@article {pmid39056464,
year = {2024},
author = {Czolk, R and Codreanu-Morel, F and de Nies, L and Busi, SB and Halder, R and Hunewald, O and Boehm, TM and Hefeng, FQ and De Beaufort, C and Wilmes, P and Ollert, M and Kuehn, A},
title = {Fecal IgE Analyses Reveal a Role for Stratifying Peanut-Allergic Patients.},
journal = {Journal of investigational allergology & clinical immunology},
volume = {},
number = {},
pages = {0},
doi = {10.18176/jiaci.1008},
pmid = {39056464},
issn = {1018-9068},
abstract = {BACKGROUND AND OBJECTIVE: Peanut allergy (PA) is an IgE-mediated food allergy with variable clinical outcomes. Mild-to-severe symptoms affect various organs and, often, the gastrointestinal tract. The role of intestine-derived IgE antibodies in astrointestinal PA symptoms is poorly understood. This study aimed to examine fecal IgE responses in PA as a novel approach to patient endotyping.

METHODS: Feces and serum samples were collected from peanut-allergic and healthy children (n=26) to identify IgE and cytokines using multiplex assays. Shotgun metagenomics DNA sequencing and allergen database comparisons made it possible to identify microbial peptides with homology to known allergens.

RESULTS: Compared to controls, fecal IgE signatures showed broad diversity and increased levels for 13 allergens, including food, venom, contact, and respiratory allergens (P<.01-.0001). Overall, fecal IgE patterns were negatively correlated compared to sera IgE patterns in PA patients, with the greatest differences recorded for peanut allergens (P<.0001). For 83% of the allergens recognized by fecal IgE, we found bacterial homologs from PA patients' gut microbiome (eg, thaumatin-like protein Acinetobacter baumannii vs Act d 2, 109/124 aa identical). Compared to controls, PA patients had higher levels of fecal IgA, IL-22, and auto-IgE binding to their own fecal proteins (P<.001). Finally, levels of fecal IgE correlated with abdominal pain scores (P<.0001), suggesting a link between local IgE production and clinical outcomes.

CONCLUSION: Fecal IgE release from the intestinal mucosa could be an underlying mechanism of severe abdominal pain through the association between leaky gut epithelia and anticommensal TH2 responses in PA.},
}

@article {pmid39056112,
year = {2024},
author = {Dong, J and Zhang, J and Cheng, S and Qin, B and Jin, K and Chen, B and Zhang, Y and Lu, J},
title = {A high-fat diet induced depression-like phenotype via hypocretin-HCRTR1 mediated inflammation activation.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d4fo00210e},
pmid = {39056112},
issn = {2042-650X},
abstract = {Background: A high-fat diet (HFD) is generally associated with an increased risk of mental disorders that constitute a sizeable worldwide health. A HFD results in the gut microbiota-brain axis being altered and linked to mental disorders. Hypocretin-1, which can promote appetite, has been previously confirmed to be associated with depression. However, no exact relationship has been found for hypocretin between depression and HFDs. Methods: Adult male SD rats were randomly assigned to either a HFD or a normal diet for eight weeks, followed by behavioral tests and plasma biochemical analyses. Then, we investigated the protein and mRNA levels of inflammation-related factors in the hippocampus. We also observed morphological changes in brain microglia and lipid accumulation. Additionally, metagenomic and metabolomic analyses of gut microbiomes were performed. 3T3-L1 cells were utilized in vitro to investigate the impact of hypocretin receptor 1 antagonists (SB334867) on lipid accumulation. To consider the connection between the brain and adipose tissue, we used a conditioned medium (CM) treated with 3T3-L1 cells to observe the activation and phagocytosis of BV2 cells. Following a 12-week period of feeding a HFD to C57BL/6 mice, a three-week intervention period was initiated during which the administration of SB334867 was observed. This was followed by a series of assessments, including monitoring of body weight changes and emotional problems, as well as attention to plasma biochemical levels and microglial cell phenotypes in the brain. Results: The HFD rats displayed anxiety and depressive-like behaviors. HFD rats exhibited increased plasma HDL, LDL, and TC levels. A HFD also causes an increase in hypocretin-1 and hypocretin-2 in the hypothalamus. Metagenomics and metabolomics revealed that the HFD caused an increase in the relative abundance of associated inflammatory bacteria and decreased the abundance of anti-inflammatory and bile acid metabolites. Compared with the CTR group, hippocampal microglia in the HFD group were significantly activated and accompanied by lipid deposition. At the same time, protein and mRNA expression levels of inflammation-related factors were increased. We found that SB334867 could significantly reduce lipid accumulation in 3T3-L1 cells after differentiation. The expression of inflammatory factors decreased in the SB334867 group. The administration of SB334867 was found to reverse the adverse effects of the HFD on body weight, depressive-like behaviour and anxiety-like mood. Furthermore, this treatment was associated with improvements in plasma biochemical levels and a reduction in the number of microglia in the brain. Conclusions: In summary, our results demonstrated that a HFD induced anxiety and depressive-like behaviors, which may be linked to the increased hypocretin-1 level and lipid accumulation. Supplementation with SB334867 improved the above. These observations highlight the possibility of hypocretin-1 inducing the risk of HFD-associated emotional dysfunctions.},
}

@article {pmid39055941,
year = {2024},
author = {Magnusson, A and Jabbari Shiadeh, SM and Ardalan, M and Swolin-Eide, D and Elfvin, A},
title = {Gut microbiota differences in five-year-old children that were born preterm with a history of necrotizing enterocolitis: A pilot trial.},
journal = {iScience},
volume = {27},
number = {7},
pages = {110325},
doi = {10.1016/j.isci.2024.110325},
pmid = {39055941},
issn = {2589-0042},
abstract = {The study explores the long-term effects of necrotizing enterocolitis (NEC) on gut microbiota in preterm infants by analyzing stool samples from 5-year-old children using shotgun metagenomic sequencing. It compares children with a history of NEC, treated surgically or medically, to preterm controls without NEC. Findings reveal persistent gut microbiota dysbiosis in NEC children, with reduced species diversity and evenness, especially in those treated surgically. The surgical NEC group had a lower Shannon index, indicating less microbial diversity. Significant differences in taxonomic profiles were observed, mainly influenced by surgical treatment. These results underscore the lasting impact of NEC and its treatment on gut microbiota, suggesting a need for strategies addressing long-term dysbiosis.},
}

@article {pmid39055364,
year = {2024},
author = {Roman-Reyna, V and Crandall, SG},
title = {Seeing in the dark: a metagenomic approach can illuminate the drivers of plant disease.},
journal = {Frontiers in plant science},
volume = {15},
number = {},
pages = {1405042},
doi = {10.3389/fpls.2024.1405042},
pmid = {39055364},
issn = {1664-462X},
}

@article {pmid39055239,
year = {2023},
author = {Sande, C and Boston, ZJ and Kalan, LR and Brennan, MB},
title = {Next Steps: Studying Diabetic Foot Infections with Next-Generation Molecular Assays.},
journal = {Current infectious disease reports},
volume = {25},
number = {12},
pages = {323-330},
doi = {10.1007/s11908-023-00822-8},
pmid = {39055239},
issn = {1523-3847},
abstract = {PURPOSE OF REVIEW: In 2019, the International Working Group on the Diabetic Foot voiced six concerns regarding the use of molecular microbiology techniques for routine diagnosis of infection complicating diabetic foot ulcers. The purpose of this review is to evaluate contemporary evidence addressing each of these concerns and describe promising avenues for continued development of molecular microbiology assays.

RECENT FINDINGS: Since 2019, the feasibility of conducting metagenomic and metatranscriptomic studies on diabetic foot ulcer samples has been shown. However, these preliminary studies used small samples with concerns for selection bias. We await larger-scale, longitudinal studies, potentially using the recently formed Diabetic Foot Consortium, to identify microbiome profiles associated with infection and patient outcomes. How these results would translate into a clinical diagnostic requires further clarification.

SUMMARY: High-throughput molecular microbiology techniques are not yet ready for clinical adoption as first-line diagnostics. However, moving from amplicon sequencing to metagenomic and metatranscriptomic studies has the potential to significantly accelerate development of assays that might meaningfully impact patient care.},
}

@article {pmid39054868,
year = {2024},
author = {Sorwar, E and Oliveira, JIN and Malar C, M and Krüger, M and Corradi, N},
title = {Assembly and comparative analyses of the Geosiphon pyriformis metagenome.},
journal = {Environmental microbiology},
volume = {26},
number = {7},
pages = {e16681},
doi = {10.1111/1462-2920.16681},
pmid = {39054868},
issn = {1462-2920},
support = {RGPIN2020-05643//Natural Sciences and Engineering Research Council/ ; RGPAS-2020-00033//Discovery Accelerator Supplements Program/ ; IT16902//Mitacs Accelerate Program/ ; },
mesh = {*Symbiosis ; *Metagenome ; Phylogeny ; Cyanobacteria/genetics/classification/metabolism ; Nostoc/genetics/metabolism ; Metagenomics ; Genome, Fungal ; Genome, Bacterial ; },
abstract = {Geosiphon pyriformis, a representative of the fungal sub-phylum Glomeromycotina, is unique in its endosymbiosis with cyanobacteria within a fungal cell. This symbiotic relationship occurs in bladders containing nuclei of G. pyriformis, Mollicutes-like bacterial endosymbionts (MRE), and photosynthetically active and dividing cells of Nostoc punctiforme. Recent genome analyses have shed light on the biology of G. pyriformis, but the genome content and biology of its endosymbionts remain unexplored. To fill this gap, we gathered and examined metagenomic data from the bladders of G. pyriformis, where N. punctiforme and MRE are located. This ensures that our analyses are focused on the organs directly involved in the symbiosis. By comparing this data with the genetic information of related cyanobacteria and MREs from other species of Arbuscular Mycorrhizal Fungi, we aimed to reveal the genetic content of these organisms and understand how they interact at a genetic level to establish a symbiotic relationship. Our analyses uncovered significant gene expansions in the Nostoc endosymbiont, particularly in mobile elements and genes potentially involved in xenobiotic degradation. We also confirmed that the MRE of Glomeromycotina are monophyletic and possess a highly streamlined genome. These genomes show dramatic differences in both structure and content, including the presence of enzymes involved in environmental sensing and stress response.},
}

*Symbiosis
*Metagenome
Phylogeny
Cyanobacteria/genetics/classification/metabolism
Nostoc/genetics/metabolism
Metagenomics
Genome, Fungal
Genome, Bacterial

@article {pmid39054479,
year = {2024},
author = {Boldrini, L and Chiloiro, G and Di Franco, S and Romano, A and Smiljanic, L and Tran, EH and Bono, F and Charles Davies, D and Lopetuso, L and De Bonis, M and Minucci, A and Giacò, L and Cusumano, D and Placidi, L and Giannarelli, D and Sala, E and Gambacorta, MA},
title = {MOREOVER: multiomics MR-guided radiotherapy optimization in locally advanced rectal cancer.},
journal = {Radiation oncology (London, England)},
volume = {19},
number = {1},
pages = {94},
pmid = {39054479},
issn = {1748-717X},
support = {Next Generation Clinician Scientist_ID 28614//Fondazione AIRC per la ricerca sul cancro ETS/ ; Next Generation Clinician Scientist_ID 28614//Fondazione AIRC per la ricerca sul cancro ETS/ ; Next Generation Clinician Scientist_ID 28614//Fondazione AIRC per la ricerca sul cancro ETS/ ; Next Generation Clinician Scientist_ID 28614//Fondazione AIRC per la ricerca sul cancro ETS/ ; Next Generation Clinician Scientist_ID 28614//Fondazione AIRC per la ricerca sul cancro ETS/ ; Next Generation Clinician Scientist_ID 28614//Fondazione AIRC per la ricerca sul cancro ETS/ ; Next Generation Clinician Scientist_ID 28614//Fondazione AIRC per la ricerca sul cancro ETS/ ; Next Generation Clinician Scientist_ID 28614//Fondazione AIRC per la ricerca sul cancro ETS/ ; Next Generation Clinician Scientist_ID 28614//Fondazione AIRC per la ricerca sul cancro ETS/ ; Next Generation Clinician Scientist_ID 28614//Fondazione AIRC per la ricerca sul cancro ETS/ ; Next Generation Clinician Scientist_ID 28614//Fondazione AIRC per la ricerca sul cancro ETS/ ; Next Generation Clinician Scientist_ID 28614//Fondazione AIRC per la ricerca sul cancro ETS/ ; Next Generation Clinician Scientist_ID 28614//Fondazione AIRC per la ricerca sul cancro ETS/ ; Next Generation Clinician Scientist_ID 28614//Fondazione AIRC per la ricerca sul cancro ETS/ ; Next Generation Clinician Scientist_ID 28614//Fondazione AIRC per la ricerca sul cancro ETS/ ; Next Generation Clinician Scientist_ID 28614//Fondazione AIRC per la ricerca sul cancro ETS/ ; Next Generation Clinician Scientist_ID 28614//Fondazione AIRC per la ricerca sul cancro ETS/ ; },
mesh = {*Rectal Neoplasms/radiotherapy/pathology/therapy ; Humans ; Neoadjuvant Therapy/methods ; Gastrointestinal Microbiome ; Magnetic Resonance Imaging ; Radiotherapy, Image-Guided/methods ; Chemoradiotherapy/methods ; Circulating Tumor DNA/genetics ; Biomarkers, Tumor ; Genomics/methods ; Male ; Female ; Multiomics ; },
abstract = {BACKGROUND: Complete response prediction in locally advanced rectal cancer (LARC) patients is generally focused on the radiomics analysis of staging MRI. Until now, omics information extracted from gut microbiota and circulating tumor DNA (ctDNA) have not been integrated in composite biomarkers-based models, thereby omitting valuable information from the decision-making process. In this study, we aim to integrate radiomics with gut microbiota and ctDNA-based genomics tracking during neoadjuvant chemoradiotherapy (nCRT).

METHODS: The main hypothesis of the MOREOVER study is that the incorporation of composite biomarkers with radiomics-based models used in the THUNDER-2 trial will improve the pathological complete response (pCR) predictive power of such models, paving the way for more accurate and comprehensive personalized treatment approaches. This is due to the inclusion of actionable omics variables that may disclose previously unknown correlations with radiomics. Aims of this study are: - to generate longitudinal microbiome data linked to disease resistance to nCRT and postulate future therapeutic strategies in terms of both type of treatment and timing, such as fecal microbiota transplant in non-responding patients. - to describe the genomics pattern and ctDNA data evolution throughout the nCRT treatment in order to support the prediction outcome and identify new risk-category stratification agents. - to mine and combine collected data through integrated multi-omics approaches (radiomics, metagenomics, metabolomics, metatranscriptomics, human genomics, ctDNA) in order to increase the performance of the radiomics-based response predictive model for LARC patients undergoing nCRT on MR-Linac.

EXPERIMENTAL DESIGN: The objective of the MOREOVER project is to enrich the phase II THUNDER-2 trial (NCT04815694) with gut microbiota and ctDNA omics information, by exploring the possibility to enhance predictive performance of the developed model. Longitudinal ctDNA genomics, microbiome and genomics data will be analyzed on 7 timepoints: prior to nCRT, during nCRT on a weekly basis and prior to surgery. Specific modelling will be performed for data harvested, according to the TRIPOD statements.

DISCUSSION: We expect to find differences in fecal microbiome, ctDNA and radiomics profiles between the two groups of patients (pCR and not pCR). In addition, we expect to find a variability in the stability of the considered omics features over time. The identified profiles will be inserted into dedicated modelling solutions to set up a multiomics decision support system able to achieve personalized treatments.},
}

*Rectal Neoplasms/radiotherapy/pathology/therapy
Humans
Neoadjuvant Therapy/methods
Gastrointestinal Microbiome
Magnetic Resonance Imaging
Radiotherapy, Image-Guided/methods
Chemoradiotherapy/methods
Circulating Tumor DNA/genetics
Biomarkers, Tumor
Genomics/methods
Male
Female
Multiomics

@article {pmid39054413,
year = {2024},
author = {Rajeev, S and Nishan, K and Dipesh, T and M, TC and Manu, V and Vida, A and Juliana, G and Surendra Kumar, M and Binod, G and Runa, J},
title = {Investigation of acute encephalitis syndrome with implementation of metagenomic next generation sequencing in Nepal.},
journal = {BMC infectious diseases},
volume = {24},
number = {1},
pages = {734},
pmid = {39054413},
issn = {1471-2334},
mesh = {Humans ; Nepal/epidemiology ; *Metagenomics/methods ; Adolescent ; Child, Preschool ; Child ; *High-Throughput Nucleotide Sequencing/methods ; Male ; Female ; *Acute Febrile Encephalopathy/epidemiology/virology ; Young Adult ; Adult ; Infant ; Encephalitis, Japanese/epidemiology/virology ; },
abstract = {BACKGROUND: The causative agents of Acute Encephalitis Syndrome remain unknown in 68-75% of the cases. In Nepal, the cases are tested only for Japanese encephalitis, which constitutes only about 15% of the cases. However, there could be several organisms, including vaccine-preventable etiologies that cause acute encephalitis, when identified could direct public health efforts for prevention, including addressing gaps in vaccine coverage.

OBJECTIVES: This study employs metagenomic next-generation-sequencing in the investigation of underlying causative etiologies contributing to acute encephalitis syndrome in Nepal.

METHODS: In this study, we investigated 90, Japanese-encephalitis-negative, banked cerebrospinal fluid samples that were collected as part of a national surveillance network in 2016 and 2017. Randomization was done to include three age groups (< 5-years; 5-14-years; >15-years). Only some metadata (age and gender) were available. The investigation was performed in two batches which included total nucleic-acid extraction, followed by individual library preparation (DNA and RNA) and sequencing on Illumina iSeq100. The genomic data were interpreted using Chan Zuckerberg-ID and confirmed with polymerase-chain-reaction.

RESULTS: Human-alphaherpes-virus 2 and Enterovirus-B were seen in two samples. These hits were confirmed by qPCR and semi-nested PCR respectively. Most of the other samples were marred by low abundance of pathogen, possible freeze-thaw cycles, lack of process controls and associated clinical metadata.

CONCLUSION: From this study, two documented causative agents were revealed through metagenomic next-generation-sequencing. Insufficiency of clinical metadata, process controls, low pathogen abundance and absence of standard procedures to collect and store samples in nucleic-acid protectants could have impeded the study and incorporated ambiguity while correlating the identified hits to infection. Therefore, there is need of standardized procedures for sample collection, inclusion of process controls and clinical metadata. Despite challenging conditions, this study highlights the usefulness of mNGS to investigate diseases with unknown etiologies and guide development of adequate clinical-management-algorithms and outbreak investigations in Nepal.},
}

Humans
Nepal/epidemiology
*Metagenomics/methods
Adolescent
Child, Preschool
Child
*High-Throughput Nucleotide Sequencing/methods
Male
Female
*Acute Febrile Encephalopathy/epidemiology/virology
Young Adult
Adult
Infant
Encephalitis, Japanese/epidemiology/virology

@article {pmid39054372,
year = {2024},
author = {Pu, Y and Sun, Z and Zhang, H and Huang, Q and Wang, Z and Mei, Z and Wang, P and Kong, M and Yang, W and Lin, C and Zhou, X and Lin, S and Huang, Q and Huang, L and Sun, L and Yuan, C and Xu, Q and Tang, H and Wang, X and Zheng, Y},
title = {Gut microbial features and circulating metabolomic signatures of frailty in older adults.},
journal = {Nature aging},
volume = {},
number = {},
pages = {},
pmid = {39054372},
issn = {2662-8465},
abstract = {Frailty, a multidimensional indicator of suboptimal aging, reflects cumulative declines across multiple physiological systems. Although age-related changes have been reported in gut microbiota, their role in healthy aging remains unclear. In this study, we calculated frailty index (FI) from 33 health-related items to reflect the overall health status of 1,821 older adults (62-96 years, 55% female) and conducted multi-omics analysis using gut metagenomic sequencing data and plasma metabolomic data. We identified 18 microbial species and 17 metabolites shifted along with frailty severity, with stronger links observed in females. The associations of nine species, including various Clostridium species and Faecalibacterium prausnitzii, with FI were reproducible in two external populations. Plasma glycerol levels, white blood cell count and kidney function partially mediated these associations. A composite microbial score derived from FI significantly predicted 2-year mortality (adjusted hazard ratio across extreme quartiles, 2.86; 95% confidence interval, 1.38-5.93), highlighting the potential of microbiota-based strategies for risk stratification in older adults.},
}

@article {pmid39054286,
year = {2024},
author = {Shoemaker, A and Maritan, A and Cosar, S and Nupp, S and Menchaca, A and Jackson, T and Dang, A and Baxter, BK and Colman, DR and Dunham, EC and Boyd, ES},
title = {Wood-Ljungdahl pathway encoding anaerobes facilitate low-cost primary production in hypersaline sediments at Great Salt Lake, Utah.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiae105},
pmid = {39054286},
issn = {1574-6941},
abstract = {Little is known of primary production in dark hypersaline ecosystems despite the prevalence of such environments on Earth today and throughout its geologic history. Here we generated and analyzed metagenome assembled genomes (MAGs) organized as operational taxonomic units (OTUs) from three depth intervals along a 30 cm sediment core from the north arm of Great Salt Lake, Utah. The sediments and associated porewaters were saturated with NaCl, exhibited redox gradients with depth, and harbored nitrogen depleted organic carbon. Metabolic predictions of MAGs representing 36 total OTUs recovered from the core indicated that communities transitioned from aerobic and heterotrophic at the surface to anaerobic and autotrophic at depth. Dark CO2 fixation was detected in sediments and the primary mode of autotrophy was predicted to be via the Wood-Ljungdahl pathway. This included novel hydrogenotrophic acetogens affiliated with the bacterial class Candidatus Bipolaricaulia. Minor populations were dependent on the Calvin Cycle and the reverse Tricarboxylic Acid Cycle, including in a novel Thermoplasmatota MAG. These results are interpreted to reflect the favorability of and selectability for populations that operate the lowest energy requiring CO2 fixation pathway known, the Wood-Ljungdahl (WL) pathway, in anoxic and hypersaline conditions that together impart a higher energy demand on cells.},
}

@article {pmid39053646,
year = {2024},
author = {Jiang, Y and Huang, X and Zhou, H and Wang, M and Wang, S and Ren, X and He, G and Xu, J and Wang, Q and Dai, M and Xiong, Y and Zhong, L and He, X and Deng, X and Pan, Y and Xu, Y and Cai, H and Jin, S and Wang, H and Huang, L},
title = {Clinical characteristics and prognosis of patients with severe pneumonia with Pneumocystis jirovecii colonization: A multicenter, retrospective study.},
journal = {Chest},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chest.2024.07.140},
pmid = {39053646},
issn = {1931-3543},
abstract = {BACKGROUND: For decades, the incidence and clinical characteristics of Pneumocystis jirovecii (P. jirovecii) colonization in patients with severe pneumonia was remained unclear.

RESEARCH QUESTION: What are the clinical features and outcomes associated with P. jirovecii colonization in individuals diagnosed with severe pneumonia?

STUDY DESIGN AND METHODS: In this multicenter, retrospective, matched study, severe pneumonia patients who underwent bronchoalveolar lavage clinical metagenomics from 2019 to 2023 in the ICUs of 17 medical centers were enrolled. Patients were diagnosed based on clinical metagenomics, pulmonary CT scans, and clinical presentations. Clinical data were collected retrospectively, and according to propensity score matching and Cox multivariate regression analysis, the prognosis of patients with P. jirovecii colonization was compared to that of P. jirovecii-negative patients.

RESULTS: 40% of P. jirovecii positive patients are considered to have P. jirovecii colonization. P. jirovecii colonization group had a higher proportion of patients with immunosuppression and a lower lymphocyte count compared to P. jirovecii-negative group. More frequent detection of cytomegalovirus, Epstein-Barr virus, human herpesvirus-6B, human herpesvirus-7, and torque teno virus in the lungs was associated with P. jirovecii colonization than with P. jirovecii negativity. By constructing two cohorts through propensity score matching, we incorporated codetected microorganisms and clinical features into a Cox proportional hazards model and revealed that P. jirovecii colonization was an independent risk factor for mortality in severe pneumonia patients. According to sensitivity analyses, which included or excluded codetected microorganisms, as well as patients not receiving TMP-SMX treatment, similar conclusions were reached.

INTERPRETATION: Immunosuppression and a reduced lymphocyte count were identified as risk factors for P. jirovecii colonization in non-PCP patients. More frequent detection of various viruses was observed in P. jirovecii colonization patients, and P. jirovecii colonization was associated with an increased 28-day mortality in patients with severe pneumonia.},
}

@article {pmid39053208,
year = {2024},
author = {Kong, Z and Wang, H and Wang, H and Man, S and Yan, Q},
title = {Magnetite-mediated shifts in denitrifying consortia in bioelectrochemical system: Insights into species selection and metabolic dynamics.},
journal = {Water research},
volume = {262},
number = {},
pages = {122132},
doi = {10.1016/j.watres.2024.122132},
pmid = {39053208},
issn = {1879-2448},
abstract = {Conductive materials, such as magnetite, are recognized for their ability to enhance electron transfer and stimulate microbial metabolic activities. This study aimed to elucidate the metabolic potential and species interactions of dominant microbial species within complex communities influenced by magnetite. It indicated that the optimal dosage of magnetite at 4.5 mg/cm[2], would significantly improve denitrification efficiency and then reduce the time for removing 50 mg/L nitrate by 24.33 %. This enhancement was attributed to the reduced charge transfer resistance and the promoted formation of extracellular polymeric substances (EPS) facilitated by magnetite. Metagenomic analysis revealed that magnetite addition mitigated the competition among truncated denitrifiers for downstream nitrogen species, diminished the contribution of bacteria with complete nitrogen metabolism pathways to denitrification, and fostered a transition towards co-denitrification through interspecies cooperation, consequently leading to decreased nitrite accumulation and increased tolerance to nitrate shock loads. Furthermore, an in-depth study on a key species, Geobacter anodireducens JN93 within the bioelectrochemical system revealed that while magnetite with varying Fe(II) and Fe(III) ratios improved denitrification performance, the metabolic potential of Geobacter sp. varied for different nitrogen metabolism pathways. Collectively, this research provides insights into the microecological effects of magnetite on denitrifying consortia by shifting interspecific interactions via enhanced electron transfer.},
}

@article {pmid39052829,
year = {2024},
author = {Chen, L and Chen, A and Zhang, XD and Saenz Robles, MT and Han, HS and Xiao, Y and Xiao, G and Pipas, JM and Weitz, DA},
title = {Targeted whole-genome recovery of single viral species in a complex environmental sample.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {121},
number = {31},
pages = {e2404727121},
doi = {10.1073/pnas.2404727121},
pmid = {39052829},
issn = {1091-6490},
support = {5R01AI153156//US National institute for health/ ; },
mesh = {*Genome, Viral/genetics ; *Simian virus 40/genetics/isolation & purification ; Metagenomics/methods ; Humans ; Adenoviruses, Human/genetics/isolation & purification ; Sewage/virology ; },
abstract = {Characterizing unknown viruses is essential for understanding viral ecology and preparing against viral outbreaks. Recovering complete genome sequences from environmental samples remains computationally challenging using metagenomics, especially for low-abundance species with uneven coverage. We present an experimental method for reliably recovering complete viral genomes from complex environmental samples. Individual genomes are encapsulated into droplets and amplified using multiple displacement amplification. A unique gene detection assay, which employs an RNA-based probe and an exonuclease, selectively identifies droplets containing the target viral genome. Labeled droplets are sorted using a microfluidic sorter, and genomes are extracted for sequencing. We demonstrate this method's efficacy by spiking two known viral genomes, Simian virus 40 (SV40, 5,243 bp) and Human Adenovirus 5 (HAd5, 35,938 bp), into a sewage sample with a final abundance in the droplets of around 0.1% and 0.015%, respectively. We achieve 100% recovery of the complete sequence of the spiked-in SV40 genome with uniform coverage distribution. For the larger HAd5 genome, we cover approximately 99.4% of its sequence. Notably, genome recovery is achieved with as few as one sorted droplet, which enables the recovery of any desired genomes in complex environmental samples, regardless of their abundance. This method enables single-genome whole-genome amplification and targeting characterizations of rare viral species and will facilitate our ability to access the mutational profile in single-virus genomes and contribute to an improved understanding of viral ecology.},
}

*Genome, Viral/genetics
*Simian virus 40/genetics/isolation & purification
Metagenomics/methods
Humans
Adenoviruses, Human/genetics/isolation & purification
Sewage/virology

@article {pmid39052651,
year = {2024},
author = {Fofanova, TY and Karandikar, UC and Auchtung, JM and Wilson, RL and Valentin, AJ and Britton, RA and Grande-Allen, KJ and Estes, MK and Hoffman, K and Ramani, S and Stewart, CJ and Petrosino, JF},
title = {A novel system to culture human intestinal organoids under physiological oxygen content to study microbial-host interaction.},
journal = {PloS one},
volume = {19},
number = {7},
pages = {e0300666},
doi = {10.1371/journal.pone.0300666},
pmid = {39052651},
issn = {1932-6203},
mesh = {Humans ; *Organoids/microbiology/metabolism ; *Oxygen/metabolism ; *Coculture Techniques/methods ; *Intestinal Mucosa/microbiology/metabolism/cytology ; Gastrointestinal Microbiome ; Host Microbial Interactions ; Bacteria, Anaerobic/growth & development/metabolism ; Intestines/microbiology/cytology ; Bacteroides thetaiotaomicron/metabolism ; },
abstract = {Mechanistic investigation of host-microbe interactions in the human gut are hindered by difficulty of co-culturing microbes with intestinal epithelial cells. On one hand the gut bacteria are a mix of facultative, aerotolerant or obligate anaerobes, while the intestinal epithelium requires oxygen for growth and function. Thus, a coculture system that can recreate these contrasting oxygen requirements is critical step towards our understanding microbial-host interactions in the human gut. Here, we demonstrate Intestinal Organoid Physoxic Coculture (IOPC) system, a simple and cost-effective method for coculturing anaerobic intestinal bacteria with human intestinal organoids (HIOs). Using commensal anaerobes with varying degrees of oxygen tolerance, such as nano-aerobe Bacteroides thetaiotaomicron and strict anaerobe Blautia sp., we demonstrate that IOPC can successfully support 24-48 hours HIO-microbe coculture. The IOPC recapitulates the contrasting oxygen conditions across the intestinal epithelium seen in vivo. The IOPC cultured HIOs showed increased barrier integrity, and induced expression of immunomodulatory genes. A transcriptomic analysis suggests that HIOs from different donors show differences in the magnitude of their response to coculture with anaerobic bacteria. Thus, the IOPC system provides a robust coculture setup for investigating host-microbe interactions in complex, patient-derived intestinal tissues, that can facilitate the study of mechanisms underlying the role of the microbiome in health and disease.},
}

Humans
*Organoids/microbiology/metabolism
*Oxygen/metabolism
*Coculture Techniques/methods
*Intestinal Mucosa/microbiology/metabolism/cytology
Gastrointestinal Microbiome
Host Microbial Interactions
Bacteria, Anaerobic/growth & development/metabolism
Intestines/microbiology/cytology
Bacteroides thetaiotaomicron/metabolism

@article {pmid39052319,
year = {2024},
author = {Liu, B and Qi, L and Zheng, Y and Zhang, C and Zhou, J and An, Z and Wang, B and Lin, Z and Yao, C and Wang, Y and Yin, G and Dong, H and Li, X and Liang, X and Han, P and Liu, M and Zhang, G and Cui, Y and Hou, L},
title = {Four years of climate warming reduced dark carbon fixation in coastal wetlands.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrae138},
pmid = {39052319},
issn = {1751-7370},
abstract = {Dark carbon fixation (DCF), conducted mainly by chemoautotrophs, contributes greatly to primary production and the global carbon budget. Understanding the response of DCF process to climate warming in coastal wetlands is of great significance for model optimization and climate change prediction. Here, based on a four-year field warming experiment (average annual temperature increase of 1.5°C), DCF rates were observed to be significantly inhibited by warming in coastal wetlands (average annual DCF decline of 21.6%, and estimated annual loss of 0.08-1.5 Tg C yr-1 in global coastal marshes), thus causing a positive climate feedback. Under climate warming, chemoautotrophic microbial abundance and biodiversity, which were jointly affected by environmental changes such as soil organic carbon and water content, were recognized as significant drivers directly affecting DCF rates. Metagenomic analysis further revealed that climate warming may alter the pattern of DCF carbon sequestration pathways in coastal wetlands, increasing the relative importance of the 3HP/4HB cycle, whereas the relative importance of the dominant chemoautotrophic carbon fixation pathways (CBB cycle and W-L pathway) may decrease due to warming stress. Collectively, our work uncovers the feedback mechanism of microbially mediated DCF to climate warming in coastal wetlands, and emphasizes a decrease in carbon sequestration through DCF activities in this globally important ecosystem under a warming climate.},
}

@article {pmid39051781,
year = {2024},
author = {Fahnøe, U and Madsen, LW and Christensen, PB and Sølund, CS and Mollerup, S and Pinholt, M and Weis, N and Øvrehus, A and Bukh, J},
title = {Effect of direct-acting antivirals on the titers of human pegivirus 1 during treatment of chronic hepatitis C patients.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0064124},
doi = {10.1128/spectrum.00641-24},
pmid = {39051781},
issn = {2165-0497},
abstract = {UNLABELLED: Coinfections with human pegivirus 1 (HPgV-1) are common in chronic hepatitis C virus (HCV) patients. However, little is known about whether HPgV-1 is affected by direct-acting antivirals during HCV treatment. Metagenomic analysis and reverse transcriptase-quantitative PCR (RT-qPCR) were performed on RNA from the plasma of 88 selected chronic HCV patients undergoing medical treatment. Twenty (23%) of these HCV patients had HPgV-1 coinfections and were followed by RT-qPCR during treatment and follow-up to investigate HPgV-1 RNA titers. Recovered sequences could be assembled to complete HPgV-1 genomes, and most formed a genotype 2 subclade. All HPgV-1 viral genomic regions were under negative purifying selection. Glecaprevir/pibrentasvir treatment in five patients did not consistently lower the genome titers of HPgV-1. In contrast, a one log10 drop of HPgV-1 titers at week 2 was observed in 10 patients during treatment with sofosbuvir-containing regimens, sustained to the end of treatment (EOT) and in two cases decreasing to below the detection limit of the assay. For the five patients treated with ledipasvir/sofosbuvir with the inclusion of pegylated interferon, titers decreased to below the detection limit at week 2 and remained undetectable to EOT. Subsequently, the HPgV-1 titer rebounded to pretreatment levels for all patients. In conclusion, we found that HCV treatment regimens that included the polymerase inhibitor sofosbuvir resulted in decreases in HPgV-1 titers, and the addition of pegylated interferon increased the effect on patients with coinfections. This points to the high specificity of protease and NS5A inhibitors toward HCV and the more broad-spectrum activity of sofosbuvir and especially pegylated interferon.

IMPORTANCE: Human pegivirus 1 coinfections are common in hepatitis C virus (HCV) patients, persisting for years. However, little is known about how pegivirus coinfections are affected by treatment with pangenotypic direct-acting antivirals (DAAs) against HCV. We identified human pegivirus by metagenomic analysis of chronic HCV patients undergoing protease, NS5A, and polymerase inhibitor treatment, in some patients with the addition of pegylated interferon, and followed viral kinetics of both viruses to investigate treatment effects. Only during HCV DAA treatment regimens that included the more broad-spectrum drug sofosbuvir could we detect a consistent decline in pegivirus titers that, however, rebounded to pretreatment levels after treatment cessation. The addition of pegylated interferon gave the highest effect with pegivirus titers decreasing to below the assay detection limit, but without clearance. These results reveal the limited effect of frontline HCV drugs on the closest related human virus, but sofosbuvir appeared to have the potential to be repurposed for other viral diseases.},
}

@article {pmid39051424,
year = {2024},
author = {Ti, J and Ning, Z and Zhang, M and Wang, S and Gan, S and Xu, Z and Di, H and Kong, S and Sun, W and He, Z},
title = {Characterization the microbial diversity and functional genes in the multi-component contaminated groundwater in a petrochemical site.},
journal = {Water environment research : a research publication of the Water Environment Federation},
volume = {96},
number = {7},
pages = {e11085},
doi = {10.1002/wer.11085},
pmid = {39051424},
issn = {1554-7531},
support = {42330714//National Natural Science Foundation of China/ ; D2021504025//Natural Science Foundation of Hebei Province/ ; },
mesh = {*Groundwater/microbiology/chemistry ; *Water Pollutants, Chemical/metabolism ; *Petroleum ; Bacteria/classification/genetics/metabolism ; Hydrocarbons/metabolism ; RNA, Ribosomal, 16S/genetics ; Biodegradation, Environmental ; Biodiversity ; Water Microbiology ; },
abstract = {Microorganisms in groundwater at petroleum hydrocarbon (PHC)-contaminated sites are crucial for PHC natural attenuation. Studies mainly focused on the microbial communities and functions in groundwater contaminated by PHC only. However, due to diverse raw and auxiliary materials and the complex production processes, in some petrochemical sites, groundwater suffered multi-component contamination, but the microbial structure remains unclear. To solve the problem, in the study, a petrochemical enterprise site, where the groundwater suffered multi-component pollution by PHC and sulfates, was selected. Using hydrochemistry, 16S rRNA gene, and metagenomic sequencing analyses, the relationships among electron acceptors, microbial diversity, functional genes, and their interactions were investigated. Results showed that different production processes led to different microbial structures. Overall, pollution reduced species richness but increased the abundance of specific species. The multi-component contamination multiplied a considerable number of hydrocarbon-degrading and sulfate-reducing microorganisms, and the introduced sulfates might have promoted the biodegradation of PHC. PRACTITIONER POINTS: The compound pollution of the site changed the microbial community structure. Sulfate can promote the degradation of petroleum hydrocarbons by hydrocarbon-degrading microorganisms. The combined contamination of petroleum hydrocarbons and sulfates will decrease the species richness but increase the abundance of endemic species.},
}

*Groundwater/microbiology/chemistry
*Water Pollutants, Chemical/metabolism
*Petroleum
Bacteria/classification/genetics/metabolism
Hydrocarbons/metabolism
RNA, Ribosomal, 16S/genetics
Biodegradation, Environmental
Biodiversity
Water Microbiology

@article {pmid39050838,
year = {2024},
author = {Li, E and Zhu, Q and Lv, Z and Xie, S and Zhang, C and Li, W and Mi, L and Liu, Q and Wang, Y and Lu, X},
title = {Visceral Leishmaniasis: A Case Confirmed by Metagenomic Next-Generation Sequencing from Northwestern China.},
journal = {Infection and drug resistance},
volume = {17},
number = {},
pages = {3153-3158},
pmid = {39050838},
issn = {1178-6973},
abstract = {Visceral leishmaniasis (VL), also known as kala-azar. It is characterized by prolonged intermittent fever, anemia, splenomegaly, hepatomegaly, and skin darkening. VL is primarily endemic in regions, such as Brazil, East Africa, and India. However, Northern Xinjiang, which is located in northwestern China, is considered a low-incidence area for VL, contributing to its status as a neglected infectious disease. In this report, we present a case of VL caused by Leishmania donovani that was diagnosed using metagenomic next-generation sequencing (mNGS). This case underscores the diagnostic value of mNGS, particularly in regions with low incidence of VL.},
}

@article {pmid39050835,
year = {2024},
author = {Chen, J and Liu, Y and Huang, S and Pang, Z and Wei, Q and Liu, Y and Qin, H and Chen, Y},
title = {Spinal Infections? mNGS Combined with Microculture and Pathology for Answers.},
journal = {Infection and drug resistance},
volume = {17},
number = {},
pages = {3025-3034},
pmid = {39050835},
issn = {1178-6973},
abstract = {INTRODUCTION: This study evaluates the efficacy of metagenomic next-generation sequencing (mNGS) in diagnosing spinal infections and developing therapeutic regimens that combine mNGS, microbiological cultures, and pathological investigations.

METHODS: Data were collected from 108 patients with suspected spinal infections between January 2022 and December 2023. Lesion tissues were obtained via C-arm assisted puncture or open surgery for mNGS, conventional microbiological culture, and pathological analysis. Personalized antimicrobial therapies were tailored based on these findings, with follow-up evaluations 7 days postoperatively. The sensitivity and specificity of mNGS were assessed, along with its impact on treatment and prognosis.

RESULTS: mNGS showed a significantly higher positive detection rate (61.20%) compared to conventional microbiological culture (30.80%) and PCT (28%). mNGS demonstrated greater sensitivity (79.41%) and negative predictive value (63.16%) than cultures (25% and 22.58%, respectively), with no significant difference in specificity and positive predictive value. Seven days post-surgery, a significant reduction in neutrophil percentage (NEUT%) was observed, though decreases in white blood cell count (WBC), erythrocyte sedimentation rate (ESR), and C-reactive protein (CRP) were not statistically significant. At the last follow-up, significant improved in Visual Analogue Scale (VAS) scores, Oswestry Disability Index (ODI), and Japanese Orthopaedic Association (JOA) scores were noted.

CONCLUSION: mNGS outperforms traditional microbiological culture in pathogen detection, especially for rare and critical pathogens. Treatment protocols combining mNGS, microbiological cultures, and pathological examinations are effective and provide valuable clinical insights for treating spinal infections.},
}

@article {pmid39050829,
year = {2024},
author = {Sun, Y and Li, Z and Li, Y and Zhang, C and Wang, M and Yu, W and Liu, G and Wang, S},
title = {The First Infant Anaerobic Meningitis Infected by Prevotella bivia: A Case Report and Literature Review.},
journal = {Infection and drug resistance},
volume = {17},
number = {},
pages = {3081-3088},
pmid = {39050829},
issn = {1178-6973},
abstract = {Anaerobic bacterial meningitis is a serious infection of the central nervous system (CNS) that leads to severe neurological complications, resulting in high levels of disability and mortality worldwide. However, accurately diagnosing and isolating the responsible pathogens remains challenging due to the difficulty in culturing anaerobic bacteria, as they require harsh anaerobic culture conditions. Anaerobic bacteria have rarely been reported in meningitis, especially in children. This report details the first infant with anaerobic meningitis caused by Prevotella bivia. Additionally, we present a case of infant anaerobic meningitis caused by P. bivia, detected using metagenomics next-generation sequencing (mNGS). Our clinical experience highlights the importance of early identification of Prevotella spp. through mNGS and anaerobic culture, the effectiveness of antimicrobial medications, and the timely implementation of carefully planned precision therapeutic regimens. Furthermore, we have conducted a comprehensive review of 10 cases of Prevotella spp. infection, summarized their clinical and laboratory examination characteristics, and identified their commonalities.},
}

@article {pmid39050629,
year = {2024},
author = {Vala, FD and Lende, SR and Solanki, VK and Jora, K and Desai, R and Sharma, P and Nathani, N and Mootapally, C},
title = {Melodious tuning of microbial dynamics in biofloc, cage, and pond culturing system: a study on Pangasius pangasius fish gut microbiome.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1434312},
pmid = {39050629},
issn = {1664-302X},
abstract = {Aquaculture, a rapidly expanding sector, meets the global surging demand for aquatic food. Pangasius, a highly valued freshwater species, has seen a significant increase in demand due to its adaptability and potential for high yields, making it a promising candidate for aquaculture in India. This study investigates the gut microbiome composition of Pangasius pangasius fish cultured in three different systems (biofloc, cage, and pond). Metagenomic DNA extraction and 16S rRNA gene-targeted sequencing were performed. Outcomes revealed distinct microbial compositions across culture types, with significant differences in species richness and diversity, specifically in the biofloc system, compared to cages and ponds. Taxonomic analysis identified prevalent phyla such as Firmicutes and Fusobacteriota, with varying abundances among culture systems. The genus-level analysis highlighted dominant genera such as Cetobacterium and WWE3. Functional profiling indicated differences in enzymatic activity and metabolic pathways, emphasizing each culture sample type's unique microbial community structures. Notably, the microbiota from BF samples exhibited significant differences and unique metabolic pathways compared to the microbiota from C and P samples, which showed greater similarity and shared several common metabolic pathways. These findings highlight substantial differences in microbial diversity across the culturing systems, reflecting the microbiota's ability to adapt to specific environments and their potential role in promoting fish growth within those environments. Overall, this study provides insights into the gut microbiome diversity and functionality in Pangasius pangasius across different aquaculture environments, contributing to a better understanding of host-microbe interactions and aquaculture management strategies.},
}

@article {pmid39050248,
year = {2024},
author = {Weston, M and Hu, H and Li, X},
title = {PSPI: A deep learning approach for prokaryotic small protein identification.},
journal = {Frontiers in genetics},
volume = {15},
number = {},
pages = {1439423},
pmid = {39050248},
issn = {1664-8021},
abstract = {Small Proteins (SPs) are pivotal in various cellular functions such as immunity, defense, and communication. Despite their significance, identifying them is still in its infancy. Existing computational tools are tailored to specific eukaryotic species, leaving only a few options for SP identification in prokaryotes. In addition, these existing tools still have suboptimal performance in SP identification. To fill this gap, we introduce PSPI, a deep learning-based approach designed specifically for predicting prokaryotic SPs. We showed that PSPI had a high accuracy in predicting generalized sets of prokaryotic SPs and sets specific to the human metagenome. Compared with three existing tools, PSPI was faster and showed greater precision, sensitivity, and specificity not only for prokaryotic SPs but also for eukaryotic ones. We also observed that the incorporation of (n, k)-mers greatly enhances the performance of PSPI, suggesting that many SPs may contain short linear motifs. The PSPI tool, which is freely available at https://www.cs.ucf.edu/∼xiaoman/tools/PSPI/, will be useful for studying SPs as a tool for identifying prokaryotic SPs and it can be trained to identify other types of SPs as well.},
}

@article {pmid39049923,
year = {2024},
author = {Treviso, RL and Sant'Anna, V and Fabricio, MF and Ayub, MAZ and Brandelli, A and Hickert, LR},
title = {Time and temperature influence on physicochemical, microbiological, and sensory profiles of yerba mate kombucha.},
journal = {Journal of food science and technology},
volume = {61},
number = {9},
pages = {1733-1742},
pmid = {39049923},
issn = {0022-1155},
abstract = {UNLABELLED: The present work aimed to evaluate the features of yerba mate kombucha during 7 days of fermentation at either 25 ºC or 30 ºC, monitoring physicochemical changes, sensory profile, and sensorial acceptance. The symbiotic microbial culture of active bacteria and yeasts (SCOBY) at the beginning and the end of the bioprocess was also identified. The yerba mate kombuchas fermented at 25 ºC for 5 days or 30 ºC for 4 days were suitable for consumption according to Brazilian standards. Acetic acid, ethanol, and chlorophyll contents were dependent on fermentation time and temperature, unlike the total phenolic content. The main yeast and bacterium in SCOBY were Brettanomyces bruxellensis and Komagataeibacter rhaeticus, respectively, which remained dominant when fermentation was conducted for up to 7 days at both temperatures. Fermentation of yerba mate infusion led to products characterized by sourness, vinegar bitter, and fermented flavors and aromas, making the acceptance of non-fermented Yerba mate preferable to fermented infusions.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13197-024-05951-z.},
}

@article {pmid39049845,
year = {2024},
author = {Yang, M and Liu, ZQ and Wang, Y and Luo, LL and Qiao, LN},
title = {Successful treatment of diffuse alveolar hemorrhage secondary to Mycoplasma pneumoniae complicated with hemophagocytic lymphohistiocytosis in children: a case report and non-systematic literature review.},
journal = {Frontiers in pediatrics},
volume = {12},
number = {},
pages = {1404872},
pmid = {39049845},
issn = {2296-2360},
abstract = {BACKGROUND: After quarantine-related measures were completely lifted in China, the respiratory infection rate of children caused by Mycoplasma pneumoniae (MP) increased significantly, and MP infection may lead to rare severe intra- and extrapulmonary manifestation. Hemophagocytic lymphohistiocytosis (HLH) and diffuse alveolar hemorrhage (DAH) are life-threatening clinical syndromes. Timely recognition may contribute to timely treatment and an improved prognosis. Currently there are no reports of children with DAH secondary to MP infection complicated with HLH.

CASE PRESENTATION: We successfully treated a previously healthy school-aged child who was admitted to the pediatric intensive care unit with fever, cough, drowsiness, and progressive dyspnea. HLH was confirmed by clinical and testing criteria, DAH was indicated by computed tomography scan of the chest, and Mycoplasma antibody detection and endotracheal aspirates pathogen metagenomic next-generation sequencing (mNGS) confirmed MP infection. After invasive mechanical ventilation, antibiotics, and glucocorticoid treatment, the patient recovered well and was discharged. At follow-up, she did not experience any more initial symptoms. For the fourth consecutive month, all indexes remained normal.

CONCLUSION: mNGS can be considered for identifying the causative agent of infection in patients with DAH and/or HLH. The clinical manifestations of DAH in children may only present as acute hypoxic respiratory failure, significantly decreased hemoglobin without bleeding elsewhere, and chest imaging findings may assist in the diagnosis of DAH. When MP infection is associated with hemocytopenia, HLH should be considered.},
}

@article {pmid39048979,
year = {2024},
author = {Jiang, C and Yang, J and Peng, X and Li, X},
title = {A permutable MLP-like architecture for disease prediction from gut metagenomic data.},
journal = {BMC bioinformatics},
volume = {25},
number = {1},
pages = {246},
pmid = {39048979},
issn = {1471-2105},
support = {82171526//National Natural Science Foundation of China/ ; 2020A38//Beijing Talents Fund/ ; SZU-BDSC-OF2024-19//National Engineering Laboratory for Big Data System Computing Technology/ ; },
mesh = {*Metagenomics/methods ; *Gastrointestinal Microbiome/genetics ; Humans ; Neural Networks, Computer ; Phylogeny ; Machine Learning ; Deep Learning ; Metagenome/genetics ; },
abstract = {Metagenomic data plays a crucial role in analyzing the relationship between microbes and diseases. However, the limited number of samples, high dimensionality, and sparsity of metagenomic data pose significant challenges for the application of deep learning in data classification and prediction. Previous studies have shown that utilizing the phylogenetic tree structure to transform metagenomic abundance data into a 2D matrix input for convolutional neural networks (CNNs) improves classification performance. Inspired by the success of a Permutable MLP-like architecture in visual recognition, we propose Metagenomic Permutator (MetaP), which applied the Permutable MLP-like network structure to capture the phylogenetic information of microbes within the 2D matrix formed by phylogenetic tree. Our experiments demonstrate that our model achieved competitive performance compared to other deep neural networks and traditional machine learning, and has good prospects for multi-classification and large sample sizes. Furthermore, we utilize the SHAP (SHapley Additive exPlanations) method to interpret our model predictions, identifying the microbial features that are associated with diseases.},
}

*Metagenomics/methods
*Gastrointestinal Microbiome/genetics
Humans
Neural Networks, Computer
Phylogeny
Machine Learning
Deep Learning
Metagenome/genetics

@article {pmid39048829,
year = {2024},
author = {Wu, K and Zhou, L and Tahon, G and Liu, L and Li, J and Zhang, J and Zheng, F and Deng, C and Han, W and Bai, L and Fu, L and Dong, X and Zhang, C and Ettema, TJG and Sousa, DZ and Cheng, L},
title = {Isolation of a methyl-reducing methanogen outside the Euryarchaeota.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {39048829},
issn = {1476-4687},
abstract = {Methanogenic archaea are main contributors to methane emissions, and have a crucial role in carbon cycling and global warming. Until recently, methanogens were confined to Euryarchaeota, but metagenomic studies revealed the presence of genes encoding the methyl coenzyme M reductase complex in other archaeal clades[1-4], thereby opening up the premise that methanogenesis is taxonomically more widespread. Nevertheless, laboratory cultivation of these non-euryarchaeal methanogens was lacking to corroborate their potential methanogenic ability and physiology. Here we report the isolation of a thermophilic archaeon LWZ-6 from an oil field. This archaeon belongs to the class Methanosuratincolia (originally affiliated with 'Candidatus Verstraetearchaeota') in the phylum Thermoproteota. Methanosuratincola petrocarbonis LWZ-6 is a strict hydrogen-dependent methylotrophic methanogen. Although previous metagenomic studies speculated on the fermentative potential of Methanosuratincolia members, strain LWZ-6 does not ferment sugars, peptides or amino acids. Its energy metabolism is linked only to methanogenesis, with methanol and monomethylamine as electron acceptors and hydrogen as an electron donor. Comparative (meta)genome analysis confirmed that hydrogen-dependent methylotrophic methanogenesis is a widespread trait among Methanosuratincolia. Our findings confirm that the diversity of methanogens expands beyond the classical Euryarchaeota and imply the importance of hydrogen-dependent methylotrophic methanogenesis in global methane emissions and carbon cycle.},
}

@article {pmid39048824,
year = {2024},
author = {Kohtz, AJ and Petrosian, N and Krukenberg, V and Jay, ZJ and Pilhofer, M and Hatzenpichler, R},
title = {Cultivation and visualization of a methanogen of the phylum Thermoproteota.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {39048824},
issn = {1476-4687},
abstract = {Methane is the second most abundant climate-active gas, and understanding its sources and sinks is an important endeavour in microbiology, biogeochemistry, and climate sciences[1,2]. For decades, it was thought that methanogenesis, the ability to conserve energy coupled to methane production, was taxonomically restricted to a metabolically specialized group of archaea, the Euryarchaeota[1]. The discovery of marker genes for anaerobic alkane cycling in metagenome-assembled genomes obtained from diverse habitats has led to the hypothesis that archaeal lineages outside the Euryarchaeota are also involved in methanogenesis[3-6]. Here we cultured Candidatus Methanosuratincola verstraetei strain LCB70, a member of the archaeal class Methanomethylicia (formerly Verstraetearchaeota) within the phylum Thermoproteota, from a terrestrial hot spring. Growth experiments combined with activity assays, stable isotope tracing, and genomic and transcriptomic analyses demonstrated that this thermophilic archaeon grows by means of methyl-reducing hydrogenotrophic methanogenesis. Cryo-electron tomography revealed that Ca. M. verstraetei are coccoid cells with archaella and chemoreceptor arrays, and that they can form intercellular bridges connecting two to three cells with continuous cytoplasm and S-layer. The wide environmental distribution of Ca. M. verstraetei suggests that they might play important and hitherto overlooked roles in carbon cycling within diverse anoxic habitats.},
}

@article {pmid39048485,
year = {2024},
author = {Pérez-Prieto, I and Plaza-Florido, A and Ubago-Guisado, E and Ortega, FB and Altmäe, S},
title = {Physical activity, sedentary behavior and microbiome: A systematic review and meta-analysis.},
journal = {Journal of science and medicine in sport},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jsams.2024.07.003},
pmid = {39048485},
issn = {1878-1861},
abstract = {BACKGROUND: The effects of physical activity and sedentary behavior on human health are well known, however, the molecular mechanisms are poorly understood. Growing evidence points to physical activity as an important modulator of the composition and function of microbial communities, while evidence of sedentary behavior is scarce. We aimed to synthesize and meta-analyze the current evidence about the effects of physical activity and sedentary behavior on microbiome across different body sites and in different populations.

METHODS: A systematic search in PubMed, Web of Science, Scopus and Cochrane databases was conducted until September 2022. Random-effects meta-analyses including cross-sectional studies (active vs. inactive/athletes vs. non-athletes) or trials reporting the chronic effect of physical activity interventions on gut microbiome alpha-diversity in healthy individuals were performed.

RESULTS: Ninety-one studies were included in this systematic review. Our meta-analyses of 2632 participants indicated no consistent effect of physical activity on microbial alpha-diversity, although there seems to be a trend toward a higher microbial richness in athletes compared to non-athletes. Most of studies reported an increase in short-chain fatty acid-producing bacteria such as Akkermansia, Faecalibacterium, Veillonella or Roseburia in active individuals and after physical activity interventions.

CONCLUSIONS: Physical activity levels were positively associated with the relative abundance of short-chain fatty acid-producing bacteria. Athletes seem to have a richer microbiome compared to non-athletes. However, high heterogeneity between studies avoids obtaining conclusive information on the role of physical activity in microbial composition. Future multi-omics studies would enhance our understanding of the molecular effects of physical activity and sedentary behavior on the microbiome.},
}

@article {pmid39048017,
year = {2024},
author = {Krukenberg, V and Kohtz, AJ and Jay, ZJ and Hatzenpichler, R},
title = {Methyl-reducing methanogenesis by a thermophilic culture of Korarchaeia.},
journal = {Nature},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41586-024-07829-8},
pmid = {39048017},
issn = {1476-4687},
abstract = {Methanogenesis mediated by archaea is the major source of methane, a strong greenhouse gas, and thus is critical for understanding Earth's climate dynamics. Recently, genes encoding diverse methanogenesis pathways were discovered in metagenome-assembled genomes affiliated with multiple archaeal phyla[1-7]. However, all experimental studies on methanogens are currently restricted to cultured representatives of the Euryarchaeota. Here we show for the first time methanogenic growth by a member of the lineage Korarchaeia within the phylum Thermoproteota (TACK superphylum)[5-7]. Following enrichment cultivation of Candidatus Methanodesulfokora washburnenis strain LCB3 we used measurements of metabolic activity and isotope tracer conversion to demonstrate methanol reduction to methane using hydrogen as electron donor. Analysis of the archaeon's circular genome and transcriptome revealed unique modifications in the energy conservation pathways linked to methanogenesis, including enzyme complexes involved in hydrogen and sulfur metabolism. The cultivation and characterization of this novel group of archaea is critical for a deeper evaluation of the diversity, physiology, and biochemistry of methanogens.},
}

@article {pmid39047732,
year = {2024},
author = {Yang, Z and Ma, J and Han, J and Li, A and Liu, G and Sun, Y and Zheng, J and Zhang, J and Chen, G and Xu, R and Sun, L and Meng, C and Gao, J and Bai, Z and Deng, W and Zhang, C and Su, J and Yao, H and Zhang, Z},
title = {Gut microbiome model predicts response to neoadjuvant immunotherapy plus chemoradiotherapy in rectal cancer.},
journal = {Med (New York, N.Y.)},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.medj.2024.07.002},
pmid = {39047732},
issn = {2666-6340},
abstract = {BACKGROUND: Accurate evaluation of the response to preoperative treatment enables the provision of a more appropriate personalized therapeutic schedule for locally advanced rectal cancer (LARC), which remains an enormous challenge, especially neoadjuvant immunotherapy plus chemoradiotherapy (nICRT).

METHODS: This prospective, multicenter cohort study enrolled patients with LARC from 6 centers who received nICRT. The dynamic variation in the gut microbiome during nICRT was evaluated. A species-level gut microbiome prediction (SPEED) model was developed and validated to predict the pathological complete response (pCR) to nICRT.

FINDINGS: A total of 50 patients were enrolled, 75 fecal samples were collected from 33 patients at different time points, and the pCR rate reached 42.4% (14/33). Lactobacillus and Eubacterium were observed to increase after nICRT. Additionally, significant differences in the gut microbiome were observed between responders and non-responders at baseline. Significantly higher abundances of Lachnospiraceaebacterium and Blautiawexlerae were found in responders, while Bacteroides, Prevotella, and Porphyromonas were found in non-responders. The SPEED model showcased a superior predictive performance with areas under the curve of 98.80% (95% confidence interval [CI]: 95.67%-100%) in the training cohort and 77.78% (95% CI: 65.42%-88.29%) in the validation cohort.

CONCLUSIONS: Programmed death 1 (PD-1) blockade plus concurrent long-course CRT showed a favorable pCR rate and is well tolerated in microsatellite-stable (MSS)/mismatch repair-proficient (pMMR) patients with LARC. The SPEED model can be used to predict the pCR to nICRT based on the baseline gut microbiome with high robustness and accuracy, thereby assisting clinical physicians in providing individualized management for patients with LARC.

FUNDING: This research was funded by the China National Natural Science Foundation (82202884).},
}

@article {pmid39047725,
year = {2024},
author = {Zhang, C and Chen, F and Wang, F and Xu, H and Xue, J and Li, Z},
title = {Mechanisms for HNH-mediated target DNA cleavage in type I CRISPR-Cas systems.},
journal = {Molecular cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.molcel.2024.06.033},
pmid = {39047725},
issn = {1097-4164},
abstract = {The metagenome-derived type I-E and type I-F variant CRISPR-associated complex for antiviral defense (Cascade) complexes, fused with HNH domains, precisely cleave target DNA, representing recently identified genome editing tools. However, the underlying working mechanisms remain unknown. Here, structures of type I-F[HNH] and I-E[HNH] Cascade complexes at different states are reported. In type I-F[HNH] Cascade, Cas8f[HNH] loosely attaches to Cascade head and is adjacent to the 5' end of the target single-stranded DNA (ssDNA). Formation of the full R-loop drives the Cascade head to move outward, allowing Cas8f[HNH] to detach and rotate ∼150° to accommodate target ssDNA for cleavage. In type I-E[HNH] Cascade, Cas5e[HNH] domain is adjacent to the 5' end of the target ssDNA. Full crRNA-target pairing drives the lift of the Cascade head, widening the substrate channel for target ssDNA entrance. Altogether, these analyses into both complexes revealed that crRNA-guided positioning of target DNA and target DNA-induced HNH unlocking are two key factors for their site-specific cleavage of target DNA.},
}

@article {pmid39047231,
year = {2024},
author = {Cao, Y and Zhang, B and Song, X and Dong, G and Zhang, Y and Chen, B},
title = {Polyhydroxybutyrate Plastics Show Rapid Disintegration and More Straightforward Biogeochemical Impacts than Polyethylene under Marine Biofragmentation.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.4c04639},
pmid = {39047231},
issn = {1520-5851},
abstract = {Although massive studies have investigated the spatiotemporally occurring marine plastisphere, a new microbial ecosystem colonizing the surfaces of plastics, the resulting biofragmentation process and impacts of plastics on biogeochemical cycles remain largely unknown. Here, we leverage synchrotron-based Fourier transform infrared spectromicroscopy (FTIR mapping) and metagenomic sequencing to explore independent marine microcosms amended with petroleum-based polyethylene (PE) and biobased polyhydroxybutyrate (PHB) plastic films. FTIR mapping results demonstrate unequal fragmentation scenarios by which the PE plastic rarely releases oxidized fragments while PHB disintegrates quickly, gradually forming fragments composed of extracellular polymeric substances resembling plastic films. Metagenomic analysis shows the critical role of hydrocarbonoclastic lineages in the biodegradation of the two plastics by the fatty acid degradation pathway, where the PE plastics host different microbial trajectories between the plastisphere (dominated by Alcanivorax) and surrounding seawater. In contrast, the PHB addition demonstrates decreased microbial richness and diversity, consistent community composition (dominated by Phaeobacter and Marinobacter), and apparently stimulated sulfur cycle and denitrification pathways in both the plastisphere and surrounding seawater. Our study gives scientific evidence on the marine biotic processes distinguishing petroleum- and biobased plastics, highlighting marine PHB input exerting straightforward impacts on the water phase and deserving critical management practices.},
}

@article {pmid39047022,
year = {2024},
author = {Lekuya, HM and Kateete, DP and Olweny, G and Kigozi, E and Kamabu, LK and Mudekereza, SP and Nantambi, R and Mbiine, R and Makumbi, F and Cose, S and Vandersteene, J and Baert, E and Kalala, JO and Galukande, M},
title = {Metagenomic sequencing of the skin microbiota of the scalp predicting the risk of surgical site infections following surgery of traumatic brain injury in sub-Saharan Africa.},
journal = {PloS one},
volume = {19},
number = {7},
pages = {e0303483},
doi = {10.1371/journal.pone.0303483},
pmid = {39047022},
issn = {1932-6203},
mesh = {Humans ; Male ; *Surgical Wound Infection/microbiology/epidemiology ; Female ; *Scalp/microbiology ; Adult ; *Microbiota/genetics ; *Metagenomics/methods ; *Brain Injuries, Traumatic/microbiology ; Prospective Studies ; Africa South of the Sahara/epidemiology ; Skin/microbiology ; Young Adult ; Adolescent ; RNA, Ribosomal, 16S/genetics ; Uganda/epidemiology ; Middle Aged ; Risk Factors ; Metagenome ; },
abstract = {BACKGROUND: Surgical site infections (SSI) are a significant concern following traumatic brain injury (TBI) surgery and often stem from the skin's microbiota near the surgical site, allowing bacteria to penetrate deeper layers and potentially causing severe infections in the cranial cavity. This study investigated the relationship between scalp skin microbiota composition and the risk of SSI after TBI surgery in sub-Saharan Africa (SSA).

METHODS: This was a prospective cohort study, enrolling patients scheduled for TBI surgery. Sterile skin swabs were taken from the surrounding normal skin of the head and stored for analysis at -80°Celcius. Patients were monitored postoperatively for up to three months to detect any occurrences of SSI. 16S rRNA sequencing was used to analyze the skin microbiota composition, identifying different taxonomic microorganisms at the genus level. The analysis compared two groups: those who developed SSI and those who did not.

RESULTS: A total of 57 patients were included, mostly male (89.5%) with a mean age of 26.5 years, predominantly from urban areas in Uganda and victims of assault. Graphical visualization and metagenomic metrics analysis revealed differences in composition, richness, and evenness of skin microbiota within samples (α) or within the community (β), and showed specific taxa (phylum and genera) associated with either the group of SSI or the No SSI.

CONCLUSIONS: Metagenomic sequencing analysis uncovered several baseline findings and trends regarding the skin microbiome's relationship with SSI risk. There is an association between scalp microbiota composition (abundancy and diversity) and SSI occurrence following TBI surgery in SSA. We hypothesize under reserve that the scalp microbiota dysbiosis could potentially be an independent predictor of the occurrence of SSI; we advocate for further studies with larger cohorts.},
}

Humans
Male
*Surgical Wound Infection/microbiology/epidemiology
Female
*Scalp/microbiology
Adult
*Microbiota/genetics
*Metagenomics/methods
*Brain Injuries, Traumatic/microbiology
Prospective Studies
Africa South of the Sahara/epidemiology
Skin/microbiology
Young Adult
Adolescent
RNA, Ribosomal, 16S/genetics
Uganda/epidemiology
Middle Aged
Risk Factors
Metagenome

@article {pmid39046290,
year = {2024},
author = {Sanz-Sáez, I and Bravo, AG and Ferri, M and Carreras, JM and Sánchez, O and Sebastian, M and Ruiz-González, C and Capo, E and Duarte, CM and Gasol, JM and Sánchez, P and Acinas, SG},
title = {Microorganisms Involved in Methylmercury Demethylation and Mercury Reduction are Widely Distributed and Active in the Bathypelagic Deep Ocean Waters.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.4c00663},
pmid = {39046290},
issn = {1520-5851},
abstract = {The ocean's mercury (Hg) content has tripled due to anthropogenic activities, and although the dark ocean (>200 m) has become an important Hg reservoir, concentrations of the toxic and bioaccumulative methylmercury (MeHg) are low and therefore very difficult to measure. As a consequence, the current understanding of the Hg cycle in the deep ocean is severely data-limited, and the factors controlling MeHg, as well as its transformation rates, remain largely unknown. By analyzing 52 globally distributed bathypelagic deep-ocean metagenomes and 26 new metatranscriptomes from the Malaspina Expedition, our study reveals the widespread distribution and expression of bacterial-coding genes merA and merB in the global bathypelagic ocean (∼4000 m depth). These genes, associated with Hg[II] reduction and MeHg demethylation, respectively, are particularly prevalent within the particle-attached fraction. Moreover, our results indicate that water mass age and the organic matter composition shaped the structure of the communities harboring merA and merB genes living in different particle size fractions, their abundance, and their expression levels. Members of the orders Corynebacteriales, Rhodobacterales, Alteromonadales, Oceanospirillales, Moraxellales, and Flavobacteriales were the main taxonomic players containing merA and merB genes in the deep ocean. These findings, together with our previous results of pure culture isolates of the deep bathypelagic ocean possessing the metabolic capacity to degrade MeHg, indicated that both methylmercury demethylation and Hg[II] reduction likely occur in the global dark ocean, the largest biome in the biosphere.},
}

@article {pmid39046276,
year = {2024},
author = {Maire, J and Collingro, A and Tandon, K and Jameson, VJ and Judd, LM and Horn, M and Blackall, LL and van Oppen, MJH},
title = {Chlamydiae as symbionts of photosynthetic dinoflagellates.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrae139},
pmid = {39046276},
issn = {1751-7370},
abstract = {Chlamydiae are ubiquitous intracellular bacteria and infect a wide diversity of eukaryotes, including mammals. However, chlamydiae have never been reported to infect photosynthetic organisms. Here, we describe a novel chlamydial genus and species, Candidatus Algichlamydia australiensis, capable of infecting the photosynthetic dinoflagellate Cladocopium sp. (originally isolated from a scleractinian coral). A. australiensis was confirmed to be intracellular by fluorescence in situ hybridization and confocal laser scanning microscopy, and temporally stable at the population level by monitoring its relative abundance across four weeks of host growth. Using a combination of short- and long-read sequencing, we recovered a high-quality (completeness 91.73% and contamination 0.27%) metagenome-assembled genome of A. australiensis. Phylogenetic analyses show that this chlamydial taxon represents a new genus and species within the Simkaniaceae family. A. australiensis possesses all the hallmark genes for chlamydiae-host interactions, including a complete type III secretion system. In addition, a type IV secretion system is encoded on a plasmid and has previously been observed for only three other chlamydial species. Twenty orthologous groups of genes are unique to A. australiensis, one of which is structurally similar to a protein known from Cyanobacteria and Archaeplastida involved in thylakoid biogenesis and maintenance, hinting at potential chlamydiae interactions with the chloroplasts of Cladocopium cells. Our study shows that chlamydiae infect dinoflagellate symbionts of cnidarians, the first photosynthetic organism reported to harbor chlamydiae, thereby expanding the breadth of chlamydial hosts and providing a new contribution to the discussion around the role of chlamydiae in the establishment of the primary plastid.},
}

@article {pmid39045787,
year = {2024},
author = {Tayebwa, DS and Hyeroba, D and Dunn, CD and Dunay, E and Richard, JC and Biryomumaisho, S and Acai, JO and Goldberg, TL},
title = {Viruses of free-roaming and hunting dogs in Uganda show elevated prevalence, richness and abundance across a gradient of contact with wildlife.},
journal = {The Journal of general virology},
volume = {105},
number = {7},
pages = {},
doi = {10.1099/jgv.0.002011},
pmid = {39045787},
issn = {1465-2099},
mesh = {Animals ; Dogs ; Uganda/epidemiology ; *Dog Diseases/virology/epidemiology/transmission ; Prevalence ; *Animals, Wild/virology ; Virome ; Viruses/classification/isolation & purification/genetics ; Metagenomics ; Anelloviridae/genetics/isolation & purification/classification ; Humans ; Virus Diseases/epidemiology/veterinary/transmission/virology ; },
abstract = {Domestic dogs (Canis lupus familiaris) live with humans, frequently contact other animals and may serve as intermediary hosts for the transmission of viruses. Free-roaming dogs, which account for over 70% of the world's domestic dog population, may pose a particularly high risk in this regard. We conducted an epidemiological study of dog viromes in three locations in Uganda, representing low, medium and high rates of contact with wildlife, ranging from dogs owned specifically for traditional hunting in a biodiversity and disease 'hotspot' to pets in an affluent suburb. We quantified rates of contact between dogs and wildlife through owner interviews and conducted canine veterinary health assessments. We then applied broad-spectrum viral metagenomics to blood plasma samples, from which we identified 46 viruses, 44 of which were previously undescribed, in three viral families, Sedoreoviridae, Parvoviridae and Anelloviridae. All 46 viruses (100 %) occurred in the high-contact population of dogs compared to 63 % and 39 % in the medium- and low-contact populations, respectively. Viral prevalence ranged from 2.1 % to 92.0 % among viruses and was highest, on average, in the high-contact population (22.3 %), followed by the medium-contact (12.3 %) and low-contact (4.8 %) populations. Viral richness (number of viruses per dog) ranged from 0 to 27 and was markedly higher, on average, in the high-contact population (10.2) than in the medium-contact (5.7) or low-contact (2.3) populations. Viral richness was strongly positively correlated with the number of times per year that a dog was fed wildlife and negatively correlated with the body condition score, body temperature and packed cell volume. Viral abundance (cumulative normalized metagenomic read density) varied 124-fold among dogs and was, on average, 4.1-fold higher and 2.4-fold higher in the high-contact population of dogs than in the low-contact or medium-contact populations, respectively. Viral abundance was also strongly positively correlated with the number of times per year that a dog was fed wildlife, negatively correlated with packed cell volume and positively correlated with white blood cell count. These trends were driven by nine viruses in the family Anelloviridae, genus Thetatorquevirus, and by one novel virus in the family Sedoreoviridae, genus Orbivirus. The genus Orbivirus contains zoonotic viruses and viruses that dogs can acquire through ingestion of infected meat. Overall, our findings show that viral prevalence, richness and abundance increased across a gradient of contact between dogs and wildlife and that the health status of the dog modified viral infection. Other ecological, geographic and social factors may also have contributed to these trends. Our finding of a novel orbivirus in dogs with high wildlife contact supports the idea that free-roaming dogs may serve as intermediary hosts for viruses of medical importance to humans and other animals.},
}

Animals
Dogs
Uganda/epidemiology
*Dog Diseases/virology/epidemiology/transmission
Prevalence
*Animals, Wild/virology
Virome
Viruses/classification/isolation & purification/genetics
Metagenomics
Anelloviridae/genetics/isolation & purification/classification
Humans
Virus Diseases/epidemiology/veterinary/transmission/virology

@article {pmid39045536,
year = {2024},
author = {Song, W and Chen, X and Yu, J and Qiao, J and Yang, J and Chen, X and Wang, Z},
title = {Effects of Bacillus altitudinis inoculants on cigar tobacco leaf fermentation.},
journal = {Frontiers in bioengineering and biotechnology},
volume = {12},
number = {},
pages = {1417601},
pmid = {39045536},
issn = {2296-4185},
abstract = {INTRODUCTION: Microbial succession and metabolic adjustment during cigar tobacco leaf (CTL) fermentation are key factors to improve the quality and flavor of CTLs. However, the interactions in the above processes remain to be further elucidated.

METHODS: Bacillus altitudinis inoculants were added to the CTLs, and metagenomics and metabolomics were used to analyze the effects of the inoculants on regulating microbial succession, metabolic shift, and aroma production during fermentation.

RESULTS AND DISCUSSION: The addition of the inoculants reinforced the CTL macromolecule transformation and facilitated the aroma production efficiently, and the total aroma production was increased by 43% compared with natural fermentation. The omics analysis showed that Staphylococcus was a main contributor to fatty acid degradation, inositol phosphate metabolism, energy supply (oxidative phosphorylation), nutrient transport (ABC transporter and phosphotransferase system [PTS]), and aroma production (terpenoid backbone biosynthesis, phenylalanine metabolism, and degradation of aromatic compounds). Furthermore, Staphylococcus was positively correlated with TCA cycle intermediates (citric acid, fumaric acid, and aconitic acid), cell wall components, peptidoglycan intermediates (GlcNAc-1-P and UDP-GlcNAc), and phytic acid degradation products (inositol). The characteristics collectively showed Staphylococcus to be the most dominant in the microbial community at the genus level during microflora succession. The addition of the inoculants supplemented the nutritional components of the CTLs, enhanced the metabolic activity and diversity of bacteria such as Corynebacterium, improved their competitive advantages in the microflora succession, and facilitated the richness of microbial communities. Additionally, a metabolic shift in nicotine degradation and NAD + anabolism from Staphylococcus to Corynebacterium in fermentation with inoculants was first observed. Meanwhile, the significantly correlative differential metabolites with Staphylococcus and Corynebacterium were a metabolic complement, thus forming a completely dynamic fermentation ecosystem. The results provided evidence for CTL fermentation optimization.},
}

@article {pmid39045243,
year = {2024},
author = {Vences-Guzmán, MÁ and Jiménez-Rodríguez, M and Lozano, L and Rojas-Juárez, S and Ramírez-Estudillo, JA and Hernández-Vázquez, ÁY and Pita-Ortiz, IY and Ramírez-Ceballos, KG and Medina-Medina, S and Sohlenkamp, C},
title = {A clinical metagenomic study of biopsies from Mexican endophthalmitis patients reveals the presence of complex bacterial communities and a diversity of resistance genes.},
journal = {Access microbiology},
volume = {6},
number = {6},
pages = {},
pmid = {39045243},
issn = {2516-8290},
abstract = {Infectious endophthalmitis is a severe ophthalmic emergency. This infection can be caused by bacteria and fungi. For efficient treatment, the administration of antimicrobial drugs to which the microbes are susceptible is essential. The aim of this study was to identify micro-organisms in biopsies of Mexican endophthalmitis patients using metagenomic next-generation sequencing and determine which antibiotic resistance genes were present in the biopsy samples. In this prospective case study, 19 endophthalmitis patients were recruited. Samples of vitreous or aqueous humour were extracted for DNA extraction for metagenomic next-generation sequencing. Analysis of the sequencing results revealed the presence of a wide variety of bacteria in the biopsies. Resistome analysis showed that homologues of antibiotic resistance genes were present in several biopsy samples. Genes possibly conferring resistance to ceftazidime and vancomycin were detected in addition to various genes encoding efflux pumps. Our findings contrast with the widespread opinion that only one or a few bacterial strains are present in the infected tissues of endophthalmitis patients. These diverse communities might host many of the resistance genes that were detected, which can further complicate the infections.},
}

@article {pmid39040200,
year = {2024},
author = {Chen, X and Balliew, J and Bauer, CX and Deegan, J and Gitter, A and Hanson, BM and Maresso, AW and Tisza, MJ and Troisi, CL and Rios, J and Mena, KD and Boerwinkle, E and Wu, F},
title = {RBD amplicon sequencing of wastewater reveals patterns of variant emergence and evolution.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
pmid = {39040200},
support = {U01 TR004355/TR/NCATS NIH HHS/United States ; },
abstract = {Rapid evolution of SARS-CoV-2 has resulted in the emergence of numerous variants, posing significant challenges to public health surveillance. Clinical genome sequencing, while valuable, has limitations in capturing the full epidemiological dynamics of circulating variants in the general population. This study utilized receptor-binding domain (RBD) amplicon sequencing of wastewater samples to monitor the SARS-CoV-2 community dynamics and evolution in El Paso, TX. Over 17 months, we identified 91 variants and observed waves of dominant variants transitioning from BA.2 to BA.2.12.1, BA.4&5, BQ.1, and XBB.1.5. Our findings demonstrated early detection of variants and identification of unreported outbreaks, while showing strong consistency with clinical genome sequencing data at the local, state, and national levels. Alpha diversity analyses revealed significant periodical variations, with the highest diversity observed in winter and the outbreak lag phases, likely due to lower competition among variants before the outbreak growth phase. The data underscores the importance of low transmission periods for rapid mutation and variant evolution. This study highlights the effectiveness of integrating RBD amplicon sequencing with wastewater surveillance in tracking viral evolution, understanding variant emergence, and enhancing public health preparedness.},
}

@article {pmid34474998,
year = {2021},
author = {Liu, C and Hu, J and Wu, Y and Irwin, DM and Chen, W and Zhang, Z and Yu, L},
title = {Comparative study of gut microbiota from captive and confiscated-rescued wild pangolins.},
journal = {Journal of genetics and genomics = Yi chuan xue bao},
volume = {48},
number = {9},
pages = {825-835},
doi = {10.1016/j.jgg.2021.07.009},
pmid = {34474998},
issn = {1673-8527},
mesh = {*Pangolins/microbiology ; *Gastrointestinal Microbiome/drug effects ; Animals, Wild ; Breeding ; Endangered Species ; Anti-Bacterial Agents/administration & dosage ; Diet ; RNA, Ribosomal, 16S/analysis/genetics ; Bacteria/classification/genetics/isolation & purification ; Metagenome ; Virulence Factors/analysis ; Carbohydrate Metabolism ; Enzymes/analysis ; },
abstract = {Pangolins are among the most critically endangered animals due to widespread poaching and worldwide trafficking. Captive breeding is considered to be one way to protect them and increase the sizes of their populations. However, comparative studies of captive and wild pangolins in the context of gut microbiota are rare. Here, the gut microbiome of captive and confiscated-rescued wild pangolins is compared, and the effects of different periods of captivity and captivity with and without antibiotic treatment are considered. We show that different diets and periods of captivity, as well as the application of antibiotic therapy, can alter gut community composition and abundance in pangolins. Compared to wild pangolins, captive pangolins have an increased capacity for chitin and cellulose/hemicellulose degradation, fatty acid metabolism, and short-chain fatty acid synthesis, but a reduced ability to metabolize exogenous substances. In addition to increasing the ability of the gut microbiota to metabolize nutrients in captivity, captive breeding imposes some risks for survival by resulting in a greater abundance of antibiotic resistance genes and virulence factors in captive pangolins than in wild pangolins. Our study is important for the development of guidelines for pangolin conservation, including health assessment, disease prevention, and rehabilitation of wild pangolin populations.},
}

*Pangolins/microbiology
*Gastrointestinal Microbiome/drug effects
Animals, Wild
Breeding
Endangered Species
Anti-Bacterial Agents/administration & dosage
Diet
RNA, Ribosomal, 16S/analysis/genetics
Bacteria/classification/genetics/isolation & purification
Metagenome
Virulence Factors/analysis
Carbohydrate Metabolism
Enzymes/analysis

@article {pmid39045130,
year = {2024},
author = {Li, J and Zhou, J and Tan, Y and Hu, C and Meng, Q and Gao, J and Xing, L},
title = {Clinical characteristics and risk factors for mortality in pneumonia-associated acute respiratory distress syndrome patients: a single center retrospective cohort study.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1396088},
pmid = {39045130},
issn = {2235-2988},
mesh = {Humans ; Retrospective Studies ; Male ; Risk Factors ; Female ; Middle Aged ; Aged ; *Respiratory Distress Syndrome/mortality ; *High-Throughput Nucleotide Sequencing ; Metagenomics/methods ; Intensive Care Units ; Adult ; Pneumonia/mortality ; },
abstract = {BACKGROUND: Pathogenic diversity may have contributed to the high mortality of pneumonia-associated acute respiratory distress syndrome (p-ARDS). Metagenomics next-generation sequencing (mNGS) serves as a valuable diagnostic tool for early pathogen identification. However, its clinical utility in p-ARDS remains understudied. There are still limited researches on the etiology, clinical characteristics and risk factors for 28-day mortality in p-ARDS patients.

METHODS: A single center retrospective cohort study of 75 p-ARDS patients was conducted. Patients were categorized into survival and deceased groups based on their 28-day outcomes. A comprehensive clinical evaluation was conducted, including baseline characteristics, laboratory indicators, outcomes and pathogen identification by mNGS and traditional microbiological testing. We then evaluated the diagnostic value of mNGS and identified clinical characteristics and risk factors for 28-day mortality in p-ARDS.

RESULT: The overall ICU mortality was 26.67%, and the 28-day mortality was 57.33%, with 32 cases (42.67%) in the survival group, and 43 cases (57.33%) in the deceased group. Patients in the deceased group were older than those in the survival group (68(59,73) years vs. 59(44,67) years, P=0.04). The average lengths of ICU and hospital stay were 9(5,13) days and 14(7,21) days, respectively. The survival group had longer lengths of ICU and hospital stay (ICU: 11(7,17) days and hospital: 17(9,27) days) compared to the deceased group (ICU: 8(4,11) days and hospital: 12(6,19) days) (P<0.05). Survival patients exhibited lower Acute Physiology and Chronic Health Evaluation (APACHE) II score on the 3rd and 7th days, higher lymphocyte counts, higher CD3[+] and CD8[+] T cell counts compared to deceased patients (P<0.05). Multivariate logistic regression analysis identified age, APACHE II scores on 3rd and 7th days, CD8[+] T cell count and length of ICU as independent risk factors for 28-day mortality in p-ARDS patients. mNGS demonstrated a significantly higher overall pathogen detection rate (70/75, 93.33%) compared to the traditional method (50/75, 66.67%, P=0.022). The average turnaround time (TAT) for mNGS was significantly shorter at 1(1,1) day compared to 4(3,5) days for the traditional method (P<0.001).

CONCLUSION: Metagenome next-generation sequencing can be used as a valuable tool for identifying pathogens in p-ARDS, reducing diagnostic time and improving accuracy. Early application of mNGS alongside traditional methods is recommended for p-ARDS. Furthermore, older age, higher APACHE II scores, lower lymphocyte counts and lymphocyte subset counts were associated with increased mortality in p-ARDS patients, highlighting the importance of timely assessment of immune status and disease severity, especially in elderly.},
}

Humans
Retrospective Studies
Male
Risk Factors
Female
Middle Aged
Aged
*Respiratory Distress Syndrome/mortality
*High-Throughput Nucleotide Sequencing
Metagenomics/methods
Intensive Care Units
Adult
Pneumonia/mortality

@article {pmid39045110,
year = {2024},
author = {Pan, Y and Qian, J and Wang, G and Zhao, H},
title = {Infective Endocarditis Caused by Streptococcus Sinensis in a Patient with Bioprosthetic Aortic Valve: A Case Report and Literature Review.},
journal = {Infection and drug resistance},
volume = {17},
number = {},
pages = {2957-2964},
pmid = {39045110},
issn = {1178-6973},
abstract = {BACKGROUND: Infective endocarditis caused by Streptococcus sinensis is exceedingly rare, with only limited cases reported. Here, we present the first documented case of prosthetic valve endocarditis attributed to Streptococcus sinensis.

CASE PRESENTATION: A 40-year-old Chinese female was admitted with a 45-day history of intermittent fever. The presumed diagnosis was a pulmonary infection and antibiotic therapies failed to alleviate her symptoms. On admission, infective endocarditis was suspected, considering the history of aortic valve replacement and recent dental procedure without prophylactic antibiotics. Transesophageal echocardiography disclosed a 3-millimeter vegetation in the prosthetic aortic valve, and metagenomic next-generation sequencing and mass spectrometry identified Streptococcus sinensis. The patient was diagnosed with infective endocarditis. Antibiotic treatments resulted in temporary clinical improvements, although fluctuations in temperature and inflammatory markers led to multiple attempts at antibiotic therapies. At last, the patient underwent an elective aortic valve replacement with a favorable prognosis.

CONCLUSION: In this case, we demonstrated prosthetic valve endocarditis caused by Streptococcus sinensis, which is an extremely rare pathogen. All reported endocarditis cases caused by Streptococcus sinensis were reviewed and summarized. Most of these patients had rheumatic heart diseases or congenital heart diseases. Antibiotic prophylaxis is important for high-risk procedures. Timely identification of the bacterium is crucial for diagnosis and treatment. Overall, infective endocarditis caused by this bacterium had a good prognosis.},
}

@article {pmid39045107,
year = {2024},
author = {Luo, W and Lin, X and Chen, Y and Luo, W and Zhang, H},
title = {Metagenomic Next-Generation Sequencing for Accurate Diagnosis of Pneumocystis jirovecii Pneumonia: A Comparative Study with Traditional Methods.},
journal = {Infection and drug resistance},
volume = {17},
number = {},
pages = {2965-2974},
pmid = {39045107},
issn = {1178-6973},
abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) is a high-throughput sequencing technique that identifies a wide array of pathogens directly from clinical specimens. This study evaluates the diagnostic value of mNGS in Pneumocystis jirovecii pneumonia (PJP) and compares its efficacy with traditional detection methods, including Grocott's Methenamine Silver (GMS) staining, serum (1-3)-β-D-Glucan (BDG) testing, and Lactate Dehydrogenase (LDH) testing.

METHODS: Seventy-eight patients hospitalized between January 2022 and March 2023 with suspected pulmonary infections were included. Patients were eligible for mNGS if they exhibited symptoms such as fever, cough, dyspnea, or progressive hypoxemia, and met specific clinical criteria for PJP. Specimens obtained included bronchoalveolar lavage fluid, sputum, and peripheral blood. Positive rates and pathogen distributions detected by mNGS and traditional methods were compared.

RESULTS: In the PJP group, 25%, 37.5%, and 9.38% of patients had solid organ tumors, corticosteroid use, and skin diseases, respectively, significantly higher than in the non-PJP group. The sensitivity and specificity of mNGS were both 100%, significantly higher than those of serum BDG (sensitivity 50%, specificity 81.8%) and LDH (sensitivity 9.3%, specificity 91.3%). Significant differences in microbial composition between the PJP and Non-PJP groups were observed. mNGS detected multiple mixed pathogens in 96.88% of PJP cases, with 68.75% exhibiting mixed bacterial and viral infections. Notably, 71% of patients improved following antibacterial treatment based on mNGS results.

CONCLUSION: mNGS technology shows superior sensitivity and specificity in diagnosing PJP and guides precise treatment for complex pulmonary infections.},
}

@article {pmid39044955,
year = {2024},
author = {Perez-Restrepo, LS and Ciuoderis, K and Usuga, J and Moreno, I and Vargas, V and Arévalo-Arbelaez, AJ and Berg, MG and Cloherty, GA and Hernández-Ortiz, JP and Osorio, JE},
title = {Mayaro Virus as the cause of Acute Febrile Illness in the Colombian Amazon Basin.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1419637},
pmid = {39044955},
issn = {1664-302X},
abstract = {INTRODUCTION: Mayaro Fever (MF) is a tropical disease caused by the Mayaro virus (MAYV), with outbreaks documented in Latin America.

METHODS: A hospital-based fever surveillance in Leticia, Colombian Amazon, collected sera from 1,460 patients aged 5-89 between December 2020 and April 2023.

RESULTS: Dengue and malaria were the main diagnoses (19.4 and 5.8%, respectively), leaving 71.4% of cases unidentified after testing. Metagenomic sequencing and real-time RT-qPCR testing identified MAYV in two patients (25-year-old male and an 80-year-old female) exhibiting typical symptoms, of MF including rash, joint pain, and fever. Phylogenetics analysis of these two viruses revealed a close relationship to Peruvian strains within the MAYV D genotype.

DISCUSSION: The study of AFI in Leticia, Colombia, identified dengue as prevalent, with malaria, COVID-19, Influenza, and Zika viruses also detected. Despite extensive testing, most cases remained unexplained until metagenomic sequencing revealed MAYV, previously unseen in Colombia but known in neighboring countries.

CONCLUSION: This study presents the first near full-length genomes of MAYV in Colombia, highlighting the need for further seroprevalence studies and enhanced surveillance to understand and control the spread of the virus in the region.},
}

@article {pmid39044948,
year = {2024},
author = {Han, N and Peng, X and Zhang, T and Qiang, Y and Li, X and Zhang, W},
title = {Temporal dynamics and species-level complexity of Prevotella spp. in the human gut microbiota: implications for enterotypes and health.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1414000},
pmid = {39044948},
issn = {1664-302X},
abstract = {The concept of "enterotypes" in microbiome research has attracted substantial interest, particularly focusing on the abundance of Prevotella spp. in the human gut. In this study, the intricate dynamics of Prevotella spp. in the human gut microbiota was investigated, based on the metagenomic method. First, 239 fecal samples from individuals across four regions of China revealed a bimodal distribution, highlighting the abundance and variability in Prevotella spp. within the Chinese population. Second, the longitudinal cohort study included 184 fecal samples from 52 time points collected from seven individuals who demonstrated either the outbreaks or disappearances of Prevotella spp., emphasizing the transient nature of Prevotella abundance levels and suggesting shifts in Prevotella "enterotypes." Furthermore, a turnover of the dominant Prevotella spp. was observed, indicating the potential presence of diverse subtypes of Prevotella enterotype. Notably, the genomic analysis demonstrated the persistence of specific Prevotella strains within individuals over extended periods, highlighting the enduring presence of Prevotella in the human gut. In conclusion, by integrating the temporal and geographical scales in our research, we gained deeper insights into the dynamics of Prevotella, emphasizing the importance of considering the dynamics at the time and species level in gut microbiota studies and their implications on human health.},
}

@article {pmid39044909,
year = {2024},
author = {Moumen, B and Samba-Louaka, C and Kimpamboudi, VAM and Boumba, AM and Ngoma, HS and Samba-Louaka, A},
title = {Metagenomic data from gutter water in the city of Pointe-Noire, Republic of Congo.},
journal = {Data in brief},
volume = {55},
number = {},
pages = {110655},
pmid = {39044909},
issn = {2352-3409},
abstract = {After Amazonia, the Congo Basin represents the second-largest tropical rainforest area in the world. This basin harbours remarkable biodiversity, yet much of its microbiological diversity within its waters, soils, and populations remains largely unexplored and undiscovered. While many initiatives to characterize global biodiversity are being undertaken, few are conducted in Africa and none of them concern the Congo Basin specifically in urban areas. In this context, we assessed the microbial diversity present in gutter water in the city of Pointe-Noire, Congo. This town has interesting characteristics as the population density is high and it is located between the Atlantic Ocean and the forest of Mayombe in Central Africa. The findings illuminate the microbial composition of surface water in Pointe-Noire. The dataset allows the identification of putative new bacteria through the assembly of 81 meta-genome-assembled genomes. It also serves as a valuable primary resource for assessing the presence of antibiotic-resistant genes, offering a useful tool for monitoring risks by public health authorities.},
}

@article {pmid39044605,
year = {2024},
author = {Xu, H and Zhang, J and Wang, F and Chen, Y and Chen, H and Feng, Y and Hou, G and Zi, J and Zhang, M and Zhou, J and Deng, L and Lin, L and Zhang, X and Liu, S},
title = {Integration of metagenomics and metaproteomics in the intestinal lavage fluids benefits construction of discriminative model and discovery of biomarkers for HBV liver diseases.},
journal = {Proteomics},
volume = {},
number = {},
pages = {e2400002},
doi = {10.1002/pmic.202400002},
pmid = {39044605},
issn = {1615-9861},
support = {2023YFC3402900//National Key Research and Development Program of China/ ; 2022YFA1304500//National Key Research and Development Program of China/ ; 2020YFE0202200//National Key Research and Development Program of China/ ; },
abstract = {Intestinal lavage fluid (IVF) containing the mucosa-associated microbiota instead of fecal samples was used to study the gut microbiota using different omics approaches. Focusing on the 63 IVF samples collected from healthy and hepatitis B virus-liver disease (HBV-LD), a question is prompted whether omics features could be extracted to distinguish these samples. The IVF-related microbiota derived from the omics data was classified into two enterotype sets, whereas the genomics-based enterotypes were poorly overlapped with the proteomics-based one in either distribution of microbiota or of IVFs. There is lack of molecular features in these enterotypes to specifically recognize healthy or HBV-LD. Running machine learning against the omics data sought the appropriate models to discriminate the healthy and HBV-LD IVFs based on selected genes or proteins. Although a single omics dataset is basically workable in such discrimination, integration of the two datasets enhances discrimination efficiency. The protein features with higher frequencies in the models are further compared between healthy and HBV-LD based on their abundance, bringing about three potential protein biomarkers. This study highlights that integration of metaomics data is beneficial for a molecular discriminator of healthy and HBV-LD, and reveals the IVF samples are valuable for microbiome in a small cohort.},
}

@article {pmid39044261,
year = {2024},
author = {Ma, S and Yin, Y and Guo, Y and Yao, C and Xu, S and Luo, Q and Yin, G and Wang, S and Wang, Q and Chen, H and Wang, R and Jin, L and Liang, G and Wang, H},
title = {The plasma viral communities associate with clinical profiles in a large-scale haematological patients cohort.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {137},
pmid = {39044261},
issn = {2049-2618},
mesh = {Humans ; Male ; Female ; *DNA Viruses/isolation & purification/genetics ; Middle Aged ; *Virus Diseases/blood/virology ; Adult ; *Hematologic Diseases/complications/blood ; *RNA Viruses/isolation & purification ; Virome ; Aged ; Torque teno virus/isolation & purification/genetics ; Cohort Studies ; Herpesvirus 4, Human/genetics/isolation & purification ; Young Adult ; },
abstract = {BACKGROUND: Haematological patients exhibit immune system abnormalities that make them susceptible to viral infections. Understanding the relationship between the virome in the blood plasma of haematological patients and their clinical characteristic is crucial for disease management. We aimed to explore the presence of viral pathogens and identify close associations between viral infections and various clinical features.

RESULTS: A total of 21 DNA viruses and 6 RNA viruses from 12 virus families were identified from 1383 patients. Patients with haematological diseases exhibited significantly higher diversity, prevalence, and co-detection rates of viral pathogens. During fever episodes, pathogen detection was notably higher, with Epstein-Barr virus (EBV) and Mucorales infections being the most probable culprits for fever symptoms in non-haematological patients. The detection rate of torque teno virus (TTV) significantly increases in haematological patients after transplantation and during primary lung infections. Additionally, TTV-positive patients demonstrate significantly higher absolute neutrophil counts, while C-reactive protein and procalcitonin levels are notably lower. Furthermore, TTV, cytomegalovirus, and parvovirus B19 (B19V) were found to be more prevalent in non-neutropenic patients, while non-viral pathogenic infections, such as Gram-negative bacteria and Mucorales, were more common in neutropenic patients. Pegivirus C (HPgV-C) infection often occurred post-transplantation, regardless of neutropenia. Additionally, some viruses such as TTV, B19V, EBV, and HPgV-C showed preferences for age and seasonal infections.

CONCLUSIONS: Analysis of the plasma virome revealed the susceptibility of haematological patients to plasma viral infections at specific disease stages, along with the occurrence of mixed infections with non-viral pathogens. Close associations were observed between the plasma virome and various clinical characteristics, as well as clinical detection parameters. Understanding plasma virome aids in auxiliary clinical diagnosis and treatment, enabling early prevention to reduce infection rates in patients and improve their quality of life. Video Abstract.},
}

Humans
Male
Female
*DNA Viruses/isolation & purification/genetics
Middle Aged
*Virus Diseases/blood/virology
Adult
*Hematologic Diseases/complications/blood
*RNA Viruses/isolation & purification
Virome
Aged
Torque teno virus/isolation & purification/genetics
Cohort Studies
Herpesvirus 4, Human/genetics/isolation & purification
Young Adult

@article {pmid39044244,
year = {2024},
author = {Glendinning, L and Jia, X and Kebede, A and Oyola, SO and Park, JE and Park, W and Assiri, A and Holm, JB and Kristiansen, K and Han, J and Hanotte, O},
title = {Altitude-dependent agro-ecologies impact the microbiome diversity of scavenging indigenous chicken in Ethiopia.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {138},
pmid = {39044244},
issn = {2049-2618},
mesh = {Animals ; *Chickens/microbiology ; Ethiopia ; *Altitude ; *Bacteria/classification/genetics/isolation & purification ; Gastrointestinal Microbiome/genetics ; Metagenome ; Cecum/microbiology ; Microbiota ; Biodiversity ; Phylogeny ; },
abstract = {BACKGROUND: Scavenging indigenous village chickens play a vital role in sub-Saharan Africa, sustaining the livelihood of millions of farmers. These chickens are exposed to vastly different environments and feeds compared to commercial chickens. In this study, we analysed the caecal microbiota of 243 Ethiopian village chickens living in different altitude-dependent agro-ecologies.

RESULTS: Differences in bacterial diversity were significantly correlated with differences in specific climate factors, topsoil characteristics, and supplemental diets provided by farmers. Microbiota clustered into three enterotypes, with one particularly enriched at high altitudes. We assembled 9977 taxonomically and functionally diverse metagenome-assembled genomes. The vast majority of these were not found in a dataset of previously published chicken microbes or in the Genome Taxonomy Database.

CONCLUSIONS: The wide functional and taxonomic diversity of these microbes highlights their importance in the local adaptation of indigenous poultry, and the significant impacts of environmental factors on the microbiota argue for further discoveries in other agro-ecologies. Video Abstract.},
}

Animals
*Chickens/microbiology
Ethiopia
*Altitude
*Bacteria/classification/genetics/isolation & purification
Gastrointestinal Microbiome/genetics
Metagenome
Cecum/microbiology
Microbiota
Biodiversity
Phylogeny

@article {pmid39044043,
year = {2024},
author = {Táncsics, A and Bedics, A and Banerjee, S and Soares, A and Baka, E and Probst, AJ and Kriszt, B},
title = {Stable-isotope probing combined with amplicon sequencing and metagenomics identifies key bacterial benzene degraders under microaerobic conditions.},
journal = {Biologia futura},
volume = {},
number = {},
pages = {},
pmid = {39044043},
issn = {2676-8607},
support = {FK 134439//National Research, Development and Innovation Office/ ; K 146358//National Research, Development and Innovation Office/ ; 899667//Horizon 2020/ ; },
abstract = {The primary aim of the present study was to reveal the major differences between benzene-degrading bacterial communities evolve under aerobic versus microaerobic conditions and to reveal the diversity of those bacteria, which can relatively quickly degrade benzene even under microaerobic conditions. For this, parallel aerobic and microaerobic microcosms were set up by using groundwater sediment of a BTEX-contaminated site and [13]C labelled benzene. The evolved total bacterial communities were first investigated by 16S rRNA gene Illumina amplicon sequencing, followed by a density gradient fractionation of DNA and a separate investigation of "heavy" and "light" DNA fractions. Results shed light on the fact that the availability of oxygen strongly determined the structure of the degrading bacterial communities. While members of the genus Pseudomonas were overwhelmingly dominant under clear aerobic conditions, they were almost completely replaced by members of genera Malikia and Azovibrio in the microaerobic microcosms. Investigation of the density resolved DNA fractions further confirmed the key role of these two latter genera in the microaerobic degradation of benzene. Moreover, analysis of a previously acquired metagenome-assembled Azovibrio genome suggested that benzene was degraded through the meta-cleavage pathway by this bacterium, with the help of a subfamily I.2.I-type catechol 2,3-dioxygenase. Overall, results of the present study implicate that under limited oxygen availability, some potentially microaerophilic bacteria play crucial role in the aerobic degradation of aromatic hydrocarbons.},
}

@article {pmid39043813,
year = {2024},
author = {Yuan, L and Zhu, XY and Lai, LM and Chen, Q and Liu, Y and Zhao, R},
title = {Clinical application and evaluation of metagenomic next-generation sequencing in pathogen detection for suspected central nervous system infections.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {16961},
pmid = {39043813},
issn = {2045-2322},
support = {grant number 2021B723//Science and Technology Program of Jiangxi Traditional Chinese Medicine/ ; SKJP220212485//the Natural Science Foundation of Jiangxi Province/ ; 82260085//the National Natural Science Fund of China/ ; },
mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Central Nervous System Infections/diagnosis/microbiology/virology ; Male ; Female ; *Metagenomics/methods ; Middle Aged ; Adult ; Retrospective Studies ; Aged ; Sensitivity and Specificity ; Adolescent ; Young Adult ; Child ; Child, Preschool ; Metagenome ; },
abstract = {Central nervous system Infections (CNSIs) is a disease characterized by complex pathogens, rapid disease progression, high mortality rate and high disability rate. Here, we evaluated the clinical value of metagenomic next generation sequencing (mNGS) in the diagnosis of central nervous system infections and explored the factors affecting the results of mNGS. We conducted a retrospective study to compare mNGS with conventional methods including culture, smear and etc. 111 suspected CNS infectious patients were enrolled in this study, and clinical data were recorded. Chi-square test were used to evaluate independent binomial variables, taking p < 0.05 as statistically significant threshold. Of the 111 enrolled cases, 57.7% (64/111) were diagnosed with central nervous system infections. From these cases, mNGS identified 39.6% (44/111) true-positive cases, 7.2% (8/111) false-positive case, 35.1% (39/111) true-negative cases, and 18.0% (20/111) false-negative cases. The sensitivity and specificity of mNGS were 68.7% (44/64) and 82.9% (39/47), respectively. Compared with culture, mNGS provided a higher pathogen detection rate in CNSIs patients (68.7% (44/64) vs. 26.5% (17/64), p < 0.0001). Compared to conventional methods, positive percent agreement and negative percent agreement was 84.60% (44/52) and 66.1% (39/59) separately. At a species-specific read number (SSRN) ≥ 2, mNGS performance in the diagnosis of definite viral encephalitis and/or meningitis was optimal (area under the curve [AUC] 0.758, 95% confidence interval [CI] 0.663-0.854). In bacterial CNSIs patients with significant CSF abnormalities (CSF WBC > 300*10[6]/L), the positive rate of CSF mNGS is higher. To sum up, conventional microbiologic testing is insufficient to detect all neuroinvasive pathogens, and mNGS exhibited satisfactory diagnostic performance in CNSIs and with an overall detection rate higher than culture (p < 0.0001).},
}

Humans
*High-Throughput Nucleotide Sequencing/methods
*Central Nervous System Infections/diagnosis/microbiology/virology
Male
Female
*Metagenomics/methods
Middle Aged
Adult
Retrospective Studies
Aged
Sensitivity and Specificity
Adolescent
Young Adult
Child
Child, Preschool
Metagenome

@article {pmid39043406,
year = {2024},
author = {Rolfe, RJ and Sheldon, SW and Kingry, LC and Petersen, JM and Maro, VP and Kinabo, GD and Saganda, W and Maze, MJ and Halliday, JEB and Nicholson, WL and Galloway, RL and Rubach, MP and Crump, JA},
title = {Metagenomic Detection of Bacterial Zoonotic Pathogens among Febrile Patients, Tanzania, 2007-2009[1].},
journal = {Emerging infectious diseases},
volume = {30},
number = {8},
pages = {1599-1608},
doi = {10.3201/eid3008.240529},
pmid = {39043406},
issn = {1080-6059},
mesh = {Humans ; Tanzania/epidemiology ; Adult ; Child, Preschool ; Adolescent ; *Metagenomics/methods ; *Fever/microbiology ; Male ; Female ; Animals ; Child ; *RNA, Ribosomal, 16S/genetics ; Young Adult ; Bacteria/genetics/classification/isolation & purification ; Bacterial Zoonoses/microbiology/epidemiology ; Bacterial Infections/microbiology/epidemiology/diagnosis ; Zoonoses/microbiology/epidemiology ; },
abstract = {Bacterial zoonoses are established causes of severe febrile illness in East Africa. Within a fever etiology study, we applied a high-throughput 16S rRNA metagenomic assay validated for detecting bacterial zoonotic pathogens. We enrolled febrile patients admitted to 2 referral hospitals in Moshi, Tanzania, during September 2007-April 2009. Among 788 participants, median age was 20 (interquartile range 2-38) years. We performed PCR amplification of V1-V2 variable region 16S rRNA on cell pellet DNA, then metagenomic deep-sequencing and pathogenic taxonomic identification. We detected bacterial zoonotic pathogens in 10 (1.3%) samples: 3 with Rickettsia typhi, 1 R. conorii, 2 Bartonella quintana, 2 pathogenic Leptospira spp., and 1 Coxiella burnetii. One other sample had reads matching a Neoerhlichia spp. previously identified in a patient from South Africa. Our findings indicate that targeted 16S metagenomics can identify bacterial zoonotic pathogens causing severe febrile illness in humans, including potential novel agents.},
}

Humans
Tanzania/epidemiology
Adult
Child, Preschool
Adolescent
*Metagenomics/methods
*Fever/microbiology
Male
Female
Animals
Child
*RNA, Ribosomal, 16S/genetics
Young Adult
Bacteria/genetics/classification/isolation & purification
Bacterial Zoonoses/microbiology/epidemiology
Bacterial Infections/microbiology/epidemiology/diagnosis
Zoonoses/microbiology/epidemiology

@article {pmid39043353,
year = {2024},
author = {Thacharodi, A and Hassan, S and Ahmed, ZHT and Singh, P and Maqbool, M and Meenatchi, R and Pugazhendhi, A and Sharma, A},
title = {The ruminant gut microbiome vs enteric methane emission: The essential microbes may help to mitigate the global methane crisis.},
journal = {Environmental research},
volume = {},
number = {},
pages = {119661},
doi = {10.1016/j.envres.2024.119661},
pmid = {39043353},
issn = {1096-0953},
abstract = {Ruminants release enteric methane into the atmosphere, significantly increasing greenhouse gas emissions and degrading the environment. A common focus of traditional mitigation efforts is on dietary management and manipulation, which may have limits in sustainability and efficacy, exploring the potential of essential microorganisms as a novel way to reduce intestinal methane emissions in ruminants; a topic that has garnered increased attention in recent years. Fermentation and feed digestion are significantly aided by essential microbes found in the rumen, such as bacteria, fungi, and archaea. The practical implications of the findings reported in various studies conducted on rumen gut concerning methane emissions may pave the way to understanding the mechanisms of CH4 production in the rumen to enhance cattle feed efficiency and mitigate CH4 emissions from livestock. This review discussed using essential bacteria to reduce intestinal methane emissions in ruminants. It investigates how particular microbial strains or consortia can alter rumen fermentation pathways to lower methane output while preserving the health and productivity of animals. We also describe the role of probiotics and prebiotics in managing methane emissions using microbial feed additives, some recent studies involving microbial interventions have been discussed. The use of new methods involving functional metagenomics and meta-transcriptomics for exploring the rumen microbiome structure has been highlighted. This review also emphasizes the challenges faced in altering the gut microbiome and future directions in this area.},
}

@article {pmid39043311,
year = {2024},
author = {Wang, X and Li, J and Wang, D and Sun, C and Zhang, X and Zhao, J and Teng, J and Wang, Q},
title = {Unveiling microplastic's role in nitrogen cycling: metagenomic insights from estuarine sediment microcosms.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {124591},
doi = {10.1016/j.envpol.2024.124591},
pmid = {39043311},
issn = {1873-6424},
abstract = {Marine microplastics (MPs) pollution, with rivers as a major source, leads to MPs accumulation in estuarine sediments, which are also nitrogen cycling hotspots. However, the impact of MPs on nitrogen cycling in estuarine sediments has rarely been documented. In this study, we conducted microcosm experiment to investigate the effects of commonly encountered polyethylene (PE) and polystyrene (PS) MPs, with two MPs concentrations (0.3% and 3% wet sediment weight) based on environmental concentration considerations and dose-response effects, on sediment dissolved oxygen (DO) diffusion capacity and microbial communities using microelectrode system and metagenomic analysis respectively. The results indicated that high concentrations of PE-MPs inhibited DO diffusion during the mid-phase of the experiment, an effect that dissipated in the later stages. Metagenomic analysis revealed that MP treatments reduced the relative abundance of dominant microbial colonies in the sediments. The PCoA results demonstrated that MPs altered the microbial community structure, particularly evident under high concentration PE-MPs treatments. Functional analysis related to the nitrogen cycle suggested that PS-MPs promoted the nitrification, denitrification, and DNRA processes, but inhibited the ANRA process, while PE-MPs had an inhibitory effect on the nitrate reduction process and the ANRA process. Additionally, the high concentration of PE-MPs treatment significantly stimulated the abundance of genus (Bacillus) by 34.1% and genes (lip, pnbA) by 100-187.5% associated with plastic degradation, respectively. Overall, in terms of microbial community structure and the abundance of nitrogen cycling functional genes, PE- and PS- MPs exhibit both similarities and differences in their impact on nitrogen cycling. Our findings highlight the complexity of MP effects on nitrogen cycling in estuarine sediments and high concentrations of PE-MP stimulated plastic-degrading genus and genes.},
}

@article {pmid39043054,
year = {2024},
author = {Perdomo, A and Calle, A},
title = {Assessment of microbial communities in a dairy farm from a food safety perspective.},
journal = {International journal of food microbiology},
volume = {423},
number = {},
pages = {110827},
doi = {10.1016/j.ijfoodmicro.2024.110827},
pmid = {39043054},
issn = {1879-3460},
abstract = {Microbial communities associated with dairy farm operations have a significant influence on food safety, dairy product quality, and animal health. This study aimed to create a microbial mapping at a dairy farm to learn about their bacterial diversity, distribution, and potential dissemination pathways. The investigation included the detection of key zoonotic pathogens, enumeration of Staphylococcus aureus and Escherichia coli as indicators of typical bacterial loads in a dairy production environment, and a microbiome analysis using metagenomics. A total of 160 samples (environmental, udder swabs, feed, feces, raw milk, and water) were collected during winter (N = 80) and spring (N = 80). In winter, Cronobacter spp. were detected in four feed and two water samples; L. monocytogenes was identified in two samples, one from feces and one from a cattle mat; E. coli O157:H7 was found in two feed samples. On the other hand, during spring, Cronobacter spp. were present in four feed samples and one hallway drain, with only one feed sample testing positive for E. coli O157:H7, while L. monocytogenes was absent during the spring season. Regarding microbial counts, there was no significant difference between the two seasons (p = 0.068) for S. aureus; however, a significant difference (p = 0.025) was observed for E. coli. Environmental microbiome analysis showed the presence of Proteobacteria (46.0 %) and Firmicutes (27.2 %) as the dominant phyla during both seasons. Moraxellaceae (11.8 %) and Pseudomonadaceae (10.62 %) were notable during winter, while Lactobacillaceae (13.0 %) and Enterobacteriaceae (12.6 %) were prominent during spring. These findings offer valuable insights into microbial distribution within a dairy farm and potential risks to animal and human health through environmental cross-contamination.},
}

@article {pmid39042309,
year = {2024},
author = {Hussan, H and Ali, MR and Lyo, V and Webb, A and Pietrzak, M and Zhu, J and Choueiry, F and Li, H and Cummings, BP and Marco, ML and Medici, V and Clinton, SK},
title = {Bariatric Surgery Is Associated with Lower Concentrations of Fecal Secondary Bile Acids and Their Metabolizing Microbial Enzymes: A Pilot Study.},
journal = {Obesity surgery},
volume = {},
number = {},
pages = {},
pmid = {39042309},
issn = {1708-0428},
support = {R35GM133510/GM/NIGMS NIH HHS/United States ; },
abstract = {INTRODUCTION: Excess body fat elevates colorectal cancer risk. While bariatric surgery (BRS) induces significant weight loss, its effects on the fecal stream and colon biology are poorly understood. Specifically, limited data exist on the impact of bariatric surgery (BRS) on fecal secondary bile acids (BA), including lithocholic acid (LCA), a putative promotor of colorectal carcinogenesis.

METHODS: This cross-sectional case-control study included 44 patients with obesity; 15 pre-BRS (controls) vs. 29 at a median of 24.1 months post-BRS. We examined the fecal concentrations of 11 BA by liquid chromatography and gene abundance of BA-metabolizing bacterial enzymes through fecal metagenomic sequencing. Differences were quantified using non-parametric tests for BA levels and linear discriminant analysis (LDA) effect size (LEfSe) for genes encoding BA-metabolizing enzymes.

RESULTS: Total fecal secondary BA concentrations trended towards lower levels post- vs. pre-BRS controls (p = 0.07). Individually, fecal LCA concentrations were significantly lower post- vs. pre-BRS (8477.0 vs. 11,914.0 uM/mg, p < 0.008). Consistent with this finding, fecal bacterial genes encoding BA-metabolizing enzymes, specifically 3-betahydroxycholanate-3-dehydrogenase (EC 1.1.1.391) and 3-alpha-hydroxycholanate dehydrogenase (EC 1.1.1.52), were also lower post- vs. pre-BRS controls (LDA of - 3.32 and - 2.64, respectively, adjusted p < 0.0001). Post-BRS fecal BA concentrations showed significant inverse correlations with weight loss, a healthy diet quality, and increased physical activity.

CONCLUSIONS: Concentrations of LCA, a secondary BA, and bacterial genes needed for BA metabolism are lower post-BRS. These changes can impact health and modulate the colorectal cancer cascade. Further research is warranted to examine how surgical alterations and the associated dietary changes impact bile acid metabolism.},
}

@article {pmid39042247,
year = {2024},
author = {Çalık Koç, G and Rezaei, F and Kahraman Ilıkkan, Ö and Bağdat, EŞ},
title = {Effect of seed priming with polyethylene glycol, distilled water, and sorbitol on physical, chemical quality parameters, and nodule microbiota of lentil.},
journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]},
volume = {},
number = {},
pages = {},
pmid = {39042247},
issn = {1678-4405},
support = {21/07//Baskent Üniversitesi/ ; },
abstract = {The aim of this study was to investigate the effects of different seed priming solutions on physical and chemical quality parameters of lentils as well as nodule bacterial diversity before sowing. Therefore, lentil seeds were treated with polyethylene glycol (PEG 6000) (15%), sorbitol (6%), and distilled water, and none pretreated lentils (Lens culinaris) were used as control. The seeds were kept in these solutions for 24 h, then dried on toweling paper for 24 h, and used for the experiment. For nodule microbiota analysis, the plant root was divided into two equal parts, upper and lower, according to the root length and all nodules were collected from each region. According to the results, it was observed that emergence and flowering started late in the control compared to other seed priming treatments. Sorbitol application was found to provide advantages in terms of germination and seedling development. PEG and distilled water (DW) treatments showed an increase in total phenolic component activity; however, no significant change was observed in DPPH radical scavenging activity. Amplicon-based metagenomic analysis revealed that sorbitol and distilled water were the seed priming solutions altering the species diversity, especially Rhizobium sp. as the genus. In the comparison of samples taken from different parts of the root nodules, more Rhizobium sp. as a genus and Rhizobium leguminosarum as the species were found in the nodules collected from the top of the root. According to the overall results of lentil pod, lentil plant, and microbiota, sorbitol and DW can be considered to be a good priming solutions.},
}

@article {pmid39042190,
year = {2024},
author = {Saket, P and Joshi, A and Yadav, AK and Bala, K},
title = {Exploring the potential of graphite material in an unplanted electroactive wetland for the remediation of synthetic wastewater containing azo dye.},
journal = {Environmental science and pollution research international},
volume = {},
number = {},
pages = {},
pmid = {39042190},
issn = {1614-7499},
support = {NASF/CA- 6031/2017-18 (GAP-303)//Indian Council of Agricultural Research/ ; MLP-037//Council of Scientific and Industrial Research, India/ ; MLP-059//Council of Scientific and Industrial Research, India/ ; DST/TMD-EWO/WTI/2K19/EWFH/2019/109 (GAP-340)]//department of science and technology, India/ ; },
abstract = {The current study was conducted to understand the sole role of graphite as a substrate material in a dual-chambered baffled electroactive wetland (EW) in the treatment of Methyl red dye-containing wastewater. The results obtained were compared with conventional gravel-based unplanted dual-chambered constructed wetlands (CW) at a lab scale. The highest dye decolorisation and COD removal efficiency achieved was 92.88 ± 1.6% and 95.78 ± 4.1%, respectively, in the electro-active wetland. Dissolved oxygen (DO) and pH conditions were appropriately maintained in both the microcosms because of separated aerobic and anaerobic chambers. UV-vis and gas chromatography-mass spectroscopy analysis revealed the production of by-products like 4-amino benzoic and N- N dimethyl phenyl-diamine of MR in microcosms and revealed further mineralisation of by-products in the aerobic zone of electroactive-wetland. Higher root growth of Cicer aerietinum and Vigna radiata was observed in the presence of effluents of baffled electroactive wetlands compared to constructed wetland, indicating a decrease in phytotoxicity. Metagenomic analysis revealed the abundance of potential microbes for MR and organic matter removal from phylum Proteobacteria, Firmicutes, Bacteroidetes, and Euryarchaeota. A batch adsorption study revealed a higher adsorption capability of graphite material in comparison to gravel. Hence, this study demonstrated that graphite is an appropriate substrate in electroactive wetland in facilitating microbial attachments and enhancing dye degradation, in addition to exhibiting superior adsorption quality.},
}

@article {pmid39041354,
year = {2024},
author = {Wang, X and Xu, H and Qin, L and Wang, H and Jiang, Y and Liu, H and Zhang, M and Pang, R and Wu, W and Li, W},
title = {Metagenomic next-generation sequencing of cerebrospinal fluid reveals etiological and microbiological features in patients with various central nervous system infections.},
journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology},
volume = {38},
number = {14},
pages = {e23812},
doi = {10.1096/fj.202400792R},
pmid = {39041354},
issn = {1530-6860},
support = {SBGJ2018077//Health Commission of Henan Province ()/ ; },
mesh = {Humans ; Male ; Female ; Middle Aged ; *High-Throughput Nucleotide Sequencing/methods ; Adult ; *Metagenomics/methods ; Aged ; *Central Nervous System Infections/cerebrospinal fluid/microbiology/diagnosis ; Adolescent ; Biomarkers/cerebrospinal fluid ; Child ; Young Adult ; Cerebrospinal Fluid/microbiology ; Aged, 80 and over ; Child, Preschool ; Metagenome ; },
abstract = {The application of metagenomic next-generation sequencing (mNGS) in pathogens detection of cerebrospinal fluid (CSF) is limited because clinical, microbiological, and biological information are not well connected. We analyzed the 428 enrolled patients' clinical features, pathogens diagnostic efficiency of mNGS in CSF, microbial community structure and composition in CSF, and correlation of microbial and clinical biomarkers in CSF. General characteristics were unspecific but helpful in formulating a differential diagnosis. CSF mNGS has a higher detection rate (34.6%) compared to traditional methods (5.4%). mNGS detection rate was higher when the time from onset to CSF collection was ≤20 days, the CSF leukocytes count was >200 × 10[6]/L, the CSF protein concentration was >1.3 g/L, or CSF glucose concentration was ≤2.5 mmol/L in non-postoperative bacterial CNS infections (CNSi). CSF was not strictly a sterile environment, and the potential pathogens may contribute to the dysbiosis of CSF microbiome. Furthermore, clinical biomarkers were significantly relevant to CNS pathogens. Clinical data are helpful in choosing a proper opportunity to obtain an accurate result of mNGS, and can speculate whether the mNGS results are correct or not. Our study is a pioneering study exploring the CSF microbiome in different CNSIs.},
}

Humans
Male
Female
Middle Aged
*High-Throughput Nucleotide Sequencing/methods
Adult
*Metagenomics/methods
Aged
*Central Nervous System Infections/cerebrospinal fluid/microbiology/diagnosis
Adolescent
Biomarkers/cerebrospinal fluid
Child
Young Adult
Cerebrospinal Fluid/microbiology
Aged, 80 and over
Child, Preschool
Metagenome

@article {pmid39041196,
year = {2024},
author = {Tan, S and Liu, L and Jiao, JY and Li, MM and Hu, CJ and Lv, AP and Qi, YL and Li, YX and Rao, YZ and Qu, YN and Jiang, HC and Soo, RM and Evans, PN and Hua, ZS and Li, WJ},
title = {Exploring the origins and evolution of oxygenic and anoxygenic photosynthesis in deeply branched Cyanobacteriota.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msae151},
pmid = {39041196},
issn = {1537-1719},
abstract = {Cyanobacteriota, the sole prokaryotes capable of oxygenic photosynthesis (OxyP), occupy a unique and pivotal role in Earth's history. While the notion that OxyP may have originated from Cyanobacteriota is widely accepted, its early evolution remains elusive. Here, by using both metagenomics and metatranscriptomics, we explore 36 metagenome-assembled genomes (MAGs) from hot spring ecosystems, belonging to two deep-branching cyanobacterial orders: Thermostichales and Gloeomargaritales. Functional investigation reveals that Thermostichales encode the crucial thylakoid membrane biogenesis protein, Vipp1. Based on the phylogenetic results, we infer that the evolution of the thylakoid membrane predates the divergence of Thermostichales from other cyanobacterial groups and that Thermostichales may be the most ancient lineage known to date to have inherited this feature from their common ancestor. Apart from OxyP, both lineages are potentially capable of sulfide-driven anoxygenic photosynthesis (AnoxyP) by linking sulfide oxidation to the photosynthetic electron transport chain. Unexpectedly, this AnoxyP capacity appears to be an acquired feature, as the key gene sqr was horizontally transferred from later-evolved cyanobacterial lineages. The presence of two D1 protein variants in Thermostichales suggests the functional flexibility of photosystems, ensuring their survival in fluctuating redox environments. Furthermore, all MAGs feature streamlined phycobilisomes with a preference for capturing longer-wavelength light, implying a unique evolutionary trajectory. Collectively, these results reveal the photosynthetic flexibility in these early-diverging cyanobacterial lineages, shedding new light on the early evolution of Cyanobacteriota and their photosynthetic processes.},
}

@article {pmid39041015,
year = {2024},
author = {Brame, JE and Liddicoat, C and Abbott, CA and Cando-Dumancela, C and Fickling, NW and Robinson, JM and Breed, MF},
title = {Urban sports fields support higher levels of soil butyrate and butyrate-producing bacteria than urban nature parks.},
journal = {Ecology and evolution},
volume = {14},
number = {7},
pages = {e70057},
pmid = {39041015},
issn = {2045-7758},
abstract = {Butyrate-producing bacteria colonise the gut of humans and non-human animals, where they produce butyrate, a short-chain fatty acid with known health benefits. Butyrate-producing bacteria also reside in soils and soil bacteria can drive the assembly of airborne bacterial communities (the aerobiome). Aerobiomes in urban greenspaces are important reservoirs of butyrate-producing bacteria as they supplement the human microbiome, but soil butyrate producer communities have rarely been examined in detail. Here, we studied soil metagenome taxonomic and functional profiles and soil physicochemical data from two urban greenspace types: sports fields (n = 11) and nature parks (n = 22). We also developed a novel method to quantify soil butyrate and characterised the in situ activity of butyrate-producing bacteria. We show that soil butyrate was higher in sports fields than nature parks and that sports fields also had significantly higher relative abundances of the terminal butyrate production genes buk and butCoAT than nature parks. Soil butyrate positively correlated with buk gene abundance (but not butCoAT). Soil moisture (r = .50), calcium (r = -.62), iron (ρ = .54), ammonium nitrogen (ρ = .58) and organic carbon (r = .45) had the strongest soil abiotic effects on soil butyrate concentrations and iron (ρ = .56) and calcium (ρ = -.57) had the strongest soil abiotic effects on buk read abundances. Overall, our findings contribute important new insights into the role of sports fields as key exposure reservoirs of butyrate producing bacteria, with important implications for the provision of microbiome-mediated human health benefits via butyrate.},
}

@article {pmid39040904,
year = {2024},
author = {Wang, C and Zhang, Y and Wang, S and Lv, X and Xu, J and Zhang, X and Yang, Q and Meng, F and Xu, B},
title = {Differential effects of domesticated and wild Capsicum frutescens L. on microbial community assembly and metabolic functions in rhizosphere soil.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1383526},
pmid = {39040904},
issn = {1664-302X},
abstract = {OBJECTIVE: Rhizosphere microorganisms play crucial roles in the growth and development of plants, disease resistance, and environmental adaptability. As the only wild pepper variety resource in China, domesticated Capsicum frutescens Linn. (Xiaomila) exhibits varying beneficial traits and affects rhizosphere microbial composition compared with its wild counterparts. In this study, we aimed to identify specific rhizosphere microbiome and metabolism patterns established during the domestication process.

METHODS: The rhizosphere microbial diversity and composition of domesticated and wild C. frutescens were detected and analyzed by metagenomics. Non-targeted metabolomics were used to explore the differences of metabolites in rhizosphere soil between wild and domesticated C. frutescens.

RESULTS: We found that the rhizosphere microbial diversity of domesticated variety was significantly different from that of the wild variety, with Massilia being its dominant bacteria. However, the abundance of certain beneficial microbes such as Gemmatimonas, Streptomyces, Rambibacter, and Lysobacter decreased significantly. The main metabolites identified in the wild variety included serylthreonine, deoxyloganic acid, vitamin C, among others. In contrast, those identified in the domesticated group were 4-hydroxy-l-glutamic acid and benzoic acid. Furthermore, the differentially enriched pathways were concentrated in tyrosine and tryptophan biosynthesis, histidine and purine-derived alkaloids biosynthesis, benzoic acid family, two-component system, etc.

CONCLUSION: This study revealed that C. frutescens established specific rhizosphere microbiota and metabolites during domestication, which has important significance for the efficient utilization of beneficial microorganisms in breeding and cultivation practices.},
}

@article {pmid39040894,
year = {2024},
author = {Feng, M and Zhang, J and Li, X and Wang, S and Li, Y and Dong, C},
title = {Case report: Suspected organizing pneumonia secondary to severe respiratory syncytial virus pneumonia in an elderly patient.},
journal = {Frontiers in medicine},
volume = {11},
number = {},
pages = {1394542},
pmid = {39040894},
issn = {2296-858X},
abstract = {Respiratory syncytial virus (RSV) usually causes acute respiratory tract infection in infants. In recent years, it has gradually become an important pathogen of lower respiratory tract infection in elderly people with an underlying disease. However, at present, the treatment of severe RSV pneumonia in adults is unclear, and organizing pneumonia (OP) after severe RSV infection has rarely been reported. We reported a 76-year-old man with multiple chronic heart and lung diseases who presented with fever, cough and progressive dyspnea. Finally, severe RSV pneumonia was diagnosed after his nasopharyngeal swabs and bronchoalveolar lavage metagenomic next-generation sequencing tests were positive for RSV. After combined treatment with oral ribavirin, intravenous immunoglobulin and corticosteroids, the patient's condition largely resolved, and he was discharged. However, when the corticosteroids were gradually tapered, the disease relapsed twice, and the patient experienced fever and aggravated dyspnea. Despite the lack of pathological evidence, we highly suspected organizing pneumonia secondary to severe RSV pneumonia based on the typical imaging manifestations and the clinical characteristics of a good response to corticosteroids. Finally, this patient was successfully treated with a course of corticosteroids and followed up for 14 months in total.},
}

@article {pmid39040893,
year = {2024},
author = {Ling, J and Liang, L and Liu, X and Wu, W and Yan, Z and Zhou, W and Jiang, Y and Kuang, L},
title = {Invasive Fusarium solani infection diagnosed by traditional microbial detection methods and metagenomic next-generation sequencing in a pediatric patient: a case report and literature review.},
journal = {Frontiers in medicine},
volume = {11},
number = {},
pages = {1322700},
pmid = {39040893},
issn = {2296-858X},
abstract = {Fusarium solani, as an opportunistic pathogen, can infect individuals with immunosuppression, neutropenia, hematopoietic stem cell transplantation (HSCT), or other high-risk factors, leading to invasive or localized infections. Particularly in patients following allogeneic HSCT, Fusarium solani is more likely to cause invasive or disseminated infections. This study focuses on a pediatric patient who underwent HSCT for severe aplastic anemia. Although initial blood cultures were negative, an abnormality was detected in the 1,3-β-D-glucan test (G test) post-transplantation. To determine the causative agent, blood samples were subjected to metagenomic next-generation sequencing (mNGS) and blood cultures simultaneously. Surprisingly, the results of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and mNGS differed slightly, with mNGS identifying Nectria haematonectria, while MALDI-TOF MS based on culture showed Fusarium solani. To clarify the results, Sanger sequencing was performed for further detection, and the results were consistent with those of MALDI-TOF MS. Since the accuracy of Sanger sequencing is higher than that of mNGS, the diagnosis was revised to invasive Fusarium solani infection. With advancements in technology, various detection methods for invasive fungi have been developed in recent years, such as mNGS, which has high sensitivity. While traditional methods may be time-consuming, they are important due to their high specificity. Therefore, in clinical practice, it is essential to utilize both traditional and novel detection methods in a complementary manner to enhance the diagnosis of invasive fungal infections.},
}

@article {pmid39040604,
year = {2024},
author = {Hasan, Z and Netherland, M and Hasan, NA and Begum, N and Yasmin, M and Ahmed, S},
title = {An insight into the vaginal microbiome of infertile women in Bangladesh using metagenomic approach.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1390088},
pmid = {39040604},
issn = {2235-2988},
mesh = {Humans ; Female ; *Vagina/microbiology ; *Metagenomics/methods ; *Infertility, Female/microbiology ; Adult ; *Microbiota/genetics ; Bangladesh ; *Bacteria/classification/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Metagenome ; Young Adult ; Lactobacillus/isolation & purification/genetics/classification ; Dysbiosis/microbiology ; Phylogeny ; },
abstract = {INTRODUCTION: The dysbiosis of vaginal microbiota is recognized as a potential underlying factor contributing to infertility in women. This study aimed to compare the vaginal microbiomes of infertile and fertile women to investigate their relationship with infertility.

METHODS: Metagenomic analysis was conducted on samples from 5 infertile and 5 fertile individuals using both amplicon 16S and metagenomics shotgun sequencing methods.

RESULTS AND DISCUSSION: In the infertile group, the bacterial community was primarily represented by three major bacterial genera: Lactobacillus (79.42%), Gardnerella (12.56%) and Prevotella (3.33%), whereas, the fertile group exhibited a more diverse composition with over 8 major bacterial genera, accompanied by significantly reduced abundance of Lactobacillus (48.79%) and Gardnerella (6.98%). At the species level, higher abundances of L. iners, L. gasseri and G. vaginalis were observed in the infertile group. Regarding the microbiome composition, only one fertile and two infertile subjects exhibited the healthiest Community State Types, CST-1, while CST-3 was observed among two infertile and one fertile subject, and CST-4 in three other fertile and one infertile subject. Overall, alpha diversity metrics indicated greater diversity and lower species richness in the control (fertile) group, while the infertile group displayed the opposite trend. However, beta-diversity analysis did not show distinct clustering of samples associated with any specific group; instead, it demonstrated CST-type specific clustering. Shotgun metagenomics further confirmed the dominance of Firmicutes, with a greater abundance of Lactobacillus species in the infertile group. Specifically, L. iners and G. vaginalis were identified as the most dominant and highly abundant in the infertile group. Fungi were only identified in the control group, dominated by Penicillium citrinum (62.5%). Metagenome-assembled genomes (MAGs) corroborated read-based taxonomic profiling, with the taxon L. johnsonii identified exclusively in disease samples. MAG identities shared by both groups include Shamonda orthobunyavirus, L. crispatus, Human endogenous retrovirus K113, L. iners, and G. vaginalis. Interestingly, the healthy microbiomes sequenced in this study contained two clusters, Penicillium and Staphylococcus haemolyticus, not found in the public dataset. In conclusion, this study suggests that lower species diversity with a higher abundance of L. iners, L. gasseri and G. vaginalis, may contribute to female infertility in our study datasets. However, larger sample sizes are necessary to further evaluate such association.},
}

Humans
Female
*Vagina/microbiology
*Metagenomics/methods
*Infertility, Female/microbiology
Adult
*Microbiota/genetics
Bangladesh
*Bacteria/classification/genetics/isolation & purification
RNA, Ribosomal, 16S/genetics
Metagenome
Young Adult
Lactobacillus/isolation & purification/genetics/classification
Dysbiosis/microbiology
Phylogeny

@article {pmid39040390,
year = {2024},
author = {Xu, Q and Han, W and Cai, Y and Yin, Y and Guo, Y and Chen, H and Wang, H},
title = {A case report of the metagenomic next-generation sequencing for timely diagnosis of a traveler with nonspecific febrile Q fever.},
journal = {Heliyon},
volume = {10},
number = {13},
pages = {e33649},
pmid = {39040390},
issn = {2405-8440},
abstract = {Q fever is a worldwide distribution disease caused by Coxiella burnetii（C. burnetii）, an obligate intracellular, Gram-negative acidophilic bacterium belonging to γ-proteobacterium. Most patients present with acute Q-fever accompanied by atypical flu-like symptoms, with only 1%-5% of cases may develop into persistent and focally infected foci, mainly manifest as endocarditis, osteomyelitis and prosthetic arthritis. In this case, the patient experienced an unexplained and uninterrupted fever up to 39.2 °C for a week, accompanied by chills and headaches, as well as abnormal liver function. The laboratory reported negative results for blood culture and respiratory-associated pathogens, however, the metagenomic next-generation sequencing (mNGS) reported that detection of 20 sequence reads of C. burnetii in the patient's peripheral blood. In addition, the patient had traveled to Sri Lanka, Iraq and Saudi Arabia before illness. In clinical, the treatment regimen was adjusted from empirically intravenous moxifloxacin 400 mg a day for 1 week to continuously oral minocyline 100 mg twice daily for 2 weeks. The patient was in good health without any adverse sequelae during outpatient visitation and the phone calls follow-up. In conclusion, the mNGS does provide an early and timely diagnostic basis for rare and difficult to culture pathogens, which contributes to the success of clinical anti-infection.},
}

@article {pmid39039769,
year = {2024},
author = {Schwab, S and Dame, RT},
title = {Identification, characterization and classification of prokaryotic nucleoid-associated proteins.},
journal = {Molecular microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1111/mmi.15298},
pmid = {39039769},
issn = {1365-2958},
support = {OCENW.GROOT.2019.012//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; VICI 016.160.613/53//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; },
abstract = {Common throughout life is the need to compact and organize the genome. Possible mechanisms involved in this process include supercoiling, phase separation, charge neutralization, macromolecular crowding, and nucleoid-associated proteins (NAPs). NAPs are special in that they can organize the genome at multiple length scales, and thus are often considered as the architects of the genome. NAPs shape the genome by either bending DNA, wrapping DNA, bridging DNA, or forming nucleoprotein filaments on the DNA. In this mini-review, we discuss recent advancements of unique NAPs with differing architectural properties across the tree of life, including NAPs from bacteria, archaea, and viruses. To help the characterization of NAPs from the ever-increasing number of metagenomes, we recommend a set of cheap and simple in vitro biochemical assays that give unambiguous insights into the architectural properties of NAPs. Finally, we highlight and showcase the usefulness of AlphaFold in the characterization of novel NAPs.},
}

@article {pmid39039586,
year = {2024},
author = {Liang, JL and Feng, SW and Jia, P and Lu, JL and Yi, X and Gao, SM and Wu, ZH and Liao, B and Shu, WS and Li, JT},
title = {Unraveling the habitat preferences, ecological drivers, potential hosts, and auxiliary metabolism of soil giant viruses across China.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {136},
pmid = {39039586},
issn = {2049-2618},
support = {42177009//National Natural Science Foundation of China/ ; 41622106//National Natural Science Foundation of China/ ; 2023YFC3207300//National Key R&D Program of China/ ; },
mesh = {China ; *Soil Microbiology ; *Metagenome ; *Ecosystem ; *Giant Viruses/genetics/classification ; Soil/chemistry ; Phylogeny ; Genome, Viral/genetics ; Metagenomics ; },
abstract = {BACKGROUND: Soil giant viruses are increasingly believed to have profound effects on ecological functioning by infecting diverse eukaryotes. However, their biogeography and ecology remain poorly understood.

RESULTS: In this study, we analyzed 333 soil metagenomes from 5 habitat types (farmland, forest, grassland, Gobi desert, and mine wasteland) across China and identified 533 distinct giant virus phylotypes affiliated with nine families, thereby greatly expanding the diversity of soil giant viruses. Among the nine families, Pithoviridae were the most diverse. The majority of phylotypes exhibited a heterogeneous distribution among habitat types, with a remarkably high proportion of unique phylotypes in mine wasteland. The abundances of phylotypes were negatively correlated with their environmental ranges. A total of 76 phylotypes recovered in this study were detectable in a published global topsoil metagenome dataset. Among climatic, geographical, edaphic, and biotic characteristics, soil eukaryotes were identified as the most important driver of beta-diversity of giant viral communities across habitat types. Moreover, co-occurrence network analysis revealed some pairings between giant viral phylotypes and eukaryotes (protozoa, fungi, and algae). Analysis of 44 medium- to high-quality giant virus genomes recovered from our metagenomes uncovered not only their highly shared functions but also their novel auxiliary metabolic genes related to carbon, sulfur, and phosphorus cycling.

CONCLUSIONS: These findings extend our knowledge of diversity, habitat preferences, ecological drivers, potential hosts, and auxiliary metabolism of soil giant viruses. Video Abstract.},
}

China
*Soil Microbiology
*Metagenome
*Ecosystem
*Giant Viruses/genetics/classification
Soil/chemistry
Phylogeny
Genome, Viral/genetics
Metagenomics

@article {pmid39039555,
year = {2024},
author = {Wang, D and Liu, L and Xu, X and Wang, C and Wang, Y and Deng, Y and Zhang, T},
title = {Distributions, interactions, and dynamics of prokaryotes and phages in a hybrid biological wastewater treatment system.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {134},
pmid = {39039555},
issn = {2049-2618},
mesh = {*Bacteriophages/genetics/classification/physiology/isolation & purification ; *Sewage/virology/microbiology ; *Wastewater/virology/microbiology ; *Bacteria/virology/genetics/classification ; Biofilms ; Metagenomics ; Water Purification/methods ; Microbiota ; },
abstract = {BACKGROUND: Understanding the interactions and dynamics of microbiotas within biological wastewater treatment systems is essential for ensuring their stability and long-term sustainability. In this study, we developed a systematic framework employing multi-omics and Hi-C sequencing to extensively investigate prokaryotic and phage communities within a hybrid biofilm and activated sludge system.

RESULTS: We uncovered distinct distribution patterns, metabolic capabilities, and activities of functional prokaryotes through the analysis of 454 reconstructed prokaryotic genomes. Additionally, we reconstructed a phage catalog comprising 18,645 viral operational taxonomic units (vOTUs) with high length and contiguity using hybrid assembly, and a distinct distribution of phages was depicted between activated sludge (AS) and biofilm. Importantly, 1340 host-phage pairs were established using Hi-C and conventional in silico methods, unveiling the host-determined phage prevalence. The majority of predicted hosts were found to be involved in various crucial metabolic processes, highlighting the potential vital roles of phages in influencing substance metabolism within this system. Moreover, auxiliary metabolic genes (AMGs) related to various categories (e.g., carbohydrate degradation, sulfur metabolism, transporter) were predicted. Subsequent activity analysis emphasized their potential ability to mediate host metabolism during infection. We also profiled the temporal dynamics of phages and their associated hosts using 13-month time-series metagenomic data, further demonstrating their tight interactions. Notably, we observed lineage-specific infection patterns, such as potentially host abundance- or phage/host ratio-driven phage population changes.

CONCLUSIONS: The insights gained from this research contribute to the growing body of knowledge surrounding interactions and dynamics of host-phage and pave the way for further exploration and potential applications in the field of microbial ecology. Video Abstract.},
}

*Bacteriophages/genetics/classification/physiology/isolation & purification
*Sewage/virology/microbiology
*Wastewater/virology/microbiology
*Bacteria/virology/genetics/classification
Biofilms
Metagenomics
Water Purification/methods
Microbiota

@article {pmid39039498,
year = {2024},
author = {Fan, Q and Tan, Z and Su, W and Li, Q and Jin, D and Du, Y and Zhang, L and Wu, S},
title = {Efficacy, safety and mechanism of Simiaoyongan decoction in the treatment of carotid atherosclerotic plaque: a randomized, double-blind, placebo-controlled clinical trial protocol.},
journal = {BMC complementary medicine and therapies},
volume = {24},
number = {1},
pages = {277},
pmid = {39039498},
issn = {2662-7671},
support = {82174340//General projects of the National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Drugs, Chinese Herbal/pharmacology/therapeutic use ; Double-Blind Method ; *Plaque, Atherosclerotic/drug therapy ; Carotid Artery Diseases/drug therapy ; Male ; Middle Aged ; Female ; Adult ; Aged ; },
abstract = {INTRODUCTION: Chronic inflammation is the major pathological feature of Atherosclerosis(As). Inflammation may accelerate plaque to develop, which is a key factor resulting in the thinning of the fibrous cap and the vulnerable rupture of plaque. Presently, clinical treatments are still lacking. It is necessary to find a safe and effective treatment for As inflammation. Simiaoyongan Decoction (SMYA) has potential anti-inflammatory and plaque protection effects. This protocol aims to evaluate the efficacy, safety, and mechanism of SMYA for patients with carotid atherosclerotic plaque.

METHODS/DESIGN: The assessment of SMYA clinical trial is designed as a randomized, double-blind, placebo-controlled study. The sample size is 86 cases in total, with 43 participants in the intervention group and the control group respectively. The intervention group takes SMYA, while the control group takes SMYA placebo. The medication lasts for 14 days every 10 weeks, with a total of 50 weeks. We will use carotid artery high resolution magnetic resonance imaging (HR-MRI) to measure plaque. The plaque minimum fiber cap thickness (PMFCT) is adopted as the primary outcome. The secondary outcomes include plaque fiber cap volume, volume percentage of fiber cap, lipid-rich necrotic core (LRNC) volume, volume percentage of LRNC, internal bleeding volume of plaque, internal bleeding volume percentage of plaque, plaque calcification volume, volume percentage of plaque calcification, lumen stenosis rate, average and a maximum of vessel wall thickness, vessel wall volume, total vessel wall load, carotid atherosclerosis score, hs-CRP, IL-1β and IL-6, the level of lipid profiles and blood glucose, blood pressure, and body weight.

DISCUSSION: We anticipate that patients with As plaque will be improved from SMYA by inhibiting inflammation to enhance plaque stability. This study analyzes plaque by using HR-MRI to evaluate the clinical efficacy and safety of SMYA. Moreover, we conduct transcriptome analysis, proteomic analysis, and metagenomic analysis of blood and stool of participants to study the mechanism of SMYA against As plaque. This is the first prospective TCM trial to observe and treat As plaque by inhibiting inflammatory reaction directly. If successful, the finding will be valuable in the treatment of As plaque and drug development, especially in the "statin era".

TRIAL REGISTRATION NUMBER: This trial is registered on Chinese Clinical Trials.gov with number ChiCTR2000039062 on October 15, 2020 (http://www.chictr.org.cn).},
}

Humans
*Drugs, Chinese Herbal/pharmacology/therapeutic use
Double-Blind Method
*Plaque, Atherosclerotic/drug therapy
Carotid Artery Diseases/drug therapy
Male
Middle Aged
Female
Adult
Aged

@article {pmid39039462,
year = {2024},
author = {Yan, L and Ye, B and Yang, M and Shan, Y and Yan, D and Fang, D and Zhang, K and Yu, Y},
title = {Gut microbiota and metabolic changes in children with idiopathic short stature.},
journal = {BMC pediatrics},
volume = {24},
number = {1},
pages = {468},
pmid = {39039462},
issn = {1471-2431},
mesh = {Humans ; *Gastrointestinal Microbiome ; Child ; Male ; Female ; *Feces/microbiology ; Case-Control Studies ; Adolescent ; Body Height ; Growth Disorders/microbiology/metabolism ; Metabolomics/methods ; Metabolome ; },
abstract = {BACKGROUND: Idiopathic short stature (ISS) is characterized by short stature with unknown causes. Recent studies showed different gut microbiota flora and reduced fecal short-chain fatty acids in ISS children. However, the roles of the microbiome and metabolites in the pathogenesis of ISS remains largely unknown.

METHODS: We recruited 51 Chinese subjects, comprising 26 ISS children and 25 normal-height control individuals. Untargeted metabolomics was performed to explore the fecal metabolic profiles between groups. A shotgun metagenomic sequencing approach was used to investigate the microbiome at the strains level. Mediation analyses were done to reveal correlations between the height standard deviation (SD) value, the gut microbiome and metabolites.

RESULTS: We detected marked differences in the composition of fecal metabolites in the ISS group, particularly a significant increase in erucic acid and a decrease in spermidine, adenosine and L-5-Hydroxytryptophan, when compared to those of controls. We further identified specific groups of bacterial strains to be associated with the different metabolic profile. Through mediation analysis, 50 linkages were established. KEGG pathway analysis of microbiota and metabolites indicated nutritional disturbances. 13 selected features were able to accurately distinguish the ISS children from the controls (AUC = 0.933 [95%CI, 79.9-100%]) by receiver operating characteristic (ROC) analysis.

CONCLUSION: Our study suggests that the microbiome and the microbial-derived metabolites play certain roles in children's growth. These findings provide a new research direction for better understanding the mechanism(s) underlying ISS.},
}

Humans
*Gastrointestinal Microbiome
Child
Male
Female
*Feces/microbiology
Case-Control Studies
Adolescent
Body Height
Growth Disorders/microbiology/metabolism
Metabolomics/methods
Metabolome

@article {pmid39039157,
year = {2024},
author = {Hatrongjit, R and Wongsurawat, T and Jenjaroenpun, P and Chopjitt, P and Boueroy, P and Akeda, Y and Okada, K and Iida, T and Hamada, S and Kerdsin, A},
title = {Genomic analysis of carbapenem- and colistin-resistant Klebsiella pneumoniae complex harbouring mcr-8 and mcr-9 from individuals in Thailand.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {16836},
pmid = {39039157},
issn = {2045-2322},
mesh = {*Colistin/pharmacology ; *Klebsiella pneumoniae/genetics/drug effects/isolation & purification ; Humans ; *Carbapenems/pharmacology ; *Anti-Bacterial Agents/pharmacology ; Thailand ; *Microbial Sensitivity Tests ; *Bacterial Proteins/genetics ; Klebsiella Infections/microbiology/epidemiology ; Male ; Plasmids/genetics ; Female ; Genomics/methods ; Drug Resistance, Bacterial/genetics ; Middle Aged ; Adult ; Carbapenem-Resistant Enterobacteriaceae/genetics/drug effects/isolation & purification ; Aged ; Genome, Bacterial ; Klebsiella ; },
abstract = {The surge in mobile colistin-resistant genes (mcr) has become an increasing public health concern, especially in carbapenem-resistant Enterobacterales (CRE). Prospective surveillance was conducted to explore the genomic characteristics of clinical CRE isolates harbouring mcr in 2015-2020. In this study, we aimed to examine the genomic characteristics and phonotypes of mcr-8 and mcr-9 harbouring carbapenem-resistant K. pneumoniae complex (CRKpnC). Polymerase chain reaction test and genome analysis identified CRKpnC strain AMR20201034 as K. pneumoniae (CRKP) ST147 and strain AMR20200784 as K. quasipneumoniae (CRKQ) ST476, harbouring mcr-8 and mcr-9, respectively. CRKQ exhibited substitutions in chromosomal-mediated colistin resistance genes (pmrB, pmrC, ramA, and lpxM), while CRKP showed two substitutions in crrB, pmrB, pmrC, lpxM and lapB. Both species showed resistance to colistin, with minimal inhibitory concentrations of 8 µg/ml for mcr-8-carrying CRKP isolate and 32 µg/ml for mcr-9-carrying CRKQ isolate. In addition, CRKP harbouring mcr-8 carried blaNDM, while CRKQ harbouring mcr-9 carried blaIMP, conferring carbapenem resistance. Analysis of plasmid replicon types carrying mcr-8 and mcr-9 showed FIA-FII (96,575 bp) and FIB-HI1B (287,118 bp), respectively. In contrast with the plasmid carrying the carbapenemase genes, the CRKQ carried blaIMP-14 on an IncC plasmid, while the CRKP harboured blaNDM-1 on an FIB plasmid. This finding provides a comprehensive insight into another mcr-carrying CRE from patients in Thailand. The other antimicrobial-resistant genes in the CRKP were blaCTX-M-15, blaSHV-11, blaOXA-1, aac(6')-Ib-cr, aph(3')-VI, ARR-3, qnrS1, oqxA, oqxB, sul1, catB3, fosA, and qacE, while those detected in CRKQ were blaOKP-B-15, qnrA1, oqxA, oqxB, sul1, fosA, and qacE. This observation highlights the importance of strengthening official active surveillance efforts to detect, control, and prevent mcr-harbouring CRE and the need for rational drug use in all sectors.},
}

*Colistin/pharmacology
*Klebsiella pneumoniae/genetics/drug effects/isolation & purification
Humans
*Carbapenems/pharmacology
*Anti-Bacterial Agents/pharmacology
Thailand
*Microbial Sensitivity Tests
*Bacterial Proteins/genetics
Klebsiella Infections/microbiology/epidemiology
Male
Plasmids/genetics
Female
Genomics/methods
Drug Resistance, Bacterial/genetics
Middle Aged
Adult
Carbapenem-Resistant Enterobacteriaceae/genetics/drug effects/isolation & purification
Aged
Genome, Bacterial
Klebsiella

@article {pmid38888585,
year = {2024},
author = {Chalita, M and Kim, YO and Park, S and Oh, HS and Cho, JH and Moon, J and Baek, N and Moon, C and Lee, K and Yang, J and Nam, GG and Jung, Y and Na, SI and Bailey, MJ and Chun, J},
title = {EzBioCloud: a genome-driven database and platform for microbiome identification and discovery.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {74},
number = {6},
pages = {},
pmid = {38888585},
issn = {1466-5034},
mesh = {*RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/isolation & purification ; *Microbiota ; *Archaea/genetics/classification ; *Genome, Bacterial ; Phylogeny ; Databases, Genetic ; Genome, Archaeal ; Sequence Analysis, DNA ; Computational Biology/methods ; },
abstract = {With the continued evolution of DNA sequencing technologies, the role of genome sequence data has become more integral in the classification and identification of Bacteria and Archaea. Six years after introducing EzBioCloud, an integrated platform representing the taxonomic hierarchy of Bacteria and Archaea through quality-controlled 16S rRNA gene and genome sequences, we present an updated version, that further refines and expands its capabilities. The current update recognizes the growing need for accurate taxonomic information as defining a species increasingly relies on genome sequence comparisons. We also incorporated an advanced strategy for addressing underrepresented or less studied lineages, bolstering the comprehensiveness and accuracy of our database. Our rigorous quality control protocols remain, where whole-genome assemblies from the NCBI Assembly Database undergo stringent screening to remove low-quality sequence data. These are then passed through our enhanced identification bioinformatics pipeline which initiates a 16S rRNA gene similarity search and then calculates the average nucleotide identity (ANI). For genome sequences lacking a 16S rRNA sequence and without a closely related genomic representative for ANI calculation, we apply a different ANI approach using bacterial core genes for improved taxonomic placement (core gene ANI, cgANI). Because of the increase in genome sequences available in NCBI and our newly introduced cgANI method, EzBioCloud now encompasses a total of 109 835 species, of which 21 964 have validly published names. 47 896 are candidate species identified either through 16S rRNA sequence similarity (phylotypes) or through whole genome ANI (genomospecies), and the remaining 39 975 were positioned in the taxonomic tree by cgANI (species clusters). Our EzBioCloud database is accessible at www.ezbiocloud.net/db.},
}

*RNA, Ribosomal, 16S/genetics
*Bacteria/genetics/classification/isolation & purification
*Microbiota
*Archaea/genetics/classification
*Genome, Bacterial
Phylogeny
Databases, Genetic
Genome, Archaeal
Sequence Analysis, DNA
Computational Biology/methods

@article {pmid39039075,
year = {2024},
author = {Stothart, MR and McLoughlin, PD and Medill, SA and Greuel, RJ and Wilson, AJ and Poissant, J},
title = {Methanogenic patterns in the gut microbiome are associated with survival in a population of feral horses.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {6012},
pmid = {39039075},
issn = {2041-1723},
support = {2016-06459//Canadian Network for Research and Innovation in Machining Technology, Natural Sciences and Engineering Research Council of Canada (NSERC Canadian Network for Research and Innovation in Machining Technology)/ ; 2019-04388//Canadian Network for Research and Innovation in Machining Technology, Natural Sciences and Engineering Research Council of Canada (NSERC Canadian Network for Research and Innovation in Machining Technology)/ ; 25046//Canada Foundation for Innovation (Fondation canadienne pour l'innovation)/ ; D20EQ-05//Morris Animal Foundation (MAF)/ ; D20EQ-05//Morris Animal Foundation (MAF)/ ; D20EQ-05//Morris Animal Foundation (MAF)/ ; },
mesh = {Animals ; Horses/microbiology ; *Gastrointestinal Microbiome/genetics ; *Feces/microbiology ; *Methane/metabolism ; Animals, Wild/microbiology ; Metagenome ; Fatty Acids, Volatile/metabolism ; Metagenomics/methods ; Male ; Female ; Canada ; },
abstract = {Gut microbiomes are widely hypothesised to influence host fitness and have been experimentally shown to affect host health and phenotypes under laboratory conditions. However, the extent to which they do so in free-living animal populations and the proximate mechanisms involved remain open questions. In this study, using long-term, individual-based life history and shallow shotgun metagenomic sequencing data (2394 fecal samples from 794 individuals collected between 2013-2019), we quantify relationships between gut microbiome variation and survival in a feral population of horses under natural food limitation (Sable Island, Canada), and test metagenome-derived predictions using short-chain fatty acid data. We report detailed evidence that variation in the gut microbiome is associated with a host fitness proxy in nature and outline hypotheses of pathogenesis and methanogenesis as key causal mechanisms which may underlie such patterns in feral horses, and perhaps, wild herbivores more generally.},
}

Animals
Horses/microbiology
*Gastrointestinal Microbiome/genetics
*Feces/microbiology
*Methane/metabolism
Animals, Wild/microbiology
Metagenome
Fatty Acids, Volatile/metabolism
Metagenomics/methods
Male
Female
Canada

@article {pmid39038938,
year = {2024},
author = {Chuang, YF and Fan, KC and Su, YY and Wu, MF and Chiu, YL and Liu, YC and Lin, CC},
title = {Precision probiotics supplement strategy in aging population based on gut microbiome composition.},
journal = {Briefings in bioinformatics},
volume = {25},
number = {4},
pages = {},
doi = {10.1093/bib/bbae351},
pmid = {39038938},
issn = {1477-4054},
support = {//Taiwan National Science and Technology Council/ ; MOST 110-2321-B-418//Ministry of Science and Technology/ ; MOHW111-TDU-B-221-114007//Ministry of Health and Welfare/ ; NYCU-FEMH 112DN11//FEMH-NYCU Joint Research Program/ ; },
mesh = {*Probiotics/therapeutic use/administration & dosage ; Humans ; *Gastrointestinal Microbiome ; Aged ; *Aging ; Female ; Male ; *Dietary Supplements ; Aged, 80 and over ; Middle Aged ; Lactobacillus/genetics ; Metagenomics/methods ; Bifidobacterium ; },
abstract = {With the increasing prevalence of age-related chronic diseases burdening healthcare systems, there is a pressing need for innovative management strategies. Our study focuses on the gut microbiota, essential for metabolic, nutritional, and immune functions, which undergoes significant changes with aging. These changes can impair intestinal function, leading to altered microbial diversity and composition that potentially influence health outcomes and disease progression. Using advanced metagenomic sequencing, we explore the potential of personalized probiotic supplements in 297 older adults by analyzing their gut microbiota. We identified distinctive Lactobacillus and Bifidobacterium signatures in the gut microbiota of older adults, revealing probiotic patterns associated with various population characteristics, microbial compositions, cognitive functions, and neuroimaging results. These insights suggest that tailored probiotic supplements, designed to match individual probiotic profile, could offer an innovative method for addressing age-related diseases and functional declines. Our findings enhance the existing evidence base for probiotic use among older adults, highlighting the opportunity to create more targeted and effective probiotic strategies. However, additional research is required to validate our results and further assess the impact of precision probiotics on aging populations. Future studies should employ longitudinal designs and larger cohorts to conclusively demonstrate the benefits of tailored probiotic treatments.},
}

*Probiotics/therapeutic use/administration & dosage
Humans
*Gastrointestinal Microbiome
Aged
*Aging
Female
Male
*Dietary Supplements
Aged, 80 and over
Middle Aged
Lactobacillus/genetics
Metagenomics/methods
Bifidobacterium

@article {pmid39038883,
year = {2024},
author = {Han, PJ and Song, L and Wen, Z and Zhu, HY and Wei, YH and Wang, JW and Bai, M and Luo, LJ and Wang, JW and Chen, SX and You, XL and Han, DY and Bai, FY},
title = {Species-level understanding of the bacterial community in Daqu based on full-length 16S rRNA gene sequences.},
journal = {Food microbiology},
volume = {123},
number = {},
pages = {104566},
doi = {10.1016/j.fm.2024.104566},
pmid = {39038883},
issn = {1095-9998},
mesh = {*RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/isolation & purification/metabolism ; *Fermentation ; China ; Microbiota ; Phylogeny ; DNA, Bacterial/genetics ; Biodiversity ; Alcoholic Beverages/microbiology/analysis ; Food Microbiology ; Metagenome ; Fermented Foods/microbiology ; },
abstract = {Daqu is used as the fermentation starter of Baijiu and contributes diversified functional microbes for saccharifying grains and converting sugars into ethanol and aroma components in Baijiu products. Daqu is mainly classified into three types, namely low (LTD), medium (MTD) and high (HTD) temperature Daqu, according to the highest temperatures reached in their fermentation processes. In this study, we used the PacBio small-molecule real-time (SMRT) sequencing technology to determine the full-length 16 S rRNA gene sequences from the metagenomes of 296 samples of different types of Daqu collected from ten provinces in China, and revealed the bacterial diversity at the species level in the Daqu samples. We totally identified 310 bacteria species, including 78 highly abundant species (with a relative abundance >0.1% each) which accounted for 91.90% of the reads from all the Daqu samples. We also recognized the differentially enriched bacterial species in different types of Daqu, and in the Daqu samples with the same type but from different provinces. Specifically, Lactobacillales, Enterobacterales and Bacillaceae were significantly enriched in the LTD, MTD and HTD groups, respectively. The potential co-existence and exclusion relationships among the bacteria species involved in all the Daqu samples and in the LTD, MTD and HTD samples from a specific region were also identified. These results provide a better understanding of the bacterial diversity in different types of Daqu at the species level.},
}

*RNA, Ribosomal, 16S/genetics
*Bacteria/genetics/classification/isolation & purification/metabolism
*Fermentation
China
Microbiota
Phylogeny
DNA, Bacterial/genetics
Biodiversity
Alcoholic Beverages/microbiology/analysis
Food Microbiology
Metagenome
Fermented Foods/microbiology

@article {pmid39038849,
year = {2024},
author = {Lee, S and Portlock, T and Le Chatelier, E and Garcia-Guevara, F and Clasen, F and Oñate, FP and Pons, N and Begum, N and Harzandi, A and Proffitt, C and Rosario, D and Vaga, S and Park, J and von Feilitzen, K and Johansson, F and Zhang, C and Edwards, LA and Lombard, V and Gauthier, F and Steves, CJ and Gomez-Cabrero, D and Henrissat, B and Lee, D and Engstrand, L and Shawcross, DL and Proctor, G and Almeida, M and Nielsen, J and Mardinoglu, A and Moyes, DL and Ehrlich, SD and Uhlen, M and Shoaie, S},
title = {Global compositional and functional states of the human gut microbiome in health and disease.},
journal = {Genome research},
volume = {},
number = {},
pages = {},
doi = {10.1101/gr.278637.123},
pmid = {39038849},
issn = {1549-5469},
abstract = {The human gut microbiota is of increasing interest, with metagenomics a key tool for analyzing bacterial diversity and functionality in health and disease. Despite increasing efforts to expand microbial gene catalogs and an increasing number of metagenome-assembled genomes, there have been few pan-metagenomic association studies and in-depth functional analyses across different geographies and diseases. Here, we explored 6014 human gut metagenome samples across 19 countries and 23 diseases by performing compositional, functional cluster, and integrative analyses. Using interpreted machine learning classification models and statistical methods, we identified Fusobacterium nucleatum and Anaerostipes hadrus with the highest frequencies, enriched and depleted, respectively, across different disease cohorts. Distinct functional distributions were observed in the gut microbiomes of both westernized and nonwesternized populations. These compositional and functional analyses are presented in the open-access Human Gut Microbiome Atlas, allowing for the exploration of the richness, disease, and regional signatures of the gut microbiota across different cohorts.},
}

@article {pmid39038424,
year = {2024},
author = {Zhu, YM and Chen, Y and Lu, H and Jin, K and Lin, Y and Ren, H and Xu, K},
title = {Simultaneous efficient removal of tetracycline and mitigation of antibiotic resistance genes enrichment by a modified activated sludge process with static magnetic field.},
journal = {Water research},
volume = {262},
number = {},
pages = {122107},
doi = {10.1016/j.watres.2024.122107},
pmid = {39038424},
issn = {1879-2448},
abstract = {To address the increasing issue of antibiotic wastewater, this study applied a static magnetic field (SMF) to the activated sludge process to increase the efficiency of tetracycline (TC) removal from swine wastewater and to reveal its enhanced mechanisms. The results demonstrated that the SMF-modified activated sludge process could achieve almost complete TC removal at sludge loading rates of 0.3 mg TC/g MLSS/d. Analysis of zeta potential and extracellular polymeric substances composition of the activated sludge revealed that SMF increased electrostatic interactions between TC and activated sludge and made activated sludge has much more binding sites, finally resulting in the increased TC biosorption. Metagenomic analysis showed that SMF promoted the enrichment of ammonia-oxidizing bacteria, TC-degrading bacteria, and aromatic compounds-degrading bacteria; it also enhanced ammonia monooxygenase- and cytochrome P450-mediated TC metabolism while upregulating functional genes associated with oxidase, reductase, and dehydrogenase - all contributing to increased TC biodegradation. Additionally, SMF mitigated the enrichment and spread of antibiotic resistance genes (ARGs) by decreasing the abundance of potential hosts of ARGs and inhibiting the upregulation of genes encoding ABC transporters and putative transposase. Based on these findings, this study demonstrates that magnetic field is an enhancement strategy with great potential to relieve the harmful impacts of the growing antibiotic wastewater problem on human health and the ecosystem.},
}

@article {pmid39038423,
year = {2024},
author = {Li, HQ and Xu, MR and An, XL and Liao, H and Li, LJ and Li, W and Su, JQ},
title = {High-risk ARGs (HRA) Chip: A high-throughput qPCR-based array for assessment of high-risk ARGs from the environment.},
journal = {Water research},
volume = {262},
number = {},
pages = {122106},
doi = {10.1016/j.watres.2024.122106},
pmid = {39038423},
issn = {1879-2448},
abstract = {The global surge in antibiotic resistance genes (ARGs) presents a serious public health challenge. While methods like metagenomic analysis and qPCR arrays have been instrumental in investigating ARG distributions and dynamics, the vast diversity of ARGs often complicates effective monitoring and risk assessment. Here, we developed a High-Risk ARGs (HRA) chip based on high-capacity quantitative PCR array targeting previously identified high-risk ARGs. These ARGs are known to be prevalent in human-related environments, exhibit gene mobility, and are present in ESKAPE pathogens. The HRA chip include 101 primer sets and the 16S rRNA gene as a reference. These primer sets consist of 34 obtained from previous studies, and 67 newly designed primer sets which were validated in silico and experimentally. Absolute quantification of targeted ARGs is accomplished by generating standard curves for all ARGs with serially ten-fold diluted mixed plasmids containing targeted ARG sequences. The amplification efficiencies of all ARGs exceed 99% via plasmid template dilution tests, suggesting high reliability in quantification. The performance of HRA chip is further evaluated by practical applications in environmental samples from wastewater treatment plants (WWTPs) and soils with various land use types and fertilization regimes. The results indicate the dynamics of high-risk ARGs during wastewater treatment process, and reveal the profiles of soil high-risk ARGs which is distinct from those derived via metagenomic approaches. These findings highlight the potentials of HRA Chip in the evaluation of anthropogenic impacts on the environmental resistome with a more focused spectrum of high-risk ARGs. Overall, the HRA Chip emerges as a powerful and efficient high-throughput tool for rapid detection and quantification of high-risk ARGs, facilitating comprehensive profiling of high-risk resistomes in environmental samples which is essential for human health risk assessment of ARGs.},
}

@article {pmid39038418,
year = {2024},
author = {Tsopanakis, V and Anastasiadou, E and Mikkelsen, MD and Meyer, AS and Pavlidis, IV},
title = {Identification and characterization of a novel thermostable PL7 alginate lyase from a submarine volcanic metagenomic library.},
journal = {Enzyme and microbial technology},
volume = {180},
number = {},
pages = {110486},
doi = {10.1016/j.enzmictec.2024.110486},
pmid = {39038418},
issn = {1879-0909},
abstract = {Seaweed biomass is as an abundant and renewable source of complex polysaccharides, including alginate which has a variety of applications. A sustainable method for exploiting alginate towards the production of valuable oligosaccharides is through enzymatic processing, using alginate lyases. Industrial refinement methods demand robust enzymes. Metagenomic libraries from extreme environments are a new source of unique enzymes with great industrial potential. Herein we report the identification of a new thermostable alginate lyase with only 58 % identity to known sequences, identified by mining a metagenomic library obtained from the hydrothermal vents of the volcano Kolumbo in the Aegean Sea (Kolumbo Alginate Lyase, KAlLy). Sequence analysis and biochemical characterization of KAlLy showed that this new alginate lyase is a Polysaccharide Lyase of family 7 (PL7) enzyme with endo- and exo-action on alginate and poly-mannuronic acid, with high activity at 60°C (56 ± 8 U/mg) and high thermostability (half-life time of 30 h at 50°C). The response surface methodology analysis revealed that the reaction optimum conditions with poly-mannuronic acid as substrate are 44°C, pH of 5.5 with 440 mM NaCl. This novel alginate lyase is a valuable addition to the toolbox of alginate modifying enzymes, due to its diverse sequence and its good thermal stability.},
}

@article {pmid39038407,
year = {2024},
author = {Rolbiecki, D and Paukszto, Ł and Krawczyk, K and Korzeniewska, E and Sawicki, J and Harnisz, M},
title = {Genomic and metagenomic analysis reveals shared resistance genes and mobile genetic elements in E. coli and Klebsiella spp. isolated from hospital patients and hospital wastewater at intra- and inter-genus level.},
journal = {International journal of hygiene and environmental health},
volume = {261},
number = {},
pages = {114423},
doi = {10.1016/j.ijheh.2024.114423},
pmid = {39038407},
issn = {1618-131X},
abstract = {Antimicrobial resistance (AMR) is a global problem that gives serious cause for concern. Hospital wastewater (HWW) is an important link between the clinical setting and the natural environment, and an escape route for pathogens that cause hospital infections, including urinary tract infections (UTI). Bacteria of the genera Escherichia and Klebsiella are common etiological factors of UTI, especially in children, and they can cause short-term infections, as well as chronic conditions. ESBL-producing Escherichia and Klebsiella have also emerged as potential indicators for estimating the burden of antimicrobial resistance under environmental conditions and the spread of AMR between clinical settings and the natural environment. In this study, whole-genome sequencing and the nanopore technology were used to analyze the complete genomes of ESBL-producing E.coli and Klebsiella spp. and the HWW metagenome, and to characterize the mechanisms of AMR. The similarities and differences in the encoded mechanisms of AMR in clinical isolates (causing UTI) and environmental strains (isolated from HWW and the HWW metagenome) were analyzed. Special attention was paid to the genetic context and the mobility of antibiotic resistance genes (ARGs) to determine the common sources and potential transmission of these genes. The results of this study suggest that the spread of drug resistance from healthcare facilities via HWW is not limited to the direct transmission of resistant clonal lines that are typically found in the clinical setting, but it also involves the indirect transfer of mobile elements carrying ARGs between bacteria colonizing various environments. Hospital wastewater could offer a supportive environment for plasmid evolution through the insertion of new ARGs, including typical chromosomal regions. These results indicate that interlined environments (hospital patients - HWW) should be closely monitored to evaluate the potential transmission routes of drug resistance in bacteria.},
}

@article {pmid39037720,
year = {2024},
author = {Du, S and Bi, L and Lin, D and Zheng, XQ and Neilson, R and Zhu, D},
title = {Viral Communities Suppress the Earthworm Gut Antibiotic Resistome by Lysing Bacteria on a National Scale.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.4c03812},
pmid = {39037720},
issn = {1520-5851},
abstract = {Earthworms are critical in regulating soil processes and act as filters for antibiotic resistance genes (ARGs). Yet, the geographic patterns and main drivers of earthworm gut ARGs remain largely unknown. We collected 52 earthworm and soil samples from arable and forest ecosystems along a 3000 km transect across China, analyzing the diversity and abundance of ARGs using shotgun metagenomics. Earthworm guts harbored a lower diversity and abundance of ARGs compared to soil, resulting in a stronger distance-decay rate of ARGs in the gut. Greater deterministic assembly processes of ARGs were found in the gut than in soil. The earthworm gut had a lower frequency of co-occurrence patterns between ARGs and mobile genetic elements (MGEs) in forest than in arable systems. Viral diversity was higher in the gut compared to soil and was negatively correlated with bacterial diversity. Bacteria such as Streptomyces and Pseudomonas were potential hosts of both viruses and ARGs. Viruses had negative effects on the diversity and abundance of ARGs, likely due to the lysis on ARG-bearing bacteria. These findings provide new insights into the variations of ARGs in the earthworm gut and highlight the vital role of viruses in the regulation of ARGs in the soil ecosystem.},
}

@article {pmid39037634,
year = {2024},
author = {Elmagzoub, WA and Idris, SM and Elnaiem, MHE and Mukhtar, ME and Eltayeb, E and Bakhiet, SM and Okuni, JB and Ojok, L and El Sanousi, SM and El Wahed, AA and Gameel, AA and Eltom, KH},
title = {Faecal microbial diversity in a cattle herd infected by Mycobacterium avium subsp. paratuberculosis: a possible effect of production status.},
journal = {World journal of microbiology & biotechnology},
volume = {40},
number = {9},
pages = {276},
pmid = {39037634},
issn = {1573-0972},
support = {Project number 404935781//Deutsche Forschungsgemeinschaft/ ; },
mesh = {Animals ; Cattle ; *Mycobacterium avium subsp. paratuberculosis/isolation & purification/genetics ; *Feces/microbiology ; *Paratuberculosis/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Cattle Diseases/microbiology ; *Milk/microbiology ; *DNA, Bacterial/genetics ; Gastrointestinal Microbiome ; Female ; Bacteria/classification/genetics/isolation & purification ; Metagenomics/methods ; },
abstract = {Mycobacterium avium subsp. paratuberculosis (MAP) causes Johne's disease, or paratuberculosis (PTB) in ruminants, besides having zoonotic potential. It possibly changes the gut microbiome, but no conclusive data are available yet. This study aimed at investigating the influence of MAP on the faecal microbiome of cattle naturally infected with PTB. In a follow up period of 10 months, PTB status was investigated in a herd of dairy cattle with history of clinical cases. Each animal was tested for MAP infection using serum and milk ELISA for MAP anti-bodies and IS900 real-time PCR and recombinase polymerase amplification assays for MAP DNA in the faeces and milk monthly for 4 successive months, then a last one after 6 months. The faecal samples were subjected to 16S rDNA metagenomic analysis using Oxford Nanopore Sequencing Technology. The microbial content was compared between animal groups based on MAP positivity rate and production status. All animals were MAP positive by one or more tests, but two animals were consistently negative for MAP DNA in the faeces. In all animals, the phyla firmicutes and bacteroidetes were highly enriched with a small contribution of proteobacteria, and increased abundance of the families Oscillospiraceae, Planococcaceae, and Streptococcacaceae was noted. Animals with high MAP positivity rate showed comparable faecal microbial content, although MAP faecal positivity had no significant effect (p > 0.05) on the microbiome. Generally, richness and evenness indices decreased with increasing positivity rate. A significantly different microbial content was found between dry cows and heifers (p < 0.05). Particularly, Oscillospiraceae and Rikenellaceae were enriched in heifers, while Planococcaceae and Streptococcaceae were overrepresented in dry cows. Furthermore, abundance of 72 genera was significantly different between these two groups (p < 0.05). Changes in faecal microbiome composition were notably associated with increasing MAP shedding in the faeces. The present findings suggest a combined influence of the production status and MAP on the cattle faecal microbiome. This possibly correlates with the fate of the infection, the concern in disease control, again remains for further investigations.},
}

Animals
Cattle
*Mycobacterium avium subsp. paratuberculosis/isolation & purification/genetics
*Feces/microbiology
*Paratuberculosis/microbiology
*RNA, Ribosomal, 16S/genetics
*Cattle Diseases/microbiology
*Milk/microbiology
*DNA, Bacterial/genetics
Gastrointestinal Microbiome
Female
Bacteria/classification/genetics/isolation & purification
Metagenomics/methods

@article {pmid39037315,
year = {2024},
author = {Marín-Paredes, R and Peña-Ocaña, BA and Martínez-Romero, E and Gutiérrez-Sarmiento, W and Ruíz-Valdiviezo, V and Jasso-Chávez, R and Servín-Garcidueñas, LE},
title = {Metagenome-Assembled Genome of "Candidatus Aramenus sp. CH1" from the Chichon volcano, Mexico.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0052624},
doi = {10.1128/mra.00526-24},
pmid = {39037315},
issn = {2576-098X},
abstract = {The Chichon volcano contains several thermal manifestations including an acidic crater lake. Here we report a metagenome-assembled genome of "Candidatus Aramenus sp. CH1," a Sulfolobales archaeon inhabiting the crater lake from the Chichon volcano. In this study, we generated a novel Aramenus genome sequence from a thermal area in Southern Mexico.},
}

@article {pmid39037310,
year = {2024},
author = {Li, M and Dong, Y and Liu, C and Liu, H and Wang, Z and Ma, J and Wang, X and Zhang, X},
title = {Metagenome-assembled bacterial genomes derived from various aging flue-cured tobacco samples.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0042724},
doi = {10.1128/mra.00427-24},
pmid = {39037310},
issn = {2576-098X},
abstract = {We recovered 16 bacterial metagenome-assembled genomes from 11 flue-cured tobacco samples with different aging stage and various geographic origins. Their sizes range from 2.3 M to 5.4 M, with GC contents of 43.17%-74.45%, completeness of 78.80%-99.25%, and contamination of 0.47%-8.56%.},
}

@article {pmid39036956,
year = {2024},
author = {Popova, AM and Jain, N and Dong, X and Abdollah-Nia, F and Britton, RA and Williamson, JR},
title = {Complete list of canonical post-transcriptional modifications in the Bacillus subtilis ribosome and their link to RbgA driven large subunit assembly.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkae626},
pmid = {39036956},
issn = {1362-4962},
support = {R01GM110248/NH/NIH HHS/United States ; //The Scripps Research Institute/ ; },
abstract = {Ribosomal RNA modifications in prokaryotes have been sporadically studied, but there is a lack of a comprehensive picture of modification sites across bacterial phylogeny. Bacillus subtilis is a preeminent model organism for gram-positive bacteria, with a well-annotated and editable genome, convenient for fundamental studies and industrial use. Yet remarkably, there has been no complete characterization of its rRNA modification inventory. By expanding modern MS tools for the discovery of RNA modifications, we found a total of 25 modification sites in 16S and 23S rRNA of B. subtilis, including the chemical identity of the modified nucleosides and their precise sequence location. Furthermore, by perturbing large subunit biogenesis using depletion of an essential factor RbgA and measuring the completion of 23S modifications in the accumulated intermediate, we provide a first look at the order of modification steps during the late stages of assembly in B. subtilis. While our work expands the knowledge of bacterial rRNA modification patterns, adding B. subtilis to the list of fully annotated species after Escherichia coli and Thermus thermophilus, in a broader context, it provides the experimental framework for discovery and functional profiling of rRNA modifications to ultimately elucidate their role in ribosome biogenesis and translation.},
}

@article {pmid39036782,
year = {2024},
author = {Cai, TT and Ma, R},
title = {Matrix Reordering for Noisy Disordered Matrices: Optimality and Computationally Efficient Algorithms.},
journal = {IEEE transactions on information theory},
volume = {70},
number = {1},
pages = {509-531},
pmid = {39036782},
issn = {0018-9448},
abstract = {Motivated by applications in single-cell biology and metagenomics, we investigate the problem of matrix reordering based on a noisy disordered monotone Toeplitz matrix model. We establish the fundamental statistical limit for this problem in a decision-theoretic framework and demonstrate that a constrained least squares estimator achieves the optimal rate. However, due to its computational complexity, we analyze a popular polynomial-time algorithm, spectral seriation, and show that it is suboptimal. To address this, we propose a novel polynomial-time adaptive sorting algorithm with guaranteed performance improvement. Simulations and analyses of two real single-cell RNA sequencing datasets demonstrate the superiority of our algorithm over existing methods.},
}

@article {pmid39035870,
year = {2024},
author = {Rabbachin, L and Nir, I and Waldherr, M and Vassallo, Y and Piñar, G and Graf, A and Kushmaro, A and Sterflinger, K},
title = {Diversity of fungi associated with petroglyph sites in the Negev Desert, Israel, and their potential role in bioweathering.},
journal = {Frontiers in fungal biology},
volume = {5},
number = {},
pages = {1400380},
pmid = {39035870},
issn = {2673-6128},
abstract = {The petroglyphs of the Negev Desert, Israel, are famous and valuable archaeological remains. Previous studies have investigated the microbial communities associated with petroglyphs and their potential role in stone deterioration; nevertheless, the role of fungi remains unclear. In this study, the fungal communities present on the stone and, as a comparison, in the surrounding environment (soil and air) at Negev petroglyph sites were analyzed by means of culture-dependent and -independent (metagenomic) techniques. The metagenomic results showed a high fungal biodiversity in the soil, and both approaches highlighted the prevalence of species producing melanized, large, thick-walled spores (mainly Alternaria spp.). From the air sampling, mostly Cladosporium spp. were retrieved. On the other hand, on the rock, the results seem to indicate a low presence of fungi, but with a rock-specialized mycobiota consisting of extremotolerant microcolonial fungi (MCF) (e.g., Vermiconidia and Coniosporium) and lichens (Flavoplaca). In addition, low proportions of cosmopolitan fungi were detected on the stone, but the comparison of the data clearly indicates that they are transients from the surrounding environment. The ability of the isolated strains to dissolve CaCO3 and therefore be a potential threat to the petroglyphs (limestone substrate) was tested, but only one strain resulted in positive acid production under laboratory conditions. Nevertheless, both lichens and MCF detected in this study are well-known stone deteriogens, which may have a significant impact on the petroglyph's deterioration.},
}

@article {pmid39035737,
year = {2024},
author = {Fan, B and Sun, X and Han, W and Zou, Y and Chen, F and Lan, F and Li, W and Mao, Y},
title = {Immune checkpoint inhibitor increased mortality in lung cancer patients with Pneumocystis jirovecii pneumonia: a comparative retrospective cohort study.},
journal = {Frontiers in oncology},
volume = {14},
number = {},
pages = {1398357},
pmid = {39035737},
issn = {2234-943X},
abstract = {INTRODUCTION: Pneumocystis jirovecii pneumonia (PJP) is a life-threatening infection in immunocompromised individuals. Immune checkpoint inhibitor (ICI) has brought significant survival benefit in lung cancer patients. Although the few studies showed there was high mortality in PJP patients with ICI use, these studies had no comparative control groups.

METHODS: A retrospective study was conducted to compare the mortality in PJP patients with lung cancer between those treated with ICI and a concurrent control group treated without ICI.

RESULTS: A total number of 20 non-human immunodeficiency virus (HIV) patients with confirmed PJP and co-existing lung cancer were included in the current study, and classified into ICI group (n=9) and non-ICI group (n=11).There was a clear trend to a shorter onset of PJP in ICI group than non-ICI group (118.9 ± 60.9 vs 253.0 ± 185.1 days), although without statistical significance (p=0.053). Bronchoscopic alveolar lavage fluid were collected from all patients and used to identify Pneumocystis jirovecii. In both groups, metagenomics next-generation sequencing (mNGS) were the most used diagnostic techniques. Within 28 days after the onset of PJP, mortality was significantly higher in the ICI group than non-ICI group (33.3% vs 0, p=0.042).

CONCLUSION: Lung cancer patients with ICI use had a higher mortality rate after PJP infection than patients without ICI use. Prospective studies with larger sample size and a multi-center design are warranted to further verify the present results.},
}

@article {pmid39035441,
year = {2024},
author = {Guan, Y and Zhao, S and Li, J and Zhang, W and Guo, Z and Luo, Y and Jiang, X and Li, J and Liu, J and Chen, X and Zhao, Z and Zhang, Z},
title = {Insights from metagenomics into gut microbiome associated with acute coronary syndrome therapy.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1369478},
pmid = {39035441},
issn = {1664-302X},
abstract = {Acute coronary syndrome (ACS) is a predominant cause of mortality, and the prompt and precise identification of this condition is crucial to minimize its impact. Recent research indicates that gut microbiota is associated with the onset, progression, and treatment of ACS. To investigate its role, we sequenced the gut microbiota of 38 ACS patients before and after percutaneous coronary intervention and statin therapy at three time points, examining differential species and metabolic pathways. We observed a decrease in the abundance of Parabacteroides, Escherichia, and Blautia in patients after treatment and an increase in the abundance of Gemalla, Klebsiella variicola, Klebsiella pneumoniae, and others. Two pathways related to sugar degradation were more abundant in patients before treatment, possibly correlated with disorders of sugar metabolism and risk factors, such as hyperglycemia, insulin resistance, and insufficient insulin secretion. Additionally, seven pathways related to the biosynthesis of vitamin K2 and its homolog were reduced after treatment, suggesting that ACS patients may gradually recover after therapy. The gut microbiota of patients treated with different statins exhibited notable differences after treatment. Rosuvastatin appeared to promote the growth of anti-inflammatory bacteria while reducing pro-inflammatory bacteria, whereas atorvastatin may have mixed effects on pro-inflammatory and anti-inflammatory bacteria while increasing the abundance of Bacteroides. Our research will provide valuable insights and enhance comprehension of ACS, leading to better patient diagnosis and therapy.},
}

@article {pmid39034696,
year = {2024},
author = {Gaudin, M and Eveillard, D and Chaffron, S},
title = {Ecological associations distribution modelling of marine plankton at a global scale.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {379},
number = {1909},
pages = {20230169},
doi = {10.1098/rstb.2023.0169},
pmid = {39034696},
issn = {1471-2970},
support = {//H2020 European Commission project AtlantECO/ ; },
mesh = {*Plankton/physiology ; *Climate Change ; *Models, Biological ; Food Chain ; Ecosystem ; Aquatic Organisms/physiology ; Oceans and Seas ; },
abstract = {Marine plankton communities form intricate networks of interacting organisms at the base of the food chain, and play a central role in regulating ocean biogeochemical cycles and climate. However, predicting plankton community shifts in response to climate change remains challenging. While species distribution models are valuable tools for predicting changes in species biogeography under climate change scenarios, they generally overlook the key role of biotic interactions, which can significantly shape ecological processes and ecosystem responses. Here, we introduce a novel statistical framework, association distribution modelling (ADM), designed to model and predict ecological associations distribution in space and time. Applied on a Tara Oceans genome-resolved metagenomics dataset, the present-day biogeography of ADM-inferred marine plankton associations revealed four major biogeographic biomes organized along a latitudinal gradient. We predicted the evolution of these biome-specific communities in response to a climate change scenario, highlighting differential responses to environmental change. Finally, we explored the functional potential of impacted plankton communities, focusing on carbon fixation, outlining the predicted evolution of its geographical distribution and implications for ecosystem function.This article is part of the theme issue 'Connected interactions: enriching food web research by spatial and social interactions'.},
}

*Plankton/physiology
*Climate Change
*Models, Biological
Food Chain
Ecosystem
Aquatic Organisms/physiology
Oceans and Seas

@article {pmid39034691,
year = {2024},
author = {Nef, C and Pierella Karlusich, JJ and Bowler, C},
title = {From nets to networks: tools for deciphering phytoplankton metabolic interactions within communities and their global significance.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {379},
number = {1909},
pages = {20230172},
doi = {10.1098/rstb.2023.0172},
pmid = {39034691},
issn = {1471-2970},
support = {//Université de Recherche Paris Sciences et Lettres/ ; //Horizon 2020 Framework Programme/ ; //Fonds Français pour l'Environnement Mondial/ ; //Simons Foundation/ ; //Agence Nationale de la Recherche/ ; //HORIZON EUROPE European Research Council/ ; },
mesh = {*Phytoplankton/metabolism/physiology ; *Food Chain ; Ecosystem ; },
abstract = {Our oceans are populated with a wide diversity of planktonic organisms that form complex dynamic communities at the base of marine trophic networks. Within such communities are phytoplankton, unicellular photosynthetic taxa that provide an estimated half of global primary production and support biogeochemical cycles, along with other essential ecosystem services. One of the major challenges for microbial ecologists has been to try to make sense of this complexity. While phytoplankton distributions can be well explained by abiotic factors such as temperature and nutrient availability, there is increasing evidence that their ecological roles are tightly linked to their metabolic interactions with other plankton members through complex mechanisms (e.g. competition and symbiosis). Therefore, unravelling phytoplankton metabolic interactions is the key for inferring their dependency on, or antagonism with, other taxa and better integrating them into the context of carbon and nutrient fluxes in marine trophic networks. In this review, we attempt to summarize the current knowledge brought by ecophysiology, organismal imaging, in silico predictions and co-occurrence networks using 'omics data, highlighting successful combinations of approaches that may be helpful for future investigations of phytoplankton metabolic interactions within their complex communities.This article is part of the theme issue 'Connected interactions: enriching food web research by spatial and social interactions'.},
}

*Phytoplankton/metabolism/physiology
*Food Chain
Ecosystem

@article {pmid39034613,
year = {2024},
author = {Krigul, KL and Feeney, RH and Wongkuna, S and Aasmets, O and Holmberg, SM and Andreson, R and Puértolas-Balint, F and Pantiukh, K and Sootak, L and Org, T and Tenson, T and Org, E and Schroeder, BO},
title = {A history of repeated antibiotic usage leads to microbiota-dependent mucus defects.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2377570},
doi = {10.1080/19490976.2024.2377570},
pmid = {39034613},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; Animals ; *Anti-Bacterial Agents/pharmacology ; Mice ; *Fecal Microbiota Transplantation ; *Mucus/metabolism/microbiology ; *Bacteria/classification/genetics/drug effects/isolation & purification/metabolism ; Intestinal Mucosa/microbiology/metabolism/drug effects ; Male ; Female ; Feces/microbiology ; Adult ; Middle Aged ; Akkermansia ; Mice, Inbred C57BL ; Colon/microbiology ; Bacteroides fragilis/drug effects ; },
abstract = {Recent evidence indicates that repeated antibiotic usage lowers microbial diversity and ultimately changes the gut microbiota community. However, the physiological effects of repeated - but not recent - antibiotic usage on microbiota-mediated mucosal barrier function are largely unknown. By selecting human individuals from the deeply phenotyped Estonian Microbiome Cohort (EstMB), we here utilized human-to-mouse fecal microbiota transplantation to explore long-term impacts of repeated antibiotic use on intestinal mucus function. While a healthy mucus layer protects the intestinal epithelium against infection and inflammation, using ex vivo mucus function analyses of viable colonic tissue explants, we show that microbiota from humans with a history of repeated antibiotic use causes reduced mucus growth rate and increased mucus penetrability compared to healthy controls in the transplanted mice. Moreover, shotgun metagenomic sequencing identified a significantly altered microbiota composition in the antibiotic-shaped microbial community, with known mucus-utilizing bacteria, including Akkermansia muciniphila and Bacteroides fragilis, dominating in the gut. The altered microbiota composition was further characterized by a distinct metabolite profile, which may be caused by differential mucus degradation capacity. Consequently, our proof-of-concept study suggests that long-term antibiotic use in humans can result in an altered microbial community that has reduced capacity to maintain proper mucus function in the gut.},
}

Humans
*Gastrointestinal Microbiome/drug effects
Animals
*Anti-Bacterial Agents/pharmacology
Mice
*Fecal Microbiota Transplantation
*Mucus/metabolism/microbiology
*Bacteria/classification/genetics/drug effects/isolation & purification/metabolism
Intestinal Mucosa/microbiology/metabolism/drug effects
Male
Female
Feces/microbiology
Adult
Middle Aged
Akkermansia
Mice, Inbred C57BL
Colon/microbiology
Bacteroides fragilis/drug effects

@article {pmid39033825,
year = {2024},
author = {Dong, Z and Han, K and Xie, Q and Lin, C and Shen, X and Hao, Y and Li, J and Xu, H and He, L and Yu, T and Kuang, W},
title = {Core antibiotic resistance genes mediate gut microbiota to intervene in the treatment of major depressive disorder.},
journal = {Journal of affective disorders},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jad.2024.07.106},
pmid = {39033825},
issn = {1573-2517},
abstract = {INTRODUCTION: The relationship between depression and gut microbiota remains unclear, but an important role of gut microbiota has been verified. The relationship between gut microbiota and antibiotic resistance genes (ARGs) may be a potential new explanatory pathway.

METHODS: We collected samples from 63 depressed patients and 30 healthy controls for metagenomic sequencing. The two groups' microbiota characteristics, functional characteristics, and ARG differences were analyzed.

RESULTS: We obtained 30 differential KEGG orthologs (KOs) and their producers in 5 genera and 7 species by HUMAnN3. We found 6 KOs from Weissella_cibaria and Lactobacillus_plantaru are potentially coring functional mechanism of gut microbiota. Different metabolites including sphingolipids, pyrans, prenol lipids, and isoflavonoids also showed significance between MDD and HC. We detected 48 significantly different ARGs: 5 ARGs up-regulated and 43 ARGs down-regulated in MDD compared to HC. Based on Cox model results, Three ARGs significantly affected drug efficacy (ARG29, ARG105, and ARG111). Eggerthella, Weissella, and Lactobacillus were correlated with different core ARGs, which indicated different mechanisms in affecting MDD.

LIMITATIONS: The present study needs to be replicated in different ethnic groups. At the same time, a larger Chinese cohort study and detailed experimental verification are also the key to further discussion.

CONCLUSION: Our findings suggest that ARGs play a role in the interplay between major depressive disorder and gut microbiota. The role of ARGs should be taken into account when understanding the relationship between depression and gut microbiota.},
}

@article {pmid39033688,
year = {2024},
author = {Berryman, MA and Ilonen, J and Triplett, EW and Ludvigsson, J},
title = {Functional metagenomic analysis reveals potential inflammatory triggers associated with genetic risk for autoimmune disease.},
journal = {Journal of autoimmunity},
volume = {148},
number = {},
pages = {103290},
doi = {10.1016/j.jaut.2024.103290},
pmid = {39033688},
issn = {1095-9157},
abstract = {To assess functional differences between the microbiomes of individuals with autoimmune risk-associated human leukocyte antigen (HLA) genetics and autoimmune protection-associated HLA, we performed a metagenomic analysis of stool samples from 72 infants in the All Babies in Southeast Sweden general-population cohort and assessed haplotype-peptide binding affinities. Infants with risk-associated HLA DR3-DQ2.5 and DR4-DQ8 had a higher abundance of known pathogen-associated molecular patterns and virulence related genes than infants with protection-associated HLA DR15-DQ6.2. However, there was limited overlap in the type of inflammatory trigger between risk groups. Supported by a high Firmicutes/Bacteroides ratio and differentially abundant flagellated species, genes related to the synthesis of flagella were prominent in those with HLA DR3-DQ2.5. However, this haplotype had a significantly lower likelihood of binding affinity to flagellin peptides. O-antigen biosynthesis genes were significantly correlated with the risk genotypes and absent from protective genotype association, supported by the differential abundance of gram-negative bacteria seen in the risk-associated groups. Genes related to vitamin B biosynthesis stood out in higher abundance in infants with HLA DR3-DQ2.5/DR4-DQ8 heterozygosity compared to those with autoimmune-protective genetics. Prevotella species and genus were significantly abundant in all infant groups with high risk for autoimmune disease. The potential inflammatory triggers associated with genetic risk for autoimmunity have significant implications. These results suggest that certain HLA haplotypes may be creating the opportunity for dysbiosis and subsequent inflammation early in life by clearing beneficial microbes or not clearing proinflammatory microbes. This HLA gatekeeping may prevent genetically at-risk individuals from benefiting from probiotic therapies by restricting the colonization of those beneficial bacteria.},
}

@article {pmid39033587,
year = {2024},
author = {Pavon, JAR and da Silva Neves, NA and Pinho, JB and de Souza, VJ and Patroca da Silva, S and Ribeiro Cruz, AC and de Almeida Medeiros, DB and Teixeira Nunes, MR and Slhessarenko, RD},
title = {Disclosing the virome of Aedes, Anopheles and Culex female mosquitoes, Alto Pantanal of Mato Grosso, Brazil, 2019.},
journal = {Virology},
volume = {598},
number = {},
pages = {110182},
doi = {10.1016/j.virol.2024.110182},
pmid = {39033587},
issn = {1096-0341},
abstract = {Using Illumina NextSeq sequencing and bioinformatics, we identified and characterized thirty-three viral sequences of unsegmented and multipartite viral families in Aedes spp., Culex sp. and Anopheles darlingi female mosquito pools from Porto São Luiz and Pirizal, Alto Pantanal. Seventeen sequences belong to unsegmented viral families, twelve represent putative novel insect-specific viruses (ISVs) within families Chuviridae (3/33; partial genomes) and coding-complete sequences of Xinmoviridae (1/33), Rhabdoviridae (2/33) and Metaviridae (6/33); and five coding-complete sequences of already-known ISVs. Notably, two putative novel rhabdoviruses, Corixo rhabdovirus 1 and 2, were phylogenetically related to Coxipo dielmovirus, but separated from other Alpharhabdovirinae genera, sharing Anopheles spp. as host. Regarding multipartite families, sixteen segments of different putative novel viruses were identified (13 coding-complete segments) within Durnavirales (4/33), Elliovirales (1/33), Hareavirales (3/33) and Reovirales (8/33) orders. Overall, this study describes twenty-eight (28/33) putative novel ISVs and five (5/33) already described viruses using metagenomics approach.},
}

@article {pmid39033282,
year = {2024},
author = {Tsola, SL and Prevodnik, AA and Sinclair, LF and Sanders, IA and Economou, CK and Eyice, Ö},
title = {Methanomethylovorans are the dominant dimethylsulfide-degrading methanogens in gravel and sandy river sediment microcosms.},
journal = {Environmental microbiome},
volume = {19},
number = {1},
pages = {51},
pmid = {39033282},
issn = {2524-6372},
support = {10.46936/10.25585/60001216//Joint Genome Institute/ ; },
abstract = {BACKGROUND: Rivers and streams are important components of the global carbon cycle and methane budget. However, our understanding of the microbial diversity and the metabolic pathways underpinning methylotrophic methane production in river sediments is limited. Dimethylsulfide is an important methylated compound, found in freshwater sediments. Yet, the magnitude of DMS-dependent methanogenesis nor the methanogens carrying out this process in river sediments have been explored before. This study addressed this knowledge gap in DMS-dependent methanogenesis in gravel and sandy river sediments.

RESULTS: Significant methane production via DMS degradation was found in all sediment  microcosms. Sandy, less permeable river sediments had higher methane yields (83 and 92%) than gravel, permeable sediments (40 and 48%). There was no significant difference between the methanogen diversity in DMS-amended gravel and sandy sediment microcosms, which Methanomethylovorans dominated. Metagenomics data analysis also showed the dominance of Methanomethylovorans and Methanosarcina. DMS-specific methyltransferase genes (mts) were found in very low relative abundances whilst the methanol-, trimethylamine- and dimethylamine-specific methyltransferase genes (mtaA, mttB and mtbB) had the highest relative abundances, suggesting their involvement in DMS-dependent methanogenesis.

CONCLUSIONS: This is the first study demonstrating a significant potential for DMS-dependent methanogenesis in river sediments with contrasting geologies. Methanomethylovorans were the dominant methylotrophic methanogen in all river sediment microcosms. Methyltransferases specific to methylotrophic substrates other than DMS are likely key enzymes in DMS-dependent methanogenesis, highlighting their versatility and importance in the methane cycle in freshwater sediments, which would warrant further study.},
}

@article {pmid39033279,
year = {2024},
author = {Trinh, P and Teichman, S and Roberts, MC and Rabinowitz, PM and Willis, AD},
title = {A cross-sectional comparison of gut metagenomes between dairy workers and community controls.},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {708},
doi = {10.1186/s12864-024-10562-1},
pmid = {39033279},
issn = {1471-2164},
support = {R35 GM133420/GM/NIGMS NIH HHS/United States ; R35 GM133420/GM/NIGMS NIH HHS/United States ; R35 GM133420/GM/NIGMS NIH HHS/United States ; T32 ES015459/ES/NIEHS NIH HHS/United States ; R21 AI168679/AI/NIAID NIH HHS/United States ; R21 AI168679/AI/NIAID NIH HHS/United States ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Cross-Sectional Studies ; *Metagenome ; Female ; Dairying ; Metagenomics/methods ; Adult ; Animals ; Middle Aged ; Bacteria/genetics/classification ; Farmers ; Male ; Drug Resistance, Bacterial/genetics ; },
abstract = {BACKGROUND: As a nexus of routine antibiotic use and zoonotic pathogen presence, the livestock farming environment is a potential hotspot for the emergence of zoonotic diseases and antibiotic resistant bacteria. Livestock can further facilitate disease transmission by serving as intermediary hosts for pathogens before a spillover event. In light of this, we aimed to characterize the microbiomes and resistomes of dairy workers, whose exposure to the livestock farming environment places them at risk for facilitating community transmission of antibiotic resistant genes and emerging zoonotic diseases.

RESULTS: Using shotgun sequencing, we investigated differences in the taxonomy, diversity and gene presence of 10 dairy farm workers and 6 community controls' gut metagenomes, contextualizing these samples with additional publicly available gut metagenomes. We found no significant differences in the prevalence of resistance genes, virulence factors, or taxonomic composition between the two groups. The lack of statistical significance may be attributed, in part, to the limited sample size of our study or the potential similarities in exposures between the dairy workers and community controls. We did, however, observe patterns warranting further investigation including greater abundance of tetracycline resistance genes and prevalence of cephamycin resistance genes as well as lower average gene diversity (even after accounting for differential sequencing depth) in dairy workers' metagenomes. We also found evidence of commensal organism association with tetracycline resistance genes in both groups (including Faecalibacterium prausnitzii, Ligilactobacillus animalis, and Simiaoa sunii).

CONCLUSIONS: This study highlights the utility of shotgun metagenomics in examining the microbiomes and resistomes of livestock workers, focusing on a cohort of dairy workers in the United States. While our study revealed no statistically significant differences between groups in taxonomy, diversity and gene presence, we observed patterns in antibiotic resistance gene abundance and prevalence that align with findings from previous studies of livestock workers in China and Europe. Our results lay the groundwork for future research involving larger cohorts of dairy and non-dairy workers to better understand the impact of occupational exposure to livestock farming on the microbiomes and resistomes of workers.},
}

Humans
*Gastrointestinal Microbiome/genetics
Cross-Sectional Studies
*Metagenome
Female
Dairying
Metagenomics/methods
Adult
Animals
Middle Aged
Bacteria/genetics/classification
Farmers
Male
Drug Resistance, Bacterial/genetics

@article {pmid39033154,
year = {2024},
author = {Wu, H and Wu, X and Wu, T and Miao, X and Zheng, S and Huang, G and Cheng, X},
title = {Detection Ewingella americana from a patient with Andersson lesion in ankylosing spondylitis by metagenomic next-generation sequencing test: a case report.},
journal = {BMC musculoskeletal disorders},
volume = {25},
number = {1},
pages = {568},
pmid = {39033154},
issn = {1471-2474},
support = {82060403//National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Spondylitis, Ankylosing/diagnosis/complications/microbiology ; Male ; *High-Throughput Nucleotide Sequencing ; Adult ; Metagenomics ; Thoracic Vertebrae/diagnostic imaging/microbiology/pathology/surgery ; },
abstract = {BACKGROUND: Andersen's lesion (AL) is a rare complication of ankylosing spondylitis (AS), characterized by nonneoplastic bone destruction, typically manifested as bone destruction and sclerosis in the vertebral body and/or intervertebral disc area. At present, there is no consensus on the pathology and etiology of AL. Repeated trauma, inflammation in essence and part of the natural history of Ankylosing spondylitis itself are the most widely recognized theories of the etiology of AL. However, positive bacteria cultured in bone biopsy of Andersen's lesion (AL) in Ankylosing spondylitis patients are extremely rare. Herein, we report a rare case of detecting Ewingella americana from a patient with Andersson lesion in ankylosing spondylitis by Metagenomic Next-Generation Sequencing (mNGS) Test.

CASE PRESENTATION: This case involved a 39-year-old male with a history of AS for 11 years, who developed AL (T11/12) in the thoracic vertebrae. After sufficient preoperative preparation, we successfully performed one-stage posterior approach corrective surgery and collected bone biopsies samples for examination. Cultured bacteria were not found, and pathological histology indicated infiltration of inflammatory cells. However, it is worth noting that we discovered a gram-negative bacterium, the Ewingella americana, through mNGS testing. Further histopathological examination suggests chronic inflammatory cell infiltration. After one-stage posterior approach corrective surgery, the patient's condition significantly improved. At the 6-month follow-up, the pain significantly decreased, and the patient returned to normal life.

CONCLUSION: We detected Ewinia americana in the bone biopsies of Andersson lesion (AL) in ankylosing spondylitis patient by mNGS.},
}

Humans
*Spondylitis, Ankylosing/diagnosis/complications/microbiology
Male
*High-Throughput Nucleotide Sequencing
Adult
Metagenomics
Thoracic Vertebrae/diagnostic imaging/microbiology/pathology/surgery

@article {pmid39033123,
year = {2024},
author = {Mercado-Evans, V and Zulk, JJ and Hameed, ZA and Patras, KA},
title = {Gestational diabetes as a risk factor for GBS maternal rectovaginal colonization: a systematic review and meta-analysis.},
journal = {BMC pregnancy and childbirth},
volume = {24},
number = {1},
pages = {488},
pmid = {39033123},
issn = {1471-2393},
support = {AI167547//National Institute of Allergy and Infectious Diseases/ ; AI173448//National Institute of Allergy and Infectious Diseases/ ; DK136201/DK/NIDDK NIH HHS/United States ; DK128053/DK/NIDDK NIH HHS/United States ; GM136554/GM/NIGMS NIH HHS/United States ; NGP10103//Burroughs Wellcome Fund/ ; },
mesh = {Humans ; *Diabetes, Gestational/epidemiology ; Female ; Pregnancy ; Risk Factors ; *Streptococcal Infections/epidemiology ; *Streptococcus agalactiae ; *Vagina/microbiology ; *Pregnancy Complications, Infectious/epidemiology/microbiology ; *Rectum/microbiology ; },
abstract = {BACKGROUND: Maternal rectovaginal colonization by group B Streptococcus (GBS) increases the risk of perinatal GBS disease that can lead to death or long-term neurological impairment. Factors that increase the risk of rectovaginal GBS carriage are incompletely understood resulting in missed opportunities for detecting GBS in risk-based clinical approaches. There is a lacking consensus on whether gestational diabetes mellitus (GDM) is a risk factor for rectovaginal GBS. This systematic review and meta-analysis aims to address current conflicting findings and determine whether GDM should be clinically considered as a risk factor for maternal GBS colonization.

METHODS: Peer-reviewed studies that provided GDM prevalence and documented GBS vaginal and/or rectal colonization in women with and without GDM were included in this analysis. From study inception to October 30, 2023, we identified 6,275 relevant studies from EMBASE and PUBMED of which 19 were eligible for inclusion. Eligible studies were analyzed and thoroughly assessed for risk of bias with a modified Newcastle-Ottawa Scale that interrogated representativeness and comparability of cohorts, quality of reporting for GDM and GBS status, and potential bias from other metabolic diseases. Results were synthesized using STATA 18 and analyzed using random-effects meta-analyses.

RESULTS: Studies encompassed 266,706 women from 10 different countries, with study periods spanning from 1981 to 2020. Meta-analysis revealed that gestational diabetes is associated with a 16% increased risk of rectovaginal GBS carriage (OR 1.16, CI 1.07-1.26, P = 0.003). We also performed subgroup analyses to assess independent effects of pregestational vs. gestational diabetes on risk of maternal GBS carriage. Pregestational diabetes (Type 1 or Type 2 diabetes mellitus) was also associated with an increased risk of 76% (pooled OR 1.76, CI 1.27-2.45, P = 0.0008).

CONCLUSIONS: This study achieved a consensus among previously discrepant observations and demonstrated that gestational diabetes and pregestational diabetes are significant risk factors for maternal rectovaginal carriage of GBS. Recognition of GDM as a risk factor during clinical decisions about GBS screening and intrapartum antibiotic prophylaxis may decrease the global burden of GBS on maternal-perinatal health.},
}

Humans
*Diabetes, Gestational/epidemiology
Female
Pregnancy
Risk Factors
*Streptococcal Infections/epidemiology
*Streptococcus agalactiae
*Vagina/microbiology
*Pregnancy Complications, Infectious/epidemiology/microbiology
*Rectum/microbiology