adult
Metabolome
Healthy Volunteers
RevDate: 2025-02-12
A metagenomic 'dark matter' enzyme catalyses oxidative cellulose conversion.
Nature [Epub ahead of print].
The breakdown of cellulose is one of the most important reactions in nature[1,2] and is central to biomass conversion to fuels and chemicals[3]. However, the microfibrillar organization of cellulose and its complex interactions with other components of the plant cell wall poses a major challenge for enzymatic conversion[4]. Here, by mining the metagenomic 'dark matter' (unclassified DNA with unknown function) of a microbial community specialized in lignocellulose degradation, we discovered a metalloenzyme that oxidatively cleaves cellulose. This metalloenzyme acts on cellulose through an exo-type mechanism with C1 regioselectivity, resulting exclusively in cellobionic acid as a product. The crystal structure reveals a catalytic copper buried in a compact jelly-roll scaffold that features a flattened cellulose binding site. This metalloenzyme exhibits a homodimeric configuration that enables in situ hydrogen peroxide generation by one subunit while the other is productively interacting with cellulose. The secretome of an engineered strain of the fungus Trichoderma reesei expressing this metalloenzyme boosted the glucose release from pretreated lignocellulosic biomass under industrially relevant conditions, demonstrating its biotechnological potential. This discovery modifies the current understanding of bacterial redox enzymatic systems devoted to overcoming biomass recalcitrance[5-7]. Furthermore, it enables the conversion of agro-industrial residues into value-added bioproducts, thereby contributing to the transition to a sustainable and bio-based economy.
Additional Links: PMID-39939775
PubMed:
Citation:
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@article {pmid39939775,
year = {2025},
author = {Santos, CA and Morais, MAB and Mandelli, F and Lima, EA and Miyamoto, RY and Higasi, PMR and Araujo, EA and Paixão, DAA and Junior, JM and Motta, ML and Streit, RSA and Morão, LG and Silva, CBC and Wolf, LD and Terrasan, CRF and Bulka, NR and Diogo, JA and Fuzita, FJ and Colombari, FM and Santos, CR and Rodrigues, PT and Silva, DB and Grisel, S and Bernardes, JS and Terrapon, N and Lombard, V and Filho, AJC and Henrissat, B and Bissaro, B and Berrin, JG and Persinoti, GF and Murakami, MT},
title = {A metagenomic 'dark matter' enzyme catalyses oxidative cellulose conversion.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {39939775},
issn = {1476-4687},
abstract = {The breakdown of cellulose is one of the most important reactions in nature[1,2] and is central to biomass conversion to fuels and chemicals[3]. However, the microfibrillar organization of cellulose and its complex interactions with other components of the plant cell wall poses a major challenge for enzymatic conversion[4]. Here, by mining the metagenomic 'dark matter' (unclassified DNA with unknown function) of a microbial community specialized in lignocellulose degradation, we discovered a metalloenzyme that oxidatively cleaves cellulose. This metalloenzyme acts on cellulose through an exo-type mechanism with C1 regioselectivity, resulting exclusively in cellobionic acid as a product. The crystal structure reveals a catalytic copper buried in a compact jelly-roll scaffold that features a flattened cellulose binding site. This metalloenzyme exhibits a homodimeric configuration that enables in situ hydrogen peroxide generation by one subunit while the other is productively interacting with cellulose. The secretome of an engineered strain of the fungus Trichoderma reesei expressing this metalloenzyme boosted the glucose release from pretreated lignocellulosic biomass under industrially relevant conditions, demonstrating its biotechnological potential. This discovery modifies the current understanding of bacterial redox enzymatic systems devoted to overcoming biomass recalcitrance[5-7]. Furthermore, it enables the conversion of agro-industrial residues into value-added bioproducts, thereby contributing to the transition to a sustainable and bio-based economy.},
}
RevDate: 2025-02-12
CmpDate: 2025-02-12
Comparing the impact of landscape on the gut microbiome of Apis mellifera in Atlantic Forest and Caatinga Biomes.
Scientific reports, 15(1):5293.
The composition of the gut microbiota in animals can be influenced by a variety of intrinsic and extrinsic factors in the host, such as diet, physiological state, and genetics. This study aimed to compare the structural composition of the gut microbiota of Apis mellifera bees from two distinct Brazilian biomes, the Atlantic Forest and the Caatinga, using high throughput 16 S rRNA sequencing. We identified a core microbiota composed of seven genera present in all samples: Lactobacillus, Commensalibacter, Rhizobiaceae, Snodgrassella, Gilliamella, Orbaceae and Bifidobacterium. These taxa accounted for 63% of all bacterial genera in the dataset. Interestingly, we observed a significantly differential abundance of the genus Apibacter between bees from the two biomes, with a marked increase in bees from Atlantic Forest. However, the overall variance in the gut structural composition attributable to landscape type, while significant, was relatively low. Notably, none of the members of the core microbiota were differently abundant between the biomes. Understanding the magnitude of landscape-associated effects on the microbiota of bees in different biomes is crucial for the accurate assessment of the impact of anthropogenic factors. These findings provide important insights into the resilience and adaptability of the honey bee gut microbiome across contrasting environments, contributing to the development of conservation and sustainable management strategies for these essential pollinators.
Additional Links: PMID-39939365
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Citation:
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@article {pmid39939365,
year = {2025},
author = {Soares, KO and Da Rocha, TF and Hale, VL and Vasconcelos, PC and do Nascimento, LJ and da Silva, NMV and Rodrigues, AE and de Oliveira, CJB},
title = {Comparing the impact of landscape on the gut microbiome of Apis mellifera in Atlantic Forest and Caatinga Biomes.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {5293},
pmid = {39939365},
issn = {2045-2322},
support = {001//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; 001//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; 88881.311776/2018-01//CAPES-PrInt Project "Omic sciences applied to the prevention of antimicrobial resistance at the human-animal-environment interface-a one health approach/ ; 88881.311776/2018-01//CAPES-PrInt Project "Omic sciences applied to the prevention of antimicrobial resistance at the human-animal-environment interface-a one health approach/ ; 3136678/2020-0//Conselho Nacional de Pesquisa e Desenvolvimento/ ; 3136678/2020-0//Conselho Nacional de Pesquisa e Desenvolvimento/ ; },
mesh = {Animals ; Bees/microbiology ; *Gastrointestinal Microbiome ; *Forests ; Brazil ; *RNA, Ribosomal, 16S/genetics ; Bacteria/classification/genetics/isolation & purification ; Ecosystem ; },
abstract = {The composition of the gut microbiota in animals can be influenced by a variety of intrinsic and extrinsic factors in the host, such as diet, physiological state, and genetics. This study aimed to compare the structural composition of the gut microbiota of Apis mellifera bees from two distinct Brazilian biomes, the Atlantic Forest and the Caatinga, using high throughput 16 S rRNA sequencing. We identified a core microbiota composed of seven genera present in all samples: Lactobacillus, Commensalibacter, Rhizobiaceae, Snodgrassella, Gilliamella, Orbaceae and Bifidobacterium. These taxa accounted for 63% of all bacterial genera in the dataset. Interestingly, we observed a significantly differential abundance of the genus Apibacter between bees from the two biomes, with a marked increase in bees from Atlantic Forest. However, the overall variance in the gut structural composition attributable to landscape type, while significant, was relatively low. Notably, none of the members of the core microbiota were differently abundant between the biomes. Understanding the magnitude of landscape-associated effects on the microbiota of bees in different biomes is crucial for the accurate assessment of the impact of anthropogenic factors. These findings provide important insights into the resilience and adaptability of the honey bee gut microbiome across contrasting environments, contributing to the development of conservation and sustainable management strategies for these essential pollinators.},
}
MeSH Terms:
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Animals
Bees/microbiology
*Gastrointestinal Microbiome
*Forests
Brazil
*RNA, Ribosomal, 16S/genetics
Bacteria/classification/genetics/isolation & purification
Ecosystem
RevDate: 2025-02-12
Metagenomic Sequencing for Personalized Treatment in Pneumonia: Does Better Detection Lead to Better Outcomes?.
Chest, 167(2):300-302.
Additional Links: PMID-39939047
Publisher:
PubMed:
Citation:
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@article {pmid39939047,
year = {2025},
author = {Wu, BG and Zinter, MS},
title = {Metagenomic Sequencing for Personalized Treatment in Pneumonia: Does Better Detection Lead to Better Outcomes?.},
journal = {Chest},
volume = {167},
number = {2},
pages = {300-302},
doi = {10.1016/j.chest.2024.08.031},
pmid = {39939047},
issn = {1931-3543},
}
RevDate: 2025-02-12
Gut microbiome composition changes in obstructive sleep apnoea syndrome also in relation to excessive daytime sleepiness.
Brain research bulletin pii:S0361-9230(25)00063-2 [Epub ahead of print].
INTRODUCTION: Obstructive sleep apnoea syndrome (OSAS) is considered a risk factor for several comorbidities. Alteration in gut microbiome was documented in OSAS animal models and in paediatric patients. This study analysed gut microbiome composition in adult patients with OSAS and compared to controls. Further, the effect of excessive daytime sleepiness (EDS) on gut microbiome was evaluated.
METHODS: Adult patients with OSAS underwent polysomnographic recording and completed the Epworth Sleepiness Scale (ESS) to assess EDS. Faecal samples were collected and compared between patients and healthy controls. Composition, community diversity, differences in taxa abundance profiles and sample dysbiosis were evaluated through 16S metagenomics and multiple bioinformatics algorithms. OSAS patients were distributed in two groups according to EDS (ESS score≥10) to assess differences in clinical, polysomnographic and faecal data.
RESULTS: Twenty-three OSAS patients were compared to 44 controls. Patients presented significant differences of gut microbiome biodiversity, specifically in qualitative alpha diversity metrics (Faith's PD Kruskal-Wallis test, p-value=0.003; Number_of_Observed_Features, p value =0.001). OSAS patients tend to cluster together, at least for Jaccard and Unweighted UniFrac distance-based PERMANOVA tests (q-values=0.02 and =0.003, respectively). Several taxa were detected as different in abundance between OSAS patients and controls, although, globally, OSAS patients cannot be considered as "dysbiotic". Differences in bacteria composition were evident between OSAS patients with and those without EDS.
CONCLUSIONS: OSAS is associated with gut microbiome alteration in adult patients. EDS in OSAS seems to characterize a different gut microbiome composition, although it can be only hypothesized a gut-mediated effect on EDS in OSAS.
Additional Links: PMID-39938754
Publisher:
PubMed:
Citation:
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@article {pmid39938754,
year = {2025},
author = {Fernandes, M and Palmieri, O and Castellana, S and Spanetta, M and Latiano, T and Lupo, C and Masi, C and Cardile, C and Calvello, C and Izzi, F and Placidi, F and Mazza, T and Mercuri, NB and Latiano, A and Liguori, C},
title = {Gut microbiome composition changes in obstructive sleep apnoea syndrome also in relation to excessive daytime sleepiness.},
journal = {Brain research bulletin},
volume = {},
number = {},
pages = {111251},
doi = {10.1016/j.brainresbull.2025.111251},
pmid = {39938754},
issn = {1873-2747},
abstract = {INTRODUCTION: Obstructive sleep apnoea syndrome (OSAS) is considered a risk factor for several comorbidities. Alteration in gut microbiome was documented in OSAS animal models and in paediatric patients. This study analysed gut microbiome composition in adult patients with OSAS and compared to controls. Further, the effect of excessive daytime sleepiness (EDS) on gut microbiome was evaluated.
METHODS: Adult patients with OSAS underwent polysomnographic recording and completed the Epworth Sleepiness Scale (ESS) to assess EDS. Faecal samples were collected and compared between patients and healthy controls. Composition, community diversity, differences in taxa abundance profiles and sample dysbiosis were evaluated through 16S metagenomics and multiple bioinformatics algorithms. OSAS patients were distributed in two groups according to EDS (ESS score≥10) to assess differences in clinical, polysomnographic and faecal data.
RESULTS: Twenty-three OSAS patients were compared to 44 controls. Patients presented significant differences of gut microbiome biodiversity, specifically in qualitative alpha diversity metrics (Faith's PD Kruskal-Wallis test, p-value=0.003; Number_of_Observed_Features, p value =0.001). OSAS patients tend to cluster together, at least for Jaccard and Unweighted UniFrac distance-based PERMANOVA tests (q-values=0.02 and =0.003, respectively). Several taxa were detected as different in abundance between OSAS patients and controls, although, globally, OSAS patients cannot be considered as "dysbiotic". Differences in bacteria composition were evident between OSAS patients with and those without EDS.
CONCLUSIONS: OSAS is associated with gut microbiome alteration in adult patients. EDS in OSAS seems to characterize a different gut microbiome composition, although it can be only hypothesized a gut-mediated effect on EDS in OSAS.},
}
RevDate: 2025-02-12
Viral Metagenomics of Hematophagous Insects Collected in the Carajas Mining Complex, Pará State, Brazil.
Acta tropica pii:S0001-706X(25)00030-0 [Epub ahead of print].
Hematophagous insects are vectors of viruses that cause diseases in humans and animals worldwide. Mosquitoes (Culicidae), biting midges (Ceratopogonidae), and sandflies (Psychodidae) were collected in three municipalities (Marabá, Canaã dos Carajás, and Curionópolis) in the state of Pará, Brazil, in 2019. Morphological keys were used for the taxonomic identification of insect species. High-throughput sequencing and metagenomic analysis were employed to characterize the viromes of the hematophagous insects. We characterized the virome of 839 insects grouped into 14 pools. A total of 729 million paired reads were generated, with 12 million viral sequences (3% of the reads). The families Reoviridae, Myoviridae, Retroviridae, and Poxviridae were found in all samples of this study. Phylogenies of RNA-dependent RNA polymerase (RdRp) from viruses of the families Chuviridae, Dicistroviridae, Flaviviridae, Iflaviridae, Mesoniviridae, Phenuiviridae, and Rhabdoviridae were performed. In this study, the first isolation of the Guaico Culex Virus (GCXV) in the northern region of Brazil was obtained from a pool of Culex (Melanoconion) spp. mosquitoes collected in Curionópolis. The data obtained in this study demonstrate that the Carajás region has an ecosystem rich in viruses. Additional studies are needed to understand the dynamics of viruses in vectors, vertebrates, and the human population in the region.
Additional Links: PMID-39938727
Publisher:
PubMed:
Citation:
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@article {pmid39938727,
year = {2025},
author = {Braga, CM and da Silva, SP and Neto, JPN and Medeiros, DBA and Cruz, ACR and Sena do Nascimento, BL and Pinheiro, LRS and Martins, LC},
title = {Viral Metagenomics of Hematophagous Insects Collected in the Carajas Mining Complex, Pará State, Brazil.},
journal = {Acta tropica},
volume = {},
number = {},
pages = {107551},
doi = {10.1016/j.actatropica.2025.107551},
pmid = {39938727},
issn = {1873-6254},
abstract = {Hematophagous insects are vectors of viruses that cause diseases in humans and animals worldwide. Mosquitoes (Culicidae), biting midges (Ceratopogonidae), and sandflies (Psychodidae) were collected in three municipalities (Marabá, Canaã dos Carajás, and Curionópolis) in the state of Pará, Brazil, in 2019. Morphological keys were used for the taxonomic identification of insect species. High-throughput sequencing and metagenomic analysis were employed to characterize the viromes of the hematophagous insects. We characterized the virome of 839 insects grouped into 14 pools. A total of 729 million paired reads were generated, with 12 million viral sequences (3% of the reads). The families Reoviridae, Myoviridae, Retroviridae, and Poxviridae were found in all samples of this study. Phylogenies of RNA-dependent RNA polymerase (RdRp) from viruses of the families Chuviridae, Dicistroviridae, Flaviviridae, Iflaviridae, Mesoniviridae, Phenuiviridae, and Rhabdoviridae were performed. In this study, the first isolation of the Guaico Culex Virus (GCXV) in the northern region of Brazil was obtained from a pool of Culex (Melanoconion) spp. mosquitoes collected in Curionópolis. The data obtained in this study demonstrate that the Carajás region has an ecosystem rich in viruses. Additional studies are needed to understand the dynamics of viruses in vectors, vertebrates, and the human population in the region.},
}
RevDate: 2025-02-12
The impact of sleeve gastrectomy on MASH development by regulating the composition of gut microbiota and metabolic homeostasis.
Biochemical and biophysical research communications, 752:151466 pii:S0006-291X(25)00180-9 [Epub ahead of print].
The prevalence of metabolic dysfunction-associated steatohepatitis (MASH) is increasing annually, which is a global public health issue. Although clinical trials are lacking, observational studies indicate that bariatric surgery can alleviate the progression of MASH. Here, we performed sleeve gastrectomy (SG) and Sham surgery on 8-week-old mice, and then fed a AMLN diet for 24 weeks to construct a diet-inducted MASH mice model after 4-week post-surgery recovery. Applying a multi-omics approach combining metagenomics, metabolomics, and transcriptomics, we found that SG prevents the development of hepatic steatosis, inflammation, and fibrosis in MASH mice not only by significantly altering the structure of gut microbiota including s_Akkermansia muciniphila, s_Alistiples dispar, g_Helicobacter and s_uc_Oscillospiraceae, but also by modulating the levels of serum metabolites including l-arginine and taurocholic acid (TCA). These results suggest that SG and the alteration of gut microbiota and its related serum metabolites can be served as the effective therapeutic strategies for MASH.
Additional Links: PMID-39938449
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PubMed:
Citation:
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@article {pmid39938449,
year = {2025},
author = {Ye, L and Yao, Z and Xuan, Q and Liu, Q and Bo, T},
title = {The impact of sleeve gastrectomy on MASH development by regulating the composition of gut microbiota and metabolic homeostasis.},
journal = {Biochemical and biophysical research communications},
volume = {752},
number = {},
pages = {151466},
doi = {10.1016/j.bbrc.2025.151466},
pmid = {39938449},
issn = {1090-2104},
abstract = {The prevalence of metabolic dysfunction-associated steatohepatitis (MASH) is increasing annually, which is a global public health issue. Although clinical trials are lacking, observational studies indicate that bariatric surgery can alleviate the progression of MASH. Here, we performed sleeve gastrectomy (SG) and Sham surgery on 8-week-old mice, and then fed a AMLN diet for 24 weeks to construct a diet-inducted MASH mice model after 4-week post-surgery recovery. Applying a multi-omics approach combining metagenomics, metabolomics, and transcriptomics, we found that SG prevents the development of hepatic steatosis, inflammation, and fibrosis in MASH mice not only by significantly altering the structure of gut microbiota including s_Akkermansia muciniphila, s_Alistiples dispar, g_Helicobacter and s_uc_Oscillospiraceae, but also by modulating the levels of serum metabolites including l-arginine and taurocholic acid (TCA). These results suggest that SG and the alteration of gut microbiota and its related serum metabolites can be served as the effective therapeutic strategies for MASH.},
}
RevDate: 2025-02-12
Comparison of clinical metagenomics with 16S rDNA Sanger sequencing for the bacteriological diagnosis of culture-negative samples.
International journal of medical microbiology : IJMM, 318:151650 pii:S1438-4221(25)00006-2 [Epub ahead of print].
BACKGROUND: Currently, diagnosis of bacterial infections is based on culture, possibly followed by the amplification and sequencing (Sanger method) of the 16S rDNA - encoding gene when cultures are negative. Clinical metagenomics (CMg), i.e. the sequencing of a sample's entire nucleic acids, may allow for the identification of bacteria not detected by conventional methods. Here, we tested the performance of CMg compared to 16S rDNA sequencing (Sanger) in 50 patients with suspected bacterial infection but negative cultures.
METHODS: This is a prospective cohort study. Fifty patients (73 samples) with negative culture and a 16S rDNA sequencing demand (Sanger) were recruited from two sites. On the same samples, CMg (Illumina NextSeq) was also performed and compared to 16S rDNA Sanger sequencing. Bacteria were identified using MetaPhlAn4.
RESULTS: Among the 73 samples, 20 (27 %, 17 patients) had a clinically relevant 16S rDNA Sanger sequencing result (used for patient management) while 11 (15 %, 9 patients) were considered contaminants. At the patient level, the sensitivity of CMg was 70 % (12/17) compared to 16S rDNA. In samples negative for 16S rDNA Sanger sequencing (n = 53), CMg identified clinically-relevant bacteria in 10 samples (19 %, 10 patients) with 14 additional bacteria.
CONCLUSIONS: CMg was not 100 % sensitive when compared to 16S, supporting that it may not be a suitable replacement. However, CMg did find additional bacteria in samples negative for 16S rDNA Sanger. CMg could therefore be positioned as a complementary to 16S rDNA Sanger sequencing.
Additional Links: PMID-39938404
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PubMed:
Citation:
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@article {pmid39938404,
year = {2025},
author = {d'Humières, C and Haviari, S and Petitjean, M and Deconinck, L and Gueye, S and Peiffer-Smadja, N and Chalal, L and Beldjoudi, N and Rossi, G and Nguyen, Y and Burdet, C and Perrineau, S and Le Pluart, D and Rahli, R and Thy, M and Szychowiak, P and Lescure, X and Leflon-Guibout, V and de Lastours, V and Ruppé, E},
title = {Comparison of clinical metagenomics with 16S rDNA Sanger sequencing for the bacteriological diagnosis of culture-negative samples.},
journal = {International journal of medical microbiology : IJMM},
volume = {318},
number = {},
pages = {151650},
doi = {10.1016/j.ijmm.2025.151650},
pmid = {39938404},
issn = {1618-0607},
abstract = {BACKGROUND: Currently, diagnosis of bacterial infections is based on culture, possibly followed by the amplification and sequencing (Sanger method) of the 16S rDNA - encoding gene when cultures are negative. Clinical metagenomics (CMg), i.e. the sequencing of a sample's entire nucleic acids, may allow for the identification of bacteria not detected by conventional methods. Here, we tested the performance of CMg compared to 16S rDNA sequencing (Sanger) in 50 patients with suspected bacterial infection but negative cultures.
METHODS: This is a prospective cohort study. Fifty patients (73 samples) with negative culture and a 16S rDNA sequencing demand (Sanger) were recruited from two sites. On the same samples, CMg (Illumina NextSeq) was also performed and compared to 16S rDNA Sanger sequencing. Bacteria were identified using MetaPhlAn4.
RESULTS: Among the 73 samples, 20 (27 %, 17 patients) had a clinically relevant 16S rDNA Sanger sequencing result (used for patient management) while 11 (15 %, 9 patients) were considered contaminants. At the patient level, the sensitivity of CMg was 70 % (12/17) compared to 16S rDNA. In samples negative for 16S rDNA Sanger sequencing (n = 53), CMg identified clinically-relevant bacteria in 10 samples (19 %, 10 patients) with 14 additional bacteria.
CONCLUSIONS: CMg was not 100 % sensitive when compared to 16S, supporting that it may not be a suitable replacement. However, CMg did find additional bacteria in samples negative for 16S rDNA Sanger. CMg could therefore be positioned as a complementary to 16S rDNA Sanger sequencing.},
}
RevDate: 2025-02-12
Metagenomic analysis of viral community during different municipal solid waste collection and treatment processes: Fate, hosts, and antibiotic resistance genes.
Journal of hazardous materials, 489:137520 pii:S0304-3894(25)00432-7 [Epub ahead of print].
Municipal solid waste (MSW) serves as effective reservoirs of viruses and virus-associated antibiotic resistance genes (vir_ARGs), posing potential risks to human health. However, the composition of viral communities in different MSW collection and treatment processes remains unclear. Here, we profiled the viral communities and vir_ARGs in MSW leachate and aerosol samples from different MSW facilities based on metagenomic and virus enrichment-based viromic sequencings. Results showed that Microviridae and Caudoviricetes_Unclassified were the dominant viral families. Viral hosts were mainly distributed in the specific functional taxa of Bacillota. Additionally, the leachate properties and bacterial community structures significantly correlated with the viral community structures, implying that these environmental factors were the important drivers for viral distribution. The co-occurrence network analysis revealed the complex relationships between vir_ARGs and bacteria, suggesting that certain vir_ARGs have a broad host spectrum. Significant differences of viruses and vir_ARGs were observed between different sample types, but the viruses and vir_ARGs showed no significant differences across three sampling sites. Overall, this study highlights novel perspectives on the changes in viruses and vir_ARGs across the whole MSW collection and treatment processes, and provides valuable insights about the environmental factors affecting the profile of viral communities. These findings are crucial for elucidating the potential risks linked to the transmission of both viruses and ARGs.
Additional Links: PMID-39938372
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PubMed:
Citation:
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@article {pmid39938372,
year = {2025},
author = {Guo, Y and Zhao, Y and Lin, K and Zheng, Q and Zhou, T},
title = {Metagenomic analysis of viral community during different municipal solid waste collection and treatment processes: Fate, hosts, and antibiotic resistance genes.},
journal = {Journal of hazardous materials},
volume = {489},
number = {},
pages = {137520},
doi = {10.1016/j.jhazmat.2025.137520},
pmid = {39938372},
issn = {1873-3336},
abstract = {Municipal solid waste (MSW) serves as effective reservoirs of viruses and virus-associated antibiotic resistance genes (vir_ARGs), posing potential risks to human health. However, the composition of viral communities in different MSW collection and treatment processes remains unclear. Here, we profiled the viral communities and vir_ARGs in MSW leachate and aerosol samples from different MSW facilities based on metagenomic and virus enrichment-based viromic sequencings. Results showed that Microviridae and Caudoviricetes_Unclassified were the dominant viral families. Viral hosts were mainly distributed in the specific functional taxa of Bacillota. Additionally, the leachate properties and bacterial community structures significantly correlated with the viral community structures, implying that these environmental factors were the important drivers for viral distribution. The co-occurrence network analysis revealed the complex relationships between vir_ARGs and bacteria, suggesting that certain vir_ARGs have a broad host spectrum. Significant differences of viruses and vir_ARGs were observed between different sample types, but the viruses and vir_ARGs showed no significant differences across three sampling sites. Overall, this study highlights novel perspectives on the changes in viruses and vir_ARGs across the whole MSW collection and treatment processes, and provides valuable insights about the environmental factors affecting the profile of viral communities. These findings are crucial for elucidating the potential risks linked to the transmission of both viruses and ARGs.},
}
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RJR Experience and Expertise
Researcher
Robbins holds BS, MS, and PhD degrees in the life sciences. He served as a tenured faculty member in the Zoology and Biological Science departments at Michigan State University. He is currently exploring the intersection between genomics, microbial ecology, and biodiversity — an area that promises to transform our understanding of the biosphere.
Educator
Robbins has extensive experience in college-level education: At MSU he taught introductory biology, genetics, and population genetics. At JHU, he was an instructor for a special course on biological database design. At FHCRC, he team-taught a graduate-level course on the history of genetics. At Bellevue College he taught medical informatics.
Administrator
Robbins has been involved in science administration at both the federal and the institutional levels. At NSF he was a program officer for database activities in the life sciences, at DOE he was a program officer for information infrastructure in the human genome project. At the Fred Hutchinson Cancer Research Center, he served as a vice president for fifteen years.
Technologist
Robbins has been involved with information technology since writing his first Fortran program as a college student. At NSF he was the first program officer for database activities in the life sciences. At JHU he held an appointment in the CS department and served as director of the informatics core for the Genome Data Base. At the FHCRC he was VP for Information Technology.
Publisher
While still at Michigan State, Robbins started his first publishing venture, founding a small company that addressed the short-run publishing needs of instructors in very large undergraduate classes. For more than 20 years, Robbins has been operating The Electronic Scholarly Publishing Project, a web site dedicated to the digital publishing of critical works in science, especially classical genetics.
Speaker
Robbins is well-known for his speaking abilities and is often called upon to provide keynote or plenary addresses at international meetings. For example, in July, 2012, he gave a well-received keynote address at the Global Biodiversity Informatics Congress, sponsored by GBIF and held in Copenhagen. The slides from that talk can be seen HERE.
Facilitator
Robbins is a skilled meeting facilitator. He prefers a participatory approach, with part of the meeting involving dynamic breakout groups, created by the participants in real time: (1) individuals propose breakout groups; (2) everyone signs up for one (or more) groups; (3) the groups with the most interested parties then meet, with reports from each group presented and discussed in a subsequent plenary session.
Designer
Robbins has been engaged with photography and design since the 1960s, when he worked for a professional photography laboratory. He now prefers digital photography and tools for their precision and reproducibility. He designed his first web site more than 20 years ago and he personally designed and implemented this web site. He engages in graphic design as a hobby.
RJR Picks from Around the Web (updated 11 MAY 2018 )
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Treating Disease with Fecal Transplantation
Fossils of miniature humans (hobbits) discovered in Indonesia
Paleontology
Dinosaur tail, complete with feathers, found preserved in amber.
Astronomy
Mysterious fast radio burst (FRB) detected in the distant universe.
Big Data & Informatics
Big Data: Buzzword or Big Deal?
Hacking the genome: Identifying anonymized human subjects using publicly available data.