@article {pmid38697552,
year = {2024},
author = {Song, K and Wang, S and Xu, X and Ma, J and Yang, Y and Zeng, Y and Li, J and Zhou, X and Zhou, Y},
title = {Benthic clade II-type nitrous oxide reducers suppress nitrous oxide emissions in shallow lakes.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {172908},
doi = {10.1016/j.scitotenv.2024.172908},
pmid = {38697552},
issn = {1879-1026},
abstract = {Shallow lakes, recognized as hotspots for nitrogen cycling, contribute to the emission of the potent greenhouse gas nitrous oxide (N2O), but the current emission estimates for this gas have a high degree of uncertainty. However, the role of N2O-reducing bacteria (N2ORB) as N2O sinks and their contribution to N2O reduction in aquatic ecosystems in response to N2O dynamics have not been determined. Here, we investigated the N2O dynamics and microbial processes in the nitrogen cycle, which included both N2O production and consumption, in five shallow lakes spanning approximately 500 km. The investigated sites exhibited N2O oversaturation, with excess dissolved N2O concentrations (ΔN2O) ranging from 0.55 ± 0.61 to 53.17 ± 15.75 nM. Sediment-bound N2O (sN2O) was significantly positively correlated with the nitrate concentration in the overlying water (p < 0.05), suggesting that nitrate accumulation contributes to benthic N2O generation. High N2O consumption activity (RN2O) corresponded to low ΔN2O. In addition, a significant negative correlation was found between RN2O and nir/nosZ, showing that bacteria encoding nosZ contributed to N2O consumption in the benthic sediments. Redundancy analysis indicated that benthic functional genes effectively reflected the variations in RN2O and ∆N2O. qPCR analysis revealed that the clade II nosZ gene was more sensitive to ΔN2O than the clade I nosZ gene. Furthermore, four novel genera of potential nondenitrifying N2ORB were identified based on metagenome-assembled genome analysis. These genera, which are affiliated with clade II, lack genes responsible for N2O production. Collectively, benthic N2ORB, especially for clade II-type N2ORB, harnesses N2O consumption activity leading to low N2O emissions from shallow lakes. This study advances our knowledge of the role of benthic clade II-type N2ORB in regulating N2O emissions in shallow lakes.},
}

@article {pmid38697527,
year = {2024},
author = {Zhu, W and Zhao, H and Ke, J and Zhang, J and Liu, X and Zhou, Y and Chen, R and Wang, A and Li, X},
title = {Deciphering the environmental adaptation and functional trait of core and noncore bacterial communities in impacted coral reef seawater.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {172897},
doi = {10.1016/j.scitotenv.2024.172897},
pmid = {38697527},
issn = {1879-1026},
abstract = {Microorganisms play pivotal roles in different biogeochemical cycles within coral reef waters. Nevertheless, our comprehension of the microbially mediated processes following environmental perturbation is still limited. To gain a deeper insight into the environmental adaptation and nutrient cycling, particularly within core and noncore bacterial communities, it is crucial to understand reef ecosystem functioning. In this study, we delved into the microbial community structure and function of seawater in a coral reef under different degrees of anthropogenic disturbance. To achieve this, we harnessed the power of 16S rRNA gene high-throughput sequencing and metagenomics techniques. The results showed that a continuous temporal succession but little spatial heterogeneity in the bacterial communities of core and noncore taxa and functional profiles involved in nitrogen (N) and phosphorus (P) cycling. Eutrophication state (i.e., nutrient concentration and turbidity) and temperature played pivotal roles in shaping both the microbial community composition and functional traits of coral reef seawater. Within this context, the core subcommunity exhibited a remarkably broader habitat niche breadth, stronger phylogenetic signals and lower environmental sensitivity when compared to the noncore taxa. Null model analysis further revealed that the core subcommunity was governed primarily by stochastic processes, while deterministic processes played a more significant role in shaping the noncore subcommunity. Furthermore, our observations indicated that changes in function related to N cycling were correlated to the variations in noncore taxa, while core taxa played a more substantial role in critical processes such as P cycling. Collectively, these findings facilitated our knowledge about environmental adaptability of core and noncore bacterial taxa and shed light on their respective roles in maintaining diverse nutrient cycling within coral reef ecosystems.},
}

@article {pmid38697408,
year = {2024},
author = {Dong, B and Peng, Y and Wang, M and Peng, C and Li, X},
title = {Multi-omics integrated analysis indicated that non-polysaccharides of Sijunzi decoction ameliorated spleen deficiency syndrome via regulating microbiota-gut-metabolites axis and exerted synergistic compatibility.},
journal = {Journal of ethnopharmacology},
volume = {},
number = {},
pages = {118276},
doi = {10.1016/j.jep.2024.118276},
pmid = {38697408},
issn = {1872-7573},
abstract = {As a classical traditional Chinese medicine formula to invigorating spleen and replenishing qi, Sijunzi decoction (SJZD) is composed of four herbs, which is applied to cure spleen deficiency syndrome (SDS) clinically. The non-polysaccharides (NPSs) of SJZD (SJZD_NPS) are important pharmacodynamic material basis. However, the amelioration mechanism of SJZD_NPS on SDS has not been fully elaborated. Additionally, the contribution of herbs compatibility to efficacy of this formula remains unclear.

AIM OF THE STUDY: The aim was to explore the underlying mechanisms of SJZD_NPS on improving SDS, and uncover the scientific connotation in SJZD compatibility.

MATERIALS AND METHODS: A strategy integrating incomplete formulae (called "Chai-fang" in Chinese) comparison, pharmacodynamics, gut microbiome, and metabolome was employed to reveal the role of each herb to SJZD compatibility against SDS. Additionally, the underlying mechanism harbored by SJZD_NPS was further explored through targeted metabolomics, network pharmacology, molecular docking, pseudo-sterile model, and metagenomics.

RESULTS: SJZD_NPS significantly alleviated diarrhea, disordered secretion of gastrointestinal hormones and neurotransmitters, damage of ileal morphology and intestinal barrier in SDS rats, which was superior to the NPSs of Chai-fang. 16S rRNA gene sequencing and metabolomics analysis revealed that SJZD_NPS effectively restored the disturbed gut microbiota community and abnormal metabolism caused by SDS, showing the most evident recovery. Moreover, SJZD_NPS recalled the levels of partial amino acids, short chain fatty acids and bile acids, which possessed strong binding affinity towards potential targets. The depletion of gut microbiota confirmed that the SDS-amelioration efficacy of SJZD_NPS is dependent on the intact gut microbiome, with the relative abundance of potential probiotics such as Lactobacillus_johnsonii and Lactobacillus_taiwanensis been enriched.

CONCLUSION: NPSs in SJZD can improve SDS-induced gastrointestinal-nervous system dysfunction through regulating microbiota-gut-metabolites axis, with four herbs exerting synergistic effects, which indicated the compatibility rationality of SJZD.},
}

@article {pmid38696985,
year = {2024},
author = {da Silva Duarte, V and de Paula Dias Moreira, L and Skeie, SB and Svalestad, F and Øyaas, J and Porcellato, D},
title = {Database selection for shotgun metaproteomic of low-diversity dairy microbiomes.},
journal = {International journal of food microbiology},
volume = {418},
number = {},
pages = {110706},
doi = {10.1016/j.ijfoodmicro.2024.110706},
pmid = {38696985},
issn = {1879-3460},
abstract = {The metaproteomics field has recently gained more and more interest as a valuable tool for studying both the taxonomy and function of microbiomes, including those used in food fermentations. One crucial step in the metaproteomics pipeline is selecting a database to obtain high-quality taxonomical and functional information from microbial communities. One of the best strategies described for building protein databases is using sample-specific or study-specific protein databases obtained from metagenomic sequencing. While this is true for high-diversity microbiomes (such as gut and soil), there is still a lack of validation for different database construction strategies in low-diversity microbiomes, such as those found in fermented dairy products where starter cultures containing few species are used. In this study, we assessed the performance of various database construction strategies applied to metaproteomics on two low-diversity microbiomes obtained from cheese production using commercial starter cultures and analyzed by LC-MS/MS. Substantial differences were detected between the strategies, and the best performance in terms of the number of peptides and proteins identified from the spectra was achieved by metagenomic-derived databases. However, extensive databases constructed from a high number of available online genomes obtained a similar taxonomical and functional annotation of the metaproteome compared to the metagenomic-derived databases. Our results indicate that, in the case of low-diversity dairy microbiomes, the use of publically available genomes to construct protein databases can be considered as an alternative to metagenome-derived databases.},
}

@article {pmid38696336,
year = {2024},
author = {Gauthier, NPG and Chan, W and Locher, K and Smailus, D and Coope, R and Charles, M and Jassem, A and Kopetzky, J and Chorlton, SD and Manges, AR},
title = {Validation of an automated, end-to-end metagenomic sequencing assay for agnostic detection of respiratory viruses.},
journal = {The Journal of infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/infdis/jiae226},
pmid = {38696336},
issn = {1537-6613},
abstract = {BACKGROUND: Current molecular diagnostics are limited in the number and type of detectable pathogens. Metagenomic next generation sequencing (mNGS) is an emerging, and increasingly feasible, pathogen-agnostic diagnostic approach. Translational barriers prohibit the widespread adoption of this technology in clinical laboratories. We validate an end-to-end mNGS assay for detection of respiratory viruses. Our assay is optimized to reduce turnaround time, lower cost-per-sample, increase throughput, and deploy secure and actionable bioinformatic results.

METHODS: We validated our assay using residual nasopharyngeal swab specimens from Vancouver General Hospital (n = 359), RT-PCR-positive, or negative for Influenza, SARS-CoV-2, and RSV. We quantified sample stability, assay precision, the effect of background nucleic acid levels, and analytical limits of detection. Diagnostic performance metrics were estimated.

RESULTS: We report that our mNGS assay is highly precise, semi-quantitative, with analytical limits of detection ranging from 103-104 copies/mL. Our assay is highly specific (100%) and sensitive (61.9% Overall: 86.8%; RT-PCR Ct < 30). Multiplexing capabilities enable processing of up to 55-specimens simultaneously on an Oxford Nanopore GridION device, with results reported within 12-hours.

CONCLUSIONS: This study outlines the diagnostic performance and feasibility of mNGS for respiratory viral diagnostics, infection control, and public health surveillance. We addressed translational barriers to widespread mNGS adoption.},
}

@article {pmid38695096,
year = {2024},
author = {Liu, H and Zhao, X and Xu, S and Zhao, L and Han, X and Xu, X and Zhao, N and Hu, L and Luo, C and Wang, X and Zhang, Q and Guo, T},
title = {Multi-omics reveal the gut microbiota-mediated severe foraging environment adaption of small wild ruminants in the Three-River-Source National Park, China.},
journal = {Integrative zoology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1749-4877.12830},
pmid = {38695096},
issn = {1749-4877},
support = {32100100//Youth Fund Project of National Natural Science Foundation of China/ ; 2022-ZJ-943Q//National Science Foundation of Qinghai Province/ ; LHZX-2022-02//Chinese Academy of Sciences-People's Government of Qinghai Province on Sanjiangyuan National Park/ ; },
abstract = {The Tibetan antelope (Pantholops hodgsonii), blue sheep (Pseudois nayaur), and Tibetan sheep (Ovis aries) are the dominant small ruminants in the Three-River-Source National Park (TRSNP). However, knowledge about the association between gut microbiota and host adaptability remains poorly understood. Herein, multi-omics sequencing approaches were employed to investigate the gut microbiota-mediated forage adaption in these ruminants. The results revealed that although wild ruminants (WR) of P. hodgsoni and P. nayaur were faced with severe foraging environments with significantly low vegetation coverage and nutrition, the apparent forage digestibility of dry matter, crude protein, and acid detergent fiber was significantly higher than that of O. aries. The 16s rRNA sequencing showed that the gut microbiota in WR underwent convergent evolution, and alpha diversity in these two groups was significantly higher than that in O. aries. Moreover, indicator species, including Bacteroidetes and Firmicutes, exhibited positive relationships with apparent forage digestibility, and their relative abundances were enriched in the gut of WR. Enterotype analysis further revealed that enterotype 1 belonged to WR, and the abundance of fatty acid synthesis metabolic pathway-related enzyme genes was significantly higher than enterotype 2, represented by O. aries. Besides, the metagenomic analysis identified 14 pathogenic bacterial species, among which 10 potentially pathogenic bacteria were significantly enriched in the gut microbiota of O. aries. Furthermore, the cellulolytic strains and genes encoding cellulase and hemicellulase were significantly enriched in WR. In conclusion, our results provide new evidence of gut microbiota to facilitate wildlife adaption in severe foraging environments of the TRSNP, China.},
}

@article {pmid38695019,
year = {2024},
author = {Luo, D and Dai, L},
title = {A 26-year-old man with multiple organ failure caused by Aeromonas dhakensis infection: a case report and literature review.},
journal = {Frontiers in medicine},
volume = {11},
number = {},
pages = {1289338},
doi = {10.3389/fmed.2024.1289338},
pmid = {38695019},
issn = {2296-858X},
abstract = {BACKGROUND: Infections in humans are mainly caused by Aeromonas hydrophila, Aeromonas caviae, and Aeromonas veronii. In recent years, Aeromonas dhakensis has been recognized as widely distributed in the environment, with strong virulence. However, this bacterial infection usually does not appear in patients with pneumonia as the first symptom.

CASE REPORT: We report a 26-year-old man who was admitted to the hospital with community-acquired pneumonia as the first symptom and developed serious conditions such as hemolytic uremic syndrome, multiple organ dysfunction, and hemorrhagic shock within a short period. He died after 13 h of admission, and the subsequent metagenomic-next generation sequencing test confirmed the finally identified pathogen of infection as A. dhakensis.

CONCLUSION: Aeromonas is a rare pathogen identified in the diagnosis of community-acquired pneumonia. Hence, doctors need to develop their experience in identifying the difference between infections caused by pathogenic microorganisms. Medical attention is essential during the occurrence of respiratory symptoms that could be controlled by empirical drugs, such as cephalosporins or quinolones. When patients with community-acquired pneumonia present hemoptysis and multiple organ dysfunction in clinical treatment, an unusual pathogen infection should be considered, and the underlying etiology should be clarified at the earliest for timely treatment.},
}

@article {pmid38694799,
year = {2024},
author = {Zhang, Y and Xue, G and Wang, F and Zhang, J and Xu, L and Yu, C},
title = {The impact of antibiotic exposure on antibiotic resistance gene dynamics in the gut microbiota of inflammatory bowel disease patients.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1382332},
doi = {10.3389/fmicb.2024.1382332},
pmid = {38694799},
issn = {1664-302X},
abstract = {BACKGROUND: While antibiotics are commonly used to treat inflammatory bowel disease (IBD), their widespread application can disturb the gut microbiota and foster the emergence and spread of antibiotic resistance. However, the dynamic changes to the human gut microbiota and direction of resistance gene transmission under antibiotic effects have not been clearly elucidated.

METHODS: Based on the Human Microbiome Project, a total of 90 fecal samples were collected from 30 IBD patients before, during and after antibiotic treatment. Through the analysis workflow of metagenomics, we described the dynamic process of changes in bacterial communities and resistance genes pre-treatment, during and post-treatment. We explored potential consistent relationships between gut microbiota and resistance genes, and established gene transmission networks among species before and after antibiotic use.

RESULTS: Exposure to antibiotics can induce alterations in the composition of the gut microbiota in IBD patients, particularly a reduction in probiotics, which gradually recovers to a new steady state after cessation of antibiotics. Network analyses revealed intra-phylum transfers of resistance genes, predominantly between taxonomically close organisms. Specific resistance genes showed increased prevalence and inter-species mobility after antibiotic cessation.

CONCLUSION: This study demonstrates that antibiotics shape the gut resistome through selective enrichment and promotion of horizontal gene transfer. The findings provide insights into ecological processes governing resistance gene dynamics and dissemination upon antibiotic perturbation of the microbiota. Optimizing antibiotic usage may help limit unintended consequences like increased resistance in gut bacteria during IBD management.},
}

@article {pmid38694752,
year = {2024},
author = {Brame, JE and Liddicoat, C and Abbott, CA and Edwards, RA and Robinson, JM and Gauthier, NE and Breed, MF},
title = {The macroecology of butyrate-producing bacteria via metagenomic assessment of butyrate production capacity.},
journal = {Ecology and evolution},
volume = {14},
number = {5},
pages = {e11239},
doi = {10.1002/ece3.11239},
pmid = {38694752},
issn = {2045-7758},
abstract = {Butyrate-producing bacteria are found in many outdoor ecosystems and host organisms, including humans, and are vital to ecosystem functionality and human health. These bacteria ferment organic matter, producing the short-chain fatty acid butyrate. However, the macroecological influences on their biogeographical distribution remain poorly resolved. Here we aimed to characterise their global distribution together with key explanatory climatic, geographical and physicochemical variables. We developed new normalised butyrate production capacity (BPC) indices derived from global metagenomic (n = 13,078) and Australia-wide soil 16S rRNA (n = 1331) data, using Geographic Information System (GIS) and modelling techniques to detail their ecological and biogeographical associations. The highest median BPC scores were found in anoxic and fermentative environments, including the human (BPC = 2.99) and non-human animal gut (BPC = 2.91), and in some plant-soil systems (BPC = 2.33). Within plant-soil systems, roots (BPC = 2.50) and rhizospheres (BPC = 2.34) had the highest median BPC scores. Among soil samples, geographical and climatic variables had the strongest overall effects on BPC scores (variable importance score range = 0.30-0.03), with human population density also making a notable contribution (variable importance score = 0.20). Higher BPC scores were in soils from seasonally productive sandy rangelands, temperate rural residential areas and sites with moderate-to-high soil iron concentrations. Abundances of butyrate-producing bacteria in outdoor soils followed complex ecological patterns influenced by geography, climate, soil chemistry and hydrological fluctuations. These new macroecological insights further our understanding of the ecological patterns of outdoor butyrate-producing bacteria, with implications for emerging microbially focused ecological and human health policies.},
}

@article {pmid38694516,
year = {2024},
author = {Sabat, AJ and Durfee, T and Baldwin, S and Akkerboom, V and Voss, A and Friedrich, AW and Bathoorn, E},
title = {The complete genome sequence of unculturable Mycoplasma faucium obtained through clinical metagenomic next-generation sequencing.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1368923},
doi = {10.3389/fcimb.2024.1368923},
pmid = {38694516},
issn = {2235-2988},
mesh = {Humans ; *Metagenomics/methods ; *Genome, Bacterial ; *High-Throughput Nucleotide Sequencing ; *Mycoplasma/genetics/isolation & purification/classification ; Mycoplasma Infections/microbiology/diagnosis ; Whole Genome Sequencing/methods ; Lung Transplantation ; Prophages/genetics ; Interspersed Repetitive Sequences/genetics ; Anti-Bacterial Agents/pharmacology/therapeutic use ; },
abstract = {INTRODUCTION: Diagnosing Mycoplasma faucium poses challenges, and it's unclear if its rare isolation is due to infrequent occurrence or its fastidious nutritional requirements.

METHODS: This study analyzes the complete genome sequence of M. faucium, obtained directly from the pus of a sternum infection in a lung transplant patient using metagenomic sequencing.

RESULTS: Genome analysis revealed limited therapeutic options for the M. faucium infection, primarily susceptibility to tetracyclines. Three classes of mobile genetic elements were identified: two new insertion sequences, a new prophage (phiUMCG-1), and a species-specific variant of a mycoplasma integrative and conjugative element (MICE). Additionally, a Type I Restriction-Modification system was identified, featuring 5'-terminally truncated hsdS pseudogenes with overlapping repeats, indicating the potential for forming alternative hsdS variants through recombination.

CONCLUSION: This study represents the first-ever acquisition of a complete circularized bacterial genome directly from a patient sample obtained from invasive infection of a primary sterile site using culture-independent, PCR-free clinical metagenomics.},
}

Humans
*Metagenomics/methods
*Genome, Bacterial
*High-Throughput Nucleotide Sequencing
*Mycoplasma/genetics/isolation & purification/classification
Mycoplasma Infections/microbiology/diagnosis
Whole Genome Sequencing/methods
Lung Transplantation
Prophages/genetics
Interspersed Repetitive Sequences/genetics
Anti-Bacterial Agents/pharmacology/therapeutic use

@article {pmid38693138,
year = {2024},
author = {Jeilu, O and Alexandersson, E and Johansson, E and Simachew, A and Gessesse, A},
title = {A novel GH3-β-glucosidase from soda lake metagenomic libraries with desirable properties for biomass degradation.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {10012},
pmid = {38693138},
issn = {2045-2322},
mesh = {*beta-Glucosidase/genetics/metabolism/chemistry ; *Lakes/microbiology ; *Biomass ; Metagenomics/methods ; Escherichia coli/genetics/metabolism ; Metagenome ; Cloning, Molecular ; Enzyme Stability ; Hydrolysis ; Hydrogen-Ion Concentration ; Cellulose/metabolism ; Temperature ; Glucose/metabolism ; },
abstract = {Beta-glucosidases catalyze the hydrolysis of the glycosidic bonds of cellobiose, producing glucose, which is a rate-limiting step in cellulose biomass degradation. In industrial processes, β-glucosidases that are tolerant to glucose and stable under harsh industrial reaction conditions are required for efficient cellulose hydrolysis. In this study, we report the molecular cloning, Escherichia coli expression, and functional characterization of a β-glucosidase from the gene, CelGH3_f17, identified from metagenomics libraries of an Ethiopian soda lake. The CelGH3_f17 gene sequence contains a glycoside hydrolase family 3 catalytic domain (GH3). The heterologous expressed and purified enzyme exhibited optimal activity at 50 °C and pH 8.5. In addition, supplementation of 1 M salt and 300 mM glucose enhanced the β-glucosidase activity. Most of the metal ions and organic solvents tested did not affect the β-glucosidase activity. However, Cu[2+] and Mn[2+] ions, Mercaptoethanol and Triton X-100 reduce the activity of the enzyme. The studied β-glucosidase enzyme has multiple industrially desirable properties including thermostability, and alkaline, salt, and glucose tolerance.},
}

*beta-Glucosidase/genetics/metabolism/chemistry
*Lakes/microbiology
*Biomass
Metagenomics/methods
Escherichia coli/genetics/metabolism
Metagenome
Cloning, Molecular
Enzyme Stability
Hydrolysis
Hydrogen-Ion Concentration
Cellulose/metabolism
Temperature
Glucose/metabolism

@article {pmid38692845,
year = {2024},
author = {Guadalupe, JJ and Pazmiño-Vela, M and Pozo, G and Vernaza, W and Ochoa-Herrera, V and Torres, ML and Torres, AF},
title = {Metagenomic analysis of microbial consortia native to the Amazon, Highlands, and Galapagos regions of Ecuador with potential for wastewater remediation.},
journal = {Environmental microbiology reports},
volume = {16},
number = {3},
pages = {e13272},
doi = {10.1111/1758-2229.13272},
pmid = {38692845},
issn = {1758-2229},
support = {//Universidad San Francisco de Quito Collaboration Grant/ ; },
mesh = {Ecuador ; *Wastewater/microbiology ; *Microbial Consortia/genetics ; *Bacteria/classification/genetics/metabolism/isolation & purification ; *Metagenomics ; Microalgae/classification/metabolism ; Water Purification ; Biodegradation, Environmental ; Metagenome ; },
abstract = {Native microbial consortia have been proposed for biological wastewater treatment, but their diversity and function remain poorly understood. This study investigated three native microalgae-bacteria consortia collected from the Amazon, Highlands, and Galapagos regions of Ecuador to assess their metagenomes and wastewater remediation potential. The consortia were evaluated for 12 days under light (LC) and continuous dark conditions (CDC) to measure their capacity for nutrient and organic matter removal from synthetic wastewater (SWW). Overall, all three consortia demonstrated higher nutrient removal efficiencies under LC than CDC, with the Amazon and Galapagos consortia outperforming the Highlands consortium in nutrient removal capabilities. Despite differences in α- and β-diversity, microbial species diversity within and between consortia did not directly correlate with their nutrient removal capabilities. However, all three consortia were enriched with core taxonomic groups associated with wastewater remediation activities. Our analyses further revealed higher abundances for nutrient removing microorganisms in the Amazon and Galapagos consortia compared with the Highland consortium. Finally, this study also uncovered the contribution of novel microbial groups that enhance wastewater bioremediation processes. These groups have not previously been reported as part of the core microbial groups commonly found in wastewater communities, thereby highlighting the potential of investigating microbial consortia isolated from ecosystems of megadiverse countries like Ecuador.},
}

Ecuador
*Wastewater/microbiology
*Microbial Consortia/genetics
*Bacteria/classification/genetics/metabolism/isolation & purification
*Metagenomics
Microalgae/classification/metabolism
Water Purification
Biodegradation, Environmental
Metagenome

@article {pmid38692373,
year = {2024},
author = {Yin, W and Li, Y and Xu, W and Bao, Y and Zhu, J and Su, X and Han, J and Chen, C and Lin, H and Sun, F},
title = {Unveiling long-term combined effect of salinity and Lead(II) on anammox activity and microbial community dynamics in saline wastewater treatment.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {130767},
doi = {10.1016/j.biortech.2024.130767},
pmid = {38692373},
issn = {1873-2976},
abstract = {The study assessed the effect of salinity and lead (Pb(II)) on the anammox sludge for nitrogen removal from saline wastewater. Results showed decreased nitrogen removal and specific anammox activity (SAA) with elevated salinity and Pb(II). SAA reduced from 541.3 ± 4.3 mg N g[-1] VSS d[-1] at 0.5 mg/L Pb(II) to 436.0 ± 0.2 mg N g[-1] VSS d[-1] at 30 g/L NaCl, further to 303.6 ± 7.1 mg N g[-1] VSS d[-1] under 30 g/L NaCl + 0.5 mg/L Pb(II). Notably, the combined inhibition at salinity (15-20 g/L NaCl) and Pb(II) (0.3-0.4 mg/L) exhibited synergistic effect, while higher salinity and Pb(II) aligned with independent inhibition models. Combined inhibition decreased protein/polysaccharides ratio, indicating more severe negative effect on anammox aggregation capacity. Metagenomics confirmed decreased Candidatus Kuenenia, and enhanced denitrification under elevated salinity and Pb(II) conditions. This study offers insights into anammox operation for treating saline wastewater with heavy metals.},
}

@article {pmid38692260,
year = {2024},
author = {Dai, B and Yang, Y and Wang, Z and Zhou, J and Wang, Z and Zhang, X and Xia, S},
title = {Refractory dissolved organic matters in sludge leachate trigger the combination of anammox and denitratation for advanced nitrogen removal.},
journal = {Water research},
volume = {257},
number = {},
pages = {121678},
doi = {10.1016/j.watres.2024.121678},
pmid = {38692260},
issn = {1879-2448},
abstract = {The cost-effective treatment of sludge leachate (SL) with high nitrogen content and refractory dissolved organic matter (rDOM) has drawn increasing attention. This study employed, for the first time, a rDOM triggered denitratation-anammox continuous-flow process to treat landfill SL. Moreover, the mechanisms of exploiting rDOM from SL as an inner carbon source for denitratation were systematically analyzed. The results demonstrated outstanding nitrogen and rDOM removal performance without any external carbon source supplement. In this study, effluent concentrations of 4.27 ± 0.45 mgTIN/L and 5.58 ± 1.64 mgTN/L were achieved, coupled with an impressive COD removal rate of 65.17 % ± 1.71 %. The abundance of bacteria belonging to the Anaerolineaceae genus, which were identified as rDOM degradation bacteria, increased from 18.23 % to 35.62 %. As a result, various types of rDOM were utilized to different extents, with proteins being the most notable, except for lignins. Metagenomic analysis revealed a preference for directing electrons towards NO3[-]-N reductase rather than NO2[-]-N reductase, indicating the coupling of denitratation bacteria and anammox bacteria (Candidatus Brocadia). Overall, this study introduced a novel synergy platform for advanced nitrogen removal in treating SL using its inner carbon source. This approach is characterized by low energy consumption and operational costs, coupled with commendable efficiency.},
}

@article {pmid38692150,
year = {2024},
author = {Cai, Y and Chen, C and Sun, T and Li, G and Wang, W and Zhao, H and An, T},
title = {Mariculture waters as yet another hotbed for the creation and transfer of new antibiotic-resistant pathogenome.},
journal = {Environment international},
volume = {187},
number = {},
pages = {108704},
doi = {10.1016/j.envint.2024.108704},
pmid = {38692150},
issn = {1873-6750},
abstract = {With the rapid growth of aquaculture globally, large amounts of antibiotics have been used to treat aquatic disease, which may accelerate induction and spread of antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARGs) in aquaculture environments. Herein, metagenomic and 16S rRNA analyses were used to analyze the potentials and co-occurrence patterns of pathogenome (culturable and unculturable pathogens), antibiotic resistome (ARGs), and mobilome (mobile genetic elements (MGEs)) from mariculture waters near 5000 km coast of South China. Total 207 species of pathogens were identified, with only 10 culturable species. Furthermore, more pathogen species were detected in mariculture waters than those in coastal waters, and mariculture waters were prone to become reservoirs of unculturable pathogens. In addition, 913 subtypes of 21 ARG types were also identified, with multidrug resistance genes as the majority. MGEs including plasmids, integrons, transposons, and insertion sequences were abundantly present in mariculture waters. The co-occurrence network pattern between pathogenome, antibiotic resistome, and mobilome suggested that most of pathogens may be potential multidrug resistant hosts, possibly due to high frequency of horizontal gene transfer. These findings increase our understanding of mariculture waters as reservoirs of antibiotic resistome and mobilome, and as yet another hotbed for creation and transfer of new antibiotic-resistant pathogenome.},
}

@article {pmid38691556,
year = {2024},
author = {Kawser, AQMR and Hoque, MN and Rahman, MS and Sakif, TI and Coffey, TJ and Islam, T},
title = {Unveiling the gut bacteriome diversity and distribution in the national fish hilsa (Tenualosa ilisha) of Bangladesh.},
journal = {PloS one},
volume = {19},
number = {5},
pages = {e0303047},
doi = {10.1371/journal.pone.0303047},
pmid = {38691556},
issn = {1932-6203},
mesh = {Animals ; Bangladesh ; *Gastrointestinal Microbiome/genetics ; *Fishes/microbiology ; *RNA, Ribosomal, 16S/genetics ; Bacteria/genetics/classification/isolation & purification ; Biodiversity ; Phylogeny ; },
abstract = {The field of fish microbiome research has rapidly been advancing, primarily focusing on farmed or laboratory fish species rather than natural or marine fish populations. This study sought to reveal the distinctive gut bacteriome composition and diversity within the anadromous fish species Tenualosa ilisha (hilsa), which holds the status of being the national fish of Bangladesh. We conducted an analysis on 15 gut samples obtained from 15 individual hilsa fishes collected from three primary habitats (e.g., freshwater = 5, brackish water = 5 and marine water = 5) in Bangladesh. The analysis utilized metagenomics based on 16S rRNA gene sequencing targeting the V3-V4 regions. Our comprehensive identification revealed a total of 258 operational taxonomic units (OTUs). The observed OTUs were represented by six phyla, nine classes, 19 orders, 26 families and 40 genera of bacteria. Our analysis unveiled considerable taxonomic differences among the habitats (freshwater, brackish water, and marine water) of hilsa fishes, as denoted by a higher level of shared microbiota (p = 0.007, Kruskal-Wallis test). Among the identified genera in the gut of hilsa fishes, including Vagococcus, Morganella, Enterobacter, Plesiomonas, Shigella, Clostridium, Klebsiella, Serratia, Aeromonas, Macrococcus, Staphylococcus, Proteus, and Hafnia, several are recognized as fish probiotics. Importantly, some bacterial genera such as Sinobaca, Synechococcus, Gemmata, Serinicoccus, Saccharopolyspora, and Paulinella identified in the gut of hilsa identified in this study have not been reported in any aquatic or marine fish species. Significantly, we observed that 67.50% (27/40) of bacterial genera were found to be common among hilsa fishes across all three habitats. Our findings offer compelling evidence for the presence of both exclusive and communal bacteriomes within the gut of hilsa fishes, exhibiting potential probiotic properties. These observations could be crucial for guiding future microbiome investigations in this economically significant fish species.},
}

Animals
Bangladesh
*Gastrointestinal Microbiome/genetics
*Fishes/microbiology
*RNA, Ribosomal, 16S/genetics
Bacteria/genetics/classification/isolation & purification
Biodiversity
Phylogeny

@article {pmid38691513,
year = {2024},
author = {Kantor, RS and Jiang, M},
title = {Considerations and Opportunities for Probe Capture Enrichment Sequencing of Emerging Viruses from Wastewater.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.4c02638},
pmid = {38691513},
issn = {1520-5851},
abstract = {Until recently, wastewater-based monitoring for pathogens of public health concern primarily used PCR-based quantification methods and targeted sequencing for specific pathogens (e.g., SARS-CoV-2). In the past three years, researchers have expanded sequencing to monitor a broad range of pathogens, applying probe capture enrichment to wastewater. The goals of those studies included (1) monitoring and expanding fundamental knowledge of disease dynamics for known pathogens and (2) evaluating the potential for early detection of emerging diseases resulting from zoonotic spillover or novel viral variants. Several studies using off-the-shelf probe panels designed for clinical and environmental surveillance reported that enrichment increased virus relative abundance but did not recover complete genomes for most nonenteric viruses. Based on our experience and recent results reported by others using these panels for wastewater, clinical, and synthetic samples, we discuss challenges and technical factors that affect the rates of false positive and false negative results. We identify trade-offs and opportunities throughout the workflow, including in wastewater sample processing, probe panel design, and bioinformatic analysis. We suggest tailored methods of virus concentration and background removal, carefully designed probe panels, and multithresholded bioinformatics analysis.},
}

@article {pmid38690990,
year = {2024},
author = {Chen, P and Chen, H and Liu, Z and Pan, X and Liu, Q and Yang, X},
title = {Fungal-bacteria interactions provide shelter for bacteria in Caesarean section scar diverticulum.},
journal = {eLife},
volume = {12},
number = {},
pages = {},
doi = {10.7554/eLife.90363},
pmid = {38690990},
issn = {2050-084X},
support = {2023A1515012940//Natural Science Foundation of Guangdong Province/ ; 2023A1515110325//Guangdong Basic and Applied Basic Research Foundation/ ; GZC20233216//Postdoctoral Fellowship Program of CPSF/ ; },
mesh = {Female ; *Cesarean Section/adverse effects ; Humans ; *Diverticulum/microbiology/metabolism ; *Bacteria/metabolism/genetics ; *Cicatrix/microbiology/metabolism ; Dysbiosis/microbiology ; Fungi/metabolism/genetics/physiology ; Microbial Interactions ; Microbiota ; },
abstract = {Caesarean section scar diverticulum (CSD) is a significant cause of infertility among women who have previously had a Caesarean section, primarily due to persistent inflammatory exudation associated with this condition. Even though abnormal bacterial composition is identified as a critical factor leading to this chronic inflammation, clinical data suggest that a long-term cure is often unattainable with antibiotic treatment alone. In our study, we employed metagenomic analysis and mass spectrometry techniques to investigate the fungal composition in CSD and its interaction with bacteria. We discovered that local fungal abnormalities in CSD can disrupt the stability of the bacterial population and the entire microbial community by altering bacterial abundance via specific metabolites. For instance, Lachnellula suecica reduces the abundance of several Lactobacillus spp., such as Lactobacillus jensenii, by diminishing the production of metabolites like Goyaglycoside A and Janthitrem E. Concurrently, Clavispora lusitaniae and Ophiocordyceps australis can synergistically impact the abundance of Lactobacillus spp. by modulating metabolite abundance. Our findings underscore that abnormal fungal composition and activity are key drivers of local bacterial dysbiosis in CSD.},
}

Female
*Cesarean Section/adverse effects
Humans
*Diverticulum/microbiology/metabolism
*Bacteria/metabolism/genetics
*Cicatrix/microbiology/metabolism
Dysbiosis/microbiology
Fungi/metabolism/genetics/physiology
Microbial Interactions
Microbiota

@article {pmid38690913,
year = {2024},
author = {Chen, Y and Dong, X and Sun, Z and Xu, C and Zhang, X and Qin, S and Geng, W and Cao, H and Zhai, B and Li, X and Wu, N},
title = {Potential coupling of microbial methane, nitrogen, and sulphur cycling in the Okinawa Trough cold seep sediments.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0349023},
doi = {10.1128/spectrum.03490-23},
pmid = {38690913},
issn = {2165-0497},
abstract = {The Okinawa Trough (OT) is a back-arc basin with a wide distribution of active cold seep systems. However, our understanding of the metabolic function of microbial communities in the cold seep sediments of the OT remains limited. In this study, we investigated the vertical profiles of functional genes involved in methane, nitrogen, and sulphur cycling in the cold seep sediments of the OT. Furthermore, we explored the possible coupling mechanisms between these biogeochemical cycles. The study revealed that the majority of genes associated with the nitrogen and sulphur cycles were most abundant in the surface sediment layers. However, only the key genes responsible for sulphur disproportionation (sor), nitrogen fixation (nifDKH), and methane metabolism (mcrABG) were more prevalent within sulfate-methane transition zone (SMTZ). Significant positive correlations (P < 0.05) were observed between functional genes involved in sulphur oxidation, thiosulphate disproportionation with denitrification, and dissimilatory nitrate reduction to ammonium (DNRA), as well as between AOM/methanogenesis and nitrogen fixation, and between sulphur disproportionation and AOM. A genome of Filomicrobium (class Alphaproteobacteria) has demonstrated potential in chemoautotrophic activities, particularly in coupling DNRA and denitrification with sulphur oxidation. Additionally, the characterized sulfate reducers such as Syntrophobacterales have been found to be capable of utilizing nitrate as an electron acceptor. The predominant methanogenic/methanotrophic groups in the OT sediments were identified as H2-dependent methylotrophic methanogens (Methanomassiliicoccales and Methanofastidiosales) and ANME-1a. This study offered a thorough understanding of microbial ecosystems in the OT cold seep sediments, emphasizing their contribution to nutrient cycling.IMPORTANCEThe Okinawa Trough (OT) is a back-arc basin formed by extension within the continental lithosphere behind the Ryukyu Trench arc system. Cold seeps are widespread in the OT. While some studies have explored microbial communities in OT cold seep sediments, their metabolic potential remains largely unknown. In this study, we used metagenomic analysis to enhance comprehension of the microbial community's role in nutrient cycling and proposed hypotheses on the coupling process and mechanisms involved in biogeochemical cycles. It was revealed that multiple metabolic pathways can be performed by a single organism or microbes that interact with each other to carry out various biogeochemical cycling. This data set provided a genomic road map on microbial nutrient cycling in OT sediment microbial communities.},
}

@article {pmid38690316,
year = {2024},
author = {Rivera-Lopez, EO and Nieves-Morales, R and Melendez-Martinez, G and Paez-Diaz, JA and Rodriguez-Carrio, SM and Rodriguez-Ramos, J and Morales-Valle, L and Rios-Velazquez, C},
title = {Sea cucumber (Holothuria glaberrima) intestinal microbiome dataset from Puerto Rico, generated by shotgun sequencing.},
journal = {Data in brief},
volume = {54},
number = {},
pages = {110421},
doi = {10.1016/j.dib.2024.110421},
pmid = {38690316},
issn = {2352-3409},
abstract = {The sea cucumber (H. glaberrima) is a species found in the shallow waters near coral reefs and seagrass beds in Puerto Rico. To characterize the microbial taxonomic composition and functional profiles present in the sea cucumber, total DNA was obtained from their intestinal system, fosmid libraries constructed, and subsequent sequencing was performed. The diversity profile displayed that the most predominant domain was Bacteria (76.56 %), followed by Viruses (23.24 %) and Archaea (0.04 %). Within the 11 phyla identified, the most abundant was Proteobacteria (73.16 %), followed by Terrabacteria group (3.20 %) and Fibrobacterota, Chlorobiota, Bacteroidota (FCB) superphylum (1.02 %). The most abundant species were Porvidencia rettgeri (21.77 %), Pseudomonas stutzeri (14.78 %), and Alcaligenes faecalis (5.00 %). The functional profile revealed that the most abundant functions are related to transporters, MISC (miscellaneous information systems), organic nitrogen, energy, and carbon utilization. The data collected in this project on the diversity and functional profiles of the intestinal system of the H. glaberrima provided a detailed view of its microbial ecology. These findings may motivate comparative studies aimed at understanding the role of the microbiome in intestinal regeneration.},
}

@article {pmid38689852,
year = {2024},
author = {Wang, T and Luo, Y and Kong, X and Yu, B and Zheng, P and Huang, Z and Mao, X and Yu, J and Luo, J and Yan, H and He, J},
title = {Genetic- and fiber-diet-mediated changes in virulence factors in pig colon contents and feces and their driving factors.},
journal = {Frontiers in veterinary science},
volume = {11},
number = {},
pages = {1351962},
doi = {10.3389/fvets.2024.1351962},
pmid = {38689852},
issn = {2297-1769},
abstract = {Virulence factors (VFs) are key factors for microorganisms to establish defense mechanisms in the host and enhance their pathogenic potential. However, the spectrum of virulence factors in pig colon and feces, as well as the influence of dietary and genetic factors on them, remains unreported. In this study, we firstly revealed the diversity, abundance and distribution characteristics of VFs in the colonic contents of different breeds of pigs (Taoyuan, Xiangcun and Duroc pig) fed with different fiber levels by using a metagenomic analysis. The analysis resulted in the identification of 1,236 virulence factors, which could be grouped into 16 virulence features. Among these, Taoyuan pigs exhibited significantly higher levels of virulence factors compared to Duroc pigs. The high-fiber diet significantly reduced the abundance of certain virulence factor categories, including iron uptake systems (FbpABC, HitABC) and Ig protease categories in the colon, along with a noteworthy decrease in the relative abundance of plasmid categories in mobile genetic elements (MGEs). Further we examined VFs in feces using absolute quantification. The results showed that high-fiber diets reduce fecal excretion of VFs and that this effect is strongly influenced by MGEs and short-chain fatty acids (SCFAs). In vitro fermentation experiments confirmed that acetic acid (AA) led to a decrease in the relative abundance of VFs (p < 0.1). In conclusion, our findings reveal for the first time how fiber diet and genetic factors affect the distribution of VFs in pig colon contents and feces and their driving factors. This information provides valuable reference data to further improve food safety and animal health.},
}

@article {pmid38689099,
year = {2024},
author = {Agustinho, DP and Fu, Y and Menon, VK and Metcalf, GA and Treangen, TJ and Sedlazeck, FJ},
title = {Unveiling microbial diversity: harnessing long-read sequencing technology.},
journal = {Nature methods},
volume = {},
number = {},
pages = {},
pmid = {38689099},
issn = {1548-7105},
support = {1U19AI144297//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; 1U19AI144297//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; 1U19AI144297//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; 1U19AI144297//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; P01-AI152999//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; P01-AI152999//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; III-2239114//National Science Foundation (NSF)/ ; EF-2126387//National Science Foundation (NSF)/ ; III-2239114//National Science Foundation (NSF)/ ; },
abstract = {Long-read sequencing has recently transformed metagenomics, enhancing strain-level pathogen characterization, enabling accurate and complete metagenome-assembled genomes, and improving microbiome taxonomic classification and profiling. These advancements are not only due to improvements in sequencing accuracy, but also happening across rapidly changing analysis methods. In this Review, we explore long-read sequencing's profound impact on metagenomics, focusing on computational pipelines for genome assembly, taxonomic characterization and variant detection, to summarize recent advancements in the field and provide an overview of available analytical methods to fully leverage long reads. We provide insights into the advantages and disadvantages of long reads over short reads and their evolution from the early days of long-read sequencing to their recent impact on metagenomics and clinical diagnostics. We further point out remaining challenges for the field such as the integration of methylation signals in sub-strain analysis and the lack of benchmarks.},
}

@article {pmid38688217,
year = {2024},
author = {Zhang, D and Li, H and Yang, Q and Xu, Y},
title = {Microbial-mediated conversion of soil organic carbon co-regulates the evolution of antibiotic resistance.},
journal = {Journal of hazardous materials},
volume = {471},
number = {},
pages = {134404},
doi = {10.1016/j.jhazmat.2024.134404},
pmid = {38688217},
issn = {1873-3336},
abstract = {The influence of organic carbon on the proliferation of antibiotic resistance genes (ARGs) in the soil has been widely documented. However, it is unclear how soil organic carbon (SOC) interacts with the evolution of antibiotic resistance in bacteria. Here, we examined the variations in ARGs abundance during SOC mineralization and explored the microbiological mechanisms and key metabolic pathways involved in their coevolution. The results showed that the SOC mineralization rate was closely correlated with ARGs abundance (p < 0.05). High organic carbon (OC) mineralization was conducive to the occurrence of multidrug resistance genes. For example, multidrug_transporter and mexB increased 2.26 and 7.83 times from the initial level. The competitor (stress) evolutionary strategy model revealed that higher OC inputs drive environmental microorganisms to evolve from stress tolerant to high resistance and strong adaptation. Meta-genomic and transcriptomic analyses revealed that the conversion process of pyruvate to acetyl-CoA to acetate was the critical metabolic pathway for the co-regulation of antibiotic resistance. Gene deletion validation trials have demonstrated that the key functional genes (ackA and pta) involved in this process can modulate the development of vancomycin and multidrug resistance. This outcome provides a preliminary framework for microbial mechanisms that target the co-regulation of microbial OC conversion and the evolution of antibiotic resistance.},
}

@article {pmid38687787,
year = {2024},
author = {Kobayashi, D and Inoue, Y and Suzuki, R and Matsuda, M and Shimoda, H and Faizah, AN and Kaku, Y and Ishijima, K and Kuroda, Y and Tatemoto, K and Virhuez-Mendoza, M and Harada, M and Nishino, A and Inumaru, M and Yonemitsu, K and Kuwata, R and Takano, A and Watanabe, M and Higa, Y and Sawabe, K and Maeda, K and Isawa, H},
title = {Identification and epidemiological study of an uncultured flavivirus from ticks using viral metagenomics and pseudoinfectious viral particles.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {121},
number = {19},
pages = {e2319400121},
doi = {10.1073/pnas.2319400121},
pmid = {38687787},
issn = {1091-6490},
support = {JP18fk0108067//Japan Agency for Medical Research and Development (AMED)/ ; JP19fk0108097//Japan Agency for Medical Research and Development (AMED)/ ; JP20wm0225009//Japan Agency for Medical Research and Development (AMED)/ ; JP21fk0108613//Japan Agency for Medical Research and Development (AMED)/ ; JP22fk0108123//Japan Agency for Medical Research and Development (AMED)/ ; JP22fk0108634//Japan Agency for Medical Research and Development (AMED)/ ; JP23fk0108625//Japan Agency for Medical Research and Development (AMED)/ ; JP23fk0108656//Japan Agency for Medical Research and Development (AMED)/ ; Strategic International Collaborative Research Program (SICORP)//MEXT | Japan Science and Technology Agency (JST)/ ; 20KC1001//Regulatory Science Research from Ministry of Health, Labor and Welfare/ ; 21KA1003//Regulatory Science Research from Ministry of Health, Labor and Welfare/ ; JP18H02856//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; JP20K15671//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; },
mesh = {Animals ; *Metagenomics/methods ; Japan/epidemiology ; *Deer/virology ; *Flavivirus/genetics/isolation & purification/classification ; *Ticks/virology ; Phylogeny ; Virome/genetics ; Virion/genetics ; Sus scrofa/virology ; High-Throughput Nucleotide Sequencing ; Humans ; Seroepidemiologic Studies ; Genome, Viral ; },
abstract = {During their blood-feeding process, ticks are known to transmit various viruses to vertebrates, including humans. Recent viral metagenomic analyses using next-generation sequencing (NGS) have revealed that blood-feeding arthropods like ticks harbor a large diversity of viruses. However, many of these viruses have not been isolated or cultured, and their basic characteristics remain unknown. This study aimed to present the identification of a difficult-to-culture virus in ticks using NGS and to understand its epidemic dynamics using molecular biology techniques. During routine tick-borne virus surveillance in Japan, an unknown flaviviral sequence was detected via virome analysis of host-questing ticks. Similar viral sequences have been detected in the sera of sika deer and wild boars in Japan, and this virus was tentatively named the Saruyama virus (SAYAV). Because SAYAV did not propagate in any cultured cells tested, single-round infectious virus particles (SRIP) were generated based on its structural protein gene sequence utilizing a yellow fever virus-based replicon system to understand its nationwide endemic status. Seroepidemiological studies using SRIP as antigens have demonstrated the presence of neutralizing antibodies against SAYAV in sika deer and wild boar captured at several locations in Japan, suggesting that SAYAV is endemic throughout Japan. Phylogenetic analyses have revealed that SAYAV forms a sister clade with the Orthoflavivirus genus, which includes important mosquito- and tick-borne pathogenic viruses. This shows that SAYAV evolved into a lineage independent of the known orthoflaviviruses. This study demonstrates a unique approach for understanding the epidemiology of uncultured viruses by combining viral metagenomics and pseudoinfectious viral particles.},
}

Animals
*Metagenomics/methods
Japan/epidemiology
*Deer/virology
*Flavivirus/genetics/isolation & purification/classification
*Ticks/virology
Phylogeny
Virome/genetics
Virion/genetics
Sus scrofa/virology
High-Throughput Nucleotide Sequencing
Humans
Seroepidemiologic Studies
Genome, Viral

@article {pmid38687700,
year = {2024},
author = {Kimemia, BB and Musila, L and Langat, S and Odoyo, E and Cinkovich, S and Abuom, D and Yalwala, S and Khamadi, S and Johnson, J and Garges, E and Ojwang, E and Eyase, F},
title = {Detection of pathogenic bacteria in ticks from Isiolo and Kwale counties of Kenya using metagenomics.},
journal = {PloS one},
volume = {19},
number = {4},
pages = {e0296597},
doi = {10.1371/journal.pone.0296597},
pmid = {38687700},
issn = {1932-6203},
mesh = {Kenya ; Animals ; *Metagenomics/methods ; *Ticks/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/isolation & purification/classification ; Humans ; Phylogeny ; },
abstract = {Ticks are arachnid ectoparasites that rank second only to mosquitoes in the transmission of human diseases including bacteria responsible for anaplasmosis, ehrlichiosis, spotted fevers, and Lyme disease among other febrile illnesses. Due to the paucity of data on bacteria transmitted by ticks in Kenya, this study undertook a bacterial metagenomic-based characterization of ticks collected from Isiolo, a semi-arid pastoralist County in Eastern Kenya, and Kwale, a coastal County with a monsoon climate in the southern Kenyan border with Tanzania. A total of 2,918 ticks belonging to 3 genera and 10 species were pooled and screened in this study. Tick identification was confirmed through the sequencing of the Cytochrome C Oxidase Subunit 1 (COI) gene. Bacterial 16S rRNA gene PCR amplicons obtained from the above samples were sequenced using the MinION (Oxford Nanopore Technologies) platform. The resulting reads were demultiplexed in Porechop, followed by trimming and filtering in Trimmomatic before clustering using Qiime2-VSearch. A SILVA database pretrained naïve Bayes classifier was used to classify the Operational Taxonomic Units (OTUs) taxonomically. The bacteria of clinical interest detected in pooled tick assays were as follows: Rickettsia spp. 59.43% of pools, Coxiella burnetii 37.88%, Proteus mirabilis 5.08%, Cutibacterium acnes 6.08%, and Corynebacterium ulcerans 2.43%. These bacteria are responsible for spotted fevers, query fever (Q-fever), urinary tract infections, skin and soft tissue infections, eye infections, and diphtheria-like infections in humans, respectively. P. mirabilis, C. acnes, and C. ulcerans were detected only in Isiolo. Additionally, COI sequences allowed for the identification of Rickettsia and Coxiella species to strain levels in some of the pools. Diversity analysis revealed that the tick genera had high levels of Alpha diversity but the differences between the microbiomes of the three tick genera studied were not significant. The detection of C. acnes, commonly associated with human skin flora suggests that the ticks may have contact with humans potentially exposing them to bacterial infections. The findings in this study highlight the need for further investigation into the viability of these bacteria and the competency of ticks to transmit them. Clinicians in these high-risk areas also need to be appraised for them to include Rickettsial diseases and Q-fever as part of their differential diagnosis.},
}

Kenya
Animals
*Metagenomics/methods
*Ticks/microbiology
*RNA, Ribosomal, 16S/genetics
*Bacteria/genetics/isolation & purification/classification
Humans
Phylogeny

@article {pmid38687074,
year = {2024},
author = {Ye, J and Huang, K and Xu, Y and Chen, N and Tu, Y and Huang, J and Shao, L and Kong, W and Zhao, D and Xie, Y},
title = {Clinical application of nanopore-targeted sequencing technology in bronchoalveolar lavage fluid from patients with pulmonary infections.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0002624},
doi = {10.1128/spectrum.00026-24},
pmid = {38687074},
issn = {2165-0497},
abstract = {The rapid and effective identification of pathogens in patients with pulmonary infections has posed a persistent challenge in medicine, with conventional microbiological tests (CMTs) proving time-consuming and less sensitive, hindering early diagnosis of respiratory infections. While there has been some research on the clinical performance of targeted sequencing technologies, limited focus has been directed toward bronchoalveolar lavage fluid (BALF). This study primarily evaluates the pathogen detection capabilities of nanopore-targeted sequencing (NTS) in BALF, providing a comprehensive analysis. The retrospective study, spanning from January 2022 to November 2023, includes 223 patients exclusively sourced from a single center. We conducted a detailed comparative analysis among NTS, targeted next-generation sequencing (tNGS), and CMTs. Initially, we compared the detection capabilities of NTS and tNGS and found no significant differences in their sensitivity and specificity. Specifically, we observed that the sensitivity of NTS was significantly higher than that of CMTs (74.83% vs 33.11%, P < 0.001). Furthermore, NTS exhibited a higher positivity rate in common pulmonary infections (62.88% vs. 23.48%) and in clinically suspected tuberculosis patients compared to CMTs (87.18% vs. 48.72%). Additionally, NTS showed less susceptibility to antibiotic interference, indicating a more sensitive detection capability, especially in detecting fastidious organisms. It complements GeneXpert in tuberculosis diagnosis and offers excellent advantages in identifying pathogens challenging for CMTs, such as non-tuberculous mycobacteria and viruses. Moreover, NTS significantly shortens the reporting time and is only a quarter of the cost of metagenomic next-generation sequencing. Clearly, NTS can facilitate faster and more cost-effective early diagnosis of respiratory infections.IMPORTANCEThis study holds paramount significance in advancing the field of respiratory infection diagnostics. By assessing the pathogen detection capabilities in bronchoalveolar lavage fluid (BALF) of patients with pulmonary infections, we illuminate the promising potential of nanopore-targeted sequencing (NTS). The findings underscore NTS as a comparable yet distinct alternative to traditional methods like comprehensive conventional microbiological tests (CMTs). Notably, NTS demonstrates a pivotal edge, expanding the spectrum of identified pathogens, particularly excelling in the detection of challenging entities like non-tuberculous mycobacteria and viruses. The study also highlights the complementary role of NTS alongside GeneXpert in the identification of tuberculosis, providing a comprehensive overview of the diagnostic landscape for respiratory infections. This insight carries significant implications for clinicians seeking rapid, cost-effective, and accurate diagnostic tools in the realm of pulmonary infections.},
}

@article {pmid38687069,
year = {2024},
author = {Ma, G and Yan, H and Tye, KD and Tang, X and Luo, H and Li, Z and Xiao, X},
title = {Effect of probiotic administration during pregnancy on the functional diversity of the gut microbiota in healthy pregnant women.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0041324},
doi = {10.1128/spectrum.00413-24},
pmid = {38687069},
issn = {2165-0497},
abstract = {UNLABELLED: Our study aims to investigate the impact of probiotic consumption during pregnancy on gut microbiota functional diversity in healthy pregnant women. Thirty-two pregnant women were randomly assigned to two groups. The probiotic group (PG) consisted of pregnant women who consumed triple viable Bifidobacterium longum, Lactobacillus delbrueckii bulgaricus, and Streptococcus thermophilus tablets from the 32nd week of pregnancy until delivery. The functional profiles of the gut microbiota were predicted through high-throughput 16S rRNA sequencing results using PICRUSt software and referencing the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. In the gut microbiota of the PG, the genera Blautia and Ruminococcus, as well as the species Subdoligranulum, showed significantly higher relative abundances compared to the control group (CG) (P < 0.05). At Level 1 of the KEGG signaling pathways, there was a significant reduction in the functional genes of the gut microbiota involved in Organismal Systems in the PG (P < 0.05). In Level 2 of the KEGG signaling pathways, there was a significant reduction in the functional genes of the gut microbiota involved in Infectious Disease in the PG (P < 0.05). In Level 3 of the KEGG signaling pathways, the PG exhibited a significant increase in the functional genes of the gut microbiota involved in ABC transporters, Oxidative phosphorylation, Folate biosynthesis, and Biotin metabolism (P < 0.05). The CG showed a significant increase in the functional genes related to Cysteine and methionine metabolism, Vitamin B6 metabolism, Tuberculosis, and Vibrio cholerae pathogenic cycle (P < 0.05). In conclusion, our findings suggest that probiotic supplementation during pregnancy has a significant impact on functional metabolism in healthy pregnant women.

IMPORTANCE: Probiotics are considered beneficial to human health. There is limited understanding of how probiotic consumption during pregnancy affects the functional diversity of the gut microbiota. The aim of our study is to investigate the impact of probiotic consumption during pregnancy on the functional diversity of the gut microbiota. Our findings suggest that probiotic supplementation during pregnancy has a significant impact on functional metabolism. This could potentially open up new avenues for preventing various pregnancy-related complications. This also provides new insights into the effects of probiotic consumption during pregnancy on the gut microbiota and offers a convenient method for exploring the potential mechanisms underlying the impact of probiotics on the gut microbiota of pregnant women.},
}

@article {pmid38687063,
year = {2024},
author = {Chen, Z and Grim, CJ and Ramachandran, P and Meng, J},
title = {Advancing metagenome-assembled genome-based pathogen identification: unraveling the power of long-read assembly algorithms in Oxford Nanopore sequencing.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0011724},
doi = {10.1128/spectrum.00117-24},
pmid = {38687063},
issn = {2165-0497},
abstract = {Oxford Nanopore sequencing is one of the high-throughput sequencing technologies that facilitates the reconstruction of metagenome-assembled genomes (MAGs). This study aimed to assess the potential of long-read assembly algorithms in Oxford Nanopore sequencing to enhance the MAG-based identification of bacterial pathogens using both simulated and mock communities. Simulated communities were generated to mimic those on fresh spinach and in surface water. Long reads were produced using R9.4.1+SQK-LSK109 and R10.4 + SQK-LSK112, with 0.5, 1, and 2 million reads. The simulated bacterial communities included multidrug-resistant Salmonella enterica serotypes Heidelberg, Montevideo, and Typhimurium in the fresh spinach community individually or in combination, as well as multidrug-resistant Pseudomonas aeruginosa in the surface water community. Real data sets of the ZymoBIOMICS HMW DNA Standard were also studied. A bioinformatic pipeline (MAGenie, freely available at https://github.com/jackchen129/MAGenie) that combines metagenome assembly, taxonomic classification, and sequence extraction was developed to reconstruct draft MAGs from metagenome assemblies. Five assemblers were evaluated based on a series of genomic analyses. Overall, Flye outperformed the other assemblers, followed by Shasta, Raven, and Unicycler, while Canu performed least effectively. In some instances, the extracted sequences resulted in draft MAGs and provided the locations and structures of antimicrobial resistance genes and mobile genetic elements. Our study showcases the viability of utilizing the extracted sequences for precise phylogenetic inference, as demonstrated by the consistent alignment of phylogenetic topology between the reference genome and the extracted sequences. R9.4.1+SQK-LSK109 was more effective in most cases than R10.4+SQK-LSK112, and greater sequencing depths generally led to more accurate results.IMPORTANCEBy examining diverse bacterial communities, particularly those housing multiple Salmonella enterica serotypes, this study holds significance in uncovering the potential of long-read assembly algorithms to improve metagenome-assembled genome (MAG)-based pathogen identification through Oxford Nanopore sequencing. Our research demonstrates that long-read assembly stands out as a promising avenue for boosting precision in MAG-based pathogen identification, thus advancing the development of more robust surveillance measures. The findings also support ongoing endeavors to fine-tune a bioinformatic pipeline for accurate pathogen identification within complex metagenomic samples.},
}

@article {pmid38686914,
year = {2024},
author = {Spatola Rossi, T and Gallia, M and Erijman, L and Figuerola, E},
title = {Biotic and abiotic factors acting on community assembly in parallel anaerobic digestion systems from a brewery wastewater treatment plant.},
journal = {Environmental technology},
volume = {},
number = {},
pages = {1-16},
doi = {10.1080/09593330.2024.2343797},
pmid = {38686914},
issn = {1479-487X},
abstract = {Anaerobic digestion is a complex microbial process that mediates the transformation of organic waste into biogas. The performance and stability of anaerobic digesters relies on the structure and function of the microbial community. In this study, we asked whether the deterministic effect of wastewater composition outweighs the effect of reactor configuration on the structure and dynamics of anaerobic digester archaeal and bacterial communities. Biotic and abiotic factors acting on microbial community assembly in two parallel anaerobic digestion systems, an upflow anaerobic sludge blanket digestor (UASB) and a closed digester tank with a solid recycling system (CDSR), from a brewery WWTP were analysed utilizing 16S rDNA and mcrA amplicon sequencing and genome-centric metagenomics. This study confirmed the deterministic effect of the wastewater composition on bacterial community structure, while the archaeal community composition resulted better explained by organic loading rate (ORL) and volatile free acids (VFA). According to the functions assigned to the differentially abundant metagenome-assembled genomes (MAGs) between reactors, CDSR was enriched in genes related to methanol and methylamines methanogenesis, protein degradation, and sulphate and alcohol utilization. Conversely, the UASB reactor was enriched in genes associated with carbohydrate and lipid degradation, as well as amino acid, fatty acid, and propionate fermentation. By comparing interactions derived from the co-occurrence network with predicted metabolic interactions of the prokaryotic communities in both anaerobic digesters, we conclude that the overall community structure is mainly determined by habitat filtering.},
}

@article {pmid38686909,
year = {2023},
author = {Liu, BY and Zhang, D and Fan, Z and Jin, JJ and Li, CH and Guo, RN and Li, XJ and Huang, Y},
title = {Role of Clinical Features, Pathogenic and Etiological Characteristics of Community-acquired Pneumonia with Type 2 Diabetes Mellitus in Early Diagnosis.},
journal = {Endocrine, metabolic & immune disorders drug targets},
volume = {},
number = {},
pages = {e221123223715},
doi = {10.2174/0118715303273741231117060753},
pmid = {38686909},
issn = {2212-3873},
abstract = {OBJECTIVE: To study the etiological characteristics of community-acquired pneumonia (CAP) combined with type 2 diabetes (T2D), providing a reference for early clinical diagnosis and treatment of the disease.

METHODS: We selected a total of 93 patients with CAP and analyzed their metagenomics nextgeneration sequencing (mNGS) data. The case group comprised 46 patients with combined CAP/T2D, and the control group comprised 47 patients without diabetes. We analyzed the pathogenic findings of the two groups.

RESULTS: There were statistically significant differences in age between the two groups (P = 0.001). Leukocytes (P = 0.012), blood platelets (P = 0.034), fibrinogen (P = 0.037), D-dimer (P = 0.000), calcitonin ogen (P = 0.015), ultrasensitive C-reactive protein or C-reactive protein (CRP) (P = 0.000), serum amyloid A (P = 0.000), and erythrocyte sedimentation rate (P = 0.003) were higher in the case group than in the control group. Albumin was lower in the case group than in the control group. All differences were statistically significant. The infection rates of Klebsiella pneumoniae (P = 0.030), Pseudomonas aeruginosa (P = 0.043), and Candida albicans (P = 0.032) were significantly different between the two groups.

CONCLUSION: Compared with those without diabetes, the infection rates of Klebsiella pneumoniae, Pseudomonas aeruginosa, and Candida albicans were higher in patients with combined CAP/T2D.},
}

@article {pmid38686450,
year = {2024},
author = {Marchi, E and Hinks, TSC and Richardson, M and Khalfaoui, L and Symon, FA and Rajasekar, P and Clifford, R and Hargadon, B and Austin, CD and MacIsaac, JL and Kobor, MS and Siddiqui, S and Mar, JS and Arron, JR and Choy, DF and Bradding, P},
title = {The effects of inhaled corticosteroids on healthy airways.},
journal = {Allergy},
volume = {},
number = {},
pages = {},
doi = {10.1111/all.16146},
pmid = {38686450},
issn = {1398-9995},
support = {211050/Z/18/z/WT_/Wellcome Trust/United Kingdom ; },
abstract = {BACKGROUND: The effects of inhaled corticosteroids (ICS) on healthy airways are poorly defined.

OBJECTIVES: To delineate the effects of ICS on gene expression in healthy airways, without confounding caused by changes in disease-related genes and disease-related alterations in ICS responsiveness.

METHODS: Randomized open-label bronchoscopy study of high-dose ICS therapy in 30 healthy adult volunteers randomized 2:1 to (i) fluticasone propionate 500 mcg bd daily or (ii) no treatment, for 4 weeks. Laboratory staff were blinded to allocation. Biopsies and brushings were analysed by immunohistochemistry, bulk RNA sequencing, DNA methylation array and metagenomics.

RESULTS: ICS induced small between-group differences in blood and lamina propria eosinophil numbers, but not in other immunopathological features, blood neutrophils, FeNO, FEV1, microbiome or DNA methylation. ICS treatment upregulated 72 genes in brushings and 53 genes in biopsies, and downregulated 82 genes in brushings and 416 genes in biopsies. The most downregulated genes in both tissues were canonical markers of type-2 inflammation (FCER1A, CPA3, IL33, CLEC10A, SERPINB10 and CCR5), T cell-mediated adaptive immunity (TARP, TRBC1, TRBC2, PTPN22, TRAC, CD2, CD8A, HLA-DQB2, CD96, PTPN7), B-cell immunity (CD20, immunoglobulin heavy and light chains) and innate immunity, including CD48, Hobit, RANTES, Langerin and GFI1. An IL-17-dependent gene signature was not upregulated by ICS.

CONCLUSIONS: In healthy airways, 4-week ICS exposure reduces gene expression related to both innate and adaptive immunity, and reduces markers of type-2 inflammation. This implies that homeostasis in health involves tonic type-2 signalling in the airway mucosa, which is exquisitely sensitive to ICS.},
}

@article {pmid38686438,
year = {2024},
author = {White, KH and Keepers, K and Kane, N and Lendemer, JC},
title = {Discovery of new genomic configuration of mating-type loci in the largest lineage of lichen-forming-fungi.},
journal = {Genome biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/gbe/evae094},
pmid = {38686438},
issn = {1759-6653},
abstract = {The genetic architecture of mating-type loci in lichen-forming fungi has been characterized in very few taxa. Despite the limited data, and in contrast to all other major fungal lineages, arrangements that have both mating-type alleles in a single haploid genome have been hypothesized to be absent from the largest lineage of lichen-forming fungi, the Lecanoromycetes. We report the discovery of both mating-type alleles from the haploid genomes of three species within this group. Our results demonstrate that Lecanoromycetes are not an outlier among Ascomycetes.},
}

@article {pmid38686186,
year = {2024},
author = {Chen, Q and Huang, X and Zhang, H and Jiang, X and Zeng, X and Li, W and Su, H and Chen, Y and Lin, F and Li, M and Gu, X and Jin, H and Wang, R and Diao, D and Wang, W and Li, J and Wei, S and Zhang, W and Liu, W and Huang, Z and Deng, Y and Luo, W and Liu, Z and Zhang, B},
title = {Characterization of tongue coating microbiome from patients with colorectal cancer.},
journal = {Journal of oral microbiology},
volume = {16},
number = {1},
pages = {2344278},
pmid = {38686186},
issn = {2000-2297},
abstract = {BACKGROUND: Tongue coating microbiota has aroused particular interest in profiling oral and digestive system cancers. However, little is known on the relationship between tongue coating microbiome and colorectal cancer (CRC).

METHODS: Metagenomic shotgun sequencing was performed on tongue coating samples collected from 30 patients with CRC, 30 patients with colorectal polyps (CP), and 30 healthy controls (HC). We further validated the potential of the tongue coating microbiota to predict the CRC by a random forest model.

RESULTS: We found a greater species diversity in CRC samples, and the nucleoside and nucleotide biosynthesis pathway was more apparent in the CRC group. Importantly, various species across participants jointly shaped three distinguishable fur types.The tongue coating microbiome profiling data gave an area under the receiver operating characteristic curve (AUC) of 0.915 in discriminating CRC patients from control participants; species such as Atopobium rimae, Streptococcus sanguinis, and Prevotella oris aided differentiation of CRC patients from healthy participants.

CONCLUSION: These results elucidate the use of tongue coating microbiome in CRC patients firstly, and the fur-types observed contribute to a better understanding of the microbial community in human. Furthermore, the tongue coating microbiota-based biomarkers provide a valuable reference for CRC prediction and diagnosis.},
}

@article {pmid38686114,
year = {2024},
author = {Zhang, D and Li, X and Wang, Y and Zhao, Y and Zhang, H},
title = {The clinical importance of metagenomic next-generation sequencing in detecting disease-causing microorganisms in cases of sepsis acquired in the community or hospital setting.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1384166},
pmid = {38686114},
issn = {1664-302X},
abstract = {OBJECTIVES: Although metagenomic next-generation sequencing (mNGS) is commonly used for diagnosing infectious diseases, clinicians face limited options due to the high costs that are not covered by basic medical insurance. The goal of this research is to challenge this bias through a thorough examination and evaluation of the clinical importance of mNGS in precisely identifying pathogenic microorganisms in cases of sepsis acquired in the community or in hospitals.

METHODS: A retrospective observational study took place at a tertiary teaching hospital in China from January to December 2021. Data on 308 sepsis patients were collected, and the performance of etiological examination was compared between mNGS and traditional culture method.

RESULTS: Two hundred twenty-nine cases were observed in the community-acquired sepsis (CAS) group and 79 cases in the hospital-acquired sepsis (HAS) group. In comparison with conventional culture, mNGS showed a significantly higher rate of positivity in both the CAS group (88.21% vs. 25.76%, adj.P < 0.001) and the HAS group (87.34% vs. 44.30%, adj.P < 0.001), particularly across various infection sites and specimens, which were not influenced by factors like antibiotic exposure or the timing and frequency of mNGS technology. Sepsis pathogens detected by mNGS were broad, especially viruses, Mycobacterium tuberculosis, and atypical pathogens, with mixed pathogens being common, particularly bacterial-viral co-detection. Based on the optimization of antimicrobial therapy using mNGS, 58 patients underwent antibiotic de-escalation, two patients were switched to antiviral therapy, and 14 patients initiated treatment for tuberculosis, resulting in a reduction in antibiotic overuse but without significant impact on sepsis prognosis. The HAS group exhibited a critical condition, poor prognosis, high medical expenses, and variations in etiology, yet the mNGS results did not result in increased medical costs for either group.

CONCLUSIONS: mNGS demonstrates efficacy in identifying multiple pathogens responsible for sepsis, with mixed pathogens of bacteria and viruses being prevalent. Variability in microbiological profiles among different infection setting underscores the importance of clinical vigilance. Therefore, the adoption of mNGS for microbiological diagnosis of sepsis warrants acknowledgment and promotion.},
}

@article {pmid38685762,
year = {2024},
author = {Ishnaiwer, M and Le Bastard, Q and Naour, M and Zeman, M and Dailly, E and Montassier, E and Batard, E and Dion, M},
title = {Efficacy of an inulin-based treatment on intestinal colonization by multidrug-resistant E. coli: insight into the mechanism of action.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2347021},
doi = {10.1080/19490976.2024.2347021},
pmid = {38685762},
issn = {1949-0984},
mesh = {Animals ; *Inulin/pharmacology/metabolism ; Mice ; *Gastrointestinal Microbiome/drug effects ; *Escherichia coli/drug effects/genetics ; *Feces/microbiology ; *Amoxicillin/pharmacology ; *Pantoprazole/pharmacology ; *Drug Resistance, Multiple, Bacterial ; beta-Lactamases/metabolism/genetics ; Dysbiosis/microbiology/drug therapy ; Anti-Bacterial Agents/pharmacology ; Escherichia coli Infections/drug therapy/microbiology ; Female ; Prebiotics/administration & dosage ; },
abstract = {Inulin, an increasingly studied dietary fiber, alters intestinal microbiota. The aim of this study was to assess whether inulin decreases intestinal colonization by multidrug resistant E. coli and to investigate its potential mechanisms of action. Mice with amoxicillin-induced intestinal dysbiosis mice were inoculated with extended spectrum beta-lactamase producing E. coli (ESBL-E. coli). The combination of inulin and pantoprazole (IP) significantly reduced ESBL-E. coli fecal titers, whereas pantoprazole alone did not and inulin had a delayed and limited effect. Fecal microbiome was assessed using shotgun metagenomic sequencing and qPCR. The efficacy of IP was predicted by increased abundance of 74 taxa, including two species of Adlercreutzia. Preventive treatments with A. caecimuris or A. muris also reduced ESBL-E. coli fecal titers. Fecal microbiota of mice effectively treated by IP was enriched in genes involved in inulin catabolism, production of propionate and expression of beta-lactamases. They also had increased beta-lactamase activity and decreased amoxicillin concentration. These results suggest that IP act through production of propionate and degradation of amoxicillin by the microbiota. The combination of pantoprazole and inulin is a potential treatment of intestinal colonization by multidrug-resistant E. coli. The ability of prebiotics to promote propionate and/or beta-lactamase producing bacteria may be used as a screening tool to identify potential treatments of intestinal colonization by multidrug resistant Enterobacterales.},
}

Animals
*Inulin/pharmacology/metabolism
Mice
*Gastrointestinal Microbiome/drug effects
*Escherichia coli/drug effects/genetics
*Feces/microbiology
*Amoxicillin/pharmacology
*Pantoprazole/pharmacology
*Drug Resistance, Multiple, Bacterial
beta-Lactamases/metabolism/genetics
Dysbiosis/microbiology/drug therapy
Anti-Bacterial Agents/pharmacology
Escherichia coli Infections/drug therapy/microbiology
Female
Prebiotics/administration & dosage

@article {pmid38685300,
year = {2024},
author = {Ma, W and An, B and Xu, X and Huo, M and Mi, K and Tian, X and Kou, Z and Tang, A and Cheng, G and Huang, L},
title = {Ceftiofur in swine manure contributes to reducing pathogens and antibiotic resistance genes during composting.},
journal = {Environmental research},
volume = {},
number = {},
pages = {119033},
doi = {10.1016/j.envres.2024.119033},
pmid = {38685300},
issn = {1096-0953},
abstract = {Aerobic composting is a common way for the disposal of feces produced in animal husbandry, and can reduce the release of antibiotic resistance genes (ARGs) from feces into the environment. In this study, we collected samples from two distinct treatments of swine manure compost with and without ceftiofur (CEF), and identified the ARGs, mobile genetic elements (MGEs), and bacterial community by metagenomic sequencing. The impacts of CEF on the bacterial community composition and fate of ARGs and MGEs were investigated. With increasing composting temperature and pH, the concentration of CEF in the manure decreased rapidly, with a degradation half-life of 1.12 d and a 100% removal rate after 10 d of aerobic composting. Metagenomics demonstrated that CEF in the manure might inhibit the growth of Firmicutes and Proteobacteria, thereby reducing some ARGs and MGEs hosted by these two bacteria, which was further confirmed by the variations of ARGs and MGEs. A further redundancy analysis suggested that pH and temperature are key environmental factors affecting ARG removal during composting, and intI1 and bacterial communities also have significant influence on ARG abundance. These results are of great significance for promoting the removal of some ARGs from animal manure by controlling some key environmental factors and the type of antibiotics used in animals.},
}

@article {pmid38685076,
year = {2024},
author = {Sun, J and Xu, X and Gao, S and Pan, Q and Liu, Z and Huang, Y and Lian, Y},
title = {Refractory pneumonia caused by Prevotella heparinolytica: a case report.},
journal = {Journal of medical case reports},
volume = {18},
number = {1},
pages = {213},
pmid = {38685076},
issn = {1752-1947},
support = {SYSD2019104//Science and Technology Program of Suzhou/ ; SDFEYBS2002//Second Affiliated Hospital of Soochow University/ ; SDFEYHT2224//Second Affiliated Hospital of Soochow University/ ; YWJKJJHKYJJ-HX05//Medical Science Research Funding Project of Beijing Medical Health Public Welfare Foundation/ ; },
mesh = {Humans ; Male ; Middle Aged ; *Prevotella/isolation & purification ; *Anti-Bacterial Agents/therapeutic use ; *Tomography, X-Ray Computed ; Bacteroidaceae Infections/drug therapy/microbiology/diagnosis ; Pneumonia, Bacterial/drug therapy/microbiology/diagnosis ; Piperacillin, Tazobactam Drug Combination/therapeutic use ; },
abstract = {BACKGROUND: Prevotella heparinolytica is a Gram-negative bacterium that is commonly found in the oral, intestinal, and urinary tracts. It has been extensively studied in lower respiratory tract infections in horses, which has heparinolytic activity and can secrete heparinase and further induces virulence factors in cells and causes disease. However, no such cases have been reported in humans.

CASE PRESENTATION: A 58-year-old male patient from China presented to the respiratory clinic in Suzhou with a productive cough producing white sputum for 20 days and fever for 3 days. Prior to this visit, a chest computed tomography scan was conducted, which revealed multiple patchy nodular opacities in both lungs. On admission, the patient presented with a temperature of 38.1 °C and a pulse rate of 110 beats per minute. Despite routine anti-infective treatment with moxifloxacin, his temperature fluctuated and the treatment was ineffective. The patient was diagnosed with Prevotella heparinolytica infection through metagenomic next-generation sequencing. Therefore, the antibiotics were switched to piperacillin-tazobactam in combination with ornidazole, which alleviated his symptoms; 1 week after discharge, the patient returned to the clinic for a follow-up chest computed tomography, and the opacities on the lungs continued to be absorbed.

CONCLUSION: Prevotella heparinolytica is an opportunistic pathogen. However, it has not been reported in human pneumonia. In refractory pneumonia, measures such as metagenomic next-generation sequencing can be used to identify pathogens and help guide antibiotic selection and early support.},
}

Humans
Male
Middle Aged
*Prevotella/isolation & purification
*Anti-Bacterial Agents/therapeutic use
*Tomography, X-Ray Computed
Bacteroidaceae Infections/drug therapy/microbiology/diagnosis
Pneumonia, Bacterial/drug therapy/microbiology/diagnosis
Piperacillin, Tazobactam Drug Combination/therapeutic use

@article {pmid38685074,
year = {2024},
author = {Tulloch, CL and Bargiela, R and Williams, GB and Chernikova, TN and Cotterell, BM and Wellington, EMH and Christie-Oleza, J and Thomas, DN and Jones, DL and Golyshin, PN},
title = {Microbial communities colonising plastics during transition from the wastewater treatment plant to marine waters.},
journal = {Environmental microbiome},
volume = {19},
number = {1},
pages = {27},
pmid = {38685074},
issn = {2524-6372},
support = {NE/S004548//Natural Environment Research Council/ ; NE/S004548//Natural Environment Research Council/ ; NE/S004548//Natural Environment Research Council/ ; NE/S004548//Natural Environment Research Council/ ; NE/S004548//Natural Environment Research Council/ ; NE/S005501/1//Natural Environment Research Council/ ; NE/S005501/1//Natural Environment Research Council/ ; NE/S004548//Natural Environment Research Council/ ; NE/S004548//Natural Environment Research Council/ ; NE/S004548//Natural Environment Research Council/ ; 81280//European Regional Development Fund/ ; 81280//European Regional Development Fund/ ; 81280//European Regional Development Fund/ ; 81280//European Regional Development Fund/ ; 81280//European Regional Development Fund/ ; 81280//European Regional Development Fund/ ; 81280//European Regional Development Fund/ ; 101000327//Horizon 2020 Framework Programme/ ; 101000327//Horizon 2020 Framework Programme/ ; 101000327//Horizon 2020 Framework Programme/ ; },
abstract = {BACKGROUND: Plastics pollution and antimicrobial resistance (AMR) are two major environmental threats, but potential connections between plastic associated biofilms, the 'plastisphere', and dissemination of AMR genes are not well explored.

RESULTS: We conducted mesocosm experiments tracking microbial community changes on plastic surfaces transitioning from wastewater effluent to marine environments over 16 weeks. Commonly used plastics, polypropylene (PP), high density polyethylene (HDPE), low density polyethylene (LDPE) and polyethylene terephthalate (PET) incubated in wastewater effluent, river water, estuarine water, and in the seawater for 16 weeks, were analysed via 16S rRNA gene amplicon and shotgun metagenome sequencing. Within one week, plastic-colonizing communities shifted from wastewater effluent-associated microorganisms to marine taxa, some members of which (e.g. Oleibacter-Thalassolituus and Sphingomonas spp., on PET, Alcanivoracaceae on PET and PP, or Oleiphilaceae, on all polymers), were selectively enriched from levels undetectable in the starting communities. Remarkably, microbial biofilms were also susceptible to parasitism, with Saprospiraceae feeding on biofilms at late colonisation stages (from week 6 onwards), while Bdellovibrionaceae were prominently present on HDPE from week 2 and LDPE from day 1. Relative AMR gene abundance declined over time, and plastics did not become enriched for key AMR genes after wastewater exposure.

CONCLUSION: Although some resistance genes occurred during the mesocosm transition on plastic substrata, those originated from the seawater organisms. Overall, plastic surfaces incubated in wastewater did not act as hotspots for AMR proliferation in simulated marine environments.},
}

@article {pmid38684965,
year = {2024},
author = {Shi, J and Li, Z and Jia, L and Ma, Y and Huang, Y and He, P and Ran, T and Liu, W and Zhang, W and Cheng, Q and Zhang, Z and Lei, Z},
title = {Castration alters the ileum microbiota of Holstein bulls and promotes beef flavor compounds.},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {426},
pmid = {38684965},
issn = {1471-2164},
support = {GSA-XMLZ-2021-01//Gansu beef cattle quality fattening project/ ; GAU-XKTD-2022-22//Discipline Team Project of Gansu Agricultural University/ ; 2020C-08//the Application of Pingliang Red Bull Planting and Breeding Combined with High-efficiency Circular Production System Construction Technology Application/ ; },
abstract = {BACKGROUND: In the beef industry, bull calves are usually castrated to improve flavor and meat quality; however, this can reduce their growth and slaughter performance. The gut microbiota is known to exert a significant influence on growth and slaughter performance. However, there is a paucity of research investigating the impact of castration on gut microbiota composition and its subsequent effects on slaughter performance and meat flavor.

RESULT: The objective of this study was to examine the processes via which castration hinders slaughter productivity and enhances meat quality. Bull and castrated calves were maintained under the same management conditions, and at slaughter, meat quality was assessed, and ileum and epithelial tissue samples were obtained. The research employed metagenomic sequencing and non-targeted metabolomics techniques to investigate the makeup of the microbiota and identify differential metabolites. The findings of this study revealed the Carcass weight and eye muscle area /carcass weight in the bull group were significantly higher than those in the steer group. There were no significant differences in the length, width, and crypt depth of the ileum villi between the two groups. A total of 53 flavor compounds were identified in the two groups of beef, of which 16 were significantly higher in the steer group than in the bull group, and 5 were significantly higher in the bull group than in the steer group. In addition, bacteria, Eukaryota, and virus species were significantly separated between the two groups. The lipid metabolism pathways of α-linolenic acid, linoleic acid, and unsaturated fatty acids were significantly enriched in the Steers group. Compared with the steer group, the organic system pathway is significantly enriched in the bull group. The study also found that five metabolites (LPC (0:0/20:3), LPC (20:3/0:0), LPE (0:0/22:5), LPE (22:5/0:0), D-Mannosamine), and three species (s_Cloning_vector_Hsp70_LexA-HP1, s_Bacteroides_Coprophilus_CAG: 333, and s_Clostridium_nexile-CAG: 348) interfere with each other and collectively have a positive impact on the flavor compounds of beef.

CONCLUSIONS: These findings provide a basic understanding that under the same management conditions, castration does indeed reduce the slaughter performance of bulls and improve the flavor of beef. Microorganisms and metabolites contribute to these changes through interactions.},
}

@article {pmid38684791,
year = {2024},
author = {Forry, SP and Servetas, SL and Kralj, JG and Soh, K and Hadjithomas, M and Cano, R and Carlin, M and Amorim, MG and Auch, B and Bakker, MG and Bartelli, TF and Bustamante, JP and Cassol, I and Chalita, M and Dias-Neto, E and Duca, AD and Gohl, DM and Kazantseva, J and Haruna, MT and Menzel, P and Moda, BS and Neuberger-Castillo, L and Nunes, DN and Patel, IR and Peralta, RD and Saliou, A and Schwarzer, R and Sevilla, S and Takenaka, IKTM and Wang, JR and Knight, R and Gevers, D and Jackson, SA},
title = {Variability and bias in microbiome metagenomic sequencing: an interlaboratory study comparing experimental protocols.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {9785},
pmid = {38684791},
issn = {2045-2322},
mesh = {Humans ; *Metagenomics/methods/standards ; *RNA, Ribosomal, 16S/genetics ; *Feces/microbiology ; *Microbiota/genetics ; Bias ; Metagenome ; Gastrointestinal Microbiome/genetics ; Sequence Analysis, DNA/methods ; Bacteria/genetics/classification/isolation & purification ; High-Throughput Nucleotide Sequencing/methods ; },
abstract = {Several studies have documented the significant impact of methodological choices in microbiome analyses. The myriad of methodological options available complicate the replication of results and generally limit the comparability of findings between independent studies that use differing techniques and measurement pipelines. Here we describe the Mosaic Standards Challenge (MSC), an international interlaboratory study designed to assess the impact of methodological variables on the results. The MSC did not prescribe methods but rather asked participating labs to analyze 7 shared reference samples (5 × human stool samples and 2 × mock communities) using their standard laboratory methods. To capture the array of methodological variables, each participating lab completed a metadata reporting sheet that included 100 different questions regarding the details of their protocol. The goal of this study was to survey the methodological landscape for microbiome metagenomic sequencing (MGS) analyses and the impact of methodological decisions on metagenomic sequencing results. A total of 44 labs participated in the MSC by submitting results (16S or WGS) along with accompanying metadata; thirty 16S rRNA gene amplicon datasets and 14 WGS datasets were collected. The inclusion of two types of reference materials (human stool and mock communities) enabled analysis of both MGS measurement variability between different protocols using the biologically-relevant stool samples, and MGS bias with respect to ground truth values using the DNA mixtures. Owing to the compositional nature of MGS measurements, analyses were conducted on the ratio of Firmicutes: Bacteroidetes allowing us to directly apply common statistical methods. The resulting analysis demonstrated that protocol choices have significant effects, including both bias of the MGS measurement associated with a particular methodological choices, as well as effects on measurement robustness as observed through the spread of results between labs making similar methodological choices. In the analysis of the DNA mock communities, MGS measurement bias was observed even when there was general consensus among the participating laboratories. This study was the result of a collaborative effort that included academic, commercial, and government labs. In addition to highlighting the impact of different methodological decisions on MGS result comparability, this work also provides insights for consideration in future microbiome measurement study design.},
}

Humans
*Metagenomics/methods/standards
*RNA, Ribosomal, 16S/genetics
*Feces/microbiology
*Microbiota/genetics
Bias
Metagenome
Gastrointestinal Microbiome/genetics
Sequence Analysis, DNA/methods
Bacteria/genetics/classification/isolation & purification
High-Throughput Nucleotide Sequencing/methods

@article {pmid38684664,
year = {2024},
author = {Ma, W and Wang, Y and Nguyen, LH and Mehta, RS and Ha, J and Bhosle, A and Mclver, LJ and Song, M and Clish, CB and Strate, LL and Huttenhower, C and Chan, AT},
title = {Gut microbiome composition and metabolic activity in women with diverticulitis.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {3612},
pmid = {38684664},
issn = {2041-1723},
support = {U01 CA176726/CA/NCI NIH HHS/United States ; R01 DK101495/DK/NIDDK NIH HHS/United States ; K23 DK125838/DK/NIDDK NIH HHS/United States ; R01 DK101495/DK/NIDDK NIH HHS/United States ; R24 DK110499/DK/NIDDK NIH HHS/United States ; },
mesh = {Humans ; Female ; *Gastrointestinal Microbiome ; Middle Aged ; *Diverticulitis/metabolism/microbiology ; *Feces/microbiology ; Aged ; Prospective Studies ; Bilophila/metabolism ; Metabolomics ; Case-Control Studies ; Clostridiales/metabolism/isolation & purification ; Bile Acids and Salts/metabolism ; Adult ; Dietary Fiber/metabolism ; Metabolome ; Metagenomics/methods ; },
abstract = {The etiopathogenesis of diverticulitis, among the most common gastrointestinal diagnoses, remains largely unknown. By leveraging stool collected within a large prospective cohort, we performed shotgun metagenomic sequencing and untargeted metabolomics profiling among 121 women diagnosed with diverticulitis requiring antibiotics or hospitalizations (cases), matched to 121 women without diverticulitis (controls) according to age and race. Overall microbial community structure and metabolomic profiles differed in diverticulitis cases compared to controls, including enrichment of pro-inflammatory Ruminococcus gnavus, 1,7-dimethyluric acid, and histidine-related metabolites, and depletion of butyrate-producing bacteria and anti-inflammatory ceramides. Through integrated multi-omic analysis, we detected covarying microbial and metabolic features, such as Bilophila wadsworthia and bile acids, specific to diverticulitis. Additionally, we observed that microbial composition modulated the protective association between a prudent fiber-rich diet and diverticulitis. Our findings offer insights into the perturbations in inflammation-related microbial and metabolic signatures associated with diverticulitis, supporting the potential of microbial-based diagnostics and therapeutic targets.},
}

Humans
Female
*Gastrointestinal Microbiome
Middle Aged
*Diverticulitis/metabolism/microbiology
*Feces/microbiology
Aged
Prospective Studies
Bilophila/metabolism
Metabolomics
Case-Control Studies
Clostridiales/metabolism/isolation & purification
Bile Acids and Salts/metabolism
Adult
Dietary Fiber/metabolism
Metabolome
Metagenomics/methods

@article {pmid38684658,
year = {2024},
author = {Rolando, JL and Kolton, M and Song, T and Liu, Y and Pinamang, P and Conrad, R and Morris, JT and Konstantinidis, KT and Kostka, JE},
title = {Sulfur oxidation and reduction are coupled to nitrogen fixation in the roots of the salt marsh foundation plant Spartina alterniflora.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {3607},
pmid = {38684658},
issn = {2041-1723},
support = {NA18OAR4170084//United States Department of Commerce | National Oceanic and Atmospheric Administration (NOAA)/ ; DEB 1754756//National Science Foundation (NSF)/ ; },
mesh = {*Nitrogen Fixation ; *Sulfur/metabolism ; *Oxidation-Reduction ; *Plant Roots/metabolism/microbiology ; *Wetlands ; *Poaceae/metabolism ; Phylogeny ; Symbiosis ; Bacteria/metabolism/genetics/classification ; Metagenome ; Sulfates/metabolism ; Nitrogen/metabolism ; },
abstract = {Heterotrophic activity, primarily driven by sulfate-reducing prokaryotes, has traditionally been linked to nitrogen fixation in the root zone of coastal marine plants, leaving the role of chemolithoautotrophy in this process unexplored. Here, we show that sulfur oxidation coupled to nitrogen fixation is a previously overlooked process providing nitrogen to coastal marine macrophytes. In this study, we recovered 239 metagenome-assembled genomes from a salt marsh dominated by the foundation plant Spartina alterniflora, including diazotrophic sulfate-reducing and sulfur-oxidizing bacteria. Abundant sulfur-oxidizing bacteria encode and highly express genes for carbon fixation (RuBisCO), nitrogen fixation (nifHDK) and sulfur oxidation (oxidative-dsrAB), especially in roots stressed by sulfidic and reduced sediment conditions. Stressed roots exhibited the highest rates of nitrogen fixation and expression level of sulfur oxidation and sulfate reduction genes. Close relatives of marine symbionts from the Candidatus Thiodiazotropha genus contributed ~30% and ~20% of all sulfur-oxidizing dsrA and nitrogen-fixing nifK transcripts in stressed roots, respectively. Based on these findings, we propose that the symbiosis between S. alterniflora and sulfur-oxidizing bacteria is key to ecosystem functioning of coastal salt marshes.},
}

*Nitrogen Fixation
*Sulfur/metabolism
*Oxidation-Reduction
*Plant Roots/metabolism/microbiology
*Wetlands
*Poaceae/metabolism
Phylogeny
Symbiosis
Bacteria/metabolism/genetics/classification
Metagenome
Sulfates/metabolism
Nitrogen/metabolism

@article {pmid38684959,
year = {2024},
author = {Sunithakumari, VS and Menon, RR and Suresh, GG and Krishnan, R and Rameshkumar, N},
title = {Characterization of a novel root-associated diazotrophic rare PGPR taxa, Aquabacter pokkalii sp. nov., isolated from pokkali rice: new insights into the plant-associated lifestyle and brackish adaptation.},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {424},
pmid = {38684959},
issn = {1471-2164},
abstract = {Salinity impacts crop growth and productivity and lowers the activities of rhizosphere microbiota. The identification and utilization of habitat-specific salinity-adapted plant growth-promoting rhizobacteria (PGPR) are considered alternative strategies to improve the growth and yields of crops in salinity-affected coastal agricultural fields. In this study, we characterize strain L1I39[T], the first Aquabacter species with PGPR traits isolated from a salt-tolerant pokkali rice cultivated in brackish environments. L1I39[T] is positive for 1-aminocyclopropane-1-carboxylate deaminase activity and nitrogen fixation and can promote pokkali rice growth by supplying fixed nitrogen under a nitrogen-deficient seawater condition. Importantly, enhanced plant growth and efficient root colonization were evident in L1I39[T]-inoculated plants grown under 20% seawater but not in zero-seawater conditions, identifying brackish conditions as a key local environmental factor critical for L1I39[T]-pokkali rice symbiosis. Detailed physiological studies revealed that L1I39[T] is well-adapted to brackish environments. In-depth genome analysis of L1I39[T] identified multiple gene systems contributing to its plant-associated lifestyle and brackish adaptations. The 16S rRNA-based metagenomic study identified L1I39[T] as an important rare PGPR taxon. Based on the polyphasic taxonomy analysis, we established strain L1I39[T] as a novel Aquabacter species and proposed Aquabacter pokkalii sp nov. Overall, this study provides a better understanding of a marine-adapted PGPR strain L1I39[T] that may perform a substantial role in host growth and health in nitrogen-poor brackish environments.},
}

@article {pmid38684473,
year = {2024},
author = {Díaz, L and Castellá, G and Bragulat, MR and Paytuví-Gallart, A and Sanseverino, W and Cabañes, FJ},
title = {Mycobiome of the external ear canal of healthy cows.},
journal = {Medical mycology},
volume = {},
number = {},
pages = {},
doi = {10.1093/mmy/myae049},
pmid = {38684473},
issn = {1460-2709},
abstract = {Malassezia yeasts belong to the normal skin microbiota of a wide range of warm-blooded animals. However, their significance in cattle is still poorly understood. In the present study, the mycobiota of the external ear canal of 20 healthy dairy Holstein cows was assessed by cytology, culture, PCR, and next-generation sequencing. The presence of Malassezia was detected in 15 cows by cytology and PCR. The metagenomic analysis revealed that Ascomycota was the predominant phylum but M. pachydermatis the main species. The Malassezia phylotype 131 was detected in low abundance. Nor M. nana nor M. equina were detected in the samples.},
}

@article {pmid38683843,
year = {2024},
author = {Hernández, AM and Alcaraz, LD and Hernández-Álvarez, C and Romero, MF and Jara-Servín, A and Barajas, H and Ramírez, CM and Peimbert, M},
title = {Revealing the microbiome diversity and biocontrol potential of field Aedes ssp.: Implications for disease vector management.},
journal = {PloS one},
volume = {19},
number = {4},
pages = {e0302328},
doi = {10.1371/journal.pone.0302328},
pmid = {38683843},
issn = {1932-6203},
mesh = {*Aedes/microbiology ; Animals ; *Microbiota ; *Mosquito Vectors/microbiology ; *RNA, Ribosomal, 16S/genetics ; Wolbachia/genetics/physiology/isolation & purification ; Larva/microbiology ; Metagenomics/methods ; Mexico ; Mosquito Control/methods ; },
abstract = {The mosquito Aedes spp. holds important relevance for human and animal health, as it serves as a vector for transmitting multiple diseases, including dengue and Zika virus. The microbiome's impact on its host's health and fitness is well known. However, most studies on mosquito microbiomes have been conducted in laboratory settings. We explored the mixed microbial communities within Aedes spp., utilizing the 16S rRNA gene for diversity analysis and shotgun metagenomics for functional genomics. Our samples, which included Ae. aegypti and Ae. albopictus, spanned various developmental stages-eggs, larvae, and adults-gathered from five semiurban areas in Mexico. Our findings revealed a substantial diversity of 8,346 operational taxonomic units (OTUs), representing 967 bacterial genera and 126,366 annotated proteins. The host developmental stage was identified as the primary factor associated with variations in the microbiome composition. Subsequently, we searched for genes and species involved in mosquito biocontrol. Wolbachia accounted for 9.6% of the 16S gene sequences. We observed a high diversity (203 OTUs) of Wolbachia strains commonly associated with mosquitoes, such as wAlb, with a noticeable increase in abundance during the adult stages. Notably, we detected the presence of the cifA and cifB genes, which are associated with Wolbachia's cytoplasmic incompatibility, a biocontrol mechanism. Additionally, we identified 221 OTUs related to Bacillus, including strains linked to B. thuringiensis. Furthermore, we discovered multiple genes encoding insecticidal toxins, such as Cry, Mcf, Vip, and Vpp. Overall, our study contributes to the understanding of mosquito microbiome biodiversity and metabolic capabilities, which are essential for developing effective biocontrol strategies against this disease vector.},
}

*Aedes/microbiology
Animals
*Microbiota
*Mosquito Vectors/microbiology
*RNA, Ribosomal, 16S/genetics
Wolbachia/genetics/physiology/isolation & purification
Larva/microbiology
Metagenomics/methods
Mexico
Mosquito Control/methods

@article {pmid38683823,
year = {2024},
author = {Procopio, N and Bonicelli, A},
title = {From flesh to bones: Multi-omics approaches in forensic science.},
journal = {Proteomics},
volume = {},
number = {},
pages = {e2200335},
doi = {10.1002/pmic.202200335},
pmid = {38683823},
issn = {1615-9861},
support = {MR/S032878/1//UK Research and Innovation/ ; },
abstract = {Recent advancements in omics techniques have revolutionised the study of biological systems, enabling the generation of high-throughput biomolecular data. These innovations have found diverse applications, ranging from personalised medicine to forensic sciences. While the investigation of multiple aspects of cells, tissues or entire organisms through the integration of various omics approaches (such as genomics, epigenomics, metagenomics, transcriptomics, proteomics and metabolomics) has already been established in fields like biomedicine and cancer biology, its full potential in forensic sciences remains only partially explored. In this review, we have presented a comprehensive overview of state-of-the-art analytical platforms employed in omics research, with specific emphasis on their application in the forensic field for the identification of the cadaver and the cause of death. Moreover, we have conducted a critical analysis of the computational integration of omics approaches, and highlighted the latest advancements in employing multi-omics techniques for forensic investigations.},
}

@article {pmid38683238,
year = {2024},
author = {Cowan, DA and Albers, SV and Antranikian, G and Atomi, H and Averhoff, B and Basen, M and Driessen, AJM and Jebbar, M and Kelman, Z and Kerou, M and Littlechild, J and Müller, V and Schönheit, P and Siebers, B and Vorgias, K},
title = {Extremophiles in a changing world.},
journal = {Extremophiles : life under extreme conditions},
volume = {28},
number = {2},
pages = {26},
pmid = {38683238},
issn = {1433-4909},
mesh = {*Extremophiles/metabolism/physiology ; Sustainable Development ; Adaptation, Physiological ; Extreme Environments ; Biotechnology ; },
abstract = {Extremophiles and their products have been a major focus of research interest for over 40 years. Through this period, studies of these organisms have contributed hugely to many aspects of the fundamental and applied sciences, and to wider and more philosophical issues such as the origins of life and astrobiology. Our understanding of the cellular adaptations to extreme conditions (such as acid, temperature, pressure and more), of the mechanisms underpinning the stability of macromolecules, and of the subtleties, complexities and limits of fundamental biochemical processes has been informed by research on extremophiles. Extremophiles have also contributed numerous products and processes to the many fields of biotechnology, from diagnostics to bioremediation. Yet, after 40 years of dedicated research, there remains much to be discovered in this field. Fortunately, extremophiles remain an active and vibrant area of research. In the third decade of the twenty-first century, with decreasing global resources and a steadily increasing human population, the world's attention has turned with increasing urgency to issues of sustainability. These global concerns were encapsulated and formalized by the United Nations with the adoption of the 2030 Agenda for Sustainable Development and the presentation of the seventeen Sustainable Development Goals (SDGs) in 2015. In the run-up to 2030, we consider the contributions that extremophiles have made, and will in the future make, to the SDGs.},
}

*Extremophiles/metabolism/physiology
Sustainable Development
Adaptation, Physiological
Extreme Environments
Biotechnology

@article {pmid38683195,
year = {2024},
author = {Cook, R and Telatin, A and Hsieh, SY and Newberry, F and Tariq, MA and Baker, DJ and Carding, SR and Adriaenssens, EM},
title = {Nanopore and Illumina sequencing reveal different viral populations from human gut samples.},
journal = {Microbial genomics},
volume = {10},
number = {4},
pages = {},
doi = {10.1099/mgen.0.001236},
pmid = {38683195},
issn = {2057-5858},
mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; *Genome, Viral ; *Gastrointestinal Microbiome/genetics ; *Feces/virology/microbiology ; Nanopores ; Nanopore Sequencing/methods ; Viruses/genetics/classification/isolation & purification ; Virome/genetics ; Sequence Analysis, DNA/methods ; },
abstract = {The advent of viral metagenomics, or viromics, has improved our knowledge and understanding of global viral diversity. High-throughput sequencing technologies enable explorations of the ecological roles, contributions to host metabolism, and the influence of viruses in various environments, including the human intestinal microbiome. However, bacterial metagenomic studies frequently have the advantage. The adoption of advanced technologies like long-read sequencing has the potential to be transformative in refining viromics and metagenomics. Here, we examined the effectiveness of long-read and hybrid sequencing by comparing Illumina short-read and Oxford Nanopore Technology (ONT) long-read sequencing technologies and different assembly strategies on recovering viral genomes from human faecal samples. Our findings showed that if a single sequencing technology is to be chosen for virome analysis, Illumina is preferable due to its superior ability to recover fully resolved viral genomes and minimise erroneous genomes. While ONT assemblies were effective in recovering viral diversity, the challenges related to input requirements and the necessity for amplification made it less ideal as a standalone solution. However, using a combined, hybrid approach enabled a more authentic representation of viral diversity to be obtained within samples.},
}

Humans
*High-Throughput Nucleotide Sequencing/methods
*Metagenomics/methods
*Genome, Viral
*Gastrointestinal Microbiome/genetics
*Feces/virology/microbiology
Nanopores
Nanopore Sequencing/methods
Viruses/genetics/classification/isolation & purification
Virome/genetics
Sequence Analysis, DNA/methods

@article {pmid38682956,
year = {2024},
author = {Pol, S and Kallonen, T and Mäklin, T and Sar, P and Hopkins, J and Soeng, S and Miliya, T and Ling, CL and Bentley, SD and Corander, J and Turner, P},
title = {Exploring the pediatric nasopharyngeal bacterial microbiota with culture-based MALDI-TOF mass spectrometry and targeted metagenomic sequencing.},
journal = {mBio},
volume = {},
number = {},
pages = {e0078424},
doi = {10.1128/mbio.00784-24},
pmid = {38682956},
issn = {2150-7511},
abstract = {UNLABELLED: The nasopharynx is an important reservoir of disease-associated and antimicrobial-resistant bacterial species. This proof-of-concept study assessed the utility of a combined culture, matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS), and targeted metagenomic sequencing workflow for the study of the pediatric nasopharyngeal bacterial microbiota. Nasopharyngeal swabs and clinical metadata were collected from Cambodian children during a hospital outpatient visit and then biweekly for 12 weeks. Swabs were cultured on chocolate and blood-gentamicin agar, and all colony morphotypes were identified by MALDI-TOF MS. Metagenomic sequencing was done on a scrape of all colonies from a chocolate agar culture and processed using the mSWEEP pipeline. One hundred one children were enrolled, yielding 620 swabs. MALDI-TOF MS identified 106 bacterial species/40 genera: 20 species accounted for 88.5% (2,190/2,474) of isolates. Colonization by Moraxella catarrhalis (92.1% of children on ≥1 swab), Haemophilus influenzae (87.1%), and Streptococcus pneumoniae (83.2%) was particularly common. In S. pneumoniae-colonized children, a median of two serotypes [inter-quartile range (IQR) 1-2, range 1-4] was detected. For the 21 bacterial species included in the mSWEEP database and identifiable by MALDI-TOF, detection by culture + MALDI-TOF MS and culture + mSWEEP was highly concordant with a median species-level agreement of 96.9% (IQR 86.8%-98.8%). mSWEEP revealed highly dynamic lineage-level colonization patterns for S. pneumoniae which were quite different to those for S. aureus. A combined culture, MALDI-TOF MS, targeted metagenomic sequencing approach for the exploration of the young child nasopharyngeal microbiome was technically feasible, and each component yielded complementary data.

IMPORTANCE: The human upper respiratory tract is an important source of disease-causing and antibiotic-resistant bacteria. However, understanding the interactions and stability of these bacterial populations is technically challenging. We used a combination of approaches to determine colonization patterns over a 3-month period in 101 Cambodian children. The combined approach was feasible to implement, and each component gave complementary data to enable a better understanding of the complex patterns of bacterial colonization.},
}

@article {pmid38682777,
year = {2024},
author = {Kunselman, E and Allard, S and Burge, C and Marshman, B and Frederick, A and Gilbert, J},
title = {Metagenome-assembled genome of withering syndrome causative agent, "Candidatus Xenohaliotis californiensis," from endangered white abalone (Haliotis sorenseni).},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0008624},
doi = {10.1128/mra.00086-24},
pmid = {38682777},
issn = {2576-098X},
abstract = {The genome of "Candidatus Xenohaliotis californiensis" was assembled from shotgun metagenomic sequencing of experimentally infected white abalone. Ninety-one percent genome completeness was achieved with low contamination. Sequencing this genome provides the opportunity to track pathogen evolution over time, conduct gene expression experiments, and study dynamics between this pathogen and its phage.},
}

@article {pmid38682769,
year = {2024},
author = {Vighnesh, L and Jagadeeshwari, U and Sasikala, C and Venkata Ramana, C},
title = {Metagenome-assembled genome of Zalaria obscura strain JY119.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0078623},
doi = {10.1128/mra.00786-23},
pmid = {38682769},
issn = {2576-098X},
abstract = {Here, we report a 22.1-Mbp genome sequence of microcolonial fungi, Zalaria obscura, isolated from a pine tree bark. The microbiome of the new fungi is predicted to be largely associated with Acidobacteriota. The genome sequence of Zalaria obscura will help us in understanding the unusual relationship with Acidobacteriota member(s).},
}

@article {pmid38682309,
year = {2024},
author = {Jingushi, K and Kawashima, A and Tanikawa, S and Saito, T and Yamamoto, A and Uemura, T and Sassi, N and Ishizuya, Y and Yamamoto, Y and Kato, T and Hatano, K and Hase, H and Nonomura, N and Tsujikawa, K},
title = {Cutibacterium acnes-derived extracellular vesicles promote tumor growth in renal cell carcinoma.},
journal = {Cancer science},
volume = {},
number = {},
pages = {},
doi = {10.1111/cas.16202},
pmid = {38682309},
issn = {1349-7006},
support = {//Kobayashi Foundation for Cancer Research/ ; //Takeda Science Foundation/ ; //Yakult Bio-Science Foundation/ ; },
abstract = {Bacterial flora are present in various parts of the human body, including the intestine, and are thought to be involved in the etiology of various diseases such as multiple sclerosis, intestinal diseases, cancer, and uterine diseases. In recent years, the presence of bacterial 16S rRNA genes has been revealed in blood, which was previously thought to be a sterile environment, and characteristic blood microbiomes have been detected in various diseases. However, the mechanism and the origin of the bacterial information are unknown. In this study, we performed 16S rRNA metagenomic analysis of bacterial DNA in serum extracellular vesicles from five healthy donors and seven patients with renal cell carcinoma and detected Cutibacterium acnes DNA as a characteristic bacterial DNA in the serum extracellular vesicles of patients with renal cell carcinoma. In addition, C. acnes DNA was significantly reduced in postoperative serum extracellular vesicles from patients with renal cell carcinoma compared with that in preoperative serum extracellular vesicles from these patients and was also detected in tumor tissue and extracellular vesicles from tumor tissue-associated microbiota, suggesting an association between C. acnes extracellular vesicles and renal cell carcinoma. C. acnes extracellular vesicles were taken up by renal carcinoma cells to enhance their proliferative potential. C. acnes extracellular vesicles also exhibited tumor-promoting activity in a mouse model of renal cancer allografts with enhanced angiogenesis. These results suggest that extracellular vesicles released by C. acnes localized in renal cell carcinoma tissues act in a tumor-promoting manner.},
}

@article {pmid38682059,
year = {2024},
author = {Dsouza, NN and Chellasamy, SK},
title = {A comparative genomic approach to decipher the mutations associated with Nipah viral human isolates from southeast Asia.},
journal = {Iranian journal of microbiology},
volume = {16},
number = {1},
pages = {104-113},
pmid = {38682059},
issn = {2008-3289},
abstract = {BACKGROUND AND OBJECTIVES: Multiple outbreaks over two decades and a high mortality rate have emphasized the Nipah virus (NiV) as a priority research area. The study focuses on identifying the mutational landscape in sequences from NiV human isolates from different geographical regions.

MATERIALS AND METHODS: Thirty-seven NiV genomes of human samples from Malaysia, Bangladesh, and India were subjected to phylogeny and metagenomic analysis to decipher the genome variability using MEGA11 software and the meta-CATS web server. Using the Single-Likelihood Ancestor Counting method, the synonymous and nonsynonymous mutations among NiV genes were identified. Further, the nonsynonymous variations were used to identify mutations in all the NiV proteins.

RESULTS: The NiV isolates were categorized into NiV-M, NiV-B, and NiV-I clades based on phylogenetic analysis. Metagenomic analysis revealed 1636 variations in the noncoding and coding regions of the genomes of the three clades of NiV. Further analysis of nonsynonymous mutations showed the phosphoprotein to be highly mutating, whereas the matrix protein was stable.

CONCLUSION: Deciphering the mutation pattern using a comparative genomics approach for human isolates provided valuable insight into the stability of NiV proteins which can be further used for understanding variations in host-pathogen interaction and developing effective therapeutic measures.},
}

@article {pmid38681899,
year = {2024},
author = {Wang, H and Lang, Y and Cai, X and Gao, L and Yang, S and Jin, J},
title = {Lessons from Multiple Infections Such as Lymphoma Complicated with Pneumocystis Infection: A Case Report.},
journal = {Infection and drug resistance},
volume = {17},
number = {},
pages = {1583-1588},
doi = {10.2147/IDR.S461607},
pmid = {38681899},
issn = {1178-6973},
abstract = {BACKGROUND: Lymphoma is complicated by intricate infections, notably Pneumocystis jirovecii pneumonia (PJP), marked by rapid progression, respiratory failure, and high mortality. Rapid diagnosis of PJP and effective administration of the first-line treatment trimethoprim-sulfamethoxazole (TMP-SMX) are important. For patients intolerant to TMP-SMX, selecting appropriate alternatives is challenging, necessitating careful decisions to optimize diagnosis and treatment. We present a lymphoma case complicated by PJP, illustrating medication adjustment until a positive response was observed.

CASE DESCRIPTION: A 41-year-old male patient with lymphoma presented with a week-long history of fever, fatigue, cough, sputum, chest tightness, and exertional dyspnea, unresponsive to treatment. Routine laboratory examinations revealed no pathogenic bacteria. PJ and Mycobacterium tuberculosis (MTB) were detected in bronchoalveolar lavage fluid (BALF) using metagenomic next-generation sequencing (mNGS). On Day 1 of admission, meropenem, TMP-SMX, and rifampicin+isoniazid+levofloxacin were administered. However, the patient developed drug-induced hepatotoxicity and gastrointestinal adverse reactions after six days of treatment. After a multidisciplinary team discussion, anti-tuberculosis therapy was stopped because of insufficient evidence of tuberculosis infection. A reduced dose of TMP-SMX with micafungin was used for PJP; however, symptoms persisted and repeated computed tomography showed extensive deterioration of bilateral pulmonary plaques. The PJP regimen was modified to include a combination of TMP-SMX and caspofungin. Due to the high fever and elevated infection indices, the patient was treated with teicoplanin to enhance the anti-infection effects. By Day 13, the patient's temperature had normalized, and infection control was achieved by Day 30. CT revealed that the infection in both lung lobes fully resolved. Subsequently, lymphoma treatment commenced.

CONCLUSION: BALF-NGS facilitates early and rapid diagnosis of PJP. mNGS reads of MTB bacillus <5 may indicate a bacterial carrier state, warranting other detection techniques to support it. There is insufficient evidence for using TMP-SMX with micafungin to treat PJP; however, TMP-SMX combined with caspofungin is suitable.},
}

@article {pmid38681728,
year = {2024},
author = {Guo, SS and Fu, G and Hu, YW and Liu, J and Wang, YZ},
title = {Application of metagenomic next-generation sequencing technology in the etiological diagnosis of peritoneal dialysis-associated peritonitis.},
journal = {Open life sciences},
volume = {19},
number = {1},
pages = {20220865},
doi = {10.1515/biol-2022-0865},
pmid = {38681728},
issn = {2391-5412},
abstract = {Pathogens detected by metagenomic next-generation sequencing (mNGS) and the laboratory blood culture flask method were compared to understand the advantages and clinical significance of mNGS assays in the etiological diagnosis of peritoneal dialysis-associated peritonitis (PDAP). The study involved a total of 37 patients from the hospital's peritoneal dialysis centre, six of whom were patients with non-peritoneal dialysis-associated peritonitis. Peritoneal dialysis samples were collected from the 37 patients, who were divided into two groups. One group's samples were cultured using conventional blood culture flasks, and the other samples underwent pathogen testing using mNGS. The results showed that the positive rate of mNGS was 96.77%, while that of the blood culture flask method was 70.97% (p < 0.05). A total of 29 pathogens were detected by mNGS, namely 24 bacteria, one fungus, and four viruses. A total of 10 pathogens were detected using the bacterial blood culture method, namely nine bacteria and one fungus. The final judgment of the PDAP's causative pathogenic microorganism was made by combining the clinical condition, response to therapy, and the whole-genome sequencing findings. For mNGS, the sensitivity was 96.77%, the specificity was 83.33%, the positive predictive value was 96.77%, and the negative predictive value was 83.33%. For the blood culture flask method, the sensitivity was 70.97%, the specificity was 100%, the positive predictive value was 100%, and the negative predictive value was 0%. In conclusion, mNGS had a shorter detection time for diagnosing peritoneal dialysis-related peritonitis pathogens, with a higher positive rate than traditional bacterial cultures, providing significant advantages in diagnosing rare pathogens.},
}

@article {pmid38681641,
year = {2024},
author = {Chukwudozie, KI and Wang, H and Wang, X and Lu, C and Xue, J and Zhang, W and Shan, T},
title = {Viral metagenomic analysis reveals diverse viruses and a novel bocaparvovirus in the enteric virome of snow leopard (Panthera uncia).},
journal = {Heliyon},
volume = {10},
number = {8},
pages = {e29799},
doi = {10.1016/j.heliyon.2024.e29799},
pmid = {38681641},
issn = {2405-8440},
abstract = {The enteric virome, comprising a complex community of viruses inhabiting the gastrointestinal tract, plays a significant role in health and disease dynamics. In this study, the fecal sample of a wild snow leopard was subjected to viral metagenomic analysis using a double barcode Illumina MiSeq platform. The resulting reads were de novo assembled into contigs with SOAPdenovo2 version r240. Additional bioinformatic analysis of the assembled genome and genome annotation was done using the Geneious prime software (version 2022.0.2). Following viral metagenomic analysis and bioinformatic analysis, a total of 7 viral families and a novel specie of bocaparvovirus tentatively named Panthera uncia bocaparvovirus (PuBOV) with GenBank accession number OQ627713 were identified. The complete genome of PuBOV was predicted to contain 3 open reading frames (ORFs), contains 5433 nucleotides and has a G + C content of 47.40 %. BLASTx analysis and pairwise sequence comparison indicated the novel virus genome was a new species in the genus Bocaparvovirus based on the species demarcation criteria of the International Committee on the Taxonomy of Viruses. This study provides valuable insights into the diversity and composition of the enteric virome in wild endangered snow leopards. The identification and characterization of viruses in wildlife is crucial for developing effective strategies to manage and mitigate potential zoonotic and other viral disease threats to human and animal health.},
}

@article {pmid38680920,
year = {2024},
author = {Li, H and Lv, Y and Zhang, Y and Wang, X and Yang, X and Qu, J},
title = {Fermentation properties and functional stability of dough starter Jiaozi and Laomian after frozen storage.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1379484},
doi = {10.3389/fmicb.2024.1379484},
pmid = {38680920},
issn = {1664-302X},
abstract = {PURPOSE: This study aims to investigate the effects of frozen storage on the stability of traditional dough starters in China.

METHODS: The microbial community structure and abundance of related metabolic genes in different fermented sourdough prepared by Jiaozi (JZ) and Laomian (LM) starters before and after frozen storage at -20°C for half a year were analyzed using the shotgun metagenomic sequencing method, and differences in characteristics of texture in steamed bread were also compared by formal methods.

RESULTS: The fermentation ability (FA) and metabolic activities of yeast in the JZH sourdough (started by JZ which was stored at -20°C for half a year) were better than those of LMH sourdough (started by LM which was stored at -20°C for half a year). The dominant genera of Acetobacter were found to be increased in the JZH0 sourdough (started by JZH and fermented for 0 h) and those of Lactobacillus were found to be decreased. Lactobacillus (98.72%), Pediococcus (0.37%), Saccharomyces (0.27%), and Acetobacter (0.01%), were dominant in sourdough LMH0 (started by LMH and fermented for 0 h). The abundances of "oxidative phosphorylation-related enzymes" and the "biosynthesis of glutamate"-related enzymes and genes related to "biosynthesis of glutamate" and "unsaturated fatty acid" were higher in JZH0 than in the JZ0 sourdough (started by JZ without being frozen and fermented for 0 h). The good FA of yeast, the acid production capacity of bacteria in the sourdough, and the quality of the JZH steamed bread (made by the JZH starter) indicated the better freezing tolerance of the microorganisms in JZ than in LM.

CONCLUSION: The conclusion of this study suggests the better application potential of the JZ as the fermentation starter in actual production.},
}

@article {pmid38680886,
year = {2024},
author = {Nimnoi, P and Pirankham, P and Srimuang, K and Ruanpanun, P},
title = {Insights into soil nematode diversity and bacterial community of Thai jasmine rice rhizosphere from different paddy fields in Thailand.},
journal = {PeerJ},
volume = {12},
number = {},
pages = {e17289},
doi = {10.7717/peerj.17289},
pmid = {38680886},
issn = {2167-8359},
mesh = {Animals ; Thailand ; *Oryza/microbiology/parasitology ; *Rhizosphere ; *Soil Microbiology ; *Nematoda/microbiology ; Bacteria/classification/isolation & purification/genetics ; Microbiota ; Soil/parasitology/chemistry ; Biodiversity ; Southeast Asian People ; },
abstract = {Globally, phytonematodes cause significant crop losses. Understanding the functions played by the plant rhizosphere soil microbiome during phytonematodes infection is crucial. This study examined the distribution of phytonematodes in the paddy fields of five provinces in Thailand, as well as determining the keystone microbial taxa in response to environmental factors that could be considered in the development of efficient biocontrol tactics in agriculture. The results demonstrated that Meloidogyne graminicola and Hirschmanniella spp. were the major and dominant phytonematodes distributed across the paddy fields of Thailand. Soil parameters (total P, Cu, Mg, and Zn) were the important factors affecting the abundance of both nematodes. Illumina next-generation sequencing demonstrated that the levels of bacterial diversity among all locations were not significantly different. The Acidobacteriota, Proteobacteria, Firmicutes, Actinobacteriota, Myxococcota, Chloroflexi, Verrucomicrobiota, Bacteroidota, Gemmatimonadota, and Desulfobacterota were the most abundant bacterial phyla observed at all sites. The number of classes of the Acidobacteriae, Clostridia, Bacilli, and Bacteroidia influenced the proportions of Hirschmanniella spp., Tylenchorhynchus spp., and free-living nematodes in the sampling dirt, whereas the number of classes of the Polyangia and Actinobacteria affected the amounts of Pratylenchus spp. in both roots and soils. Soil organic matter, N, and Mn were the main factors that influenced the structure of the bacterial community. Correlations among rhizosphere microbiota, soil nematodes, and soil properties will be informative data in considering phytonematode management in a rice production system.},
}

Animals
Thailand
*Oryza/microbiology/parasitology
*Rhizosphere
*Soil Microbiology
*Nematoda/microbiology
Bacteria/classification/isolation & purification/genetics
Microbiota
Soil/parasitology/chemistry
Biodiversity
Southeast Asian People

@article {pmid38680269,
year = {2024},
author = {Huang, HY and Bu, KP and Liu, JW and Wei, J},
title = {Overlapping infections of Mycobacterium canariasense and Nocardia farcinica in an immunocompetent patient: A case report.},
journal = {World journal of clinical cases},
volume = {12},
number = {12},
pages = {2079-2085},
doi = {10.12998/wjcc.v12.i12.2079},
pmid = {38680269},
issn = {2307-8960},
abstract = {BACKGROUND: Infections by non-tuberculous mycobacteria (NTM) have become more common in recent years. Mycobacterium canariasense (M. canariasense) was first reported as an opportunistic pathogen in 2004, but there have been very few case reports since then. Nocardia is a genus of aerobic and Gram-positive bacilli, and these species are also opportunistic pathogens and in the Mycobacteriales order. Conventional methods for diagnosis of NTM are inefficient. Metagenomic next-generation sequencing (mNGS) can rapidly detect many pathogenic microorganisms, even rare species. Most NTM and Nocardia infections occur in immunocompromised patients with atypical clinical symptoms. There are no previous reports of infection by M. canariasense and Nocardia farcinica (N. farcinica), especially in immunocompetent patients. This case report describes an immunocompetent 52-year-old woman who had overlapping infections of M. canariasense, N. farcinica, and Candida parapsilosis (C. parapsilosis) based on mNGS.

CASE SUMMARY: A 52-year-old woman presented with a productive cough and chest pain for 2 wk, and recurrent episodes of moderate-grade fever for 1 wk. She received antibiotics for 1 wk at a local hospital, and experienced defervescence, but the productive cough and chest pain persisted. We collected samples of a lung lesion and alveolar lavage fluid for mNGS. The lung tissue was positive for M. canariasense, N. farcinica, and C. parapsilosis, and the alveolar lavage fluid was positive for M. canariasense. The diagnosis was pneumonia, and application of appropriate antibiotic therapy cured the patient.

CONCLUSION: Etiological diagnosis is critical for patients with infectious diseases. mNGS can identify rare and novel pathogens, and does not require a priori knowledge.},
}

@article {pmid38679334,
year = {2024},
author = {Fang, Y and Wang, J and Sun, J and Su, Z and Chen, S and Xiao, J and Ni, J and Hu, Z and He, Y and Shen, S and Deng, F},
title = {RNA viromes of Dermacentor nuttalli ticks reveal a novel uukuvirus in Qīnghǎi Province, China.},
journal = {Virologica Sinica},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.virs.2024.04.006},
pmid = {38679334},
issn = {1995-820X},
abstract = {Ticks are a major parasite on the Qīnghǎi-Tibet Plateau, western China, and represent an economic burden to agriculture and animal husbandry. Despite research on tick-borne pathogens that threaten humans and animals, the viromes of dominant tick species remain unknown. In this study, we collected Dermacentor nuttalli ticks near Qīnghǎi Lake and identified 13 viruses belonging to at least six families through metagenomic sequencing. Four viruses were of high abundance in pools, including Xīnjiāng tick-associated virus 1 (XJTAV1), and three novel viruses: Qīnghǎi Lake virus 1, Qīnghǎi Lake virus 2 (QHLV1, and QHLV2, unclassified), and Qīnghǎi Lake virus 3 (QHLV3, genus Uukuvirus of family Phenuiviridae in order Bunyavirales), which lacks the M segment. The minimum infection rates of the four viruses among the tick groups were 8.2%, 49.5%, 6.2%, and 24.7%, respectively, suggesting the prevalence of these viruses in D. nuttalli ticks. A putative M segment of QHLV3 was identified from next-generation sequencing data and further characterized for its signal peptide cleavage site, N-glycosylation, and transmembrane region. Furthermore, we probed the L, M, and S segments of other viruses using the putative M segment sequence with sequencing data of other tick pools. By revealing the viromes of D. nuttalli ticks, this study enhances our understanding of tick-borne viral communities in highland regions. The putative M segment identified in a novel uukuvirus suggests that previously identified uukuviruses without M segments should have had the same genome organization as typical bunyaviruses. These results will facilitate virus discovery and our understanding of the phylogeny of tick-borne uukuviruses.},
}

@article {pmid38679240,
year = {2024},
author = {Chen, C and Gong, H and Wei, Y and Xu, T and Li, J and Ding, GC},
title = {Promoting agricultural waste-driven denitrification and nitrogen sequestration with nano-enabled strategy.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {130746},
doi = {10.1016/j.biortech.2024.130746},
pmid = {38679240},
issn = {1873-2976},
abstract = {Nanotechnology and biotechnology offer promising avenues for bolstering food security through the facilitation of soil nitrogen (N) sequestration and the reduction of nitrate leaching. Nonetheless, a comprehensive and mechanistic evaluation of their effectiveness and safety remains unclear. In this study, a soil remediation strategy employing nano-Fe3O4 and straw in N-contaminated soil was developed to elucidate N retention mechanisms via diverse metagenomics techniques. The findings revealed that subsoil amended with straw, particularly in conjunction with nano-Fe3O4, significantly increased subsoil N content (53.2%) and decreased nitrate concentration (74.6%) in leachate. Furthermore, the enrichment of functional genes associated with N-cycling, sulfate, nitrate, and iron uptake, along with chemotaxis, and responses to environmental stimuli or microbial collaboration, effectively mitigates nitrate leaching while enhancing soil N sequestration. This study introduces a pioneering approach utilizing nanomaterials in soil remediation, thereby offering the potential for the cultivation of safe vegetables in high N input greenhouse agriculture.},
}

@article {pmid38678973,
year = {2024},
author = {Hoepers, PG and Nunes, PLF and Almeida-Souza, HO and Martins, MM and Carvalho, RDO and Dreyer, CT and Aburjaile, FF and Sommerfeld, S and Azevedo, V and Fonseca, BB},
title = {Harnessing probiotics capability to combat Salmonella Heidelberg and improve intestinal health in broilers.},
journal = {Poultry science},
volume = {103},
number = {7},
pages = {103739},
doi = {10.1016/j.psj.2024.103739},
pmid = {38678973},
issn = {1525-3171},
abstract = {The poultry industry faces significant challenges in controlling Salmonella contamination while reducing antibiotic use, particularly with the emergence of Salmonella Heidelberg (SH) strains posing risks to food safety and public health. Probiotics, notably lactic acid bacteria (LAB) and Saccharomyces boulardii (SB) offer promising alternatives for mitigating Salmonella colonization in broilers. Understanding the efficacy of probiotics in combating SH and their impact on gut health and metabolism is crucial for improving poultry production practices and ensuring food safety standards. This study aimed to assess the inhibitory effects of LAB and SB against SH both in vitro and in vivo broilers, while also investigating their impact on fecal metabolites and caecal microbiome composition. In vitro analysis demonstrated strong inhibition of SH by certain probiotic strains, such as Lactiplantibacillus plantarum (LP) and Lacticaseibacillus acidophilus (LA), while others like SB and Lactobacillus delbrueckii (LD) did not exhibit significant inhibition. In vivo testing revealed that broilers receiving probiotics had significantly lower SH concentrations in cecal content compared to the positive control (PC) at all ages, indicating a protective effect of probiotics against SH colonization. Metagenomic analysis of cecal-content microbiota identified predominant bacterial families and genera, highlighting changes in microbiota composition with age and probiotic supplementation. Additionally, fecal metabolomics profiling showed alterations in metabolite concentrations, suggesting reduced oxidative stress, intestinal inflammation, and improved gut health in probiotic-supplemented birds. These findings underscore the potential of probiotics to mitigate SH colonization and improve broiler health while reducing reliance on antibiotics.},
}

@article {pmid38678728,
year = {2024},
author = {Tyagi, S and Katara, P},
title = {A metagenome-wide association study of gut microbiome in patients with AMD, ASD, RA, T2D & VKH diseases.},
journal = {Computational biology and chemistry},
volume = {110},
number = {},
pages = {108076},
doi = {10.1016/j.compbiolchem.2024.108076},
pmid = {38678728},
issn = {1476-928X},
abstract = {Clinical studies have already illustrated the associations between gut microbes and diseases, yet fundamental questions remain unclear that how we can universalize this knowledge. Considering the important role of human gut microbial composition in maintaining overall health, it is important to understand the microbial diversity and altered disease conditions of the human gut. Metagenomics provides a way to analyze and understand the microbes and their role in a community manner. It provides qualitative as well as quantitative measurements, in terms of relative abundance. Various studies are already going on to find out the association between microbes and diseases; still, the mined knowledge is limited. Considering the current scenario, using the targeted metagenomics approach, we analyzed the gut microbiome of 99 samples from healthy and diseased individuals. Our metagenomic analysis mainly targeted five diseased microbiomes (i.e., Age-related macular degeneration, Autism spectrum disorder, Rheumatoid arthritis, Type 2 diabetes and Vogt-Koyanagi harada), with compare to healthy microbiome, and reported disease-associated microbiome shift in different conditions.},
}

@article {pmid38678707,
year = {2024},
author = {Guruge, KS and Goswami, P and Kanda, K and Abeynayaka, A and Kumagai, M and Watanabe, M and Tamamura-Andoh, Y},
title = {Plastiome: Plastisphere-enriched mobile resistome in aquatic environments.},
journal = {Journal of hazardous materials},
volume = {471},
number = {},
pages = {134353},
doi = {10.1016/j.jhazmat.2024.134353},
pmid = {38678707},
issn = {1873-3336},
abstract = {Aquatic microplastics (MPs) act as reservoirs for microbial communities, fostering the formation of a mobile resistome encompassing diverse antibiotic (ARGs) and biocide/metal resistance genes (BMRGs), and mobile genetic elements (MGEs). This collective genetic repertoire, referred to as the "plastiome," can potentially perpetuate environmental antimicrobial resistance (AMR). Our study examining two Japanese rivers near Tokyo revealed that waterborne MPs are primarily composed of polyethylene and polypropylene fibers and sheets of diverse origin. Clinically important genera like Exiguobacterium and Eubacterium were notably enriched on MPs. Metagenomic analysis uncovered a 3.46-fold higher enrichment of ARGs on MPs than those in water, with multidrug resistance genes (MDRGs) and BMRGs prevailing, particularly within MPs. Specific ARG and BMRG subtypes linked to resistance to vancomycin, beta-lactams, biocides, arsenic, and mercury showed selective enrichment on MPs. Network analysis revealed intense associations between host genera with ARGs, BMRGs, and MGEs on MPs, emphasizing their role in coselection. In contrast, river water exhibited weaker associations. This study underscores the complex interactions shaping the mobile plastiome in aquatic environments and emphasizes the global imperative for research to comprehend and effectively control AMR within the One Health framework.},
}

@article {pmid38678508,
year = {2024},
author = {Tang, Z and Wang, H and Liu, Y and Wang, C and Li, X and Yang, Q},
title = {Current status and new experimental diagnostic methods of invasive fungal infections after hematopoietic stem cell transplantation.},
journal = {Archives of microbiology},
volume = {206},
number = {5},
pages = {237},
pmid = {38678508},
issn = {1432-072X},
support = {22072005//National Natural Science Foundation of China/ ; 22072005//National Natural Science Foundation of China/ ; 22072005//National Natural Science Foundation of China/ ; 22072005//National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Hematopoietic Stem Cell Transplantation/adverse effects ; *Invasive Fungal Infections/diagnosis ; Fluorescence Resonance Energy Transfer ; High-Throughput Nucleotide Sequencing ; Biosensing Techniques/methods ; },
abstract = {Invasive fungal infections (IFIs) are common and life-threatening complications in post-hematopoietic stem cell transplantation (post-HSCT) recipients, Severe IFIs can lead to systemic infection and organ damage, which results in high mortality in HSCT recipients. With the development of the field of fungal infection diagnosis, more and more advanced non-culture diagnostic tools have been developed, such as glip biosensors, metagenomic next-generation sequencing, Magnetic Nanoparticles and Identified Using SERS via AgNPs[+] , and artificial intelligence-assisted diagnosis. The advanced diagnostic approaches contribute to the success of HSCT and improve the overall survival of post-HSCT leukemia patients by supporting therapeutical decisions. This review provides an overview of the characteristics of two high-incidence IFIs in post-HSCT recipients and discusses some of the recently developed IFI detection technologies. Additionally, it explores the potential application of cationic conjugated polymer fluorescence resonance energy transfer (CCP-FRET) technology for IFI detection. The aim is to offer insights into selecting appropriate IFI detection methods and gaining an understanding of novel fungal diagnostic approaches in laboratory settings.},
}

Humans
*Hematopoietic Stem Cell Transplantation/adverse effects
*Invasive Fungal Infections/diagnosis
Fluorescence Resonance Energy Transfer
High-Throughput Nucleotide Sequencing
Biosensing Techniques/methods

@article {pmid38678226,
year = {2024},
author = {Alexa, EA and Cobo-Díaz, JF and Renes, E and O Callaghan, TF and Kilcawley, K and Mannion, D and Skibinska, I and Ruiz, L and Margolles, A and Fernández-Gómez, P and Alvarez-Molina, A and Puente-Gómez, P and Crispie, F and López, M and Prieto, M and Cotter, PD and Alvarez-Ordóñez, A},
title = {The detailed analysis of the microbiome and resistome of artisanal blue-veined cheeses provides evidence on sources and patterns of succession linked with quality and safety traits.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {78},
pmid = {38678226},
issn = {2049-2618},
support = {818368//European Commission under the European Union´s Horizon 2020 research and innovation program/ ; 818368//European Commission under the European Union´s Horizon 2020 research and innovation program/ ; 818368//European Commission under the European Union´s Horizon 2020 research and innovation program/ ; 818368//European Commission under the European Union´s Horizon 2020 research and innovation program/ ; 818368//European Commission under the European Union´s Horizon 2020 research and innovation program/ ; AGL2016-78085-P//Ministry of Science and Innovation of the Spanish Government/ ; AGL2016-78085-P//Ministry of Science and Innovation of the Spanish Government/ ; AGL2016-78085-P//Ministry of Science and Innovation of the Spanish Government/ ; },
mesh = {*Cheese/microbiology ; *Microbiota/genetics ; *Food Microbiology ; Bacteria/classification/genetics ; Caves/microbiology ; Corynebacterium/genetics ; Longitudinal Studies ; Metagenome ; Lactococcus/genetics/classification ; RNA, Ribosomal, 16S/genetics ; Staphylococcus/genetics/classification ; Food Safety ; },
abstract = {BACKGROUND: Artisanal cheeses usually contain a highly diverse microbial community which can significantly impact their quality and safety. Here, we describe a detailed longitudinal study assessing the impact of ripening in three natural caves on the microbiome and resistome succession across three different producers of Cabrales blue-veined cheese.

RESULTS: Both the producer and cave in which cheeses were ripened significantly influenced the cheese microbiome. Lactococcus and the former Lactobacillus genus, among other taxa, showed high abundance in cheeses at initial stages of ripening, either coming from the raw material, starter culture used, and/or the environment of processing plants. Along cheese ripening in caves, these taxa were displaced by other bacteria, such as Tetragenococcus, Corynebacterium, Brevibacterium, Yaniella, and Staphylococcus, predominantly originating from cave environments (mainly food contact surfaces), as demonstrated by source-tracking analysis, strain analysis at read level, and the characterization of 613 metagenome-assembled genomes. The high abundance of Tetragenococcus koreensis and Tetragenococcus halophilus detected in cheese has not been found previously in cheese metagenomes. Furthermore, Tetragenococcus showed a high level of horizontal gene transfer with other members of the cheese microbiome, mainly with Lactococcus and Staphylococcus, involving genes related to carbohydrate metabolism functions. The resistome analysis revealed that raw milk and the associated processing environments are a rich reservoir of antimicrobial resistance determinants, mainly associated with resistance to aminoglycosides, tetracyclines, and β-lactam antibiotics and harbored by aerobic gram-negative bacteria of high relevance from a safety point of view, such as Escherichia coli, Salmonella enterica, Acinetobacter, and Klebsiella pneumoniae, and that the displacement of most raw milk-associated taxa by cave-associated taxa during ripening gave rise to a significant decrease in the load of ARGs and, therefore, to a safer end product.

CONCLUSION: Overall, the cave environments represented an important source of non-starter microorganisms which may play a relevant role in the quality and safety of the end products. Among them, we have identified novel taxa and taxa not previously regarded as being dominant components of the cheese microbiome (Tetragenococcus spp.), providing very valuable information for the authentication of this protected designation of origin artisanal cheese. Video Abstract.},
}

*Cheese/microbiology
*Microbiota/genetics
*Food Microbiology
Bacteria/classification/genetics
Caves/microbiology
Corynebacterium/genetics
Longitudinal Studies
Metagenome
Lactococcus/genetics/classification
RNA, Ribosomal, 16S/genetics
Staphylococcus/genetics/classification
Food Safety

@article {pmid38678116,
year = {2024},
author = {Zhou, Y and Shen, N and Luo, L and Liu, Y and Cao, Q},
title = {Clinical and metagenomic characteristics of lymphadenopathy related to fever of unknown origin in children.},
journal = {Pediatric research},
volume = {},
number = {},
pages = {},
pmid = {38678116},
issn = {1530-0447},
abstract = {BACKGROUND: Diagnosis of fever of unknown origin remains challenge for pediatricians. Lymphadenopathy is a separate entity that mainly originates from infection or malignancy.

METHODS: 168 patients with FUO accompanied by lymphadenectasis were reviewed. 33 lymph node tissue samples were examined by mNGS. Differences in clinical characteristics were compared among different disease groups. The value of mNGS in diagnosing and improving the clinical situation was assessed.

RESULTS: Multivariate analysis revealed that hepatosplenomegaly and LDH levels were associated with infectious diseases. Arthralgia was correlated with non-infectious inflammatory diseases. Weight loss and a node located in supraclavicular region may indicate neoplastic diseases. mNGS-positive rate was 60.60%, higher than that obtained with traditional methods. Treatment for 3/4 patients was adjusted according to the pathogen detected by mNGS, and antibiotics uses was discontinued or degraded in over 1/2 of the patients according to mNGS results.

CONCLUSIONS: Clinical characteristics of children with lymphadenopathy related to FUO have limited diagnostic value for distinguishing different kinds of diseases, while mNGS of lymph node tissue serves as a useful tool for identifying infectious diseases, especially those caused by rare pathogens. mNGS results can lead to not only adjustments in targeted treatment but also further confirmation of underlying diseases.

IMPACT STATEMENT: 1. The clinical features of children with FUO and lymphadenopathy differ according to disease group,although multivariate analysis indicated little diagnostic value for these features. 2. mNGS on lymph node tissue from children with FUO may serve as a efficient tool for distinguishing infectious diseases from other diseases. This is especially useful when a diagnosis cannot be determined with traditional methods. 3. mNGS targeted treatment can be administered in a timely manner and some underlying diseases can be indicated.},
}

@article {pmid38677439,
year = {2024},
author = {Luo, X and Hounmanou, YMG and Ndayisenga, F and Yu, Z},
title = {Spontaneous fermentation mitigates the frequency of genes encoding antimicrobial resistance spreading from the phyllosphere reservoir to the diet.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {172712},
doi = {10.1016/j.scitotenv.2024.172712},
pmid = {38677439},
issn = {1879-1026},
abstract = {The phyllosphere microbiome of vegetable products constitutes an important reservoir for multidrug resistant bacteria and Antibiotic Resistance Genes (ARG). Vegetable products including fermented products such as Paocai therefore may serve as a shuttle for extrinsic microorganisms with ARGs into the gut of consumers. Here we study the effect of fermentation on Paocai ARG dissemination by metagenomic analysis. Microbial abundance and diversity of the Paocai microbiome were diminished during fermentation, which correlated with the reduction of abundance in ARGs. Specifically, as fermentation progressed, Enterobacterales overtook Pseudomonadales as the predominant ARG carriers, and Lactobacillales and Enterobacteriales became the determinants of Paocai resistome variation. Moreover, the dual effect of microbes and metal resistance genes (MRGs) was the major contributor driving Paocai resistome dynamics. We recovered several metagenome-assembled genomes (MAGs) carrying acquired ARGs in the phyllosphere microbiome. ARGs of potential clinical and epidemiological relevance such as tet M and emrB-qacA, were mainly hosted by non-dominant bacterial genera. Overall, our study provides evidence that changes in microbial community composition by fermentation aid in constraining ARG dispersal from raw ingredients to the human microbiome but does not eliminate them.},
}

@article {pmid38677385,
year = {2024},
author = {Wang, YC and Fu, HM and Shen, Y and Wang, J and Wang, N and Chen, YP and Yan, P},
title = {Biosynthetic potential of uncultured anammox community bacteria revealed through multi-omics analysis.},
journal = {Bioresource technology},
volume = {401},
number = {},
pages = {130740},
doi = {10.1016/j.biortech.2024.130740},
pmid = {38677385},
issn = {1873-2976},
abstract = {Microbial secondary metabolites (SMs) and their derivatives have been widely used in medicine, agriculture, and energy. Growing needs for renewable energy and the challenges posed by antibiotic resistance, cancer, and pesticides emphasize the crucial hunt for new SMs. Anaerobic ammonium-oxidation (anammox) systems harbor many uncultured or underexplored bacteria, representing potential resources for discovering novel SMs. Leveraging HiFi long-read metagenomic sequencing, 1,040 biosynthetic gene clusters (BGCs) were unearthed from the anammox microbiome with 58% being complete and showcasing rich diversity. Most of them showed distant relations to known BGCs, implying novelty. Members of the underexplored lineages (Chloroflexota and Planctomycetota) and Proteobacteria contained lots of BGCs, showcasing substantial biosynthetic potential. Metaproteomic results indicated that Planctomycetota members harbored the most active BGCs, particularly those involved in producing potential biofuel-ladderane. Overall, these findings underscore that anammox microbiomes could serve as valuable resources for mining novel BGCs and discovering new SMs for practical application.},
}

@article {pmid38677229,
year = {2024},
author = {Chen, WL and Zhang, M and Wang, JG and Huang, WJ and Wu, Q and Zhu, XP and Li, N and Wu, Q and Guo, W and Chen, J},
title = {Microbial mechanisms of C/N/S geochemical cycling during low-water-level sediment remediation in urban rivers.},
journal = {Journal of environmental management},
volume = {359},
number = {},
pages = {120962},
doi = {10.1016/j.jenvman.2024.120962},
pmid = {38677229},
issn = {1095-8630},
abstract = {Low-water-level regulation has been effectively implemented in the restoration of urban river sediments in Guangzhou City, China. Further investigation is needed to understand the microbial mechanisms involved in pollutant degradation in low-water-level environments. This study examined sediment samples from nine rivers, including low-water-level rivers (LW), tidal waterways (TW), and enclosed rivers (ER). Metagenomic high-throughput sequencing and the Diting pipeline were utilized to investigate the microbial mechanisms involved in sediment C/N/S geochemical cycling during low-water-level regulation. The results reveal that the degree of pollution in LW sediment is lower compared to TW and ER sediment. LW sediment exhibits a higher capacity for pollutant degradation and elimination of black, odorous substances due to its stronger microbial methane oxidation, nitrification, denitrification, anammox, and oxidation of sulfide, sulfite, and thiosulfate. Conversely, TW and ER sediment showcase greater microbial methanogenesis, anaerobic fermentation, and sulfide generation abilities, leading to the persistence of black, odorous substances. Factors such as grit and silt content, nitrate, and ammonia concentrations impacted microbial metabolic pathways. Low-water-level regulation improved the micro-environment for functional microbes, facilitating pollutant removal and preventing black odorous substance accumulation. These findings provide insights into the microbial mechanisms underlying low-water-level regulation technology for sediment restoration in urban rivers.},
}

@article {pmid38677068,
year = {2024},
author = {Duan, LY and Zhang, Y and Li, YY and Li, XQ and Liu, YQ and Li, BL and Ding, CY and Ren, XM and Duan, PF and Han, H and Chen, ZJ},
title = {Effects of combined microplastic and cadmium pollution on sorghum growth, Cd accumulation, and rhizosphere microbial functions.},
journal = {Ecotoxicology and environmental safety},
volume = {277},
number = {},
pages = {116380},
doi = {10.1016/j.ecoenv.2024.116380},
pmid = {38677068},
issn = {1090-2414},
abstract = {The interaction between microplastics (MPs) and cadmium (Cd) poses a threat to agricultural soil environments, and their effects on plant growth and rhizosphere microbial community functions are not yet clear. In this study, energy sorghum was used as a test plant to investigate the effects of two types of MPs, polystyrene (PS) and polyethylene (PE), at different particle sizes (13 μm, 550 μm) and concentrations (0.1%, 1% w/w), and Cd, as well as their interactions, on the growth of sorghum in a soil-cultivation pot experiment. The results showed that the combined effects of MP and Cd pollution on the dry weight and Cd accumulation rate in sorghum varied depending on the type, concentration, and particle size of the MPs, with an overall trend of increasing stress from combined pollution with increasing Cd content and accumulation. High-throughput sequencing analysis revealed that combined MP and Cd pollution increased bacterial diversity, and the most significant increase was observed in the abundance-based coverage estimator (ACE), Shannon, and Sobs indices in the 13 μm 1% PS+Cd treatment group. Metagenomic analysis based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathways revealed that 19 groups of metabolic pathways, including microbial metabolism and methane metabolism, differed significantly under combined MP and Cd pollution. Hierarchical clustering results indicated that Cd treatment and combined MP and Cd treatment affected the abundances of sorghum rhizosphere soil nitrogen (N) and phosphorus (P) cycling genes and that the type of MP present was an important factor affecting N and P cycling genes. The results of this study provide a basis for exploring the toxic effects of combined MP and Cd pollution and for conducting soil environmental risk assessments.},
}

@article {pmid38677036,
year = {2024},
author = {Al-Faliti, M and Wang, P and Smith, AL and Delgado Vela, J},
title = {Phage phylogeny, molecular signaling, and auxiliary antimicrobial resistance in aerobic and anaerobic membrane bioreactors.},
journal = {Water research},
volume = {256},
number = {},
pages = {121620},
doi = {10.1016/j.watres.2024.121620},
pmid = {38677036},
issn = {1879-2448},
abstract = {Phage emit communication signals that inform their lytic and lysogenic life cycles. However, little is known regarding the abundance and diversity of the genes associated with phage communication systems in wastewater treatment microbial communities. This study focused on phage communities within two distinct biochemical wastewater environments, specifically aerobic membrane bioreactors (AeMBRs) and anaerobic membrane bioreactors (AnMBRs) exposed to varying antibiotic concentrations. Metagenomic data from the bench-scale systems were analyzed to explore phage phylogeny, life cycles, and genetic capacity for antimicrobial resistance and quorum sensing. Two dominant phage families, Schitoviridae and Peduoviridae, exhibited redox-dependent dynamics. Schitoviridae prevailed in anaerobic conditions, while Peduoviridae dominated in aerobic conditions. Notably, the abundance of lytic and lysogenic proteins varied across conditions, suggesting the coexistence of both life cycles. Furthermore, the presence of antibiotic resistance genes (ARGs) within viral contigs highlighted the potential for phage to transfer ARGs in AeMBRs. Finally, quorum sensing genes in the virome of AeMBRs indicated possible molecular signaling between phage and bacteria. Overall, this study provides insights into the dynamics of viral communities across varied redox conditions in MBRs. These findings shed light on phage life cycles, and auxiliary genetic capacity such as antibiotic resistance and bacterial quorum sensing within wastewater treatment microbial communities.},
}

@article {pmid38676863,
year = {2024},
author = {Xiang, F and Han, L and Jiang, S and Xu, X and Zhang, Z},
title = {Black soldier fly larvae mitigate greenhouse gas emissions from domestic biodegradable waste by recycling carbon and nitrogen and reconstructing microbial communities.},
journal = {Environmental science and pollution research international},
volume = {},
number = {},
pages = {},
pmid = {38676863},
issn = {1614-7499},
support = {42377002//Major Research Plan/ ; 32171466//Major Research Plan/ ; },
abstract = {Black soldier fly larvae have been proven to reduce greenhouse gas emissions in the treatment of organic waste. However, the microbial mechanisms involved have not been fully understood. The current study mainly examined the dynamic changes of carbon and nitrogen, greenhouse gas emissions, the succession of microbial community structure, and changes in functional gene abundance in organic waste under larvae treatment and non-aeration composting. Thirty percent carbon and 55% nitrogen in the organic waste supplied were stored in larvae biomass. Compared to the non-aeration composting, the larvae bioreactor reduced the proportion of carbon and nitrogen converted into greenhouse gases (CO2, CH4, and N2O decreased by 62%, 87%, and 95%, respectively). 16S rRNA sequencing analysis indicated that the larvae bioreactor increased the relative abundance of Methanophaga, Marinobacter, and Campylobacter during the bioprocess, enhancing the consumption of CH4 and N2O. The metagenomic data showed that the intervention of larvae reduced the ratio of (nirK + nirS + nor)/nosZ in the residues, thereby reducing the emission of N2O. Larvae also increased the functional gene abundance of nirA, nirB, nirD, and nrfA in the residues, making nitrite more inclined to be reduced to ammonia instead of N2O. The larvae bioreactor mitigated greenhouse gas emissions by redistributing carbon and nitrogen and remodeling microbiomes during waste bioconversion, giving related enterprises a relative advantage in carbon trading.},
}

@article {pmid38676557,
year = {2024},
author = {Glasl, B and Luter, HM and Damjanovic, K and Kitzinger, K and Mueller, AJ and Mahler, L and Engelberts, JP and Rix, L and Osvatic, JT and Hausmann, B and Séneca, J and Daims, H and Pjevac, P and Wagner, M},
title = {Co-occurring nitrifying symbiont lineages are vertically inherited and widespread in marine sponges.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrae069},
pmid = {38676557},
issn = {1751-7370},
abstract = {Ammonia-oxidising archaea and nitrite-oxidising bacteria are common members of marine sponge microbiomes. They derive energy for carbon fixation and growth from nitrification - the aerobic oxidation of ammonia to nitrite and further to nitrate - and are proposed to play essential roles in the carbon and nitrogen cycling of sponge holobionts. In this study, we characterise two novel nitrifying symbiont lineages, Candidatus Nitrosokoinonia and Candidatus Nitrosymbion in the marine sponge Coscinoderma matthewsi using a combination of molecular tools, in situ visualisation, and physiological rate measurements. Both represent a new genus in the ammonia-oxidising archaeal class Nitrososphaeria and the nitrite-oxidising bacterial order Nitrospirales, respectively. Furthermore, we show that larvae of this viviparous sponge are densely colonised by representatives of Ca. Nitrosokoinonia and Ca. Nitrosymbion indicating vertical transmission. In adults, the representatives of both symbiont genera are located extracellularly in the mesohyl. Comparative metagenome analyses and physiological data suggest that ammonia-oxidising archaeal symbionts of the genus Ca. Nitrosokoinonia strongly rely on endogenously produced nitrogenous compounds (i.e., ammonium, urea, nitriles/cyanides, and creatinine) rather than on exogenous ammonium sources taken up by the sponge. Additionally, the nitrite-oxidising bacterial symbionts of the genus Ca. Nitrosymbion may reciprocally support the ammonia-oxidisers with ammonia via the utilisation of sponge-derived urea and cyanate. Comparative analyses of published environmental 16S rRNA gene amplicon data revealed that Ca. Nitrosokoinonia and Ca. Nitrosymbion are widely distributed and predominantly associated with marine sponges and corals, suggesting a broad relevance of our findings.},
}

@article {pmid38675971,
year = {2024},
author = {Jitvaropas, R and Sawaswong, V and Poovorawan, Y and Auysawasdi, N and Vuthitanachot, V and Wongwairot, S and Rodkvamtook, W and Lindroth, E and Payungporn, S and Linsuwanon, P},
title = {Identification of Bacteria and Viruses Associated with Patients with Acute Febrile Illness in Khon Kaen Province, Thailand.},
journal = {Viruses},
volume = {16},
number = {4},
pages = {},
pmid = {38675971},
issn = {1999-4915},
support = {N41A640077//Research Grants for Talented Mid-Career Researchers, The National Research Council of Thailand (NRCT)/ ; HEAF67300057//Thailand Science Research and Innovation Fund Chulalongkorn University/ ; P0081_18_AF activity 05.01 and 05.02//Global Emerging Infections Surveillance (GEIS)/ ; },
mesh = {Humans ; Thailand/epidemiology ; Female ; Male ; Middle Aged ; Adult ; *Dengue/virology/epidemiology ; *Fever/virology ; Young Adult ; Adolescent ; Phylogeny ; Aged ; Child ; Scrub Typhus/microbiology/epidemiology/virology ; Bacteria/genetics/isolation & purification/classification ; Child, Preschool ; Coinfection/virology/microbiology/epidemiology ; Viruses/genetics/classification/isolation & purification ; Culicidae/virology/microbiology ; Animals ; Dengue Virus/genetics/classification/isolation & purification ; Rickettsia Infections/epidemiology/microbiology/virology ; },
abstract = {The majority of cases of undifferentiated acute febrile illness (AFI) in the tropics have an undefined etiology. In Thailand, AFI accounts for two-thirds of illnesses reported to the Ministry of Public Health. To characterize the bacterial and viral causes of these AFIs, we conducted molecular pathogen screening and serological analyses in patients who sought treatment in Chum Phae Hospital, Khon Kaen province, during the period from 2015 to 2016. Through integrated approaches, we successfully identified the etiology in 25.5% of cases, with dengue virus infection being the most common cause, noted in 17% of the study population, followed by scrub typhus in 3.8% and rickettsioses in 6.8%. Further investigations targeting viruses in patients revealed the presence of Guadeloupe mosquito virus (GMV) in four patients without other pathogen co-infections. The characterization of four complete genome sequences of GMV amplified from AFI patients showed a 93-97% nucleotide sequence identity with GMV previously reported in mosquitoes. Nucleotide substitutions resulted in amino acid differences between GMV amplified from AFI patients and mosquitoes, observed in 37 positions. However, these changes had undergone purifying selection pressure and potentially had a minimal impact on protein function. Our study suggests that the GMV strains identified in the AFI patients are relatively similar to those previously reported in mosquitoes, highlighting their potential role associated with febrile illness.},
}

Humans
Thailand/epidemiology
Female
Male
Middle Aged
Adult
*Dengue/virology/epidemiology
*Fever/virology
Young Adult
Adolescent
Phylogeny
Aged
Child
Scrub Typhus/microbiology/epidemiology/virology
Bacteria/genetics/isolation & purification/classification
Child, Preschool
Coinfection/virology/microbiology/epidemiology
Viruses/genetics/classification/isolation & purification
Culicidae/virology/microbiology
Animals
Dengue Virus/genetics/classification/isolation & purification
Rickettsia Infections/epidemiology/microbiology/virology

@article {pmid38675947,
year = {2024},
author = {Luo, R and Guan, A and Ma, B and Gao, Y and Peng, Y and He, Y and Xu, Q and Li, K and Zhong, Y and Luo, R and Cao, R and Jin, H and Lin, Y and Shang, P},
title = {Developmental Dynamics of the Gut Virome in Tibetan Pigs at High Altitude: A Metagenomic Perspective across Age Groups.},
journal = {Viruses},
volume = {16},
number = {4},
pages = {},
pmid = {38675947},
issn = {1999-4915},
mesh = {Animals ; *Altitude ; Swine ; *Virome/genetics ; *Metagenomics ; *Gastrointestinal Microbiome/genetics ; Tibet ; Viruses/genetics/classification ; Metagenome ; Female ; Genome, Viral ; },
abstract = {Tibetan pig is a geographically isolated pig breed that inhabits high-altitude areas of the Qinghai-Tibetan plateau. At present, there is limited research on viral diseases in Tibetan pigs. This study provides a novel metagenomic exploration of the gut virome in Tibetan pigs (altitude ≈ 3000 m) across three critical developmental stages, including lactation, nursery, and fattening. The composition of viral communities in the Tibetan pig intestine, with a dominant presence of Microviridae phages observed across all stages of development, in combination with the previous literature, suggest that it may be associated with geographical locations with high altitude. Functional annotation of viral operational taxonomic units (vOTUs) highlights that, among the constantly increasing vOTUs groups, the adaptability of viruses to environmental stressors such as salt and heat indicates an evolutionary response to high-altitude conditions. It shows that the lactation group has more abundant viral auxiliary metabolic genes (vAMGs) than the nursery and fattening groups. During the nursery and fattening stages, this leaves only DNMT1 at a high level. which may be a contributing factor in promoting gut health. The study found that viruses preferentially adopt lytic lifestyles at all three developmental stages. These findings not only elucidate the dynamic interplay between the gut virome and host development, offering novel insights into the virome ecology of Tibetan pigs and their adaptation to high-altitude environments, but also provide a theoretical basis for further studies on pig production and epidemic prevention under extreme environmental conditions.},
}

Animals
*Altitude
Swine
*Virome/genetics
*Metagenomics
*Gastrointestinal Microbiome/genetics
Tibet
Viruses/genetics/classification
Metagenome
Female
Genome, Viral

@article {pmid38675943,
year = {2024},
author = {Bandoo, RA and Kraberger, S and Varsani, A},
title = {Two Novel Geminiviruses Identified in Bees (Apis mellifera and Nomia sp.).},
journal = {Viruses},
volume = {16},
number = {4},
pages = {},
doi = {10.3390/v16040602},
pmid = {38675943},
issn = {1999-4915},
mesh = {Animals ; Bees/virology ; *Geminiviridae/genetics/classification/isolation & purification ; *Genome, Viral ; *Phylogeny ; Metagenomics ; DNA, Viral/genetics ; },
abstract = {Members of the Geminviridae family are circular single-stranded DNA plant-infecting viruses, some of which impact global food production. Geminiviruses are vectored by sap-feeding insects such as leafhoppers, treehoppers, aphids, and whiteflies. Additionally, geminivirus sequences have also been identified in other insects such as dragonflies, mosquitoes, and stingless bees. As part of a viral metagenomics study on honeybees and solitary bees (Nomia sp.), two geminivirus genomes were identified. These represent a novel citlodavirus (from honeybees collected from Westmoreland, Jamaica) and a mastrevirus-like genome (from a solitary bee collected from Tempe, Arizona, USA). The novel honeybee-derived citlodavirus genome shares ~61 to 69% genome-wide nucleotide pairwise identity with other citlodavirus genome sequences and is most closely related to the passion fruit chlorotic mottle virus identified in Brazil. Whereas the novel solitary bee-derived mastrevirus-like genome shares ~55 to 61% genome-wide nucleotide identity with other mastreviruses and is most closely related to tobacco yellow dwarf virus identified in Australia, based on pairwise identity scores of the full genome, replication-associated protein, and capsid protein sequences. Previously, two geminiviruses in the Begomovirus genus were identified in samples of stingless bee (Trigona spp.) samples. Here, we identify viruses that represent two new species of geminiviruses from a honeybee and a solitary bee, which continues to demonstrate that plant pollinators can be utilized for the identification of plant-infecting DNA viruses in ecosystems.},
}

Animals
Bees/virology
*Geminiviridae/genetics/classification/isolation & purification
*Genome, Viral
*Phylogeny
Metagenomics
DNA, Viral/genetics

@article {pmid38675877,
year = {2024},
author = {Zhao, H and Yang, M and Fan, X and Gui, Q and Yi, H and Tong, Y and Xiao, W},
title = {A Metagenomic Investigation of Potential Health Risks and Element Cycling Functions of Bacteria and Viruses in Wastewater Treatment Plants.},
journal = {Viruses},
volume = {16},
number = {4},
pages = {},
doi = {10.3390/v16040535},
pmid = {38675877},
issn = {1999-4915},
support = {32071570//National Natural Science Foundation of China/ ; 202303AP140004//the Science and Technology Planning Project in Key Areas of Yunnan Province/ ; },
mesh = {*Metagenomics ; *Wastewater/virology/microbiology ; *Bacteria/genetics/classification/isolation & purification ; *Sewage/virology/microbiology ; Humans ; *Viruses/genetics/classification/isolation & purification ; Metagenome ; Bacteriophages/genetics/isolation & purification/classification ; Virome/genetics ; Water Purification ; Animals ; },
abstract = {The concentration of viruses in sewage sludge is significantly higher (10-1000-fold) than that found in natural environments, posing a potential risk for human and animal health. However, the composition of these viruses and their role in the transfer of pathogenic factors, as well as their role in the carbon, nitrogen, and phosphorus cycles remain poorly understood. In this study, we employed a shotgun metagenomic approach to investigate the pathogenic bacteria and viral composition and function in two wastewater treatment plants located on a campus. Our analysis revealed the presence of 1334 amplicon sequence variants (ASVs) across six sludge samples, with 242 ASVs (41.22% of total reads) identified as pathogenic bacteria. Arcobacter was found to be the most dominant pathogen accounting for 6.79% of total reads. The virome analysis identified 613 viral genera with Aorunvirus being the most abundant genus at 41.85%. Approximately 0.66% of these viruses were associated with human and animal diseases. More than 60% of the virome consisted of lytic phages. Host prediction analysis revealed that the phages primarily infected Lactobacillus (37.11%), Streptococcus (21.11%), and Staphylococcus (7.11%). Furthermore, our investigation revealed an abundance of auxiliary metabolic genes (AMGs) involved in carbon, nitrogen, and phosphorus cycling within the virome. We also detected a total of 113 antibiotic resistance genes (ARGs), covering major classes of antibiotics across all samples analyzed. Additionally, our findings indicated the presence of virulence factors including the clpP gene accounting for approximately 4.78%, along with toxin genes such as the RecT gene representing approximately 73.48% of all detected virulence factors and toxin genes among all samples analyzed. This study expands our understanding regarding both pathogenic bacteria and viruses present within sewage sludge while providing valuable insights into their ecological functions.},
}

*Metagenomics
*Wastewater/virology/microbiology
*Bacteria/genetics/classification/isolation & purification
*Sewage/virology/microbiology
Humans
*Viruses/genetics/classification/isolation & purification
Metagenome
Bacteriophages/genetics/isolation & purification/classification
Virome/genetics
Water Purification
Animals

@article {pmid38675851,
year = {2024},
author = {Luqman, M and Duhan, N and Temeeyasen, G and Selim, M and Jangra, S and Mor, SK},
title = {Geographical Expansion of Avian Metapneumovirus Subtype B: First Detection and Molecular Characterization of Avian Metapneumovirus Subtype B in US Poultry.},
journal = {Viruses},
volume = {16},
number = {4},
pages = {},
doi = {10.3390/v16040508},
pmid = {38675851},
issn = {1999-4915},
mesh = {Animals ; *Metapneumovirus/genetics/classification/isolation & purification ; *Paramyxoviridae Infections/veterinary/virology/epidemiology ; *Poultry Diseases/virology/epidemiology ; *Phylogeny ; *Turkeys/virology ; *Genome, Viral ; United States/epidemiology ; Chickens/virology ; Poultry/virology ; Metagenomics ; Disease Outbreaks/veterinary ; },
abstract = {Avian metapneumovirus (aMPV), classified within the Pneumoviridae family, wreaks havoc on poultry health. It typically causes upper respiratory tract and reproductive tract infections, mainly in turkeys, chickens, and ducks. Four subtypes of AMPV (A, B, C, D) and two unclassified subtypes have been identified, of which subtypes A and B are widely distributed across the world. In January 2024, an outbreak of severe respiratory disease occurred on turkey and chicken farms across different states in the US. Metagenomics sequencing of selected tissue and swab samples confirmed the presence of aMPV subtype B. Subsequently, all samples were screened using an aMPV subtype A and B multiplex real-time RT-PCR kit. Of the 221 farms, 124 (56%) were found to be positive for aMPV-B. All samples were negative for subtype A. Six whole genomes were assembled, five from turkeys and one from chickens; all six assembled genomes showed 99.29 to 99.98% nucleotide identity, indicating a clonal expansion event for aMPV-B within the country. In addition, all six sequences showed 97.74 to 98.58% nucleotide identity with previously reported subtype B sequences, e.g., VCO3/60616, Hungary/657/4, and BR/1890/E1/19. In comparison to these two reference strains, the study sequences showed unique 49-62 amino acid changes across the genome, with maximum changes in glycoprotein (G). One unique AA change from T (Threonine) to I (Isoleucine) at position 153 in G protein was reported only in the chicken aMPV sequence, which differentiated it from turkey sequences. The twelve unique AA changes along with change in polarity of the G protein may indicate that these unique changes played a role in the adaptation of this virus in the US poultry. This is the first documented report of aMPV subtype B in US poultry, highlighting the need for further investigations into its genotypic characterization, pathogenesis, and evolutionary dynamics.},
}

Animals
*Metapneumovirus/genetics/classification/isolation & purification
*Paramyxoviridae Infections/veterinary/virology/epidemiology
*Poultry Diseases/virology/epidemiology
*Phylogeny
*Turkeys/virology
*Genome, Viral
United States/epidemiology
Chickens/virology
Poultry/virology
Metagenomics
Disease Outbreaks/veterinary

@article {pmid38675747,
year = {2024},
author = {Zhang, LN and Tan, JT and Ng, HY and Liao, YS and Zhang, RQ and Chan, KH and Hung, IF and Lam, TT and Cheung, KS},
title = {Association between Gut Microbiota Composition and Long-Term Vaccine Immunogenicity following Three Doses of CoronaVac.},
journal = {Vaccines},
volume = {12},
number = {4},
pages = {},
doi = {10.3390/vaccines12040365},
pmid = {38675747},
issn = {2076-393X},
support = {COVID1903010//Food and Health Bureau, The Government of HKSAR/ ; },
abstract = {BACKGROUND: Neutralizing antibody level wanes with time after COVID-19 vaccination. We aimed to study the relationship between baseline gut microbiota and immunogenicity after three doses of CoronaVac.

METHODS: This was a prospective cohort study recruiting three-dose CoronaVac recipients from two centers in Hong Kong. Blood samples were collected at baseline and one year post-first dose for virus microneutralization (vMN) assays to determine neutralization titers. The primary outcome was high immune response (defined as with vMN titer ≥ 40). Shotgun DNA metagenomic sequencing of baseline fecal samples identified potential bacterial species and metabolic pathways using Linear Discriminant Analysis Effect Size (LEfSe) analysis. Univariate and multivariable logistic regression models were used to identify high response predictors.

RESULTS: In total, 36 subjects were recruited (median age: 52.7 years [IQR: 47.9-56.4]; male: 14 [38.9%]), and 18 had low immune response at one year post-first dose vaccination. Eubacterium rectale (log10LDA score = 4.15, p = 0.001; relative abundance of 1.4% vs. 0, p = 0.002), Collinsella aerofaciens (log10LDA score = 3.31, p = 0.037; 0.39% vs. 0.18%, p = 0.038), and Streptococcus salivarius (log10LDA score = 2.79, p = 0.021; 0.05% vs. 0.02%, p = 0.022) were enriched in low responders. The aOR of high immune response with E. rectale, C. aerofaciens, and S. salivarius was 0.03 (95% CI: 9.56 × 10[-4]-0.32), 0.03 (95% CI: 4.47 × 10[-4]-0.59), and 10.19 (95% CI: 0.81-323.88), respectively. S. salivarius had a positive correlation with pathways enriched in high responders like incomplete reductive TCA cycle (log10LDA score = 2.23). C. aerofaciens similarly correlated with amino acid biosynthesis-related pathways. These pathways all showed anti-inflammation functions.

CONCLUSION: E. rectale,C. aerofaciens, and S. salivarius correlated with poorer long-term immunogenicity following three doses of CoronaVac.},
}

@article {pmid38675716,
year = {2024},
author = {Chudan, S and Kurakawa, T and Nishikawa, M and Nagai, Y and Tabuchi, Y and Ikushiro, S and Furusawa, Y},
title = {Beneficial Effects of Dietary Fiber in Young Barley Leaf on Gut Microbiota and Immunity in Mice.},
journal = {Molecules (Basel, Switzerland)},
volume = {29},
number = {8},
pages = {},
doi = {10.3390/molecules29081897},
pmid = {38675716},
issn = {1420-3049},
support = {20K05929//Japan Society for the Promotion of Science/ ; n/a//Takeda Science Foundation/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Hordeum/chemistry ; *Dietary Fiber/pharmacology ; *Plant Leaves/chemistry ; Mice ; Retinal Dehydrogenase/metabolism ; Butyrates/metabolism ; Feces/microbiology ; },
abstract = {The health benefits of young barley leaves, rich in dietary fiber, have been studied for several decades; however, their beneficial effects on the intestinal microenvironment remain to be elucidated. To investigate the effects of young barley leaf-derived dietary fiber (YB) on the gut microbiota and immunity, mice were fed an AIN-93G diet containing cellulose or YB and subjected to subsequent analysis. The population of MHC-II-positive conventional dendritic cells (cDCs) and CD86 expression in the cDCs of Peyer's patches were elevated in the YB-fed mice. MHC-II and CD86 expression was also elevated in the bone marrow-derived DCs treated with YB. 16S-based metagenomic analysis revealed that the gut microbiota composition was markedly altered by YB feeding. Among the gut microbiota, Lachnospiraceae, mainly comprising butyrate-producing NK4A136 spp., were overrepresented in the YB-fed mice. In fact, fecal butyrate concentration was also augmented in the YB-fed mice, which coincided with increased retinaldehyde dehydrogenase (RALDH) activity in the CD103[+] cDCs of the mesenteric lymph nodes. Consistent with elevated RALDH activity, the population of colonic IgA[+] plasma cells was higher in the YB-fed mice than in the parental control mice. In conclusion, YB has beneficial effects on the gut microbiota and intestinal immune system.},
}

Animals
*Gastrointestinal Microbiome/drug effects
*Hordeum/chemistry
*Dietary Fiber/pharmacology
*Plant Leaves/chemistry
Mice
Retinal Dehydrogenase/metabolism
Butyrates/metabolism
Feces/microbiology

@article {pmid38674803,
year = {2024},
author = {Arteaga-Muller, GY and Flores-Treviño, S and Bocanegra-Ibarias, P and Robles-Espino, D and Garza-González, E and Fabela-Valdez, GC and Camacho-Ortiz, A},
title = {Changes in the Progression of Chronic Kidney Disease in Patients Undergoing Fecal Microbiota Transplantation.},
journal = {Nutrients},
volume = {16},
number = {8},
pages = {},
doi = {10.3390/nu16081109},
pmid = {38674803},
issn = {2072-6643},
mesh = {Humans ; *Renal Insufficiency, Chronic/therapy/microbiology ; *Fecal Microbiota Transplantation ; Male ; Female ; *Disease Progression ; Middle Aged ; Double-Blind Method ; *Gastrointestinal Microbiome ; Aged ; *Feces/microbiology ; Dysbiosis/therapy ; Treatment Outcome ; Adult ; Creatinine/blood ; },
abstract = {Chronic kidney disease (CKD) is a progressive loss of renal function in which gut dysbiosis is involved. Fecal microbiota transplantation (FMT) may be a promising alternative for restoring gut microbiota and treating CKD. This study evaluated the changes in CKD progression in patients treated with FMT. Patients with diabetes and/or hypertension with CKD clinical stages 2, 3, and 4 in this single-center, double-blind, randomized, placebo-controlled clinical trial (NCT04361097) were randomly assigned to receive either FMT or placebo capsules for 6 months. Laboratory and stool metagenomic analyses were performed. A total of 28 patients were included (15 FMT and 13 placebo). Regardless of CKD stages, patients responded similarly to FMT treatment. More patients (53.8%) from the placebo group progressed to CKD than the FMT group (13.3%). The FMT group maintained stable renal function parameters (serum creatinine and urea nitrogen) compared to the placebo group. Adverse events after FMT treatment were mild or moderate gastrointestinal symptoms. The abundance of Firmicutes and Actinobacteria decreased whereas Bacteroidetes, Proteobacteria and Roseburia spp. increased in the FMT group. CKD patients showed less disease progression after FMT administration. The administration of oral FMT in patients with CKD is a safe strategy, does not represent a risk, and has potential benefits.},
}

Humans
*Renal Insufficiency, Chronic/therapy/microbiology
*Fecal Microbiota Transplantation
Male
Female
*Disease Progression
Middle Aged
Double-Blind Method
*Gastrointestinal Microbiome
Aged
*Feces/microbiology
Dysbiosis/therapy
Treatment Outcome
Adult
Creatinine/blood

@article {pmid38674796,
year = {2024},
author = {Chang, WL and Chen, YE and Tseng, HT and Cheng, CF and Wu, JH and Hou, YC},
title = {Gut Microbiota in Patients with Prediabetes.},
journal = {Nutrients},
volume = {16},
number = {8},
pages = {},
doi = {10.3390/nu16081105},
pmid = {38674796},
issn = {2072-6643},
support = {TCRD-TPE-109-RT-10//Taipei Tzu Chi Hospital/ ; TCRD-TPE-111-65//Taipei Tzu Chi Hospital/ ; TCRD-TPE-112-RT-9//Taipei Tzu Chi Hospital/ ; TCRD-TPE-108-38//Taipei Tzu Chi Hospital/ ; },
mesh = {Humans ; *Prediabetic State/microbiology ; *Gastrointestinal Microbiome ; Middle Aged ; Adult ; Male ; Female ; *Feces/microbiology ; Aged ; Young Adult ; Adolescent ; RNA, Ribosomal, 16S/genetics ; Blood Glucose/metabolism ; Diabetes Mellitus, Type 2/microbiology ; Bacteria/classification/genetics/isolation & purification ; Dietary Fiber/administration & dosage ; },
abstract = {Prediabetes is characterized by abnormal glycemic levels below the type 2 diabetes threshold, and effective control of blood glucose may prevent the progression to type 2 diabetes. While the association between the gut microbiota, glucose metabolism, and insulin resistance in diabetic patients has been established in previous studies, there is a lack of research regarding these aspects in prediabetic patients in Asia. We aim to investigate the composition of the gut microbiota in prediabetic patients and their differences compared to healthy individuals. In total, 57 prediabetic patients and 60 healthy adult individuals aged 18 to 65 years old were included in this study. Biochemistry data, fecal samples, and 3 days of food records were collected. Deoxyribonucleic acid extraction and next-generation sequencing via 16S ribosomal ribonucleic acid metagenomic sequencing were conducted to analyze the relationship between the gut microbiota and dietary habits. Prediabetic patients showed a lower microbial diversity than healthy individuals, with 9 bacterial genera being less abundant and 14 others more abundant. Prediabetic patients who consumed a low-carbohydrate (LC) diet exhibited higher diversity in the gut microbiota than those who consumed a high-carbohydrate diet. A higher abundance of Coprococcus was observed in the prediabetic patients on an LC diet. Compared to healthy individuals, the gut microbiota of prediabetic patients was significantly different, and adopting an LC diet with high dietary fiber consumption may positively impact the gut microbiota. Future studies should aim to understand the relationship between the gut microbiota and glycemic control in the Asian population.},
}

Humans
*Prediabetic State/microbiology
*Gastrointestinal Microbiome
Middle Aged
Adult
Male
Female
*Feces/microbiology
Aged
Young Adult
Adolescent
RNA, Ribosomal, 16S/genetics
Blood Glucose/metabolism
Diabetes Mellitus, Type 2/microbiology
Bacteria/classification/genetics/isolation & purification
Dietary Fiber/administration & dosage

@article {pmid38674771,
year = {2024},
author = {Gómez, F and Rodríguez, N and Rodríguez-Manfredi, JA and Escudero, C and Carrasco-Ropero, I and Martínez, JM and Ferrari, M and De Angelis, S and Frigeri, A and Fernández-Sampedro, M and Amils, R},
title = {Association of Acidotolerant Cyanobacteria to Microbial Mats below pH 1 in Acidic Mineral Precipitates in Río Tinto River in Spain.},
journal = {Microorganisms},
volume = {12},
number = {4},
pages = {},
doi = {10.3390/microorganisms12040829},
pmid = {38674771},
issn = {2076-2607},
abstract = {This report describes acidic microbial mats containing cyanobacteria that are strongly associated to precipitated minerals in the source area of Río Tinto. Río Tinto (Huelva, Southwestern Spain) is an extreme acidic environment where iron and sulfur cycles play a fundamental role in sustaining the extremely low pH and the high concentration of heavy metals, while maintaining a high level of microbial diversity. These multi-layered mineral deposits are stable all year round and are characterized by a succession of thick greenish-blue and brownish layers mainly composed of natrojarosite. The temperature and absorbance above and below the mineral precipitates were followed and stable conditions were detected inside the mineral precipitates. Different methodologies, scanning and transmission electron microscopy, immunological detection, fluorescence in situ hybridization, and metagenomic analysis were used to describe the biodiversity existing in these microbial mats, demonstrating, for the first time, the existence of acid-tolerant cyanobacteria in a hyperacidic environment of below pH 1. Up to 0.46% of the classified sequences belong to cyanobacterial microorganisms, and 1.47% of the aligned DNA reads belong to the Cyanobacteria clade.},
}

@article {pmid38674713,
year = {2024},
author = {Iani, FCM and de Campos, GM and Adelino, TER and da Silva, AS and Kashima, S and Alcantara, LCJ and Sampaio, SC and Giovanetti, M and Elias, MC and Slavov, SN},
title = {Metagenomic Analysis for Diagnosis of Hemorrhagic Fever in Minas Gerais, Brazil.},
journal = {Microorganisms},
volume = {12},
number = {4},
pages = {},
doi = {10.3390/microorganisms12040769},
pmid = {38674713},
issn = {2076-2607},
support = {2017/23205-8; 2021/11944-6; 2022/00910-6; 2022/10278-5//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; },
abstract = {Viral hemorrhagic fever poses a significant public health challenge due to its severe clinical presentation and high mortality rate. The diagnostic process is hindered by similarity of symptoms across different diseases and the broad spectrum of pathogens that can cause hemorrhagic fever. In this study, we applied viral metagenomic analysis to 43 serum samples collected by the Public Health Laboratory (Fundação Ezequiel Dias, FUNED) in Minas Gerais State, Brazil, from patients diagnosed with hemorrhagic fever who had tested negative for the standard local hemorrhagic disease testing panel. This panel includes tests for Dengue virus (DENV) IgM, Zika virus IgM, Chikungunya virus IgM, yellow fever IgM, Hantavirus IgM, Rickettsia rickettsii IgM/IgG, and Leptospira interrogans IgM, in addition to respective molecular tests for these infectious agents. The samples were grouped into 18 pools according to geographic origin and analyzed through next-generation sequencing on the NextSeq 2000 platform. Bioinformatic analysis revealed a prevalent occurrence of commensal viruses across all pools, but, notably, a significant number of reads corresponding to the DENV serotype 2 were identified in one specific pool. Further verification via real-time PCR confirmed the presence of DENV-2 RNA in an index case involving an oncology patient with hemorrhagic fever who had initially tested negative for anti-DENV IgM antibodies, thereby excluding this sample from initial molecular testing. The complete DENV-2 genome isolated from this patient was taxonomically classified within the cosmopolitan genotype that was recently introduced into Brazil. These findings highlight the critical role of considering the patient's clinical condition when deciding upon the most appropriate testing procedures. Additionally, this study showcases the potential of viral metagenomics in pinpointing the viral agents behind hemorrhagic diseases. Future research is needed to assess the practicality of incorporating metagenomics into standard viral diagnostic protocols.},
}

@article {pmid38674701,
year = {2024},
author = {Li, C and Han, G and Huang, L and Lu, Y and Xia, Y and Zhang, N and Liu, Q and Xu, J},
title = {Metagenomic Analyses Reveal Gut Microbial Profiles of Cnaphalocrocis medinalis Driven by the Infection of Baculovirus CnmeGV.},
journal = {Microorganisms},
volume = {12},
number = {4},
pages = {},
doi = {10.3390/microorganisms12040757},
pmid = {38674701},
issn = {2076-2607},
support = {BK20191216//the Natural science Foundation of Jiangsu Province/ ; NAES069AM04 and NAES-EE-041//the National Agricultural Basic Long-Term Scientific and Technological Work/ ; CX(22)1009//the Jiangsu Agricultural Science and Technology Innovation Fund/ ; YZ2021049 and YZ2021034//Yangzhou Science and Technology Project/ ; },
abstract = {The composition of microbiota in the digestive tract gut is essential for insect physiology, homeostasis, and pathogen infection. Little is known about the interactions between microbiota load and oral infection with baculoviruses. CnmeGV is an obligative baculovirus to Cnaphalocrocis medinalis. We investigated the impact of CnmeGV infection on the structure of intestinal microbes of C. medinalis during the initial infection stage. The results revealed that the gut microbiota profiles were dynamically driven by pathogen infection of CnmeGV. The numbers of all the OTU counts were relatively higher at the early and later stages, while the microbial diversity significantly increased early but dropped sharply following the infection. The compositional abundance of domain bacteria Firmicutes developed substantially higher. The significantly enriched and depleted species can be divided into four groups at the species level. Fifteen of these species were ultimately predicted as the biomarkers of CnmeGV infection. CnmeGV infection induces significant enrichment of alterations in functional genes related to metabolism and the immune system, encompassing processes such as carbohydrate, amino acid, cofactor, and vitamin metabolism. Finally, the study may provide an in-depth analysis of the relationship between host microbiota, baculovirus infection, and pest control of C. medinalis.},
}

@article {pmid38674691,
year = {2024},
author = {Deryabin, D and Lazebnik, C and Vlasenko, L and Karimov, I and Kosyan, D and Zatevalov, A and Duskaev, G},
title = {Broiler Chicken Cecal Microbiome and Poultry Farming Productivity: A Meta-Analysis.},
journal = {Microorganisms},
volume = {12},
number = {4},
pages = {},
doi = {10.3390/microorganisms12040747},
pmid = {38674691},
issn = {2076-2607},
support = {22-16-00036//Russian Science Foundation/ ; FNWZ-2022-0010//research project/ ; },
abstract = {The cecal microbial community plays an important role in chicken growth and development via effective feed conversion and essential metabolite production. The aim of this study was to define the microbial community's variants in chickens' ceca and to explore the most significant association between the microbiome compositions and poultry farming productivity. The meta-analysis included original data from 8 control broiler chicken groups fed with a standard basic diet and 32 experimental groups supplemented with various feed additives. Standard Illumina 16S-RNA gene sequencing technology was used to characterize the chicken cecal microbiome. Zootechnical data sets integrated with the European Production Effectiveness Factor (EPEF) were collected. Analysis of the bacterial taxa abundance and co-occurrence in chicken cecal microbiomes revealed two alternative patterns: Bacteroidota-dominated with decreased alpha biodiversity; and Bacillota-enriched, which included the Actinomycetota, Cyanobacteriota and Thermodesulfobacteriota phyla members, with increased biodiversity indices. Bacillota-enriched microbiome groups showed elevated total feed intake (especially due to the starter feed intake) and final body weight, and high EPEF values, while Bacteroidota-dominated microbiomes were negatively associated with poultry farming productivity. The meta-analysis results lay the basis for the development of chicken growth-promoting feed supplementations, aimed at the stimulation of beneficial and inhibition of harmful bacterial patterns, where relevant metagenomic data can be a tool for their control and selection.},
}

@article {pmid38674657,
year = {2024},
author = {Zhang, M and Zhou, Y and Cui, X and Zhu, L},
title = {The Potential of Co-Evolution and Interactions of Gut Bacteria-Phages in Bamboo-Eating Pandas: Insights from Dietary Preference-Based Metagenomic Analysis.},
journal = {Microorganisms},
volume = {12},
number = {4},
pages = {},
doi = {10.3390/microorganisms12040713},
pmid = {38674657},
issn = {2076-2607},
support = {32270546//National Natural Science Foundation of China/ ; },
abstract = {Bacteria and phages are two of the most abundant biological entities in the gut microbiome, and diet and host phylogeny are two of the most critical factors influencing the gut microbiome. A stable gut bacterial community plays a pivotal role in the host's physiological development and immune health. A phage is a virus that directly infects bacteria, and phages' close associations and interactions with bacteria are essential for maintaining the stability of the gut bacterial community and the entire microbial ecosystem. Here, we utilized 99 published metagenomic datasets from 38 mammalian species to investigate the relationship (diversity and composition) and potential interactions between gut bacterial and phage communities and the impact of diet and phylogeny on these communities. Our results highlight the co-evolutionary potential of bacterial-phage interactions within the mammalian gut. We observed a higher alpha diversity in gut bacteria than in phages and identified positive correlations between bacterial and phage compositions. Furthermore, our study revealed the significant influence of diet and phylogeny on mammalian gut bacterial and phage communities. We discovered that the impact of dietary factors on these communities was more pronounced than that of phylogenetic factors at the order level. In contrast, phylogenetic characteristics had a more substantial influence at the family level. The similar omnivorous dietary preference and closer phylogenetic relationship (family Ursidae) may contribute to the similarity of gut bacterial and phage communities between captive giant panda populations (GPCD and GPYA) and omnivorous animals (OC; including Sun bear, brown bear, and Asian black bear). This study employed co-occurrence microbial network analysis to reveal the potential interaction patterns between bacteria and phages. Compared to other mammalian groups (carnivores, herbivores, and omnivores), the gut bacterial and phage communities of bamboo-eating species (giant pandas and red pandas) exhibited a higher level of interaction. Additionally, keystone species and modular analysis showed the potential role of phages in driving and maintaining the interaction patterns between bacteria and phages in captive giant pandas. In sum, gaining a comprehensive understanding of the interaction between the gut microbiota and phages in mammals is of great significance, which is of great value in promoting healthy and sustainable mammals and may provide valuable insights into the conservation of wildlife populations, especially endangered animal species.},
}

@article {pmid38674651,
year = {2024},
author = {Zhu, P and Hou, J and Xiong, Y and Xie, R and Wang, Y and Wang, F},
title = {Expanded Archaeal Genomes Shed New Light on the Evolution of Isoprenoid Biosynthesis.},
journal = {Microorganisms},
volume = {12},
number = {4},
pages = {},
doi = {10.3390/microorganisms12040707},
pmid = {38674651},
issn = {2076-2607},
support = {42230401//National Natural Science Foundation of China/ ; WH510244001//Shanghai Jiao Tong University 2030 Project/ ; 2023M742235//China Postdoctoral Science Foundation/ ; },
abstract = {Isoprenoids and their derivatives, essential for all cellular life on Earth, are particularly crucial in archaeal membrane lipids, suggesting that their biosynthesis pathways have ancient origins and play pivotal roles in the evolution of early life. Despite all eukaryotes, archaea, and a few bacterial lineages being known to exclusively use the mevalonate (MVA) pathway to synthesize isoprenoids, the origin and evolutionary trajectory of the MVA pathway remain controversial. Here, we conducted a thorough comparison and phylogenetic analysis of key enzymes across the four types of MVA pathway, with the particular inclusion of metagenome assembled genomes (MAGs) from uncultivated archaea. Our findings support an archaeal origin of the MVA pathway, likely postdating the divergence of Bacteria and Archaea from the Last Universal Common Ancestor (LUCA), thus implying the LUCA's enzymatic inability for isoprenoid biosynthesis. Notably, the Asgard archaea are implicated in playing central roles in the evolution of the MVA pathway, serving not only as putative ancestors of the eukaryote- and Thermoplasma-type routes, but also as crucial mediators in the gene transfer to eukaryotes, possibly during eukaryogenesis. Overall, this study advances our understanding of the origin and evolutionary history of the MVA pathway, providing unique insights into the lipid divide and the evolution of early life.},
}

@article {pmid38674647,
year = {2024},
author = {Wu, J and Xu, W and Xu, Y and Su, H and Hu, X and Cao, Y and Zhang, J and Wen, G},
title = {Impact of Organic Carbons Addition on the Enrichment Culture of Nitrifying Biofloc from Aquaculture Water: Process, Efficiency, and Microbial Community.},
journal = {Microorganisms},
volume = {12},
number = {4},
pages = {},
doi = {10.3390/microorganisms12040703},
pmid = {38674647},
issn = {2076-2607},
support = {NSFC 32373135//National Natural Science Foundation of China/ ; },
abstract = {In this study, we developed a rapid and effective method for enriching the culture of nitrifying bioflocs (NBF) from aquacultural brackish water. The self-designed mixotrophic mediums with a single or mixed addition of sodium acetate, sodium citrate, and sucrose were used to investigate the enrichment process and nitrification efficiency of NBF in small-scale reactors. The results showed that NBF with an MLVSSs from 1170.4 mg L[-1] to 2588.0 mg L[-1] were successfully enriched in a period of less than 16 days. The citrate group performed the fastest enrichment time of 10 days, while the sucrose group had the highest biomass of 2588.0 ± 384.7 mg L[-1]. In situ testing showed that the highest nitrification efficiency was achieved in the citrate group, with an ammonia oxidation rate of 1.45 ± 0.34 mg N L[-1] h[-1], a net nitrification rate of 2.02 ± 0.20 mg N L[-1] h[-1], and a specific nitrification rate of 0.72 ± 0.14 mg N g[-1] h[-1]. Metagenomic sequencing revealed that Nitrosomonas (0.0~1.0%) and Nitrobacter (10.1~26.5%) were dominant genera for AOB and NOB, respectively, both of which had the highest relative abundances in the citrate group. Linear regression analysis further demonstrated significantly positive linear relations between nitrification efficiencies and nitrifying bacterial genera and gene abundance in NBF. The results of this study provide an efficient enrichment culture method of NBF for the operation of biofloc technology aquaculture systems, which will further promote its wide application in modern intensive aquaculture.},
}

@article {pmid38674632,
year = {2024},
author = {Couto, RDS and Abreu, WU and Rodrigues, LRR and Marinho, LF and Morais, VDS and Villanova, F and Pandey, RP and Deng, X and Delwart, E and da Costa, AC and Leal, E},
title = {Genomoviruses in Liver Samples of Molossus molossus Bats.},
journal = {Microorganisms},
volume = {12},
number = {4},
pages = {},
doi = {10.3390/microorganisms12040688},
pmid = {38674632},
issn = {2076-2607},
abstract = {CRESS-DNA encompasses a broad spectrum of viruses documented across diverse organisms such as animals, plants, diatoms, fungi, and marine invertebrates. Despite this prevalence, the full extent of these viruses' impact on the environment and their respective hosts remains incompletely understood. Furthermore, an increasing number of viruses within this category lack detailed characterization. This investigation focuses on unveiling and characterizing viruses affiliated with the Genomoviridae family identified in liver samples from the bat Molossus molossus. Leveraging viral metagenomics, we identified seven sequences (MmGmV-PA) featuring a circular DNA genome housing two ORFs encoding replication-associated protein (Rep) and capsid protein (Cap). Predictions based on conserved domains typical of the Genomoviridae family were established. Phylogenetic analysis revealed the segregation of these sequences into two clades aligning with the genera Gemycirculavirus (MmGmV-06-PA and MmGmV-07-PA) and Gemykibivirus (MmGmV-01-PA, MmGmV-02-PA, MmGmV-03-PA, MmGmV-05-PA, and MmGmV-09-PA). At the species level, pairwise comparisons based on complete nucleotide sequences indicated the potential existence of three novel species. In summary, our study significantly contributes to an enhanced understanding of the diversity of Genomoviridae within bat samples, shedding light on previously undiscovered viral entities and their potential ecological implications.},
}

@article {pmid38673740,
year = {2024},
author = {Matys, J and Kensy, J and Gedrange, T and Zawiślak, I and Grzech-Leśniak, K and Dobrzyński, M},
title = {A Molecular Approach for Detecting Bacteria and Fungi in Healthcare Environment Aerosols: A Systematic Review.},
journal = {International journal of molecular sciences},
volume = {25},
number = {8},
pages = {},
doi = {10.3390/ijms25084154},
pmid = {38673740},
issn = {1422-0067},
mesh = {*Fungi/genetics ; *Aerosols ; *Bacteria/genetics/classification/isolation & purification ; *Air Microbiology ; Humans ; Health Facilities ; },
abstract = {Molecular methods have become integral to microbiological research for microbial identification. This literature review focuses on the application of molecular methods in examining airborne bacteria and fungi in healthcare facilities. In January 2024, a comprehensive electronic search was carried out in esteemed databases including PubMed, Web of Science, and Scopus, employing carefully selected keywords such as ((bacteria) OR (virus) OR (fungi)) AND (aerosol) AND ((hospital) OR (healthcare) OR (dental office)) AND ((molecular) OR (PCR) OR (NGS) OR (RNA) OR (DNA) OR (metagenomic) OR (microarray)), following the PRISMA protocol. The review specifically targets healthcare environments with elevated concentrations of pathogenic bacteria. A total of 487 articles were initially identified, but only 13 met the inclusion criteria and were included in the review. The study disclosed that the prevalent molecular methodology for appraising aerosol quality encompassed the utilization of the PCR method, incorporating either 16S rRNA (bacteria) or 18S rRNA (fungi) amplification techniques. Notably, five diverse molecular techniques, specifically PFGE, DGGE, SBT, LAMP, and DNA hybridization methods, were implemented in five distinct studies. These molecular tests exhibited superior capabilities compared to traditional bacterial and fungal cultures, providing precise strain identification. Additionally, the molecular methods allowed the detection of gene sequences associated with antibiotic resistance. In conclusion, molecular testing offers significant advantages over classical microbiological culture, providing more comprehensive information.},
}

*Fungi/genetics
*Aerosols
*Bacteria/genetics/classification/isolation & purification
*Air Microbiology
Humans
Health Facilities

@article {pmid38672848,
year = {2024},
author = {Tenea, GN and Reyes, P and Molina, D},
title = {Fungal Mycobiome of Mature Strawberry Fruits (Fragaria x ananassa Variety 'Monterey') Suggests a Potential Market Site Contamination with Harmful Yeasts.},
journal = {Foods (Basel, Switzerland)},
volume = {13},
number = {8},
pages = {},
doi = {10.3390/foods13081175},
pmid = {38672848},
issn = {2304-8158},
support = {7874/2023//Universidad Técnica del Norte/ ; },
abstract = {An amplicon metagenomic approach based on the ITS2 region of fungal rDNA was used to investigate the diversity of fungi associated with mature strawberries collected from a volcanic orchard and open-air market stands. Based on the Kruskal-Wallis test, no statistically significant differences were observed in both non-phylogenetic and phylogenetic alpha diversity indices. According to beta diversity analyses, significant differences in fungal communities were found between groups (orchard vs. market). Taxonomic assignment of amplicon sequence variables (ASVs) revealed 7 phyla and 31 classes. The prevalent fungal phyla were Basidiomycota (29.59-84.58%), Ascomycota (15.33-70.40%), and Fungi-phy-Insertae-sedis (0.45-2.89%). The most predominant classes among the groups were Saccharomycetes in the market group, and Microbotryomycetes and Tremellomycetes in the orchard group. Based on the analysis of microbiome composition (ANCOM), we found that the most differentially fungal genera were Hanseniaspora, Kurtzmaniella, and Phyllozyma. Endophytic yeasts Curvibasidium cygneicollum were prevalent in both groups, while Candida railenensis was detected in fruits originating only from the market. In addition, Rhodotorula graminis (relative abundance varying from 1.7% to 21.18%) and Papiliotrema flavescens (relative abundance varying from 1.58% to 16.55%) were detected in all samples regardless of origin, while Debaryomyces prosopidis was detected in samples from the market only, their relative abundance varying with the sample (from 0.80% to 19.23%). Their role in fruit quality and safety has not been yet documented. Moreover, several clinically related yeasts, such as Meyerozyma guilliermondii and Candida parapsilosis, were detected in samples only from the market. Understanding the variety and makeup of the mycobiome in ripe fruits during the transition from the orchard to the market is crucial for fruit safety after harvest.},
}

@article {pmid38672421,
year = {2024},
author = {Zhang, L and Tang, X and Fan, C and Ren, S and Cheng, Q and Zhou, H and Liu, K and Jia, S and Zhang, Y},
title = {Dysbiosis of Gut Microbiome Aggravated Male Infertility in Captivity of Plateau Pika.},
journal = {Biomolecules},
volume = {14},
number = {4},
pages = {},
doi = {10.3390/biom14040403},
pmid = {38672421},
issn = {2218-273X},
support = {LHZX-2023-02//Sanjiangyuan National Park Collaborative Research Special Fund/ ; 31670394, U21A20186//National Natural Science Foundation of China/ ; 2021-ZJ-Y01//Qinghai innovation platform construction project by Chinese Academy of Sciences/ ; },
mesh = {Animals ; Male ; *Gastrointestinal Microbiome ; *Dysbiosis/microbiology/metabolism ; *Infertility, Male/microbiology/metabolism ; *Testosterone/metabolism ; *Lagomorpha/microbiology ; Testis/microbiology/metabolism ; Fatty Acids, Volatile/metabolism ; },
abstract = {Captivity is an important and efficient technique for rescuing endangered species. However, it induces infertility, and the underlying mechanism remains obscure. This study used the plateau pika (Ochotona curzoniae) as a model to integrate physiological, metagenomic, metabolomic, and transcriptome analyses and explore whether dysbiosis of the gut microbiota induced by artificial food exacerbates infertility in captive wild animals. Results revealed that captivity significantly decreased testosterone levels and the testicle weight/body weight ratio. RNA sequencing revealed abnormal gene expression profiles in the testicles of captive animals. The microbial α-diversity and Firmicutes/Bacteroidetes ratio were drastically decreased in the captivity group. Bacteroidetes and Muribaculaceae abundance notably increased in captive pikas. Metagenomic analysis revealed that the alteration of flora increased the capacity for carbohydrate degradation in captivity. The levels of microbe metabolites' short-chain fatty acids (SCFAs) were significantly high in the captive group. Increasing SCFAs influenced the immune response of captivity plateau pikas; pro-inflammatory cytokines were upregulated in captivity. The inflammation ultimately contributed to male infertility. In addition, a positive correlation was observed between Gastranaerophilales family abundance and testosterone concentration. Our results provide evidence for the interactions between artificial food, the gut microbiota, and male infertility in pikas and benefit the application of gut microbiota interference in threatened and endangered species.},
}

Animals
Male
*Gastrointestinal Microbiome
*Dysbiosis/microbiology/metabolism
*Infertility, Male/microbiology/metabolism
*Testosterone/metabolism
*Lagomorpha/microbiology
Testis/microbiology/metabolism
Fatty Acids, Volatile/metabolism

@article {pmid38672407,
year = {2024},
author = {Schiano-Lomoriello, D and Abicca, I and Contento, L and Gabrielli, F and Alfonsi, C and Di Pietro, F and Papa, FT and Ballesteros-Sánchez, A and Sánchez-González, JM and Rocha-De-Lossada, C and Mazzotta, C and Giannaccare, G and Bonzano, C and Borroni, D},
title = {Infectious Keratitis: Characterization of Microbial Diversity through Species Richness and Shannon Diversity Index.},
journal = {Biomolecules},
volume = {14},
number = {4},
pages = {},
doi = {10.3390/biom14040389},
pmid = {38672407},
issn = {2218-273X},
mesh = {*Keratitis/microbiology ; Humans ; *Biodiversity ; Bacteria/genetics/classification/isolation & purification ; DNA, Bacterial/genetics ; Microbiota/genetics ; },
abstract = {Purpose: To characterize microbial keratitis diversity utilizing species richness and Shannon Diversity Index. Methods: Corneal impression membrane was used to collect samples. All swabs were processed and analyzed by Biolab Laboratory (level V-SSN Excellence: ISO 9001:2015), Biolab Srl (Ascoli Piceno, Italy). DNA extraction, library preparation, and sequencing were performed in all samples. After sequencing, low-quality and polyclonal sequences were filtered out by the Ion software. At this point, we employed Kraken2 for microbial community analysis in keratitis samples. Nuclease-free water and all the reagents included in the experiment were used as a negative control. The primary outcome was the reduction in bacterial DNA (microbial load) at T1, expressed as a percentage of the baseline value (T0). Richness and Shannon alpha diversity metrics, along with Bray-Curtis beta diversity values, were calculated using the phyloseq package in R. Principal coordinate analysis was also conducted to interpret these metrics. Results: 19 samples were included in the study. The results exhibited a motley species richness, with the highest recorded value surpassing 800 species. Most of the samples displayed richness values ranging broadly from under 200 to around 600, indicating considerable variability in species count among the keratitis samples. Conclusions: A significant presence of both typical and atypical bacterial phyla in keratitis infections, underlining the complexity of the disease's microbial etiology.},
}

*Keratitis/microbiology
Humans
*Biodiversity
Bacteria/genetics/classification/isolation & purification
DNA, Bacterial/genetics
Microbiota/genetics

@article {pmid38672329,
year = {2024},
author = {Zhao, H and Mo, Q and Kulyar, MF and Guan, J and Zhang, X and Luo, X and Li, J},
title = {Metagenomic Analysis Reveals A Gut Microbiota Structure and Function Alteration between Healthy and Diarrheic Juvenile Yaks.},
journal = {Animals : an open access journal from MDPI},
volume = {14},
number = {8},
pages = {},
doi = {10.3390/ani14081181},
pmid = {38672329},
issn = {2076-2615},
support = {2022YFN0037//Sichuan Provincial Department of Science and Technology/ ; 2021-NK-A5//Qinghai Science and Technology Major Program/ ; 2022YFD1601603//National Key Research and Development Program of China/ ; },
abstract = {Diarrhea-induced mortality among juvenile yaks is highly prevalent in the pastoral areas of the Qinghai-Tibet plateau. Although numerous diseases have been linked to the gut microbial community, little is known about how diarrhea affects the gut microbiota in yaks. In this work, we investigated and compared changes in the gut microbiota of juvenile yaks with diarrhea. The results demonstrated a considerable drop in the alpha diversity of the gut microbiota in diarrheic yaks, accompanied by Eysipelatoclostridium, Parabacteroides, and Escherichia-Shigella, which significantly increased during diarrhea. Furthermore, a PICRust analysis verified the elevation of the gut-microbial metabolic pathways in diarrhea groups, including glycine, serine, and threonine metabolism, alanine, aspartate, oxidative phosphorylation, glutamate metabolism, antibiotic biosynthesis, and secondary metabolite biosynthesis. Taken together, our study showed that the harmful bacteria increased, and beneficial bacteria decreased significantly in the gut microbiota of yaks with diarrhea. Moreover, these results also indicated that the dysbiosis of the gut microbiota may be a significant driving factor of diarrhea in yaks.},
}

@article {pmid38671923,
year = {2024},
author = {Yue, Y and Yang, HJ and Zhang, T and Li, C and Kim, MJ and Kim, KN and Park, S},
title = {Porcine Brain Enzyme Hydrolysate Enhances Immune Function and Antioxidant Defense via Modulation of Gut Microbiota in a Cyclophosphamide-Induced Immunodeficiency Model.},
journal = {Antioxidants (Basel, Switzerland)},
volume = {13},
number = {4},
pages = {},
doi = {10.3390/antiox13040476},
pmid = {38671923},
issn = {2076-3921},
support = {23-12//the "Food Functionality Evaluation program" under the Ministry of Agriculture, Food and Rural Affairs/ ; },
abstract = {This study examined how consuming porcine brain enzyme hydrolysate (PBEH) affects the immune function and composition of the gut microbiota in an immunodeficient animal model. Male Wistar rats aged 6 weeks were fed casein (control), 100 mg/kg body weight (BW), red ginseng extract (positive-control), and 6, 13, and 26 mg PBEH per kg BW (PBEH-L, PBEH-M, and PBEH-H, respectively) daily for 4 weeks. At 30 min after consuming assigned compounds, they were orally administered cyclophosphamide (CTX; 5 mg/kg BW), an immunosuppressive agent, to suppress the immune system by inhibiting the proliferation of lymphocytes. The normal-control rats were fed casein and water instead of CTX. Natural killer cell activity and splenocyte proliferation induced by 1 μg/mL lipopolysaccharide were lower in the control group than the normal-control group, and they significantly increased with PBEH consumption, particularly at high doses. The PBEH consumption increased dose-dependently in the Th1/Th2 ratio compared to the control. The lipid peroxide contents were lower in the PBEH group than in the control group. Moreover, PBEH m and PBEH-H consumption mitigated white pulp cell damage, reduced red pulp congestion, and increased spleen mast cells in the histological analysis. Intestinal microbiota composition demonstrated differences between the groups at the genus levels, with Akkermansia being more abundant in the control group than the normal-control group and the PBEH-H group showing a decrease. However, Bifidobacterium decreased in the control group but increased in the PBEH-H group. The β-diversity revealed distinct microbial communities of PBEH and positive-control groups compared to the control group (p < 0.05). The metagenome predictions revealed that PBEH-H influenced amino acid metabolism, antioxidant defense, insulin sensitivity, and longevity pathways. In conclusion, PBEH-H intake boosted immune responses and reduced lipid peroxides by modulating gut microbiota composition. These findings suggest that PBEH-H has the potential as a dietary supplement for improving immune function and gut health in individuals with immunodeficiency.},
}

@article {pmid38670851,
year = {2024},
author = {Chen, H and Zhan, M and Liu, S and Balloux, F and Wang, H},
title = {Unraveling the potential of metagenomic next-generation sequencing in infectious disease diagnosis: Challenges and prospects.},
journal = {Science bulletin},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.scib.2024.04.033},
pmid = {38670851},
issn = {2095-9281},
}

@article {pmid38670644,
year = {2024},
author = {Akinsuyi, OS and Xhumari, J and Ojeda, A and Roesch, LFW},
title = {Gut permeability among Astronauts during Space missions.},
journal = {Life sciences in space research},
volume = {41},
number = {},
pages = {171-180},
doi = {10.1016/j.lssr.2024.03.003},
pmid = {38670644},
issn = {2214-5532},
mesh = {*Space Flight ; *Astronauts ; Humans ; Animals ; *Permeability ; *Gastrointestinal Microbiome ; Mice ; Transcriptome ; Gastrointestinal Tract/microbiology ; },
abstract = {The space environment poses substantial challenges to human physiology, including potential disruptions in gastrointestinal health. Gut permeability has only recently become widely acknowledged for its potential to cause adverse effects on a systemic level, rendering it a critical factor to investigate in the context of spaceflight. Here, we propose that astronauts experience the onset of leaky gut during space missions supported by transcriptomic and metagenomic analysis of human and murine samples. A genetic map contributing to intestinal permeability was constructed from a systematic review of current literature. This was referenced against our re-analysis of three independent transcriptomic datasets which revealed significant changes in gene expression patterns associated with the gut barrier. Specifically, in astronauts during flight, we observed a substantial reduction in the expression genes that are crucial for intestinal barrier function, goblet cell development, gut microbiota modulation, and immune responses. Among rodent spaceflight studies, differential expression of cytokines, chemokines, and genes which regulate mucin production and post-translational modifications suggest a similar dysfunction of intestinal permeability. Metagenomic analysis of feces from two murine studies revealed a notable reduction probiotic, short chain fatty acid-producing bacteria and an increase in the Gram-negative pathogens, including Citrobacter rodentium, Enterobacter cloacea, Klebsiella aerogenes, and Proteus hauseri which promote LPS circulation, a recipe for barrier disruption and systemic inflammatory activation. These findings emphasize the critical need to understand the underlying mechanisms and develop interventions to maintain gastrointestinal health in space.},
}

*Space Flight
*Astronauts
Humans
Animals
*Permeability
*Gastrointestinal Microbiome
Mice
Transcriptome
Gastrointestinal Tract/microbiology

@article {pmid38670293,
year = {2024},
author = {Clagnan, E and Petrini, S and Pioli, S and Piergiacomo, F and Aziz Chowdhury, A and Brusetti, L and Foladori, P},
title = {Conventional activated sludge vs. photo-sequencing batch reactor for enhanced nitrogen removal in municipal wastewater: Microalgal-bacterial consortium and pathogenic load insights.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {130735},
doi = {10.1016/j.biortech.2024.130735},
pmid = {38670293},
issn = {1873-2976},
abstract = {Municipal wastewater treatment plants are mostly based on traditional activated sludge (AS) processes. These systems are characterised by major drawbacks: high energy consumption, large amount of excess sludge and high greenhouse gases emissions. Treatment through microalgal-bacterial consortia (MBC) is an alternative and promising solution thanks to lower energy consumption and emissions, biomass production and water sanitation. Here, microbial difference between a traditional anaerobic sludge (AS) and a consortium-based system (photo-sequencing batch reactor (PSBR)) with the same wastewater inlet were characterised through shotgun metagenomics. Stable nitrification was achieved in the PSBR ensuring ammonium removal > 95 % and significant total nitrogen removal thanks to larger flocs enhancing denitrification. The new system showed enhanced pathogen removal, a higher abundance of photosynthetic and denitrifying microorganisms with a reduced emissions potential identifying this novel PSBR as an effective alternative to AS.},
}