@article {pmid39434181,
year = {2024},
author = {Chen, CZ and Li, P and Liu, L and Sun, YJ and Ju, WM and Li, ZH},
title = {Seasonal variations of microbial communities and viral diversity in fishery-enhanced marine ranching sediments: insights into metabolic potentials and ecological interactions.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {209},
pmid = {39434181},
issn = {2049-2618},
support = {42277269//National Natural Science Foundation of China/ ; 42277269//National Natural Science Foundation of China/ ; 42277269//National Natural Science Foundation of China/ ; 42277269//National Natural Science Foundation of China/ ; KLMR-2022-03//Key Laboratory of Marine Ranching, Ministry of Agriculture and Rural Affairs, China/ ; KLMR-2022-03//Key Laboratory of Marine Ranching, Ministry of Agriculture and Rural Affairs, China/ ; KLMR-2022-03//Key Laboratory of Marine Ranching, Ministry of Agriculture and Rural Affairs, China/ ; KLMR-2022-03//Key Laboratory of Marine Ranching, Ministry of Agriculture and Rural Affairs, China/ ; },
abstract = {BACKGROUND: The ecosystems of marine ranching have enhanced marine biodiversity and ecological balance and have promoted the natural recovery and enhancement of fishery resources. The microbial communities of these ecosystems, including bacteria, fungi, protists, and viruses, are the drivers of biogeochemical cycles. Although seasonal changes in microbial communities are critical for ecosystem functioning, the current understanding of microbial-driven metabolic properties and their viral communities in marine sediments remains limited. Here, we employed amplicon (16S and 18S) and metagenomic approaches aiming to reveal the seasonal patterns of microbial communities, bacterial-eukaryotic interactions, whole metabolic potential, and their coupling mechanisms with carbon (C), nitrogen (N), and sulfur (S) cycling in marine ranching sediments. Additionally, the characterization and diversity of viral communities in different seasons were explored in marine ranching sediments.

RESULTS: The current study demonstrated that seasonal variations dramatically affected the diversity of microbial communities in marine ranching sediments and the bacterial-eukaryotic interkingdom co-occurrence networks. Metabolic reconstruction of the 113 medium to high-quality metagenome-assembled genomes (MAGs) was conducted, and a total of 8 MAGs involved in key metabolic genes and pathways (methane oxidation - denitrification - S oxidation), suggesting a possible coupling effect between the C, N, and S cycles. In total, 338 viral operational taxonomic units (vOTUs) were identified, all possessing specific ecological characteristics in different seasons and primarily belonging to Caudoviricetes, revealing their widespread distribution and variety in marine sediment ecosystems. In addition, predicted virus-host linkages showed that high host specificity was observed, with few viruses associated with specific hosts.

CONCLUSIONS: This finding deepens our knowledge of element cycling and viral diversity in fisheries enrichment ecosystems, providing insights into microbial-virus interactions in marine sediments and their effects on biogeochemical cycling. These findings have potential applications in marine ranching management and ecological conservation. Video Abstract.},
}

@article {pmid39434178,
year = {2024},
author = {van Gogh, M and Louwers, JM and Celli, A and Gräve, S and Viveen, MC and Bosch, S and de Boer, NKH and Verheijden, RJ and Suijkerbuijk, KPM and Brand, EC and Top, J and Oldenburg, B and de Zoete, MR},
title = {Next-generation IgA-SEQ allows for high-throughput, anaerobic, and metagenomic assessment of IgA-coated bacteria.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {211},
pmid = {39434178},
issn = {2049-2618},
abstract = {BACKGROUND: The intestinal microbiota plays a significant role in maintaining systemic and intestinal homeostasis, but can also influence diseases such as inflammatory bowel disease (IBD) and cancer. Certain bacterial species within the intestinal tract can chronically activate the immune system, leading to low-grade intestinal inflammation. As a result, plasma cells produce high levels of secretory antigen-specific immunoglobulin A (IgA), which coats the immunostimulatory bacteria. This IgA immune response against intestinal bacteria may be associated with the maintenance of homeostasis and health, as well as disease. Unraveling this dichotomy and identifying the immunostimulatory bacteria is crucial for understanding the relationship between the intestinal microbiota and the immune system, and their role in health and disease. IgA-SEQ technology has successfully identified immunostimulatory, IgA-coated bacteria from fecal material. However, the original technology is time-consuming and has limited downstream applications. In this study, we aimed to develop a next-generation, high-throughput, magnet-based sorting approach (ng-IgA-SEQ) to overcome the limitations of the original IgA-SEQ protocol.

RESULTS: We show, in various settings of complexity ranging from simple bacterial mixtures to human fecal samples, that our magnetic 96-well plate-based ng-IgA-SEQ protocol is highly efficient at sorting and identifying IgA-coated bacteria in a high-throughput and time efficient manner. Furthermore, we performed a comparative analysis between different IgA-SEQ protocols, highlighting that the original FACS-based IgA-SEQ approach overlooks certain nuances of IgA-coated bacteria, due to the low yield of sorted bacteria. Additionally, magnetic-based ng-IgA-SEQ allows for novel downstream applications. Firstly, as a proof-of-concept, we performed metagenomic shotgun sequencing on 10 human fecal samples to identify IgA-coated bacterial strains and associated pathways and CAZymes. Secondly, we successfully isolated and cultured IgA-coated bacteria by performing the isolation protocol under anaerobic conditions.

CONCLUSIONS: Our magnetic 96-well plate-based high-throughput next-generation IgA-SEQ technology efficiently identifies a great number of IgA-coated bacteria from fecal samples. This paves the way for analyzing large cohorts as well as novel downstream applications, including shotgun metagenomic sequencing, culturomics, and various functional assays. These downstream applications are essential to unravel the role of immunostimulatory bacteria in health and disease. Video Abstract.},
}

@article {pmid39433961,
year = {2024},
author = {Li, J and Shen, N and He, W and Pan, Y and Wu, J and Zhao, R and Mo, X and Li, Y},
title = {Gut microbiome impact on childhood allergic rhinitis and house dust mite IgE responses.},
journal = {Pediatric research},
volume = {},
number = {},
pages = {},
pmid = {39433961},
issn = {1530-0447},
abstract = {BACKGROUND: The correlation between the gut microbiota and airway inflammation in childhood allergic rhinitis (AR), particularly concerning allergen exposure, remains insufficiently explored. This study aimed to link gut microbiota changes with house dust mite (HDM)-specific IgE responses in pediatric AR.

METHODS: Using metagenomic shotgun sequencing, we compared the fecal microbiota of 60 children with HDM-AR to 48 healthy controls (HC), analyzing the link to IgE reactions. We examined the effects of oral Escherichia (E.) fergusonii treatment in mice sensitized with ovalbumin and HDM on allergic symptoms, mucosal cell infiltration, Th1/Th2/Tregs balance in the spleen, serum cytokine levels, and E. fergusonii presence in feces.

RESULTS: Children with HDM-AR have a less diverse gut microbiome and lower levels of E. fergusonii compared to controls, with a negative correlation between E. fergusonii abundance and HDM-specific IgE levels. In mice sensitized with OVA and HDM, oral administration of E. fergusonii improved allergic symptoms, reduced nasal eosinophils/mast cells infiltration and adjusted Th cell populations towards a non-allergic profile in splenic lymphocytes with exception of IFN-γ change in serum.

CONCLUSION: These findings underline the potential of targeting gut microbiota, particularly E. fergusonii, in managing childhood HDM-AR, suggesting a promising approach for future interventions.

IMPACT: The composition and distribution of gut microbiota in children with HDM-AR are significant changed. The abundance of Escherichia genus is decreased in HDM-AR children. HDM-specific IgE levels are strongly negatively associated with E. fergusonii abundance. Oral administration of E. fergusonii effectively suppresses allergic responses in murine model. These findings offer novel insights into the diagnosis and treatment of HDM-AR, which suggested that E. fergusonii holds promise as a potential therapeutic avenue for managing HDM-AR.},
}

@article {pmid39433727,
year = {2024},
author = {Lemaire, ON and Wegener, G and Wagner, T},
title = {Ethane-oxidising archaea couple CO2 generation to F420 reduction.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {9065},
pmid = {39433727},
issn = {2041-1723},
support = {WA 4053/2-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; WE 5492/1-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; WA 4053/1-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; },
mesh = {*Oxidation-Reduction ; *Carbon Dioxide/metabolism ; *Ethane/metabolism/chemistry ; Archaea/metabolism/genetics ; Aldehyde Oxidoreductases/metabolism/genetics/chemistry ; Multienzyme Complexes/metabolism/genetics/chemistry ; Crystallography, X-Ray ; Archaeal Proteins/metabolism/genetics/chemistry ; Anaerobiosis ; Ferredoxins/metabolism ; Riboflavin/analogs & derivatives ; },
abstract = {The anaerobic oxidation of alkanes is a microbial process that mitigates the flux of hydrocarbon seeps into the oceans. In marine archaea, the process depends on sulphate-reducing bacterial partners to exhaust electrons, and it is generally assumed that the archaeal CO2-forming enzymes (CO dehydrogenase and formylmethanofuran dehydrogenase) are coupled to ferredoxin reduction. Here, we study the molecular basis of the CO2-generating steps of anaerobic ethane oxidation by characterising native enzymes of the thermophile Candidatus Ethanoperedens thermophilum obtained from microbial enrichment. We perform biochemical assays and solve crystal structures of the CO dehydrogenase and formylmethanofuran dehydrogenase complexes, showing that both enzymes deliver electrons to the F420 cofactor. Both multi-metalloenzyme harbour electronic bridges connecting CO and formylmethanofuran oxidation centres to a bound flavin-dependent F420 reductase. Accordingly, both systems exhibit robust coupled F420-reductase activities, which are not detected in the cell extract of related methanogens and anaerobic methane oxidisers. Based on the crystal structures, enzymatic activities, and metagenome mining, we propose a model in which the catabolic oxidising steps would wire electron delivery to F420 in this organism. Via this specific adaptation, the indirect electron transfer from reduced F420 to the sulphate-reducing partner would fuel energy conservation and represent the driving force of ethanotrophy.},
}

*Oxidation-Reduction
*Carbon Dioxide/metabolism
*Ethane/metabolism/chemistry
Archaea/metabolism/genetics
Aldehyde Oxidoreductases/metabolism/genetics/chemistry
Multienzyme Complexes/metabolism/genetics/chemistry
Crystallography, X-Ray
Archaeal Proteins/metabolism/genetics/chemistry
Anaerobiosis
Ferredoxins/metabolism
Riboflavin/analogs & derivatives

@article {pmid39433639,
year = {2024},
author = {Davidson, IM and Nikbakht, E and Haupt, LM and Ashton, KJ and Dunn, PJ},
title = {Methodological approaches in 16S sequencing of female reproductive tract in fertility patients: a review.},
journal = {Journal of assisted reproduction and genetics},
volume = {},
number = {},
pages = {},
pmid = {39433639},
issn = {1573-7330},
abstract = {BACKGROUND: The female genital tract microbiome has become a particular area of interest in improving assisted reproductive technology (ART) outcomes with the emergence of next-generation sequencing (NGS) technology. However, NGS assessment of microbiomes currently lacks uniformity and poses significant challenges for accurate and precise bacterial population representation.

OBJECTIVE: As multiple NGS platforms and assays have been developed in recent years for microbiome investigation-including the advent of long-read sequencing technologies-this work aimed to identify current trends and practices undertaken in female genital tract microbiome investigations.

RESULTS: Areas like sample collection and transport, DNA extraction, 16S amplification vs. metagenomics, NGS library preparation, and bioinformatic analysis demonstrated a detrimental lack of uniformity. The lack of uniformity present is a significant limitation characterised by gap discrepancies in generation and interpretation of results. Minimal consistency was observed in primer design, DNA extraction techniques, sample transport, and bioinformatic analyses.

CONCLUSION: With third-generation sequencing technology highlighted as a promising tool in microbiota-based research via full-length 16S rRNA sequencing, there is a desperate need for future studies to investigate and optimise methodological approaches of the genital tract microbiome to ensure better uniformity of methods and results interpretation to improve clinical impact.},
}

@article {pmid39432998,
year = {2024},
author = {Ma, ZS and Li, L},
title = {Identifications of the potential in-silico biomarkers in lung cancer tissue microbiomes.},
journal = {Computers in biology and medicine},
volume = {183},
number = {},
pages = {109231},
doi = {10.1016/j.compbiomed.2024.109231},
pmid = {39432998},
issn = {1879-0534},
abstract = {It is postulated that the tumor tissue microbiome is one of the enabling characteristics that can either promote or suppress the ability of tumors to acquire certain hallmarks of cancer. This underscores its critical importance in carcinogenesis, cancer progression, and therapy responses. However, characterizing the tumor microbiomes is extremely challenging because of their low biomass and severe difficulties in controlling laboratory-borne contaminants, which is further aggravated by lack of comprehensively effective computational approaches to identify unique or enriched microbial species associated with cancers. Here we take advantage of a recent computational framework by Ma (2024), termed metagenome comparison (MC) framework (MCF), which can detect treatment-specific, unique or enriched OMUs (operational metagenomic unit), or US/ES (unique/enriched species) when adapted for this study. We apply the MCF to reanalyze four lung cancer tissue microbiome datasets, which include samples from Lung Adenocarcinoma (LUAD), Lung Squamous Cell Carcinoma (LUSC), and their adjacent normal tissue (NT) controls. Our analysis is structured around three distinct schemes: Scheme I-separately detecting the US/ES for each of the four lung cancer microbiome datasets; Scheme II-consolidation of the four datasets followed by detection of US/ES in the combined datasets; Scheme III-construction of the union and intersection sets of US/ES derived from the results of the preceding two schemes. The generated lists of US/ES, including enriched microbial phyla, likely hold significant biomedical value for developing diagnostic and prognostic biomarkers for lung cancer risk assessment, improving the efficacy of immunotherapy, and designing novel microbiome-based therapies in lung cancer research.},
}

@article {pmid39432940,
year = {2024},
author = {Aseem, A and Sagar, P and Reddy, NS and Veleri, S},
title = {The antimicrobial resistance profile in poultry of Central and Southern India is evolving with distinct features.},
journal = {Comparative immunology, microbiology and infectious diseases},
volume = {114},
number = {},
pages = {102255},
doi = {10.1016/j.cimid.2024.102255},
pmid = {39432940},
issn = {1878-1667},
abstract = {Antimicrobial resistance (AMR) is fast emerging and is depleting antibiotics repertoire. Poultry is a major source for AMR because focus to enhance its production by modern practices widely uses antibiotics. India and China are major producers of meat and have hotspots of AMR. The Central and Southern India were predicted as emerging hotspots for AMR in poultry but no data available to substantiate it. To this end, we collected chicken feces from poultry farms in these regions and isolated genomic DNA. Further, shotgun whole genome sequencing was performed for metagenomics analysis. For the first time, we report the AMR gene profiles in poultry from Kerala and Telangana. The samples exhibited a higher prevalence of gram-negative and anaerobic species. The high priority pathogens in India were detected, like E.coli, Clostridium perfringens, Klebsiella pneumonia Staphylococcus aureus, Enterococcous faecalis, Pseudomonas aeruginosa, Bacteriodes fragiles. Conspicuously, the Southern India had the highest abundance of AMR genes than the Central India. E.coli was significantly more prevalent in the southernmost zone of India than in other sites. Our data had many common AMR profile features of the European Union (EU) poultry farms but lacked mcr-1, which was a lately emerged AMR gene in E.coli. Our data revealed the extent of AMR gene evolved in the Central and Southern India. It is comparable to the EU data but severity is lesser than in the EU.},
}

@article {pmid39432783,
year = {2024},
author = {Oguro-Igashira, E and Murakami, M and Mori, R and Kuwahara, R and Kihara, T and Kohara, M and Fujiwara, M and Motooka, D and Okuzaki, D and Arase, M and Toyota, H and Peng, S and Ogino, T and Kitabatake, Y and Morii, E and Hirota, S and Ikeuchi, H and Umemoto, E and Kumanogoh, A and Takeda, K},
title = {The pyruvate-GPR31 axis promotes transepithelial dendrite formation in human intestinal dendritic cells.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {121},
number = {44},
pages = {e2318767121},
doi = {10.1073/pnas.2318767121},
pmid = {39432783},
issn = {1091-6490},
support = {JP21H050430//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; JP21K07895//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; JP21gm1010004//Japan Agency for Medical Research and Development (AMED)/ ; JPMJSP213//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; J178501002//BD Biosciences (Becton Dickenson Biosciences)/ ; },
mesh = {Humans ; *Receptors, G-Protein-Coupled/metabolism ; *Dendritic Cells/metabolism ; *Pyruvic Acid/metabolism ; Intestinal Mucosa/metabolism/cytology ; Dendrites/metabolism ; Gastrointestinal Microbiome ; Signal Transduction ; Induced Pluripotent Stem Cells/metabolism/cytology ; Organoids/metabolism ; Intestines/cytology ; },
abstract = {The intestinal lumen is rich in gut microbial metabolites that serve as signaling molecules for gut immune cells. G-protein-coupled receptors (GPCRs) sense metabolites and can act as key mediators that translate gut luminal signals into host immune responses. However, the impacts of gut microbe-GPCR interactions on human physiology have not been fully elucidated. Here, we show that GPR31, which is activated by the gut bacterial metabolite pyruvate, is specifically expressed on type 1 conventional dendritic cells (cDC1s) in the lamina propria of the human intestine. Using human induced pluripotent stem cell-derived cDC1s and a monolayer human gut organoid coculture system, we show that cDC1s extend their dendrites toward pyruvate on the luminal side, forming transepithelial dendrites (TED). Accordingly, GPR31 activation via pyruvate enhances the fundamental function of cDC1 by allowing efficient uptake of gut luminal antigens, such as dietary compounds and bacterial particles through TED formation. Our results highlight the role of GPCRs in tuning the human gut immune system according to local metabolic cues.},
}

Humans
*Receptors, G-Protein-Coupled/metabolism
*Dendritic Cells/metabolism
*Pyruvic Acid/metabolism
Intestinal Mucosa/metabolism/cytology
Dendrites/metabolism
Gastrointestinal Microbiome
Signal Transduction
Induced Pluripotent Stem Cells/metabolism/cytology
Organoids/metabolism
Intestines/cytology

@article {pmid39432658,
year = {2024},
author = {Liu, B and Dai, W and Wei, J and Sun, S and Chen, W and Deng, Y},
title = {Knowledge framework and emerging trends of invasive pulmonary fungal infection: A bibliometric analysis (2003-2023).},
journal = {Medicine},
volume = {103},
number = {42},
pages = {e40068},
doi = {10.1097/MD.0000000000040068},
pmid = {39432658},
issn = {1536-5964},
mesh = {Humans ; *Bibliometrics ; Invasive Fungal Infections/epidemiology ; Lung Diseases, Fungal/epidemiology/microbiology ; COVID-19/epidemiology ; },
abstract = {The rising number of immunocompromised people has increased concerns about fungal infections as a severe public health issue. Invasive pulmonary fungal infections (IPFIs) are prevalent and often fatal, particularly for those with weakened immune systems. Understanding IPFIs is crucial. The work aims to offer a concise overview of the field's characteristics, main research areas, development paths, and trends. This study searched the Web of Science Core Collection on June 5, 2024, collecting relevant academic works from 2003 to 2023. Analysis was conducted using CiteSpace, VOSviewer, Bibliometrix Package in R, Microsoft Excel 2019, and Scimago Graphica. The study indicated that the USA, the University of Manchester, and Denning DW led in productivity and impact, while the Journal of Fungi topped the list in terms of publication volume and citations. High-frequency terms include "fungal infection," "invasive," "diagnosis," and "epidemiology." Keyword and trend analysis identified "influenza," "COVID-19," "invasive pulmonary aspergillosis," and "metagenomic next-generation sequencing" as emerging research areas. Over the last 2 decades, research on IPFI has surged, with topics becoming more profound. These insights offer key guidance on current trends, gaps, and the trajectory of IPFI studies.},
}

Humans
*Bibliometrics
Invasive Fungal Infections/epidemiology
Lung Diseases, Fungal/epidemiology/microbiology
COVID-19/epidemiology

@article {pmid39432094,
year = {2024},
author = {Shafana Farveen, M and Narayanan, R},
title = {Omic-driven strategies to unveil microbiome potential for biodegradation of plastics: a review.},
journal = {Archives of microbiology},
volume = {206},
number = {11},
pages = {441},
pmid = {39432094},
issn = {1432-072X},
mesh = {*Biodegradation, Environmental ; *Plastics/metabolism ; *Microbiota ; Bacteria/metabolism/genetics/classification ; Proteomics ; Genomics ; Microbial Consortia ; },
abstract = {Plastic waste accumulation has lately been identified as the leading and pervasive environmental concern, harming all living beings, natural habitats, and the global market. Given this issue, developing ecologically friendly solutions, such as biodegradation instead of standard disposal, is critical. To effectively address and develop better strategies, it is critical to understand the inter-relationship between microorganisms and plastic, the role of genes and enzymes involved in this process. However, the complex nature of microbial communities and the diverse mechanisms involved in plastic biodegradation have hindered the development of efficient plastic waste degradation strategies. Omics-driven approaches, encompassing genomics, transcriptomics and proteomics have revolutionized our understanding of microbial ecology and biotechnology. Therefore, this review explores the application of omics technologies in plastic degradation studies and discusses the key findings, challenges, and future prospects of omics-based approaches in identifying novel plastic-degrading microorganisms, enzymes, and metabolic pathways. The integration of omics technologies with advanced molecular technologies such as the recombinant DNA technology and synthetic biology would guide in the optimization of microbial consortia and engineering the microbial systems for enhanced plastic biodegradation under various environmental conditions.},
}

*Biodegradation, Environmental
*Plastics/metabolism
*Microbiota
Bacteria/metabolism/genetics/classification
Proteomics
Genomics
Microbial Consortia

@article {pmid39432083,
year = {2024},
author = {Xu, X and Liu, X and Liu, L and Chen, J and Guan, J and Luo, D},
title = {Metagenomic and transcriptomic profiling of the hypoglycemic and hypotriglyceridemic actions of Tremella fuciformis-derived polysaccharides in high-fat-diet- and streptozotocin-treated mice.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d4fo01870b},
pmid = {39432083},
issn = {2042-650X},
abstract = {Mushroom polysaccharides have great anti-diabetes potential. The fruiting body of Tremella fuciformis is rich in polysaccharides. However, few studies have been performed to date on T. fuciformis-derived polysaccharides (TPs) in terms of anti-diabetes potential. Our previous studies showed that novel TPs with medium molecular weights exhibited the highest anti-skin aging activities among the tested samples in D-galactose-treated mice. In the present study, the effects of these novel TPs, named TP, on high-fat-diet- and streptozotocin-treated mice were assessed, and their potential biological mechanisms were explored by metagenomic and transcriptomic analyses. Oral administration of TP markedly reduced blood glucose and TG levels, alleviated emaciation, improved anti-oxidant capacity, and protected the functions of β-cells at a dose of 100 mg kg[-1] in diabetic mice. Meanwhile, the taxonomic compositions and functional properties of fecal microbiota were altered considerably by TP, as evidenced by partial restoration of the imbalanced gut microbiota and the higher abundances of Bacteroides, Phocaeicola, Bifidobacterium, and Alistipes compared to the model mice, corresponding to the upregulation of four enriched KEGG pathways of microbial communities such as the digestive system, cardiovascular disease, parasitic infectious disease, and cell growth and death. Further transcriptomic analysis of liver tissues identified 35 enriched KEGG pathways associated with metabolism and cellular signaling processes in response to TP. These results demonstrated the biological mechanisms underlying the hypoglycemic and hypotriglyceridemic activities of TP. The findings expanded our understanding of the anti-diabetic mechanisms for mushroom polysaccharides and provided new clues for future studies.},
}

@article {pmid39431871,
year = {2024},
author = {Tuladhar, ET and Chalise, BS and Khadka, B and Tamang, M and Neupane, J and Poudel, S and Droit, L and Mihindukulasuriya, KA and Elong Ngono, A and Basaula, YN and Shresta, S and Wang, D and Manandhar, KD},
title = {Human immunodeficiency virus-1 genome from patient with fever, Nepal.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0076824},
doi = {10.1128/mra.00768-24},
pmid = {39431871},
issn = {2576-098X},
abstract = {A patient with fever presented to the referral infectious disease hospital in Kathmandu, Nepal. Metagenomic sequencing of the patient's serum recovered a near-complete genome of human immunodeficiency virus-1 (HIV-1), distinct from previous HIV-1 genomes from Nepal in GenBank. It shared 92.48% nucleotide identity with an HIV-1 subtype C isolate from India.},
}

@article {pmid39431789,
year = {2024},
author = {Bickerstaff, JRM and Walsh, T and Court, L and Pandey, G and Ireland, K and Cousins, D and Caron, V and Wallenius, T and Slipinski, A and Rane, R and Escalona, HE},
title = {Chromosome structural rearrangements in invasive haplodiploid ambrosia beetles revealed by the genomes of Euwallacea fornicatus (Eichhoff) and Euwallacea similis (Ferrari) (Coleoptera, Curculionidae, Scolytinae).},
journal = {Genome biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/gbe/evae226},
pmid = {39431789},
issn = {1759-6653},
abstract = {Bark and ambrosia beetles are among the most ecologically and economically damaging introduced plant pests worldwide. Life history traits including polyphagy, haplodiploidy, inbreeding polygyny and symbiosis with fungi contribute to their dispersal and impact. Species vary in their interactions with host trees, with many attacking stressed or recently dead trees, such as the globally distributed E. similis (Ferrari). Other species, like the Polyphagous Shot Hole Borer (PSHB) Euwallacea fornicatus (Eichhoff), can attack over 680 host plants and is causing considerable economic damage in several countries. Despite their notoriety, publicly accessible genomic resources for Euwallacea Hopkins species are scarce, hampering our understanding of their invasive capabilities as well as modern control measures, surveillance and management. Using a combination of long and short read sequencing platforms we assembled and annotated high quality (BUSCO > 98% complete) pseudo-chromosome level genomes for these species. Comparative macro-synteny analysis identified an increased number of pseudo-chromosome scaffolds in the haplodiploid inbreeding species of Euwallacea compared to diploid outbred species, due to fission events. This suggests that life history traits can impact chromosome structure. Further, the genome of E. fornicatus had a higher relative proportion of repetitive elements, up to 17% more, than E. similis. Metagenomic assembly pipelines identified microbiota associated with both species including Fusarium fungal symbionts and a novel Wolbachia strain. These novel genomes of haplodiploid inbreeding species will contribute to the understanding of how life history traits are related to their evolution and to the management of these invasive pests.},
}

@article {pmid39431768,
year = {2024},
author = {Tutagata, J and Pocquet, N and Trouche, B and Reveillaud, J},
title = {Dissection of Mosquito Ovaries, Midgut, and Salivary Glands for Microbiome Analyses at the Organ Level.},
journal = {Journal of visualized experiments : JoVE},
volume = {},
number = {212},
pages = {},
doi = {10.3791/67128},
pmid = {39431768},
issn = {1940-087X},
mesh = {Animals ; Female ; *Salivary Glands/microbiology ; *Microbiota/physiology ; *Ovary/microbiology ; Dissection/methods ; Culicidae/microbiology ; },
abstract = {The global burden of mosquito-transmitted diseases, including malaria, dengue, West Nile, Zika, Usutu, and yellow fever, continues to increase, posing a significant public health threat. With the rise of insecticide resistance and the absence of effective vaccines, new strategies are emerging that focus on the mosquito's microbiota. Nevertheless, the majority of symbionts remain resistant to cultivation. Characterizing the diversity and function of bacterial genomes in mosquito specimens, therefore, relies on metagenomics and subsequent assembly and binning strategies. The obtention and analysis of Metagenome-Assembled Genomes (MAGs) from separated organs can notably provide key information about the specific role of mosquito-associated microbes in the ovaries (the reproductive organs), the midgut (key for food digestion and immunity), or the salivary glands (essential for the transmission of vector-borne diseases as pathogens must colonize them to enter the saliva and reach the bloodstream during a blood meal). These newly reconstructed genomes can then pave the way for the development of novel vector biocontrol strategies. To this aim, it is required to isolate mosquito organs while avoiding cross-contamination between them or with microorganisms present in other mosquito organs. Here, we describe an optimized and contamination-free dissection protocol for studying mosquito microbiome at the organ level.},
}

Animals
Female
*Salivary Glands/microbiology
*Microbiota/physiology
*Ovary/microbiology
Dissection/methods
Culicidae/microbiology

@article {pmid39431465,
year = {2024},
author = {Hagan, J},
title = {Mapping the spread of antibiotic resistance genes in the coastal microbiome.},
journal = {BioTechniques},
volume = {},
number = {},
pages = {1-4},
doi = {10.1080/07366205.2024.2416379},
pmid = {39431465},
issn = {1940-9818},
abstract = {StandfirstCoastal environments are becoming increasingly exposed to antibiotics through anthropogenic inputs. But how could emerging metagenomic techniques be used to map the spread of antibiotic resistance genes in the coastal microbiome?[Formula: see text].},
}

@article {pmid39431456,
year = {2024},
author = {Batty, CA and Pearson, VK and Olsson-Francis, K and Morgan, G},
title = {Volatile organic compounds (VOCs) in terrestrial extreme environments: implications for life detection beyond Earth.},
journal = {Natural product reports},
volume = {},
number = {},
pages = {},
doi = {10.1039/d4np00037d},
pmid = {39431456},
issn = {1460-4752},
abstract = {Covering: 1961 to 2024Discovering and identifying unique natural products/biosignatures (signatures that can be used as evidence for past or present life) that are abundant, and complex enough that they indicate robust evidence of life is a multifaceted process. One distinct category of biosignatures being explored is organic compounds. A subdivision of these compounds not yet readily investigated are volatile organic compound (VOCs). When assessing these VOCs as a group (volatilome) a fingerprint of all VOCs within an environment allows the complex patterns in metabolic data to be unravelled. As a technique already successfully applied to many biological and ecological fields, this paper explores how analysis of volatilomes in terrestrial extreme environments could be used to enhance processes (such as metabolomics and metagenomics) already utilised in life detection beyond Earth. By overcoming some of the complexities of collecting VOCs in remote field sites, a variety of lab based analytical equipment and techniques can then be utilised. Researching volatilomics in astrobiology requires time to characterise the patterns of VOCs. They must then be differentiated from abiotic (non-living) signals within extreme environments similar to those found on other planetary bodies (analogue sites) or in lab-based simulated environments or microcosms. Such an effort is critical for understanding data returned from past or upcoming missions, but it requires a step change in approach which explores the volatilome as a vital additional tool to current 'Omics techniques.},
}

@article {pmid39431411,
year = {2024},
author = {Sobala, ŁF},
title = {LukProt: A database of eukaryotic predicted proteins designed for investigations of animal origins.},
journal = {Genome biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/gbe/evae231},
pmid = {39431411},
issn = {1759-6653},
abstract = {The origins and early evolution of animals is a subject with many outstanding questions. One problem faced by researchers trying to answer them is the absence of a comprehensive database with sequences from non-bilaterians. Publicly available data is plentiful but scattered and often not associated with proper metadata. A new database presented in this paper, LukProt, is an attempt at solving this issue. The database contains protein sequences obtained mostly from genomic, transcriptomic and metagenomic studies and is an extension of EukProt (Richter et al., 2022, Peer Community Journal, 2, e56). LukProt adopts the EukProt naming conventions and includes data from 216 additional animals. The database is associated with a taxonomic grouping (taxogroup) scheme suitable for studying early animal evolution. Minor updates to the database will contain species additions or metadata corrections and major updates will synchronize LukProt to each new version of EukProt and releases are permanently stored on Zenodo (https://doi.org/10.5281/zenodo.7089120). A BLAST server to search the database is available at https://lukprot.hirszfeld.pl/. Users are invited to participate in maintaining and correcting LukProt. As it can be searched without downloading locally, the database can be a convenient resource not only for evolutionary biologists, but for the broader scientific community as well.},
}

@article {pmid39431214,
year = {2024},
author = {Zhu, X and Chen, J and Wu, S and Zeng, J and Sun, Y and Wu, X},
title = {Empyema Caused by Mixed Infection with Streptococcus intermedius and Streptococcus constellatus in a Patient with Previous Surgery for Oral Carcinoma: A Case Report.},
journal = {Infection and drug resistance},
volume = {17},
number = {},
pages = {4447-4454},
pmid = {39431214},
issn = {1178-6973},
abstract = {BACKGROUND: The incidence of community-acquired empyema caused by the Streptococcus anginosus group (SAG) has been on the rise in the 2020s. To the best of our knowledge, while empyema caused individually by either strain has been reported, there are no reports on empyema caused by concurrent infection with these two strains. Here, we report for the first time empyema caused by concurrent infection with Streptococcus intermedius and Streptococcus constellatus (both SAG species) in a postoperative patient who had been treated for floor of the mouth carcinoma.

CASE PRESENTATION: A 61-year-old male patient who had undergone surgical treatment for floor of the mouth carcinoma 2 year earlier suddenly presented with left-sided chest pain. Chest computed tomography (CT) revealed encapsulated pleural effusion on the left side, which was diagnosed as empyema. Metagenomic next-generation sequencing(mNGS) of the pleural fluid sample indicated mixed infection caused by Streptococcus intermedius and Streptococcus constellatus. The patient's condition improved about 5 weeks after treatment with thoracic fluid drainage and cephalosporin antibiotics.

CONCLUSION: This case highlights the possibility of concurrent infection with two SAG strains in patients with empyema. Currently, it is unclear whether there is a definitive relationship between a surgical history of carcinoma of the floor of the mouth and empyema caused by infection with SAG strains. This case could, perhaps, serve as a reference for future related research on the topic.},
}

@article {pmid39431056,
year = {2024},
author = {Han, L and Hu, C and Du, Z and Yu, H and Du, Y and Li, L and Li, F and Wang, Y and Gao, X and Sun, X and Zhang, Z and Qin, Y},
title = {Association of glycerolipid metabolism with gut microbiota disturbances in a hamster model of high-fat diet-induced hyperlipidemia.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1439744},
pmid = {39431056},
issn = {2235-2988},
mesh = {Animals ; *Hyperlipidemias/metabolism/microbiology ; *Gastrointestinal Microbiome ; *Diet, High-Fat/adverse effects ; Cricetinae ; *Disease Models, Animal ; *Liver/metabolism ; Male ; *Lipid Metabolism ; *Feces/microbiology ; Metabolomics ; Bacteria/classification/isolation & purification/metabolism/genetics ; Metagenomics ; Lipids/blood ; },
abstract = {BACKGROUND: High-fat diet (HFD)-induced hyperlipidemia, which is associated with gut microbiota disturbances, remains a major public health challenge. Glycerolipid metabolism is responsible for lipid synthesis and is thus involved in the development of hyperlipidemia. However, possible association between the HFD-modulated gut microbiome and the glycerolipid metabolism pathway remains unclear.

METHODS: Hamsters were fed a HFD for 4 weeks to establish a hyperlipidemia model. Fecal, plasma and liver samples collected from hamsters fed a HFD or a normal chow diet (NCD) were used for integrative metagenomic and untargeted metabolomic analyses to explore changes in the composition and functions of the gut microbiota, and relevant metabolites. Spearman rank correlation analysis was used to explore correlations between gut microbes and circulating glycerolipid metabolites, gut microbes and lipids, and circulating glycerolipid metabolites and lipids.

RESULTS: The gut microbial composition of HFD hamsters showed significant alterations at the phylum, genus, and species levels that were skewed toward metabolic disorders compared with that of NCD hamsters. Functional characterization by KEGG analysis identified enrichment of the glycerolipid metabolism pathway in the gut microbiome of HFD hamsters. Plasma and liver metabolomics further indicated the upregulation and enrichment of glycerolipid metabolites in HFD hamsters. The Faecalibaculum, Allobaculum, and Eubacterium genera were positively correlated with plasma glycerolipid metabolites and lipid indices.

CONCLUSION: The findings of this study suggest an association between glycerolipid metabolism and the HFD-modulated gut microbiome that is involved in the development of hyperlipidemia.},
}

Animals
*Hyperlipidemias/metabolism/microbiology
*Gastrointestinal Microbiome
*Diet, High-Fat/adverse effects
Cricetinae
*Disease Models, Animal
*Liver/metabolism
Male
*Lipid Metabolism
*Feces/microbiology
Metabolomics
Bacteria/classification/isolation & purification/metabolism/genetics
Metagenomics
Lipids/blood

@article {pmid39430957,
year = {2024},
author = {Yao, QH and Xia, XJ and Zhi, HL and Liu, ZH},
title = {Extensive erythematous plaques of fungal origin in an overseas student: Cutaneous manifestation of coccidioidomycosis.},
journal = {Medical mycology case reports},
volume = {46},
number = {},
pages = {100674},
pmid = {39430957},
issn = {2211-7539},
abstract = {We present a case of Coccidioides posadasii infection which was contracted during study abroad. This coccidioidomycosis showed atypical manifestations and was diagnosed by a combination of tissue biopsy, metagenomic next-generation sequencing, internal transcribed spacer sequencing and culture. Initial treatment with fluconazole was not effective. Antifungal therapy was switched to voriconazole based on drug sensitivity results with good result. This case demonstrates the clinical significance of combining multiple diagnostic methods.},
}

@article {pmid39430728,
year = {2025},
author = {Zhang, Y and Xue, B and Mao, Y and Chen, X and Yan, W and Wang, Y and Wang, Y and Liu, L and Yu, J and Zhang, X and Chao, S and Topp, E and Zheng, W and Zhang, T},
title = {High-throughput single-cell sequencing of activated sludge microbiome.},
journal = {Environmental science and ecotechnology},
volume = {23},
number = {},
pages = {100493},
pmid = {39430728},
issn = {2666-4984},
abstract = {Wastewater treatment plants (WWTPs) represent one of biotechnology's largest and most critical applications, playing a pivotal role in environmental protection and public health. In WWTPs, activated sludge (AS) plays a major role in removing contaminants and pathogens from wastewater. While metagenomics has advanced our understanding of microbial communities, it still faces challenges in revealing the genomic heterogeneity of cells, uncovering the microbial dark matter, and establishing precise links between genetic elements and their host cells as a bulk method. These issues could be largely resolved by single-cell sequencing, which can offer unprecedented resolution to show the unique genetic information. Here we show the high-throughput single-cell sequencing to the AS microbiome. The single-amplified genomes (SAGs) of 15,110 individual cells were clustered into 2,454 SAG bins. We find that 27.5% of the genomes in the AS microbial community represent potential novel species, highlighting the presence of microbial dark matter. Furthermore, we identified 1,137 antibiotic resistance genes (ARGs), 10,450 plasmid fragments, and 1,343 phage contigs, with shared plasmid and phage groups broadly distributed among hosts, indicating a high frequency of horizontal gene transfer (HGT) within the AS microbiome. Complementary analysis using 1,529 metagenome-assembled genomes from the AS samples allowed for the taxonomic classification of 98 SAG bins, which were previously unclassified. Our study establishes the feasibility of single-cell sequencing in characterizing the AS microbiome, providing novel insights into its ecological dynamics, and deepening our understanding of HGT processes, particularly those involving ARGs. Additionally, this valuable tool could monitor the distribution, spread, and pathogenic hosts of ARGs both within AS environments and between AS and other environments, which will ultimately contribute to developing a health risk evaluation system for diverse environments within a One Health framework.},
}

@article {pmid39430384,
year = {2024},
author = {Takahashi, Y and Niwa, H and Ebisuda, Y and Mukai, K and Yoshida, T and Raidal, S and Padalino, B and Ohmura, H},
title = {Increased freedom of head movement mitigates stress and bacterial load in the airways of horses during transport.},
journal = {Frontiers in veterinary science},
volume = {11},
number = {},
pages = {1477653},
pmid = {39430384},
issn = {2297-1769},
abstract = {INTRODUCTION: Protection of horse welfare during transport is crucial. The aim of this study was to determine the effect of head and neck restraint on behavior and airway bacteria.

METHODS: In a randomized crossover study, six healthy Thoroughbreds were transported by road for 22 h in an individual bay with tight head restraint (50 cm short-rope) or loose head restraint (95 cm long-rope). Behavioral parameters relating to head position, eating, and stress were monitored during transportation. Tracheal wash samples were obtained 6 days before and immediately after transport for bacterial culture and metagenomic analysis.

RESULTS AND DISCUSSION: Compared to before transport, bacterial load (CFU/mL) after transport was significantly increased in the short-rope group (p = 0.04), whereas no changes were observed in the long-rope group. Transport significantly reduced Simpson index at phylum, class, order, and family levels in both groups (p < 0.001) of tracheal microbiota. In both groups, this reduction was associated with increases in the dominant members of relative abundance at phylum (Firmicutes: +24% in long-rope and +14% in short-rope), class (Bacilli: +20% in long-rope and +22% in short-rope) and family (Streptococcaceae: +22% in long-rope and +23% in short-rope) levels. Licking behavior during transportation with short-rope restraint was more frequent than in horses with long-rope restraint. These results suggest loose head restraint during transportation is likely to ameliorate stress and mitigate the associated increased bacterial load in the lower airways associated with transport. Further, head position during transportation is likely a more important determinant of airway hygiene and distress than duration of travel.},
}

@article {pmid39429886,
year = {2024},
author = {Peng, X and Feng, K and Yang, X and He, Q and Zhao, B and Li, T and Wang, S and Deng, Y},
title = {iNAP 2.0: Harnessing metabolic complementarity in microbial network analysis.},
journal = {iMeta},
volume = {3},
number = {5},
pages = {e235},
pmid = {39429886},
issn = {2770-596X},
abstract = {With the widespread adoption of metagenomic sequencing, new perspectives have emerged for studying microbial ecological networks, yielding metabolic evidence of interspecies interactions that traditional co-occurrence networks cannot infer. This protocol introduces the integrated Network Analysis Pipeline 2.0 (iNAP 2.0), which features an innovative metabolic complementarity network for microbial studies from metagenomics sequencing data. iNAP 2.0 sets up a four-module process for metabolic interaction analysis, namely: (I) Prepare genome-scale metabolic models; (II) Infer pairwise interactions of genome-scale metabolic models; (III) Construct metabolic interaction networks; and (IV) Analyze metabolic interaction networks. Starting from metagenome-assembled or complete genomes, iNAP 2.0 offers a variety of methods to quantify the potential and trends of metabolic complementarity between models, including the PhyloMint pipeline based on phylogenetic distance-adjusted metabolic complementarity, the SMETANA (species metabolic interaction analysis) approach based on cross-feeding substrate exchange prediction, and metabolic distance calculation based on parsimonious flux balance analysis (pFBA). Notably, iNAP 2.0 integrates the random matrix theory (RMT) approach to find the suitable threshold for metabolic interaction network construction. Finally, the metabolic interaction networks can proceed to analysis using topological feature analysis such as hub node determination. In addition, a key feature of iNAP 2.0 is the identification of potentially transferable metabolites between species, presented as intermediate nodes that connect microbial nodes in the metabolic complementarity network. To illustrate these new features, we use a set of metagenome-assembled genomes as an example to comprehensively document the usage of the tools. iNAP 2.0 is available at https://inap.denglab.org.cn for all users to register and use for free.},
}

@article {pmid39429879,
year = {2024},
author = {Lu, YX and Yang, JB and Li, CY and Tian, YH and Chang, RR and Kong, DS and Yang, SL and Wang, YF and Zhang, YB and Zhu, XS and Pan, WH and Kong, SY},
title = {Efficient and easy-to-use capturing three-dimensional metagenome interactions with GutHi-C.},
journal = {iMeta},
volume = {3},
number = {5},
pages = {e227},
pmid = {39429879},
issn = {2770-596X},
abstract = {Hi-C can obtain three-dimensional chromatin structure information and is widely used for genome assembly. We constructed the GutHi-C technology. As shown in the graphical abstract, it is a highly efficient and quick-to-operate method and can be widely used for human, livestock, and poultry gut microorganisms. It provides a reference for the Hi-C methodology of the microbial metagenome. DPBS, Dulbecco's phosphate-buffered saline; Hi-C, high-through chromatin conformation capture; LB, Luria-Bertani; NGS, next-generation sequencing; PCR, polymerase chain reaction; QC, quality control.},
}

@article {pmid39429745,
year = {2024},
author = {Fazal, BZ and Yahya, NA and Ling, CMWV and Wei, YC and Leow, TC and Halim, MA and Balakrishnan, KN and Budiman, C and Amin, Z},
title = {16S rRNA metagenomics data on the bacterial communities in Poring Hot Spring, Sabah, Malaysia.},
journal = {Data in brief},
volume = {57},
number = {},
pages = {110935},
pmid = {39429745},
issn = {2352-3409},
abstract = {Hot springs are known to harbor potentially unique microorganisms due to the extreme temperatures in which they thrive and their biotechnologically important enzymes that are active at high temperature, which are beneficial for various industries. Sabah, Malaysia, houses several hot springs, yet knowledge of their microbiological diversity remains limited. Here, the raw sequence data of bacterial communities in a hot spring through metagenomic analysis are revealed. The data were obtained by collecting water and sediment samples from Poring Hot Spring (PHS) in Ranau, Sabah, and their bacterial diversity was analyzed using 16S rRNA amplicon sequencing targeting the V3-V4 regions. The analysis identified bacterial diversity in both water and sediment samples, with 35 phyla, 76 families, and 90 genera in water, and 38 phyla, 114 families, and 128 genera in sediment. Proteobacteria dominated the water samples (87 %), while Cyanobacteria were most abundant in sediment samples (51 %). The most abundant genera in water were Tepidimonas, Hydrogenophilus and Methylothermus, whereas Geitlerinema, Calothrix and Nitrospira dominated the sediment. Sediment samples exhibited higher bacterial richness and diversity compared to water samples, as indicated by α-diversity analysis. Sequences and sample data are deposited in the NCBI Sequence Read Archive under Bioproject ID PRJNA982554 (Accession number: SRX20671661 to SRX20671666) at https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA982554&o=acc_s%3Aa).},
}

@article {pmid39429648,
year = {2024},
author = {Li, Z and Xu, B and Liu, J},
title = {Acute fibrinous and organizing pneumonia associated with Candida: A case report.},
journal = {Respiratory medicine case reports},
volume = {52},
number = {},
pages = {102120},
pmid = {39429648},
issn = {2213-0071},
abstract = {BACKGROUND: Acute fibrinous and organizing pneumonia (AFOP) is a rare form of pneumonia, is characterized by the deposition of fibrin in alveoli, the formation of fibrin spheres, and deposition of fibrin in alveolar junctions and bronchioles adjacent to or adjacent to the alveoli, forming institutional loose connective tissue.The clinical characteristics of AFOP lack specificity. We report a special case of AFOP that may be associated with Candida, so as to improve our understanding and diagnosis of AFOP.

RESULT: In this patient who was early misdiagnosed with community-acquired pneumonia (CAP), the empirical anti-infective treatment was ineffective, and various infectious and non-infectious factors were excluded. Flexible bronchoscopy was subsequently performed, and metagenomics Next Generation Sequencing (mNGS) of Bronchoalveolar lavage fluid (BALF) showed Candida albicans, and further ultrasound interventional percutaneous and lung puncture biopsy was performed to diagnose AFOP according to pathology, while mNGS of lung pathological tissue also suggested Candid. The patient recovered well on corticosteroids.

CONCLUSION: The clinical manifestation, laboratory examination and imaging examination of AFOP has no specificity, lung biopsy and pathological examination should be carried out to make a clear diagnosis by comprehensively considering the clinical manifestations, auxiliary examination, pathology and other aspects of the patients. After definite diagnosis, it is still necessary to rule out various diseases and environmental exposure and further classify them as idiopathic or secondary, so as to choose monotherapy or combination therapy.},
}

@article {pmid39428758,
year = {2024},
author = {Minot, SS and Mayer-Blackwell, K and Fiore-Gartland, A and Johnson, A and Self, S and Bhatti, P and Yao, L and Liu, L and Sun, X and Jinfa, Y and Kublin, J},
title = {Species- and subspecies-level characterization of health-associated bacterial consortia that colonize the human gut during infancy.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2414975},
doi = {10.1080/19490976.2024.2414975},
pmid = {39428758},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome ; Infant ; *Feces/microbiology ; *Bacteria/classification/genetics/isolation & purification ; Male ; Female ; Metagenomics ; Microbial Consortia ; Metagenome ; Infant, Newborn ; Cohort Studies ; Cystic Fibrosis/microbiology ; },
abstract = {BACKGROUND: The human gut microbiome develops rapidly during infancy, a key window of development coinciding with the maturation of the adaptive immune system. However, little is known about the microbiome growth dynamics over the first few months of life and whether there are any generalizable patterns across human populations. We performed metagenomic sequencing on stool samples (n = 94) from a cohort of infants (n = 15) at monthly intervals in the first 6 months of life, augmenting our dataset with seven published studies for a total of 4,441 metagenomes from 1,162 infants.

RESULTS: Strain-level de novo analysis was used to identify 592 of the most abundant organisms in the infant gut microbiome. Previously unrecognized consortia were identified which exhibited highly correlated abundances across samples and were composed of diverse species spanning multiple genera. Analysis of a published cohort of infants with cystic fibrosis identified one such novel consortium of diverse Enterobacterales which was positively correlated with weight gain. While all studies showed an increased community stability during the first year of life, microbial dynamics varied widely in the first few months of life, both by study and by individual.

CONCLUSION: By augmenting published metagenomic datasets with data from a newly established cohort, we were able to identify novel groups of organisms that are correlated with measures of robust human development. We hypothesize that the presence of these groups may impact human health in aggregate in ways that individual species may not in isolation.},
}

Humans
*Gastrointestinal Microbiome
Infant
*Feces/microbiology
*Bacteria/classification/genetics/isolation & purification
Male
Female
Metagenomics
Microbial Consortia
Metagenome
Infant, Newborn
Cohort Studies
Cystic Fibrosis/microbiology

@article {pmid39428055,
year = {2024},
author = {Hazra, D and Chawla, K and Fayaz, SM and Sintchenko, V and Magazine, R and Martinez, E and Pandey, A},
title = {The impact of anti-tuberculosis treatment on respiratory tract microbiome in pulmonary tuberculosis.},
journal = {Microbes and infection},
volume = {},
number = {},
pages = {105432},
doi = {10.1016/j.micinf.2024.105432},
pmid = {39428055},
issn = {1769-714X},
abstract = {The growing evidence has underscored the significance of interactions between the host and microbiota in respiratory health, presenting a novel perspective on disease management. Yet, comprehension of the respiratory microbiome shifts before and after anti-tuberculosis treatment is limited. This study compares respiratory microbiome profiles in untreated tuberculosis (UTB) and completed TB treatment (CTB) cases with healthy controls, using 16S rRNA sequencing on sputum samples. Significant reduction in sputum microbial alpha diversity was observed in both TB groups when compared to healthy controls (P<0.05). Beta diversity analysis showed distinct clustering (P<0.05). Linear discriminant analysis revealed an abundance of potentially pathogenic bacterial genera like Haemophilus, Pseudomonas, and Mycobacterium in the UTB group, while Streptococcus, Rothia, and Neisseria dominated in CTB samples. Healthy sputum microbiomes were enriched with Prevotella, Fusobacterium, Porphyromonadaceae_unclassified, Peptostreptococcus. Moreover, predicted bacterial functional pathways showed significant differences among the three groups, mainly related to nutrient metabolism. These findings indicated significant microbial dysbiosis in sputum samples recovered from patients with pulmonary TB with an elevated presence of potentially pathogenic bacteria, depletion of beneficial genera, and downregulation of several essential metabolic pathways. Further exploration of respiratory microbiome-based diagnostic biomarkers and their role in targeted treatment strategies in tuberculosis is warranted.},
}

@article {pmid39427901,
year = {2024},
author = {Shruti, VC and Kutralam-Muniasamy, G and Pérez-Guevara, F},
title = {Viruses in the era of microplastics and plastispheres: Analytical methods, advances and future directions.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {177010},
doi = {10.1016/j.scitotenv.2024.177010},
pmid = {39427901},
issn = {1879-1026},
abstract = {Research on microplastics and plastispheres now incorporates the study of viruses to evaluate their effects on the environment and human health. Sharing these new discoveries with the scientific community is crucial to fostering further research and collaborations. However, the current research and methodologies used are fragmented. To address this issue, this paper reviews the literature and the use of methodology developments in each study, identifying four emerging research areas: (1) viral interactions with microplastics; (2) viral population, diversity, and function in plastispheres; (3) the effects of viruses and plastic particles in host-associated environments; and (4) the impacts of viruses within plastispheres. To that end, the article is structured to streamline navigation and help readers easily access existing approaches, recent advancements, key findings, challenges, and opportunities in these areas. Our synthesis reveals that research methods include biochemical assays, omics techniques, spectroscopic analysis, and molecular and bioinformatic tools. Various mechanisms enable viruses to attach to microplastics and plastispheres, leading to widespread distribution and contributing to toxic effects and gene transfer. While the growing evidence is intriguing, there is still much to uncover about their ecological interactions, functions, and impacts.},
}

@article {pmid39427542,
year = {2024},
author = {Kuai, Y and Yao, Z and Pang, T and Wang, L and Gong, X and Cheng, Y and Liu, X and Fu, Q and Wang, S},
title = {Chronic dietary deoxynivalenol exposure interferes the intestinal microbial community structure and antibiotic resistome in laying hens.},
journal = {Ecotoxicology and environmental safety},
volume = {286},
number = {},
pages = {117213},
doi = {10.1016/j.ecoenv.2024.117213},
pmid = {39427542},
issn = {1090-2414},
abstract = {Antibiotic resistance genes (ARGs) are critical emerging pollutants that have attracted considerable attention. Deoxynivalenol (DON) is one of the most prevalent mycotoxins in cereal crops worldwide, arising severe health hazards to both humans and animals. Even if numerous researches argue in favor of a notorious influence of DON on the gut, the effects of dietary DON exposure on the ARG profile in poultry intestine remain obscure. In this study, two separate feeding experiments using Jing Tint 6 laying hens exposed to 4.5 or 9.0 mg/kg DON were performed to explore the impact of dietary DON exposure on the microbial community structure and the profiles of ARGs in the intestine via 16S rDNA sequencing and metagenomics sequencing, respectively. In addition, growth performance and intestinal barrier function were also determined to assess the feasibility of using DON-contaminated feedstuffs inappropriate for pigs' consumption in laying hens. Chronic ingestion of DON at 9.0 mg/kg did not alter zootechnical parameters. However, histomorphological impairments were observed in liver and jejunum. Additionally, metagenomic sequencing revealed that dietary DON exposure at 9.0 mg/kg level dramatically changed the gut microbial structure and shifted the ARG profile. The abundance of tetracycline ARG subtype in the layer cecum was decreased, whereas the abundance of vancomycin ARG subtype was increased upon DON exposure. Co-occurrence network analysis identified that Prevotella was the major ARG host in the intestine of laying hens. In summary, our findings demonstrated that DON-contaminated feedstuffs inappropriate for pigs' consumption should be prudently used in hen production, and shed new light on the interactions between mycotoxins and ARGs in the poultry intestine.},
}

@article {pmid39427349,
year = {2024},
author = {Zhou, L and Zhang, X and Zhang, X and Wu, P and Wang, A},
title = {Insights into the carbon and nitrogen metabolism pathways in mixed-autotrophy/heterotrophy anammox consortia in response to temperature reduction.},
journal = {Water research},
volume = {268},
number = {Pt A},
pages = {122642},
doi = {10.1016/j.watres.2024.122642},
pmid = {39427349},
issn = {1879-2448},
abstract = {While the multi-coupled anammox system boasts a substantial research foundation, the specific characteristics of its synergistic metabolic response to decreased temperatures, particularly within the range of 13-15 °C, remained elusive. In this study, we delve into the intricate carbon and nitrogen metabolism pathways of mixed-autotrophy/heterotrophy anammox consortia under conditions of temperature reduction. Our macrogenomic analyses reveal a compelling phenomenon: the stimulation of functional genes responsible for complete denitrification, suggesting an enhancement of this process during temperature reduction. This adaptation likely contributes to maintaining system performance amidst environmental challenges. Further metabolic functional recombination analyses highlight a dramatic shift in microbial community composition, with denitrifying MAGs (metagenome-assembled genomes) experiencing a substantial increase in abundance (up to 200 times) compared to autotrophic MAGs. This proliferation underscores the strong stimulatory effect of temperature reduction on denitrifying species. Notably, autotrophic MAGs play a pivotal role in supporting the glycolytic processes of denitrifying MAGs, underscoring the intricate interdependencies within the consortia. Moreover, metabolic variations in amino acid composition among core MAGs emerge as a crucial adaptation mechanism. These differences facilitate the preservation of enzyme activity and enhance the consortia's resilience to low temperatures. Together, these findings offer a comprehensive understanding of the microbial synergistic metabolism within mixed-autotrophy/heterotrophy anammox consortia under temperature reduction, shedding light on their metabolic flexibility and resilience in dynamic environments.},
}

@article {pmid39427267,
year = {2024},
author = {Singh, AB and Paul, T and Shukla, SP and Kumar, S and Kumar, S and Kumar, G and Kumar, K},
title = {Gut microbiome as biomarker for triclosan toxicity in Labeo rohita: bioconcentration, immunotoxicity and metagenomic profiling.},
journal = {Ecotoxicology (London, England)},
volume = {},
number = {},
pages = {},
pmid = {39427267},
issn = {1573-3017},
support = {DST/TMD-EWO-WTI/2K19/EWFH/2019/214//Department of Science and Technology, Ministry of Science and Technology, India/ ; },
abstract = {Triclosan (TCS) is a lipophilic, broad spectrum antimicrobial agent commonly used in personal care products with a projected continuous escalation in aquatic environments in the post COVID 19 era. There is rich documentation in the literature on the alteration of physiological responses in fish due to TCS exposure; however, studies on gut associated bacteria of fish are still scarce. This is the first attempt to determine changes in bacterial community structure due to exposure of TCS on Labeo rohita, a commercially essential freshwater species, using 16S V3-V4 region ribosomal RNA (rRNA) next-generation sequencing (NGS). Chronic exposure of TCS at environmentally realistic concentrations viz. 1/5th (T1: 0.129 mg/L) and 1/10th (T2: 0.065 mg/L) of LC50 for 28 days resulted in the dose dependent bioconcentration of TCS in the fish gut. Prolonged exposure to TCS leads to disruption of gut bacteria evidenced by down regulation of the host immune system. Additionally, high-throughput sequencing analysis showed alternation in the abundance and diversity of microbial communities in the gut, signifying Proteobacteria and Verrucomicrobia as dominant phyla. Significant changes were also observed in the relative abundance of Chloroflexi and Gammatimonadetes phyla in TCS exposed groups. The study revealed that gut microbiome can be used as a biomarker in assessing the degree of TCS toxicity in commercially important fish species.},
}

@article {pmid39386691,
year = {2024},
author = {Gustafson, KL and Rodriguez, TR and McAdams, ZL and Coghill, LM and Ericsson, AC and Franklin, CL},
title = {Failure of colonization following gut microbiota transfer exacerbates DSS-induced colitis.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {39386691},
issn = {2692-8205},
support = {T32 GM008396/GM/NIGMS NIH HHS/United States ; T32 OD011126/OD/NIH HHS/United States ; U42 OD010918/OD/NIH HHS/United States ; },
abstract = {To study the impact of differing specific pathogen-free gut microbiomes (GMs) on a murine model of inflammatory bowel disease, selected GMs were transferred using embryo transfer (ET), cross-fostering (CF), and co-housing (CH). Prior work showed that the GM transfer method and the microbial composition of donor and recipient GMs can influence microbial colonization and disease phenotypes in dextran sodium sulfate-induced colitis. When a low richness GM was transferred to a recipient with a high richness GM via CH, the donor GM failed to successfully colonize, and a more severe disease phenotype resulted when compared to ET or CF, where colonization was successful. By comparing CH and gastric gavage for fecal material transfer, we isolated the microbial component of this effect and determined that differences in disease severity and survival were associated with microbial factors rather than the transfer method itself. Mice receiving a low richness GM via CH and gastric gavage exhibited greater disease severity and higher expression of pro-inflammatory immune mediators compared to those receiving a high richness GM. This study provides valuable insights into the role of GM composition and colonization in disease modulation.},
}

@article {pmid39426981,
year = {2024},
author = {Lu, C and Liu, D and Wu, Q and Zeng, J and Xiong, Y and Luo, T},
title = {EphA2 blockage ALW-II-41-27 alleviates atherosclerosis by remodeling gut microbiota to regulate bile acid metabolism.},
journal = {NPJ biofilms and microbiomes},
volume = {10},
number = {1},
pages = {108},
pmid = {39426981},
issn = {2055-5008},
support = {2023NSFSC1631//Department of Science and Technology of Sichuan Province (Sichuan Provincial Department of Science and Technology)/ ; 2023YFS0116//Department of Science and Technology of Sichuan Province (Sichuan Provincial Department of Science and Technology)/ ; 2022YFS0604//Department of Science and Technology of Sichuan Province (Sichuan Provincial Department of Science and Technology)/ ; Q22066//Education Department of Sichuan Province/ ; },
mesh = {Animals ; *Atherosclerosis/metabolism/microbiology ; *Gastrointestinal Microbiome/drug effects ; *Bile Acids and Salts/metabolism ; Mice ; *Receptor, EphA2/metabolism ; *Diet, High-Fat/adverse effects ; Male ; Humans ; Disease Models, Animal ; Plaque, Atherosclerotic/etiology ; Mice, Inbred C57BL ; Bacteria/classification/isolation & purification/genetics/metabolism ; Dysbiosis ; },
abstract = {Coronary artery disease (CAD), a critical condition resulting from systemic inflammation, metabolic dysfunction, and gut microbiota dysbiosis, poses a global public health challenge. ALW-II-41-27, a specific inhibitor of the EphA2 receptor, has shown anti-inflammatory prosperities. However, the impact of ALW-II-41-27 on atherosclerosis has not been elucidated. This study aimed to examine the roles of pharmacologically inhibiting EphA2 and the underlying mechanism in ameliorating atherosclerosis. ALW-II-41-27 was administered to apoE[-/-] mice fed a high-fat diet via intraperitoneal injection. We first discovered that ALW-II-41-27 led to a significant reduction in atherosclerotic plaques, evidenced by reduced lipid and macrophage accumulation, alongside an increase in collagen and smooth muscle cell content. ALW-II-41-27 also significantly lowered plasma and hepatic cholesterol levels, as well as the colonic inflammation. Furthermore, gut microbiota was analyzed by metagenomics and plasma metabolites by untargeted metabolomics. ALW-II-41-27-treated mice enriched Enterococcus, Akkermansia, Eggerthella and Lactobaccilus, accompanied by enhanced secondary bile acids production. To explore the causal link between ALW-II-41-27-associated gut microbiota and atherosclerosis, fecal microbiota transplantation was employed. Mice that received ALW-II-41-27-treated mouse feces exhibited the attenuated atherosclerotic plaque. In clinical, lower plasma DCA and HDCA levels were determined in CAD patients using quantitative metabolomics and exhibited a negative correlation with higher monocytes EphA2 expression. Our findings underscore the potential of ALW-II-41-27 as a novel therapeutic agent for atherosclerosis, highlighting its capacity to modulate gut microbiota composition and bile acid metabolism, thereby offering a promising avenue for CAD.},
}

Animals
*Atherosclerosis/metabolism/microbiology
*Gastrointestinal Microbiome/drug effects
*Bile Acids and Salts/metabolism
Mice
*Receptor, EphA2/metabolism
*Diet, High-Fat/adverse effects
Male
Humans
Disease Models, Animal
Plaque, Atherosclerotic/etiology
Mice, Inbred C57BL
Bacteria/classification/isolation & purification/genetics/metabolism
Dysbiosis

@article {pmid39426960,
year = {2024},
author = {Zheng, M and Wen, L and He, C and Chen, X and Si, L and Li, H and Liang, Y and Zheng, W and Guo, F},
title = {Sequencing-guided re-estimation and promotion of cultivability for environmental bacteria.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {9051},
pmid = {39426960},
issn = {2041-1723},
support = {No. 31670492//National Natural Science Foundation of China (National Science Foundation of China)/ ; No. 32270006//National Natural Science Foundation of China (National Science Foundation of China)/ ; No. 2021J01027//Natural Science Foundation of Fujian Province (Fujian Provincial Natural Science Foundation)/ ; },
mesh = {*RNA, Ribosomal, 16S/genetics ; *Sewage/microbiology ; *Metagenomics/methods ; *Bacteria/genetics/classification/isolation & purification/metabolism ; *Soil Microbiology ; Phylogeny ; DNA, Bacterial/genetics ; Sequence Analysis, DNA ; },
abstract = {The low cultivability of environmental bacteria has been widely acknowledged, but most previous estimates focused on the proportion of cultivable cells rather than cultivable taxa. Here, we estimate the proportions of cultivable cells and cultivable taxa for two sample types (soil and activated sludge) using cell counting, 16S rRNA gene amplicon sequencing, metagenomics, and cultivation on agar plates under various conditions. We find that the proportion of cultivable taxa exceeds that of cultivable cells at the sample level. A large proportion of cultivable taxa are taxonomically novel but tend to be present at very low abundance on agar plates, forming microcolonies, and some of them cease to grow during subculture. Compared with uncultivable taxa (under the conditions used in our study), cultivatable taxa tend to display higher metabolic activity as inferred by measuring rRNA copies per cell. Finally, we use the generated taxonomic and genomic information as a guide to isolate a strain representing a yet-uncultured class within the Bacteroidota and to enhance the cultivable diversity of Burkholderiales from activated sludge.},
}

*RNA, Ribosomal, 16S/genetics
*Sewage/microbiology
*Metagenomics/methods
*Bacteria/genetics/classification/isolation & purification/metabolism
*Soil Microbiology
Phylogeny
DNA, Bacterial/genetics
Sequence Analysis, DNA

@article {pmid39426578,
year = {2024},
author = {Tao, Y and Zeng, Y and Zeng, R and Gou, X and Zhou, X and Zhang, J and Nhamdriel, T and Fan, G},
title = {The total alkaloids of Berberidis Cortex alleviate type 2 diabetes mellitus by regulating gut microbiota, inflammation and liver gluconeogenesis.},
journal = {Journal of ethnopharmacology},
volume = {},
number = {},
pages = {118957},
doi = {10.1016/j.jep.2024.118957},
pmid = {39426578},
issn = {1872-7573},
abstract = {Type 2 diabetes mellitus (T2DM) has become a public health problem worldwide. There is growing interest in finding drugs to treat T2DM from herbal medicine. Berberidis Cortex is a traditional Tibetan herb commonly used in the treatment of T2DM, and alkaloids are its main active components. However, the anti-diabetic mechanisms of the total alkaloids of Berberidis Cortex (TBC) remain unclear.

AIM OF THE STUDY: The aim of this study was to evaluate the anti-T2DM efficacy of TBC and reveal the mechanisms behind its effects.

MATERIALS AND METHODS: UPLC-Q-Exactive Orbitrap MS technology was employed to qualitatively identify alkaloid components in TBC. T2DM rat models were induced by high-fat diet combined with streptozotocin, and then treated with different doses of TBC (43.5, 87, 174 mg/kg/d) for 40 days. Biochemical parameters, such as fasting blood glucose (FBG), oral glucose tolerance test (OGTT), glycated serum protein (GSP), homeostatic model assessment of insulin resistance (HOMA-IR), total cholesterol (TC), triglycerides (TG), and low-density lipoprotein cholesterol (LDL-C), alongside H&E and PAS staining were used to evaluate the anti-diabetic activity of TBC. More importantly, metagenomics, transcriptomics, targeted metabolomics, and western blot analysis were integrated to reveal the underlying mechanisms of TBC for T2DM treatment.

RESULTS: TBC significantly reduced the levels of FBG, OGTT, GSP, HOMA-IR, TC, TG, and LDL-C, and improved the histopathological alterations of pancreatic and liver tissues in T2D rats. It also reduced serum levels of lipopolysaccharide (LPS) and several pro-inflammatory cytokines (IL-6, IL-1β and TNF-α). Gut microbiome analysis by metagenomics proved that TBC could improve gut microbiota dysbiosis, including an increase in some beneficial bacteria (e.g., Bifidobacterium pseudolongum and Lactobacillus acidophilus) and a decrease in some harmful bacteria (e.g., Marvinbryantia and Parabacteroides). Western blot analysis found that TBC significantly up-regulated the expression of three intestinal barrier related tight junction proteins (ZO-1, occludin, and claudin-1), and effectively suppressed several key proteins in the TLR4/MyD88/NF-κB inflammatory cascade, including TLR4, MyD88 and p-NF-κB p65. Moreover, hepatic transcriptomics analysis further revealed the regulatory role of TBC on gluconeogenesis related genes, such as Pgc, and Creb1. Targeted metabolomics and western blot analysis showed that TBC improved BAs dysregulation in T2DM rats, specifically increasing TCDCA and CA levels, thereby activating several proteins in the FXR/FGF15 signaling axis (i.e., FXR, FGF15 and FGFR4), and then decreased the expression of p-CREB1 and PGC-1α to inhibit liver gluconeogenesis.

CONCLUSIONS: TBC can significantly improve hyperglycemia, insulin resistance, hyperlipidemia, and inflammation in T2DM rats. The mechanism is related to the regulation of multiple links, including improving gut microbiota dysbiosis, protecting the intestinal barrier by up-regulating the expression of three tight junction proteins, reducing inflammation by inhibiting the LPS/TLR4/MyD88/NF-κB pathway, and inhibiting liver gluconeogenesis by regulating BAs/FXR/FGF15 and CREB1/PGC-1α signaling pathways.},
}

@article {pmid39426464,
year = {2024},
author = {Tang, Y and Liu, X and Zhu, S and Jia, M and Liu, JX and Sun, HZ},
title = {New insights into the enteric methane production based on the archaeal genome map of ruminant gastrointestinal tract.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2024.09.016},
pmid = {39426464},
issn = {2090-1224},
abstract = {INTRODUCTION: As one of the important components of ruminant gastrointestinal tract (GIT) microbiome, archaea are involved in many biological processes, especially methanogenesis. However, the diversity and individual metabolic characteristics of archaea in this habitat remain largely understudied, partly due to the lack of a unified reference genome catalog.

OBJECTIVES: This study aimed to construct a unified genome map for taxonomic and functional exploration of ruminant GIT archaea in the future.

METHODS: We collected archaeal genomes from public sources and new data of this study. We performed phylogenetic analysis, functional genomics analyses, prophages identification based on the genomes. Using collected genomes as a reference, we conducted metagenomic and metatranscriptomic analyses on rumen fluid samples from 18 dairy cows with different methane (CH4) production.

RESULTS: We constructed the ruminant GIT archaeal genomes (RGAG) by compiling 405 strain-level (160 species) non-redundant archaeal genomes from more than 10 ruminant species. The functional heterogeneity and methanogenic structure within RGAG was investigated. RGAG possessed 1,124 (99.5 %) unknown microbial biosynthetic gene clusters. A survey of RGAG-borne prophages identified 63 prophages with 122 host-beneficial genes and 18 auxiliary metabolic genes (AMGs). The pipeline for both metagenomics and metatranscriptomics generated in the study revealed the roles of archaeal genomes under-assessed in general analyses of muti-omics. The highly expressed genus Methanosphaera was negatively correlated with CH4 production.

CONCLUSION: A unified genome map of ruminant GIT archaea is constructed in the study. Functional genomics indicates that the multifaceted functions of RGAG remains undiscovered. Multi-omics analyses reveals the advantages of metatranscriptomics over metagenomics in studying rumen archaeal communities. Differences in rumen archaeal community structure among cattle with different CH4 production may reflect the balance between rumen hydrogen production and methanogenesis. Our work provides new understanding of archaeal functions in the ruminant GIT and potential targets for future CH4 reduction.},
}

@article {pmid39426111,
year = {2024},
author = {Shang, KM and Elsheikha, HM and Ma, H and Wei, YJ and Zhao, JX and Qin, Y and Li, JM and Zhao, ZY and Zhang, XX},
title = {Metagenomic profiling of cecal microbiota and antibiotic resistome in rodents.},
journal = {Ecotoxicology and environmental safety},
volume = {286},
number = {},
pages = {117186},
doi = {10.1016/j.ecoenv.2024.117186},
pmid = {39426111},
issn = {1090-2414},
abstract = {The rodent gut microbiota is a known reservoir of antimicrobial resistance, yet the distribution of antibiotic resistance genes (ARGs) within rodent cecal microbial communities and the specific bacterial species harboring these ARGs remain largely underexplored. This study employed high-throughput sequencing of 122 samples from five distinct rodent species to comprehensively profile the diversity and distribution of ARGs and to identify the bacterial hosts of these genes. A gene catalog of the rodent cecal microbiome was constructed, comprising 22,757,369 non-redundant genes. Analysis of the microbial composition and diversity revealed that Bacillota and Bacteroidota were the dominant bacterial phyla across different rodent species, with significant variations in species composition among the rodents. In total, 3703 putative antimicrobial resistance protein-coding genes were identified, corresponding to 392 unique ARG types classified into 32 resistance classes. The most enriched ARGs in the rodent cecal microbiome were associated with multidrug resistance, followed by glycopeptide and elfamycin antibiotics. Procrustes analysis demonstrated a correlation between the structure of the microbial community and the resistome. Metagenomic assembly-based host tracking indicated that most ARG-carrying contigs originated from the bacterial family Oscillospiraceae. Additionally, 130 ARGs showed significant correlations with mobile genetic elements. These findings provide new insights into the cecal microbiota and the prevalence of ARGs across five rodent species. Future research on a wider range of wild rodent species carrying ARGs will further elucidate the mechanisms underlying the transmission of antimicrobial resistance.},
}

@article {pmid39425237,
year = {2024},
author = {Zelasko, S and Swaney, MH and Sandstrom, S and Davenport, TC and Seroogy, CM and Gern, JE and Kalan, LR and Currie, CR},
title = {Upper respiratory microbial communities of healthy populations are shaped by niche and age.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {206},
pmid = {39425237},
issn = {2049-2618},
support = {F30AI169759/NH/NIH HHS/United States ; T32AI055397/NH/NIH HHS/United States ; U19AI104317/NH/NIH HHS/United States ; U19AI104317/NH/NIH HHS/United States ; U19AI142720/NH/NIH HHS/United States ; U19AI142720/NH/NIH HHS/United States ; },
mesh = {Humans ; *Microbiota ; *Mouth/microbiology ; Adult ; Infant ; Female ; *Bacteria/classification/genetics/isolation & purification ; Male ; Age Factors ; Child, Preschool ; Healthy Volunteers ; Metagenomics/methods ; Respiratory System/microbiology ; Metagenome ; },
abstract = {BACKGROUND: Alterations in upper respiratory microbiomes have been implicated in shaping host health trajectories, including by limiting mucosal pathogen colonization. However, limited comparative studies of respiratory microbiome development and functioning across age groups have been performed. Herein, we perform shotgun metagenomic sequencing paired with pathogen inhibition assays to elucidate differences in nasal and oral microbiome composition and intermicrobial interactions across healthy 24-month-old infant (n = 229) and adult (n = 100) populations.

RESULTS: We find that beta diversity of nasal and oral microbiomes varies with age, with nasal microbiomes showing greater population-level variation compared to oral microbiomes. Infant microbiome alpha diversity was significantly lower across nasal samples and higher in oral samples, relative to adults. Accordingly, we demonstrate significant differences in genus- and species-level composition of microbiomes between sites and age groups. Antimicrobial resistome patterns likewise varied across body sites, with oral microbiomes showing higher resistance gene abundance compared to nasal microbiomes. Biosynthetic gene clusters encoding specialized metabolite production were found in higher abundance across infant oral microbiomes, relative to adults. Investigation of pathogen inhibition revealed greater inhibition of gram-negative and gram-positive bacteria by oral commensals, while nasal isolates had higher antifungal activity.

CONCLUSIONS: In summary, we identify significant differences in the microbial communities inhabiting nasal and oral cavities of healthy infants relative to adults. These findings inform our understanding of the interactions impacting respiratory microbiome composition and functions related to colonization resistance, with important implications for host health across the lifespan. Video Abstract.},
}

Humans
*Microbiota
*Mouth/microbiology
Adult
Infant
Female
*Bacteria/classification/genetics/isolation & purification
Male
Age Factors
Child, Preschool
Healthy Volunteers
Metagenomics/methods
Respiratory System/microbiology
Metagenome

@article {pmid39425038,
year = {2024},
author = {Woldeyohannis, NN and Desta, AF},
title = {Metagenome-based microbial community analysis of urine-derived fertilizer.},
journal = {BMC microbiology},
volume = {24},
number = {1},
pages = {418},
pmid = {39425038},
issn = {1471-2180},
mesh = {Humans ; *Fertilizers/analysis ; *Urine/microbiology ; *Bacteria/genetics/classification/isolation & purification ; *Struvite ; *Metagenome ; Microbiota/genetics ; Metagenomics/methods ; DNA, Bacterial/genetics ; Phylogeny ; },
abstract = {Phosphorus is essential for food production and its supply is limited. Urine is an excellent source of phosphorus and one way to produce fertilizer is through conversion of urine to struvite (MgNH3PO4.6H2O). The present study aimed to understand the bacterial portion of the microbial community composition and dynamics of plasmid-mediated antimicrobial resistant genes during the optimized process of struvite production from composite human urine. Samples for DNA extraction was collected from fresh urine, stored urine and struvite during the process of struvite production. Shotgun metagenomic analysis was employed to understand the bacterial community. The most dominant phyla in the fresh and stored urine samples were Pseudomonadata, which comprised of 60% and 43% respectively, followed by Bacillota, comprised of 25% and 39% respectively. The struvite sample was dominated by the phylum Bacilliota (61%), Pseudomonadota (18%) and bacteroidota (12%). Members of the above phyla persisted in dominating each sample accordingly. Member of the family Morganellaceae was dominant in the fresh sample while the stored urine and struvite samples were dominated by the family Clostridiaceae. A decrease of members of the class Gammaproteobacteria was observed from the fresh to the struvite sample though not statistically significant. The genus Pseudomonas remained to be the most dominant member of Gammaproteobacteria in the fresh and stored urine sample with OTU count of 12,116 and 6,155 with a marked decrease by half in the stored sample. On the other hand, members of the genera Clostridium, Enterococcus, Bacteroides in the stored samples and Clostridium, Alkaliphilus and Pseudomonas in the struvite samples were dominant. 96% of the identified genera were shared in all the samples and the antimicrobial resistance genes (ARGs) identified in the fresh urine were shared by the struvite but not by the stored urine (e.g. sul, cat, aph and aac members). The presence of high abundance of ARGs in struvite needs attention in the persistence and transmissibility of the ARGs before application for agriculture.},
}

Humans
*Fertilizers/analysis
*Urine/microbiology
*Bacteria/genetics/classification/isolation & purification
*Struvite
*Metagenome
Microbiota/genetics
Metagenomics/methods
DNA, Bacterial/genetics
Phylogeny

@article {pmid39424897,
year = {2024},
author = {Jia, X and Wang, W and Wu, M and Pang, L and Yang, C and Ling, Y and Yi, Z and Zhang, X},
title = {Empirical assessment of the enrichment-based metagenomic methods in identifying diverse respiratory pathogens.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {24493},
pmid = {39424897},
issn = {2045-2322},
support = {81801991//the National Natural Science Foundation of China/ ; GW VI-11.1-09//three-Year Initiative Plan for Strengthening Public Health System Construction in Shanghai/ ; GWVI-2.2//three-Year Initiative Plan for Strengthening Public Health System Construction in Shanghai/ ; GWVI-11.1-15//three-Year Initiative Plan for Strengthening Public Health System Construction in Shanghai/ ; 20Y11911300//the 2020 Shanghai Science and Technology Innovation Action Plan Medical Innovation Research Special Project/ ; SHDC12022121//the Shanghai Hospital Development Center Foundation/ ; 2017ZX10103009-001//the National Science and Technology Major Project of China/ ; 2018ZX10305409-001-005//the National Science and Technology Major Project of China/ ; },
mesh = {*Metagenomics/methods ; Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Respiratory Tract Infections/microbiology/virology/diagnosis ; Bacteria/genetics/isolation & purification/classification ; Metagenome ; Viruses/genetics/isolation & purification/classification ; },
abstract = {Probe-based nucleic acid enrichment represents an effective route to enhance the detection capacity of next-generation sequencing (NGS) in a set of clinically diverse and relevant microbial species. In this study, we assessed the effect of the enrichment-based sequencing on identifying respiratory infections using tiling RNA probes targeting 76 respiratory pathogens and sequenced using both Illumina and Oxford Nanopore platforms. Forty respiratory swab samples pre-tested for a panel of respiratory pathogens by qPCR were used to benchmark the sequencing data. We observed a general improvement in sensitivity after enrichment. The overall detection rate increased from 73 to 85% after probe capture detected by Illumina. Moreover, enrichment with probe sets boosted the frequency of unique pathogen reads by 34.6 and 37.8-fold for Illumina DNA and cDNA sequencing, respectively. This also resulted in significant improvements on genome coverage especially in viruses. Despite these advantages, we found that library pooling may cause reads mis-assignment, probably due to crosstalk issues arise from post-capture PCR and from pooled sequencing, thus increasing the risk of bleed-through signal. Taken together, an overall improvement in the breadth and depth of pathogen coverage is achieved using enrichment-based sequencing method. For future applications, automated library processing and pooling-free sequencing could enhance the precision and timeliness of probe enrichment-based clinical metagenomics.},
}

*Metagenomics/methods
Humans
*High-Throughput Nucleotide Sequencing/methods
*Respiratory Tract Infections/microbiology/virology/diagnosis
Bacteria/genetics/isolation & purification/classification
Metagenome
Viruses/genetics/isolation & purification/classification

@article {pmid39424349,
year = {2024},
author = {Zhang, Y and Wang, Z and Wang, F and Zhou, H and Zhang, L and Xie, B},
title = {Anaerobic Degradation of Aromatic and Aliphatic Biodegradable Plastics: Potential Mechanisms and Pathways.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.4c07554},
pmid = {39424349},
issn = {1520-5851},
abstract = {Biodegradable plastics (BDPs) have been widely used as substitutes for traditional plastics, and their environmental fate is a subject of intense research interest. Compared with the aerobic degradation of BDPs, their biodegradability under anaerobic conditions in environmental engineering systems remains poorly understood. This study aimed to investigate the degradability of BDPs composed of poly(butylene adipate-co-terephthalate) (PBAT), poly(lactide acid) (PLA), and their blends, and explore the mechanism underlying their microbial degradation under conditions of anaerobic digestion (AD). The BDPs readily depolymerized under thermophilic conditions but were hydrolyzed at a slow rate under conditions of mesophilic AD. After 45 days of thermophilic AD, a decrease in the molecular weight and significant increase in the production of methane and carbon dioxide production were observed. Network and metagenomics analyses identified AD as reservoirs of plastic-degrading bacteria that produce multiple plastic-degrading enzymes. PETase was identified as the most abundant plastic-degrading enzyme. A potential pathway for the anaerobic biodegradation of BDPs was proposed herein. The polymers of high molecular weight were subjected to abiotic hydrolysis to form oligomers and monomers, enabling subsequent microbial hydrolysis and acetogenesis. Ultimately, complete degradation was achieved predominantly via the pathway involved in the conversion of acetic acid to methane. These findings provide novel insight into the mechanism underlying the anaerobic degradation of BDPs and the microbial resources crucial for the efficient degradation of BDPs.},
}

@article {pmid39424030,
year = {2024},
author = {Wan, P and Liu, Y and Li, B and Yu, X and Jiang, L and Lv, W},
title = {Yeast-enhanced activated sludge for improved nitrogen removal in wastewater treatment: Focus on dissolved organic nitrogen degradation.},
journal = {Environmental research},
volume = {},
number = {},
pages = {120181},
doi = {10.1016/j.envres.2024.120181},
pmid = {39424030},
issn = {1096-0953},
abstract = {Dissolved organic nitrogen (DON) in effluent of wastewater treatment plants (WWTP), particularly hydrophilic DON, is usually more effective than dissolved inorganic nitrogen (DIN) in stimulating phytoplankton growth and increases the risk of eutrophication in receiving waterbodies. Proteins, amino acids, and nucleic acids, which are the main sources of DON in the effluent, are produced during the hydrolysis of extracellular polymeric substances (EPS) in activated sludge. Herein, a yeast strain Candida tropicalis O2, which was highly efficient in degrading DON in EPS was screened. Within 48-hour batch experiments, the DON removal rates of the extracted hydrophilic and hydrophobic EPS reached 68.26% and 59.27%, respectively. During the continuous 35-day operation of sequencing batch bioreactor (SBR) fed with synthetic wastewater, the yeast-enhanced activated sludge (AS-Y) reactor demonstrated a marked improvement in removing various pollutants compared to the traditional activated sludge (AS) reactor. Specifically, DON removal increased by 1.53 mg/L (24.75%), hydrophilic DON by 1.24 mg/L (27.13%), hydrophobic DON by 0.28 mg/L (12.08%), and COD removal by 4.04 mg/L (6.48%). Although the DIN removal decreased by 0.38 mg/L (3.86%), it did not attenuate the overall TN removal from the system, and an additional TN reduction of 1.15 mg/L (7.13%) was achieved. Metagenomic analysis showed that adding strain O2 slightly inhibited the DIN metabolism, and the relative abundances of napB, nirK/S, norB/C, and nosZ involved in denitrification somewhat decreased. Kyoto Encyclopedia of Genes and Genomes and Carbohydrate-Active Enzymes annotations revealed that adding strain O2 promoted amino acid and carbohydrate metabolism. The increased relative abundance of Candida indicated that strain O2 was able to colonize the sludge in AS-Y reactor, which was conducive to synergistic interactions with other microorganisms. This study provided a novel method for in situ improving nitrogen removal in WWTP and reducing the eutrophication risk of the effluent to receiving waterbodies.},
}

@article {pmid39423892,
year = {2024},
author = {Ouyang, W and Huang, Y and Li, C and Huang, W and Yuan, S and Liu, H},
title = {Control of dissolved H2 concentration enhances electron generation, transport and TCE reduction by indigenous microbial community.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {177014},
doi = {10.1016/j.scitotenv.2024.177014},
pmid = {39423892},
issn = {1879-1026},
abstract = {Electrokinetic enhanced bioremediation (EK-Bio) is practical for trichloroethene (TCE) dechlorination because the cathode can produce a wide range of dissolved H2 (DH) concentrations of 1.3-0 mg/L from the electrode to the aquifer. In this study, TCE dechlorination was investigated under different DH concentrations. The mechanisms were discussed by analyzing the microbial community structure and abundance of organohalide-respiring bacteria (OHRB) using 16S rRNA, and the gene abundances of key enzymes in the TCE electron transport chain using metagenomic analysis. The results showed that the moderate DH concentration of 0.19-0.53 mg/L exhibited the most pronounced TCE dechlorination, even better than the higher DH concentrations, due to the optimal redox environment, the enrichments of OHRB, reductive dehalogenase (rdhA) genes and key enzyme genes in the electron generation and transport chain. More electrons were obtained from H2 metabolism by Dehalobacter by promoting the formation of [NiFe] hydrogenase (HupS/L/C) or from glycolysis by versatile OHRB by stimulating the formation of formate and enriching formate dehydrogenase (FDH) under moderate DH conditions. In addition, the enhanced amino acid metabolism improved the vitamin K cycle for electron transport and enriched the reductive dechlorinating enzyme (RDase) genes. This study identifies the optimal DH concentration that facilitates bioremediation efficiency, provides insights into microbial community shifts and key enzymatic pathways in EK-Bio remediation.},
}

@article {pmid39423786,
year = {2024},
author = {Ren, H and Wang, R and Ying, L and Iyobosa, E and Chen, G and Zang, D and Tong, M and Li, E and Nerenberg, R},
title = {Removal of sulfamethoxazole in an algal-bacterial membrane aerated biofilm reactor: Microbial responses and antibiotic resistance genes.},
journal = {Water research},
volume = {268},
number = {Pt A},
pages = {122595},
doi = {10.1016/j.watres.2024.122595},
pmid = {39423786},
issn = {1879-2448},
abstract = {Antibiotics are frequently detected in wastewater, but often are poorly removed in conventional wastewater treatment processes. Combining microalgal and nitrifying bacterial processes may provide synergistic removal of antibiotics and ammonium. In this research, we studied the removal of the antibiotic sulfamethoxazole (SMX) in two different reactors: a conventional nitrifying bacterial membrane aerated biofilm reactor (bMABR) and algal-bacterial membrane aerated biofilm reactor (abMABR) systems. We investigated the synergistic removal of antibiotics and ammonium, antioxidant activity, microbial communities, antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and their potential hosts. Our findings show that the abMABR maintained a high sulfamethoxazole (SMX) removal efficiency, with a minimum of 44.6 % and a maximum of 75.8 %, despite SMX inhibition, it maintained a consistent 25.0 % ammonium removal efficiency compared to the bMABR. Through a production of extracellular polymeric substances (EPS) with increased proteins/polysaccharides (PN/PS), the abMABR possibly allowed the microalgae-bacteria consortium to protect the bacteria from SMX inactivation. The activity of antioxidant enzymes caused by SMX was reduced by 62.1-98.5 % in the abMABR compared to the bMABR. Metagenomic analysis revealed that the relative abundance of Methylophilus, Pseudoxanthomonas, and Acidovorax in the abMABR exhibited a significant positive correlation with SMX exposure and reduced nitrate concentrations and SMX removal. Sulfonamide ARGs (sul1 and sul2) appeared to be primarily responsible for defense against SMX stress, and Hyphomicrobium and Nitrosomonas were the key carriers of ARGs. This study demonstrated that the abMABR system has great potential for removing SMX and reducing the environmental risks of ARGs.},
}

@article {pmid39423213,
year = {2024},
author = {Ma, J and Yang, X and He, J},
title = {Comprehensive gut microbiota composition and microbial interactions among the three age groups.},
journal = {PloS one},
volume = {19},
number = {10},
pages = {e0305583},
doi = {10.1371/journal.pone.0305583},
pmid = {39423213},
issn = {1932-6203},
mesh = {Humans ; *Gastrointestinal Microbiome ; Aged ; Aged, 80 and over ; Adult ; Middle Aged ; Male ; Aging ; Young Adult ; Microbial Interactions ; Female ; Bacteria/genetics/classification ; Age Factors ; Archaea/genetics ; },
abstract = {There is a growing interest in studying the microbiota associated with aging by integrating multiple longevity researches while minimizing the influence of confounding factors. Here, we reprocessed metagenomic sequencing data from four different aging research studies and evaluated potential confounding factors in order to minimize the batch effect. Subsequently, we detected the diversity and abundance of the gut microbiome in three different age cohorts. Out of 1053 different bacteria species, only four showed substantial depletion across different age groups: Ligilactobacillus ruminis, Turicibacter sp. H121, Blautia massiliensis, and Anaerostipes hadrus. Archaea accumulated more in young individuals compared to elderly and centenarians. Candida albicans was more prevalent in centenarians, but Nakaseomyces glabratus (also known as Candida glabrata) was more common in elderly adults. Shuimuvirus IME207 showed a significant increase in centenarians compared to both control groups. In addition, we utilized a Fisher's exact test to investigate topological properties of differentially abundant microbiota in the co-occurrence network of each age group. Microbial signatures specific to different age stages were identified based on the condition: the reads showing differential abundance were higher compared to the other age groups. Lastly, we selected Methanosarcina sp. Kolksee for the Y group, Prevotella copri for the E group and Shuimuvirus IME207 for the C group as representatives of age-related characteristics to study how their interactions change during the aging process. Our results provide crucial insights into the gut microbiome's ecological dynamics in relation to the aging process.},
}

Humans
*Gastrointestinal Microbiome
Aged
Aged, 80 and over
Adult
Middle Aged
Male
Aging
Young Adult
Microbial Interactions
Female
Bacteria/genetics/classification
Age Factors
Archaea/genetics

@article {pmid39422492,
year = {2024},
author = {Lu, F and Huang, T and Chen, R and Yin, H},
title = {Multi-omics analysis reveals the interplay between pulmonary microbiome and host in immunocompromised patients with sepsis-induced acute lung injury.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0142424},
doi = {10.1128/spectrum.01424-24},
pmid = {39422492},
issn = {2165-0497},
abstract = {UNLABELLED: The mechanisms behind the high inflammatory state and immunocompromise in severe sepsis remain unclear. While microbiota's role in immune regulation is known, the impact of pulmonary microbiota on sepsis progression is not fully understood. This study aims to investigate pulmonary microbial characteristics in septic patients and their relationship with host immune-related genes and clinical features. Fifty-four sepsis patients were divided into the immunocompromised host (ICH) group (n = 18) and the control group (n = 36). Bronchoalveolar lavage fluid (BALF) was analyzed using metagenomic next-generation sequencing (mNGS) to assess the pulmonary microbiome, and transcriptomic sequencing evaluated host gene expression. The pulmonary microbiota network in the ICH group showed notable alterations. Symbiotic bacteria like Streptococcus salivarius and Streptococcus oralis were key taxa in the control group. In contrast, opportunistic pathogens such as Campylobacter concisus and Prevotella melaninogenica, typically linked to infections in various body sites, dominated in the ICH group. Transcriptomic analysis revealed differential genes between the two groups. The downregulated differential genes in the ICH group were primarily enriched in pathways related to T-cell activation and the Type I interferon signaling pathway, both crucial for the immune system. Further correlation analysis identified significant associations between certain microbes and host genes, as well as clinical indicators, particularly with species like Campylobacter concisus, Streptococcus salivarius, Streptococcus oralis, and several species of Veillonella. These findings suggest that alterations in the pulmonary microbiome, especially the presence of opportunistic pathogens, may contribute to immune dysregulation in immunocompromised septic patients, warranting further research to explore causal relationships.

IMPORTANCE: Recent research has substantiated the significant role of microbiota in immune regulation, which could influence high inflammatory state and immunocompromise in patients with severe sepsis, as well as provide new opportunities for acute lung injury induced by sepsis diagnosis and treatment. Our study identified some potential critical microbes (Campylobacter concisus and several species of Veillonella), which were correlated with immune-related genes and might be the novel target to regulate immunotherapy in sepsis.},
}

@article {pmid39422474,
year = {2024},
author = {Zhu, Q and Huang, S and Gonzalez, A and McGrath, I and McDonald, D and Haiminen, N and Armstrong, G and Vázquez-Baeza, Y and Yu, J and Kuczynski, J and Sepich-Poore, GD and Swafford, AD and Das, P and Shaffer, JP and Lejzerowicz, F and Belda-Ferre, P and Havulinna, AS and Méric, G and Niiranen, T and Lahti, L and Salomaa, V and Kim, H-C and Jain, M and Inouye, M and Gilbert, JA and Knight, R},
title = {Correction for Zhu et al., "Phylogeny-Aware Analysis of Metagenome Community Ecology Based on Matched Reference Genomes while Bypassing Taxonomy".},
journal = {mSystems},
volume = {},
number = {},
pages = {e0128924},
doi = {10.1128/msystems.01289-24},
pmid = {39422474},
issn = {2379-5077},
}

@article {pmid39422129,
year = {2024},
author = {Kanti Nath, B and Gupta, SD and Talukder, S and Tonu, NS and Raidal, SR and Forwood, JK and Sarker, S},
title = {Metagenomic Detection of Multiple Viruses in Monk Parakeet (Myiopsitta monachus) in Australia.},
journal = {Veterinary medicine and science},
volume = {10},
number = {6},
pages = {e70083},
doi = {10.1002/vms3.70083},
pmid = {39422129},
issn = {2053-1095},
mesh = {Animals ; *Feces/virology/microbiology ; *Parakeets/virology ; Bird Diseases/virology/epidemiology/microbiology ; Australia ; Adenoviridae/isolation & purification/classification/genetics ; Parvoviridae/isolation & purification/genetics/classification ; Phylogeny ; Circovirus/genetics/isolation & purification/classification ; High-Throughput Nucleotide Sequencing/veterinary ; Victoria ; Circoviridae/isolation & purification/genetics/classification ; Virome ; Metagenomics ; },
abstract = {BACKGROUND: Birds are known to harbour many pathogens, including circovirus, herpesviruses, adenoviruses and Chlamydia psittaci. Some of these pose zoonotic risks, while others, such as beak and feather disease virus (BFDV), have a significant impact on the conservation of endangered bird species.

OBJECTIVES: This study was aimed to determine the faecal virome of a group of apparently healthy Monk parakeet using high-throughput sequencing.

METHODS: Fresh faecal samples were collected from four Monk parakeets at a pet shop in Melbourne, Australia. Virus enrichment and nucleic acid extraction were performed on the faecal samples, followed by high-throughput sequencing at the Australian Genome Research Facility (AGRF).

RESULTS: Utilising an established pipeline for high-throughput sequencing data analysis, this study revealed the presence of three viruses of the families Circoviridae, Parvoviridae and Adenoviridae. Subsequent sequence comparison and phylogenetic analyses further confirmed that the detected viruses belong to the genera Chaphamaparvovirus (unassigned species), Circovirus (species Circovirus parrot) and Siadenovirus (species Siadenovirus viridis).

CONCLUSION: Despite non-pathogenicity, the existence of multiple viruses within a bird species underscores the risk of these viruses spreading into the pet trade. Detection and a better understanding of avian viruses are crucial for the establishment of appropriate management and biosecurity measures in the domestic and international bird trade, which ultimately supports the conservation of vulnerable bird species.},
}

Animals
*Feces/virology/microbiology
*Parakeets/virology
Bird Diseases/virology/epidemiology/microbiology
Australia
Adenoviridae/isolation & purification/classification/genetics
Parvoviridae/isolation & purification/genetics/classification
Phylogeny
Circovirus/genetics/isolation & purification/classification
High-Throughput Nucleotide Sequencing/veterinary
Victoria
Circoviridae/isolation & purification/genetics/classification
Virome
Metagenomics

@article {pmid39421628,
year = {2024},
author = {Shaykhutdinov, IH and Iliasov, PV and Limareva, LV and Sustretov, AS and Kokorev, DA and Sokolov, AV},
title = {Biomineralization of Human Genomic DNA into ZIF-8, a Zeolite-Like Metal-Organic Framework.},
journal = {Sovremennye tekhnologii v meditsine},
volume = {16},
number = {1},
pages = {5-13},
pmid = {39421628},
issn = {2309-995X},
mesh = {Humans ; *Metal-Organic Frameworks/chemistry ; *DNA ; *Zeolites/chemistry ; Biomineralization ; Genome, Human ; Imidazoles/chemistry ; },
abstract = {UNLABELLED: The aim of the study was to assess the capabilities of human genomic DNA biomineralization into ZIF-8 metal-organic framework (MOF) preserving DNA sequence integrity after the encapsulation cycle and composite dissolving. The study is an initial stage of the project aimed at developing an abiotic vector to be used when working with native nucleic acids of an arbitrary size based on DNA@ZIF-8 composite.

MATERIALS AND METHODS: We studied human genomic DNA isolated from lymphocytes of peripheral blood of healthy volunteers using Proba-NK kit (DNA-Technology LLC, Russia). Genomic DNA purity and concentration was estimated spectrophotometrically at 260/280 nm using Tecan Infinity 200 Pro plate reader (Tecan Instruments, Austria). ZIF-8 was synthesized in the physiological conditions (37°C) by mixing zinc salt and 2-methylimidazole aqueous solutions at different molar ratios. Human genomic DNA was encapsulated into ZIF-8 in similar conditions. The obtained MOF and DNA@ZIF-8 composite were studied using X-ray powder diffraction at the Phaser D2 XRPD device (Bruker, USA), and the specific surface area was estimated using Autosorb iQ porosimetry analyzer (Quantachrome, USA). The encapsulated DNA was quantified by dissolving DNA@ZIF-8 composite in the citrate buffer. DNA integrity was assessed by real-time allele-specific PCR (AS-PCR) using the kits for single nucleotide polymorphisms (Lytech, Russia) at the Quantstudio 6 Pro PCR machine (Thermo Scientific, USA). In case of using the kits with electrophoretic detection, the amplification was performed on the thermal cycler T100 (Thermo Scientific, USA).

RESULTS: The polymer ZIF-8 and DNA@ZIF-8 composite were obtained at different molar ratios of zinc ions and 2-methylimidazole. We characterized their structure and specific surface area. Genomic DNA biomineralization efficacy was found to be about 7-8%. PCR indicated the integrity of non-selectively chosen loci within the biomineralized DNA.

CONCLUSION: The study confirmed the possibility of human genomic DNA encapsulation into ZIF-8 metal-organic framework. After the biomineralization, DNA was found to preserve feasibility to be used in studies to investigate genetic constructs.},
}

Humans
*Metal-Organic Frameworks/chemistry
*DNA
*Zeolites/chemistry
Biomineralization
Genome, Human
Imidazoles/chemistry

@article {pmid39421601,
year = {2024},
author = {Dopson, M and Rezaei Somee, M and González-Rosales, C and Lui, LM and Turner, S and Buck, M and Nilsson, E and Westmeijer, G and Ashoor, K and Nielsen, TN and Mehrshad, M and Bertilsson, S},
title = {Novel candidate taxa contribute to key metabolic processes in Fennoscandian Shield deep groundwaters.},
journal = {ISME communications},
volume = {4},
number = {1},
pages = {ycae113},
pmid = {39421601},
issn = {2730-6151},
abstract = {The continental deep biosphere contains a vast reservoir of microorganisms, although a large proportion of its diversity remains both uncultured and undescribed. In this study, the metabolic potential (metagenomes) and activity (metatranscriptomes) of the microbial communities in Fennoscandian Shield deep subsurface groundwaters were characterized with a focus on novel taxa. DNA sequencing generated 1270 de-replicated metagenome-assembled genomes and single-amplified genomes, containing 7 novel classes, 34 orders, and 72 families. The majority of novel taxa were affiliated with Patescibacteria, whereas among novel archaea taxa, Thermoproteota and Nanoarchaeota representatives dominated. Metatranscriptomes revealed that 30 of the 112 novel taxa at the class, order, and family levels were active in at least one investigated groundwater sample, implying that novel taxa represent a partially active but hitherto uncharacterized deep biosphere component. The novel taxa genomes coded for carbon fixation predominantly via the Wood-Ljungdahl pathway, nitrogen fixation, sulfur plus hydrogen oxidation, and fermentative pathways, including acetogenesis. These metabolic processes contributed significantly to the total community's capacity, with up to 9.9% of fermentation, 6.4% of the Wood-Ljungdahl pathway, 6.8% of sulfur plus 8.6% of hydrogen oxidation, and energy conservation via nitrate (4.4%) and sulfate (6.0%) reduction. Key novel taxa included the UBA9089 phylum, with representatives having a prominent role in carbon fixation, nitrate and sulfate reduction, and organic and inorganic electron donor oxidation. These data provided insights into deep biosphere microbial diversity and their contribution to nutrient and energy cycling in this ecosystem.},
}

@article {pmid39421252,
year = {2024},
author = {Klaassens, ES and Baak, ML and Mekkes, NJ and Bongoni, R and Schaubeck, M},
title = {Effect of protein modification in synbiotic infant formula on probiotic metabolic activity and bacterial composition in an infant gut-model.},
journal = {Microbiome research reports},
volume = {3},
number = {3},
pages = {38},
pmid = {39421252},
issn = {2771-5965},
abstract = {Aim: Microbial colonization of the neonatal gut is pivotal in priming the infant's immune system. Human milk (HM) is the best nutrition for infants and supports the development of the microbiota due to prebiotic compounds and probiotic microorganisms. When exclusive breastfeeding is not possible, infant formula (IF) with probiotics is a strategy to support the infant's microbiome development. However, knowledge about the effects of the infant gut microbiota and different compounds in IF on individual probiotic strains is limited, as strain-level detection in a complex ecosystem is challenging. The aim of the present study was to show the effects of IF with different protein forms on the metabolic activity of two probiotic strains isolated from HM in a complex ecosystem. Methods: By using an ex-vivo infant gut model containing infant donor-microbiota, the effects of IF with either intact or extensively hydrolyzed protein on the metabolic activity of the donor microbiota, as well as two probiotic strains [Limosilactobacillus fermentum (L. fermentum) CECT 5716 (Lf) and Bifidobacterium breve (B. breve) DSM 32583 (Bb)], were analyzed. A new bioinformatic pipeline combined with a specific infant microbiome database was used to explore shotgun metagenome datasets (1200 Megabases) for taxonomic identification and strain-level tracking. Results: Both protein forms (i.e., intact or extensively hydrolyzed protein) in IF supported infant gut microbial metabolic activity equally, as evidenced by similar levels of short-chain fatty acids (SCFAs). Interestingly, gut microbial metabolic activity was found to be differently activated in a strain-dependent manner. Taxonomic profiling of the microbiome at the strain level enabled monitoring of the prevalence and abundance of both probiotic strains, even in a complex ecosystem. Conclusion: Food matrix and host microbiota interactions should be considered when evaluating strain-specific probiotic effects in the future.},
}

@article {pmid39421249,
year = {2024},
author = {Mueller, KD and Panzetta, ME and Davey, L and McCann, JR and Rawls, JF and Flores, GE and Valdivia, RH},
title = {Pangenomic analysis identifies correlations between Akkermansia species and subspecies and human health outcomes.},
journal = {Microbiome research reports},
volume = {3},
number = {3},
pages = {33},
pmid = {39421249},
issn = {2771-5965},
abstract = {Aim: Akkermansia are common members of the human gastrointestinal microbiota. The prevalence of these mucophilic bacteria, especially Akkermansia muciniphila (A. muciniphila), correlates with immunological and metabolic health. The genus Akkermansia in humans includes species with significantly larger genomes than A. muciniphila, leading us to postulate that this added genetic content may influence how they impact human metabolic and immunological health. Methods: We conducted a pangenomic analysis of 234 Akkermansia complete or near-complete genomes. We also used high-resolution species and subspecies assignments to reanalyze publicly available metagenomic datasets to determine if there are relationships between Akkermansia species and A. muciniphila clades with various disease outcomes. Results: Analysis of genome-wide average nucleotide identity, 16S rRNA gene identity, conservation of core Akkermansia genes, and analysis of the fatty acid composition of representative isolates support the partitioning of the genus Akkermansia into several species. In addition, A. muciniphila sensu stricto, the most prevalent Akkermansia species in humans, should be subdivided into two subspecies. For a pediatric cohort, we observed species-specific correlations between Akkermansia abundance with baseline obesity or after various interventions. For inflammatory bowel disease cohorts, we identified a decreased abundance of Akkermansia in patients with ulcerative colitis or Crohn's disease, which was species and subspecies-dependent. In patients undergoing immune checkpoint inhibitor therapies for non-small cell lung carcinoma, we observed a significant association between one A. muciniphila subspecies and survival outcomes. Conclusion: Our findings suggest that the prevalence of specific Akkermansia species and/or subspecies can be crucial in evaluating their association with human health, particularly in different disease contexts, and is an important consideration for their use as probiotics.},
}

@article {pmid39420944,
year = {2024},
author = {Chen, X and Zou, T and Ding, G and Jiang, S},
title = {Findings and methodologies in oral phageome research: a systematic review.},
journal = {Journal of oral microbiology},
volume = {16},
number = {1},
pages = {2417099},
pmid = {39420944},
issn = {2000-2297},
abstract = {BACKGROUND: The oral microbiome serves as both an indicator and a mediator of oral health. Evidence indicates that bacteriophages (phages) are widely present in the oral microbiome and exhibit diverse classifications and interactions with human cells and other microbes. These phages constitute the oral phageome, which potentially exerts significant yet unexplored effects on the interplay between oral and general health.

METHODS: Three databases (PubMed/MEDLINE, Embase and Scopus) were searched for metagenomic analyses that investigated the oral phageome. Eligible studies were synthesized based on their methodological approaches and findings.

RESULTS: A total of 14 articles were included in this systematic review. Among the 14 articles included, there were six studies that discussed disease-related alterations, along with a discursive examination of additional variables such as sampling niches, external interventions and methodologies. The phages that infect Streptococcus Actinomyces Haemophilus, and Veillonella have been discovered to be associated with chronic periodontitis, caries, and pancreatic ductal carcinoma.

CONCLUSIONS: This systematic review focuses on findings and methodologies in oral phageome studies, which were conducted using highly heterogeneous methodologies that explored the oral phageome in multiple directions while placing constraints on quantitative statistics. Combining different kinds of sample types, utilizing the characteristics of different methods, involving both DNA and RNA phages, and differentiating lysogenic and lytic phages should be the distinction of further studies.},
}

@article {pmid39420836,
year = {2024},
author = {Qu, W and Xu, Y and Yang, J and Shi, H and Wang, J and Yu, X and Chen, J and Wang, B and Zhuoga, D and Luo, M and Liu, R},
title = {Berberine alters the gut microbiota metabolism and impairs spermatogenesis.},
journal = {Acta biochimica et biophysica Sinica},
volume = {},
number = {},
pages = {},
doi = {10.3724/abbs.2024174},
pmid = {39420836},
issn = {1745-7270},
abstract = {Berberine (BBR) is used to treat diarrhea clinically. However, its reproductive toxicity is unclear. This study aims to investigate the impact of BBR on the male reproductive system. Intragastric BBR administration for 14 consecutive days results in a significant decrease in the serum testosterone concentration, epididymal sperm concentration, mating rate and fecundity of male mice. Testicular treatment with testosterone propionate (TP) partially reverses the damage caused by BBR to the male reproductive system. Mechanistically, the decrease in Muribaculaceae abundance in the gut microbiota of mice is the principal cause of the BBR-induced decrease in the sperm concentration. Both fecal microbiota transplantation (FMT) and polyethylene glycol (PEG) treatment demonstrate that Muribaculaceae is necessary for spermatogenesis. The intragastric administration of Muribaculaceae intestinale to BBR-treated mice restores the sperm concentration and testosterone levels. Metabolomic analysis reveals that BBR affects arginine and proline metabolism, of which ornithine level is downregulated. Combined analysis via 16S rRNA metagenomics sequencing and metabolomics shows that Muribaculaceae regulates ornithine level. The transcriptomic results of the testes indicate that the expressions of genes related to the low-density lipoprotein receptor (LDLR)-mediated testosterone synthesis pathway decrease after BBR administration. The transcriptional activity of the Ldlr gene in TM3 cells is increased with increased ornithine supplementation in the culture media, leading to increased testosterone synthesis. Overall, this study reveals an association between a BBR-induced decrease in Muribaculaceae abundance and defective spermatogenesis, providing a prospective therapeutic approach for addressing infertility-related decreases in serum testosterone triggered by changes in the gut microbiota composition.},
}

@article {pmid39420635,
year = {2024},
author = {Li, C and Sun, L and Jia, Z and Tang, Y and Liu, X and Zhang, J and Müller, C},
title = {Microbial Inoculants Drive Changes in Soil and Plant Microbiomes and Improve Plant Functions in Abandoned Mine Restoration.},
journal = {Plant, cell & environment},
volume = {},
number = {},
pages = {},
doi = {10.1111/pce.15215},
pmid = {39420635},
issn = {1365-3040},
support = {//Jinchi Zhang acknowledges the funding support from Jiangsu Science and Technology Plan Project (BE2022420); the Innovation and Promotion of Forestry Science and Technology Program of Jiangsu Province (LYKJ[2021]30); the Scientific Research Project of Baishanzu National Park (2021ZDLY01); and the Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD). Chong Li is grateful for the partial financial support from the Postgraduate Research and Practice Innovation Program of Jiangsu Province (KYCX21_0915), and the China Scholarship Council (202108320300)./ ; },
abstract = {The application of microbial inoculants holds promise for the sustainable restoration of abandoned mine sites by affecting soil nutrients and microbial communities. However, the responses of plant microbial communities to microbial inoculants in mine restoration remain largely unknown. To bridge this knowledge gap, we conducted a 4-year field experiment at an abandoned carbonate mine site to assess the impacts of microbial inoculants on the soil-plant microbiome. Our findings revealed that microbial inoculants significantly changed roots, fine root bacterial and fungal communities. Further, no significant correlations were observed between the soil-plant nutrient content (Z-score) and microbial alpha diversity. However, a significantly positive correlation was found between the relative abundance of the keystone ecological cluster (Module #1) and soil-plant nutrient content. The application of microbial inoculants also increased complexity, albeit decreased stability of plant microbiome networks, alongside a reduction in stochastic assembly. Conversely, they decreased the complexity but increased the stability of soil microbiome networks, accompanied by an increase in stochastic assembly. Notably, the number of specifically enriched microbiome functional traits of roots and root nodules under the microbial inoculant treatments surpassed that of the control. In summary, our findings underscored the potential of microbial inoculants to enhance soil-plant functionality at abandoned mine restoration sites.},
}

@article {pmid39420033,
year = {2024},
author = {Majzoub, ME and Paramsothy, S and Haifer, C and Parthasarathy, R and Borody, TJ and Leong, RW and Kamm, MA and Kaakoush, NO},
title = {The phageome of patients with ulcerative colitis treated with donor fecal microbiota reveals markers associated with disease remission.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {8979},
pmid = {39420033},
issn = {2041-1723},
support = {988415//Crohn's and Colitis Foundation (Crohn's & Colitis Foundation)/ ; APP2011047//Department of Health | National Health and Medical Research Council (NHMRC)/ ; Investigator grant//Department of Health | National Health and Medical Research Council (NHMRC)/ ; Scientia fellowship//University of New South Wales (UNSW Australia)/ ; },
mesh = {Humans ; *Colitis, Ulcerative/therapy/microbiology/virology ; *Fecal Microbiota Transplantation ; *Bacteriophages/genetics/isolation & purification/physiology ; *Gastrointestinal Microbiome/genetics ; *Feces/microbiology/virology ; Double-Blind Method ; Male ; Female ; Metagenomics/methods ; Adult ; Dysbiosis/microbiology/therapy ; Middle Aged ; Virome/genetics ; Remission Induction ; Anti-Bacterial Agents/therapeutic use ; Biomarkers ; },
abstract = {Bacteriophages are influential within the human gut microbiota, yet they remain understudied relative to bacteria. This is a limitation of studies on fecal microbiota transplantation (FMT) where bacteriophages likely influence outcome. Here, using metagenomics, we profile phage populations - the phageome - in individuals recruited into two double-blind randomized trials of FMT in ulcerative colitis. We leverage the trial designs to observe that phage populations behave similarly to bacterial populations, showing temporal stability in health, dysbiosis in active disease, modulation by antibiotic treatment and by FMT. We identify a donor bacteriophage putatively associated with disease remission, which on genomic analysis was found integrated in a bacterium classified to Oscillospiraceae, previously isolated from a centenarian and predicted to produce vitamin B complex except B12. Our study provides an in-depth assessment of phage populations during different states and suggests that bacteriophage tracking has utility in identifying determinants of disease activity and resolution.},
}

Humans
*Colitis, Ulcerative/therapy/microbiology/virology
*Fecal Microbiota Transplantation
*Bacteriophages/genetics/isolation & purification/physiology
*Gastrointestinal Microbiome/genetics
*Feces/microbiology/virology
Double-Blind Method
Male
Female
Metagenomics/methods
Adult
Dysbiosis/microbiology/therapy
Middle Aged
Virome/genetics
Remission Induction
Anti-Bacterial Agents/therapeutic use
Biomarkers

@article {pmid39419961,
year = {2024},
author = {Becsei, Á and Fuschi, A and Otani, S and Kant, R and Weinstein, I and Alba, P and Stéger, J and Visontai, D and Brinch, C and de Graaf, M and Schapendonk, CME and Battisti, A and De Cesare, A and Oliveri, C and Troja, F and Sironen, T and Vapalahti, O and Pasquali, F and Bányai, K and Makó, M and Pollner, P and Merlotti, A and Koopmans, M and Csabai, I and Remondini, D and Aarestrup, FM and Munk, P},
title = {Author Correction: Time-series sewage metagenomics distinguishes seasonal, human-derived and environmental microbial communities potentially allowing source-attributed surveillance.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {8953},
doi = {10.1038/s41467-024-53282-6},
pmid = {39419961},
issn = {2041-1723},
}

@article {pmid39419776,
year = {2024},
author = {Ma, M and Ardalan, A and Van Dyk, A and Charles, TC and Horsman, GP},
title = {Discovery of a Glyphosate Oxidase in Nature.},
journal = {FEMS microbiology letters},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsle/fnae086},
pmid = {39419776},
issn = {1574-6968},
abstract = {Glyphosate is the most used herbicide on Earth. After a half-century of use we know only two biodegradative pathways, each of which appears to degrade glyphosate incidentally. One pathway begins with oxidation of glyphosate catalyzed by glycine oxidase (GO). To date, no naturally-occurring GO enzymes preferentially oxidize glyphosate but nonetheless are sufficiently active to initiate its degradation. However, GO enzymes that preferentially oxidize glyphosate over glycine - i.e. glyphosate oxidases - may have evolved in environments facing prolonged glyphosate exposure. To test this hypothesis, we screened a metagenomic library from glyphosate-exposed agricultural soil and identified a glyphosate oxidase from clone 11AW19 (GO19) that prefers glyphosate over glycine by four orders of magnitude. This is the first GO isolated from a natural source exhibiting a glyphosate preference. Not only have we discovered the first glyphosate oxidase in nature, but we have also demonstrated the utility of functional metagenomics to find a glyphosate oxidase with greater catalytic efficiency and specificity than those engineered using directed evolution.},
}

@article {pmid39419193,
year = {2024},
author = {Chen, H and Zeng, M and Batool, SS and Zhao, Y and Yu, Z and Zhou, J and Liu, K and Huang, J},
title = {Metagenomic analysis reveals effects of gut microbiome in response to neoadjuvant chemoradiotherapy in advanced rectal cancer.},
journal = {Genomics},
volume = {},
number = {},
pages = {110951},
doi = {10.1016/j.ygeno.2024.110951},
pmid = {39419193},
issn = {1089-8646},
abstract = {Neoadjuvant chemoradiotherapy can enhance survival rate of patients with advanced rectal cancer, but its effectiveness varies considerably. Previous studies have indicated that gut microbes may serve as biomarkers for predicting treatment efficacy. However, the specific roles of the gut microbiome in patients who have good response to nCRT remains unclear. In this study, shotgun metagenomic sequencing technology was used to analyze the fecal microbiome of patients with varying responses to nCRT. Our findings revealed that beneficial intestinal bacteria and genes from different metabolic pathways (carbohydrate metabolism, amino acid metabolism, and sulfur metabolism) were significantly enriched in patients with good response. Additionally, causal relationship in which microbial-derived GDP-D-rhamnose and butyrate could influence the response to nCRT was clarified. Our results offered new insights into the different response to nCRT, and provided valuable reference points for improving the effectiveness of nCRT in patients with advanced colorectal cancer.},
}

@article {pmid39418906,
year = {2024},
author = {Zhao, W and Ma, H and Gao, Z and Li, D and Lin, Y and Wu, C and Wei, L},
title = {Uncovering the toxic effects and adaptive mechanisms of aminated polystyrene nanoplastics on microbes in sludge anaerobic digestion system: Insight from extracellular to intracellular.},
journal = {Journal of hazardous materials},
volume = {480},
number = {},
pages = {136163},
doi = {10.1016/j.jhazmat.2024.136163},
pmid = {39418906},
issn = {1873-3336},
abstract = {The impacts of polystyrene nanoplastics (PS NPs) with amino functional groups on sludge anaerobic digestion process and the underlying microbial feedbacks remains unclear. Herein, PS NPs coated with and without amino functional groups were employed to explore their impacts on the sludge digestion performance. Experimental results showed that aminated PS NPs (PS-NH2) deteriorated the methane yield and hydrolysis rate. The Derjaguin-Landau-Verwey-Overbeek theory analysis suggested that the PS-NH2 decreased the interaction energy barrier, making it easier to contact with sludge and disrupting the structure of extracellular polymeric substances. Metagenomic analysis showed that the abundance of functional microbes (e.g., Longilinea, Leptolinea, and Methanosarcina) decreased, accompanied with lower network complexity and fewer keystone taxa. Molecular docking revealed that PS-NH2 occupy the antioxidant enzyme active binding sites through hydrogen bonding and hydrophobic interactions, impairing degradation of reactive oxygen species. The severe intracellular oxidative stress up-regulated genes associated with quorum sensing (e.g., luxI and luxR) and protein biosynthesis (e.g., algA, trpG and trpE), and further inducing compact tryptophan-like proteins as a defense against NPs. These findings provide new understanding of the toxic effects from PS-NH2 in biological systems and offer valuable insights into the regulation strategies aimed at alleviating NPs inhibition.},
}

@article {pmid39418853,
year = {2024},
author = {Aydin, F and Tarhane, S and Karakaya, E and Abay, S and Kayman, T and Güran, Ö and Bozkurt, E and Üzüm, N and Avci, A and Olgun, K and Jablonski, D and Güran, C and Burçin Saticioğlu, İ},
title = {Helicobacter cappadocius sp. nov., from lizards: The first psychrotrophic Helicobacter species.},
journal = {Systematic and applied microbiology},
volume = {47},
number = {6},
pages = {126557},
doi = {10.1016/j.syapm.2024.126557},
pmid = {39418853},
issn = {1618-0984},
abstract = {It was aimed to determine the prevalence of Helicobacter in some reptilian and amphibian species in Türkiye and to describe the bacteria. For this purpose, 73 cloacal swab samples were used as material. The description of the isolates was performed by detailed phenotypic tests, whole genome analyses, and MALDI-TOF MS. As a result of the phenotypic analysis, two helical, curved Gram-negative, motile isolates were recovered. It was determined through the analysis of 16S rRNA gene sequences that two isolates belonged to the genus Helicobacter. These isolates were found to be in a distinct group from other Helicobacter species. However, the 16S rRNA sequence did not match any identified species, with the closest match being Helicobacter mustelae strain R85-13-6[T], which had an identity level of 96.2 %. Additionally, it was found that strains faydin-H75[T] and faydin-H76 had a 99.3 % identity level for their 16S rRNA genes. After conducting dDDH and ANI analyses, it was found that strains faydin-H75[T] and their close neighbors H.anseris ATCC BAA-1299[T] shared 13.5 % and 68.8 % similarity, respectively. The genome size of the strains was 1.7 Mb while G + C contents were 33.5 %. Metagenomic analyses using IMNGS and Protologger tools revealed the presence of faydin-H75[T] in various lizard species with high similarity, confirming its broad distribution and host specificity. The results indicated that these two strains represent a novel species, for which we propose the name Helicobacter cappadocius with faydin-H75[T] (=NCTC014972 = LMG 33382 = DSM117062) as the respective type strain. The current novel species is the first Helicobacter species to exhibit a psychrotrophic feature.},
}

@article {pmid39418785,
year = {2024},
author = {Chen, J and Su, Z and Li, F and Cao, F and Xiong, F and Jiang, B and Xing, Y and Wen, D},
title = {The variation of resistome, mobilome and pathogen in domestic and industrial wastewater treatment systems.},
journal = {Environment international},
volume = {193},
number = {},
pages = {109051},
doi = {10.1016/j.envint.2024.109051},
pmid = {39418785},
issn = {1873-6750},
abstract = {Wastewater treatment plants (WWTPs), including both domestic and industrial facilities, are key contributors to antibiotic resistance genes (ARGs) and human pathogens in the environment. However, the characteristics and dissemination mechanisms of ARGs in domestic (SD) and industrial (SI) wastewater treatment systems remain unclear, leading to uncertainties in risk assessment. Based on metagenomic analysis, we observed significant differences in the compositions of resistome (ARGs and metal resistance genes, MRGs), mobilome (mobile genetic elements, MGEs), and bacterial community between SD and SI. SI exhibited lower diversity of ARGs but higher abundance of MRGs compared to SD. The removal efficiency of resistome was lower in the SI than that in the SD. MGEs emerged as the primary driver of ARG dissemination in the WWTPs, followed by the bacterial community. Environmental conditions (physicochemical parameters, heavy metals, and antibiotics) indirectly influenced the variation of resistome. Significantly, environmental conditions and MGEs highly influenced the composition of resistome in the SI, while bacterial community more associated with resistome in the SD. Additionally, we identified 36 human bacterial pathogens as potential hosts of ARGs, MRGs, and MGEs in wastewater samples. This study provides new insights on the dissemination mechanisms and risk assessment of antimicrobial resistance in the different types of WWTPs.},
}

@article {pmid39418776,
year = {2024},
author = {Xie, Q and Sun, J and Sun, M and Wang, Q and Wang, M},
title = {Perturbed microbial ecology in neuromyelitis optica spectrum disorder: Evidence from the gut microbiome and fecal metabolome.},
journal = {Multiple sclerosis and related disorders},
volume = {92},
number = {},
pages = {105936},
doi = {10.1016/j.msard.2024.105936},
pmid = {39418776},
issn = {2211-0356},
abstract = {BACKGROUND: Neuromyelitis optica spectrum disorder (NMOSD) is a central nervous system inflammatory demyelinating immune-mediated ailment, which is influenced by genetic, epigenetic, and environmental elements. The escalating incidence of NMOSD in recent years implies alterations in environmental risk factors. Recent research has established a correlation between gut microbiomes and the development of NMOSD.

METHODS: Metagenomic shotgun sequencing and gas chromatography-mass spectrometry (GC-MS) were employed to assess alterations of the structure and function in the fecal microbiome, as well as levels of short-chain fatty acids (SCFAs) in fecal and blood samples, among individuals with neuromyelitis optica spectrum disorder (NMOSD) during the acute phase (n = 25), the remission phase (n = 11), and a group of healthy controls (HCs) (n = 24). We further explored the correlation between gut microbiota and the pathogenesis of NMOSD through fecal microbiota transplantation (FMT). The gut microbiome from human donors diagnosed with NMOSD or HCs was transplanted into germ-free mice, followed by an analysis of the alterations in the structure and functionality of the transplanted mice's gut microbiome. Additionally, the impact of microbiome transfer on the immunity and spinal cord of germ-free mice was assessed through various techniques, including ELISA, flow cytometry, western blot, histopathology, and transcriptome sequencing.

RESULTS: (1) At the taxonomic levels of genus and species, there were significant differences in the α-diversity of the microbiome between HCs and NMOSD patients in the acute phase, with NMOSD patients having higher species diversity. (2) In the acute phase, the gut microbiota of NMOSD patients was characterized by Ruminococcaceae_unclassified, Campylobacter, Parabacteroides, Lactobacillus, Akkermansia, Streptococcus oralis, Clostridium leptum, Clostridium asparagiforme, Firmicutes bacterium CAG 238, and Lactobacillus fermentum. (3) The relative abundances of Coprobacter, Turicimonas, Gemmiger, Enterobacter, Roseburia sp.CAG 471, Veillonella tobetsuensis, Proteobacteria bacterium CAG 139, Ruminococcus bicirculans, Lactococcus lactis, Flavonifractor plautii, and Streptococcus cristatus were notably lower in patients experiencing remission compared to NMOSD patients in the acute phase, On the other hand, the relative abundances of Flavonifractor (P = 0.049) and Clostridium aldenense (P = 0.049) were significantly higher. Following medication, the gut microbiome distribution in NMOSD patients during remission closely resembled that of healthy controls (HCs). (4) Compared with HCs, acetate levels in the feces of patients with NMOSD in the acute phase were significantly lower. (5) In addition, we transplanted feces from NMOSD patients into germ-free mice and revealed a significant increase in the levels of IL-6, IL-17A, and IL-23 in the blood of mice belonging to the NMOSD fecal transplantation (NFMT) group. Additionally, the IL-10 level exhibited a significant reduction. Moreover, the proportion of Th17 cells displayed a significant increase, while the proportion of Treg cells exhibited a significant decrease in the spleens of NFMT mice.

CONCLUSION: Patients in the acute phase of neuromyelitis optica spectrum disorder (NMOSD) exhibited imbalances in their gut microbiota and a deficiency in short-chain fatty acids (SCFAs). Following drug treatment, the composition of intestinal microbes in NMOSD patients during the remission phase closely resembled that of the healthy control population. The FMT experiment provided evidence of the significant association between intestinal flora and the pathogenesis of NMOSD. Consequently, investigating gut microbiota and identifying novel microbial markers hold promise for the diagnosis and treatment of NMOSD patients.},
}

@article {pmid39418385,
year = {2024},
author = {Lien, YW and Amendola, D and Lee, KS and Bartlau, N and Xu, J and Furusawa, G and Polz, MF and Stocker, R and Weiss, GL and Pilhofer, M},
title = {Mechanism of bacterial predation via ixotrophy.},
journal = {Science (New York, N.Y.)},
volume = {386},
number = {6719},
pages = {eadp0614},
doi = {10.1126/science.adp0614},
pmid = {39418385},
issn = {1095-9203},
mesh = {*Cryoelectron Microscopy ; Type VI Secretion Systems/metabolism/genetics ; Single-Cell Analysis ; Bacteria/metabolism/genetics ; },
abstract = {Ixotrophy is a contact-dependent predatory strategy of filamentous bacteria in aquatic environments for which the molecular mechanism remains unknown. We show that predator-prey contact can be established by gliding motility or extracellular assemblages we call "grappling hooks." Cryo-electron microscopy identified the grappling hooks as heptamers of a type IX secretion system substrate. After close predator-prey contact is established, cryo-electron tomography and functional assays showed that puncturing by a type VI secretion system mediated killing. Single-cell analyses with stable isotope-labeled prey revealed that prey components are taken up by the attacker. Depending on nutrient availability, insertion sequence elements toggle the activity of ixotrophy. A marine metagenomic time series shows coupled dynamics of ixotrophic bacteria and prey. We found that the mechanism of ixotrophy involves multiple cellular machineries, is conserved, and may shape microbial populations in the environment.},
}

*Cryoelectron Microscopy
Type VI Secretion Systems/metabolism/genetics
Single-Cell Analysis
Bacteria/metabolism/genetics

@article {pmid39418300,
year = {2024},
author = {Zhang, Y and Mao, M and Zhang, R and Liao, YT and Wu, VCH},
title = {DeepPL: A deep-learning-based tool for the prediction of bacteriophage lifecycle.},
journal = {PLoS computational biology},
volume = {20},
number = {10},
pages = {e1012525},
doi = {10.1371/journal.pcbi.1012525},
pmid = {39418300},
issn = {1553-7358},
abstract = {Bacteriophages (phages) are viruses that infect bacteria and can be classified into two different lifecycles. Virulent phages (or lytic phages) have a lytic cycle that can lyse the bacteria host after their infection. Temperate phages (or lysogenic phages) can integrate their phage genomes into bacterial chromosomes and replicate with bacterial hosts via the lysogenic cycle. Identifying phage lifecycles is a crucial step in developing suitable applications for phages. Compared to the complicated traditional biological experiments, several tools have been designed for predicting phage lifecycle using different algorithms, such as random forest (RF), linear support-vector classifier (SVC), and convolutional neural network (CNN). In this study, we developed a natural language processing (NLP)-based tool-DeepPL-for predicting phage lifecycles via nucleotide sequences. The test results showed that our DeepPL had an accuracy of 94.65% with a sensitivity of 92.24% and a specificity of 95.91%. Moreover, DeepPL had 100% accuracy in lifecycle prediction on the phages we isolated and biologically verified previously in the lab. Additionally, a mock phage community metagenomic dataset was used to test the potential usage of DeepPL in viral metagenomic research. DeepPL displayed a 100% accuracy for individual phage complete genomes and high accuracies ranging from 71.14% to 100% on phage contigs produced by various next-generation sequencing technologies. Overall, our study indicates that DeepPL has a reliable performance on phage lifecycle prediction using the most fundamental nucleotide sequences and can be applied to future phage and metagenomic research.},
}

@article {pmid39418241,
year = {2024},
author = {Song, C and Liu, F and Mei, Y and Cai, W and Cheng, K and Guo, D and Liu, Y and Shi, H and Duan, DD and Liu, Z},
title = {Integrated metagenomic and metabonomic mechanisms for the therapeutic effects of Duhuo Jisheng decoction on intervertebral disc degeneration.},
journal = {PloS one},
volume = {19},
number = {10},
pages = {e0310014},
doi = {10.1371/journal.pone.0310014},
pmid = {39418241},
issn = {1932-6203},
mesh = {Animals ; *Intervertebral Disc Degeneration/drug therapy/metabolism/microbiology ; *Drugs, Chinese Herbal/pharmacology/therapeutic use ; *Metabolomics/methods ; Rats ; *Gastrointestinal Microbiome/drug effects ; Male ; *Rats, Sprague-Dawley ; *Metagenomics/methods ; Metabolome/drug effects ; Feces/microbiology ; Disease Models, Animal ; },
abstract = {Intervertebral disc degeneration (IVDD) is a prevalent orthopedic condition with lower back pain as the predominant clinical presentation that challenges clinical treatment with few therapeutic options. Duhuo Jisheng Decoction (DHJSD) has been proven effective in the therapy of IVDD, but the precise underlying mechanisms remain not fully elucidated. The current study was designed to test our hypothesis that DHJSD may systematically correct the phenotypic disruption of the gut microbiota and changes in the serum metabolome linked to IVDD. Analysis of the active ingredients of DHJSD by ultra high performance liquid chromatography. An integrated metagenomic and metabonomic approach was used to analyze feces and blood samples from normal and IVDD rats. Compared to the control group, fiber ring pinning on the caudal 3 to caudal 5 segments of the rats caused IVDD and significantly altered the compositions of the intestinal microbiota and serum metabolites. Integrated analysis revealed commonly-altered metabolic pathways shared by both intestinal microbiota and serum metabolome of the IVDD rats. DHJSD inhibited the degenerative process and restored the compositions of the perturbed gut microbiota, particularly the relative abundance of commensal microbes of the Prevotellaceae family. DHJSD also corrected the altered metabolic pathways involved in the metabolism of glycine, serine, threonine, valine, the citric acid cycle, and biosynthesis of leucine and isoleucine. DHJSD inhibited the disc degeneration process by an integrated metagenomic and metabonomic mechanism to restore the microbiome profile and normalize the metabonomic pathways.},
}

Animals
*Intervertebral Disc Degeneration/drug therapy/metabolism/microbiology
*Drugs, Chinese Herbal/pharmacology/therapeutic use
*Metabolomics/methods
Rats
*Gastrointestinal Microbiome/drug effects
Male
*Rats, Sprague-Dawley
*Metagenomics/methods
Metabolome/drug effects
Feces/microbiology
Disease Models, Animal

@article {pmid39417646,
year = {2024},
author = {Wang, Q and Geng, L and Gao, Z and Sun, Y and Li, X and Sun, S and Luo, Y},
title = {Microalgae Enhances the Adaptability of Epiphytic Bacteria to Sulfamethoxazole Stress and Proliferation of Antibiotic Resistance Genes Mediated by Integron.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.4c04925},
pmid = {39417646},
issn = {1520-5851},
abstract = {The transmission of ARGs in the microalgae-associated epiphytic bacteria remains unclear under antibiotic exposure, apart from altering the microbial community structure. In this study, Chlorella vulgaris cocultured with bacteria screened from surface water was examined to explore the spread of ARGs in the presence of sulfamethoxazole (SMX). The extracellular polymers released by Chlorella vulgaris could reduce antibiotic-induced collateral damage to bacteria, thus increasing the diversity of the microalgae-associated epiphytic bacteria. The abundances of sul1 and intI1 in the phycosphere at 1 mg/L SMX dose increased by 290 and 28 times, respectively. Metagenomic sequencing further confirmed that SMX bioaccumulation stimulated the horizontal transfer of sul1 mediated by intI1 in the microalgae-associated epiphytic bacteria, while reactive oxygen species (ROS)-mediated oxidative stress induced the SOS response and thus enhanced the transformation of sul1 in the J group. This is the first study to verify that microalgae protect bacteria from antibiotic damage and hinder the spread of ARGs mediated by SOS response, while the transfer of ARGs mediated by integron is promoted due to the bioaccumulation of SMX in the phycosphere. The results contribute to present comprehensive understanding of the risk of ARG proliferation by the presence of emerging contaminants residues in river.},
}

@article {pmid39417540,
year = {2024},
author = {Ginatt, AA and Berihu, M and Castel, E and Medina, S and Carmi, G and Faigenboim-Doron, A and Sharon, I and Tal, O and Droby, S and Somera, T and Mazzola, M and Eizenberg, H and Freilich, S},
title = {A metabolic modeling-based framework for predicting trophic dependencies in native rhizobiomes of crop plants.},
journal = {eLife},
volume = {13},
number = {},
pages = {},
doi = {10.7554/eLife.94558},
pmid = {39417540},
issn = {2050-084X},
support = {US-5390-21//United States-Israel Binational Agricultural Research and Development Fund/ ; },
mesh = {*Rhizosphere ; *Malus/microbiology/metabolism ; *Microbiota ; Plant Roots/microbiology/metabolism ; Soil Microbiology ; Bacteria/metabolism/genetics/classification ; Crops, Agricultural/microbiology ; Metabolomics/methods ; Models, Biological ; },
abstract = {The exchange of metabolites (i.e., metabolic interactions) between bacteria in the rhizosphere determines various plant-associated functions. Systematically understanding the metabolic interactions in the rhizosphere, as well as in other types of microbial communities, would open the door to the optimization of specific predefined functions of interest, and therefore to the harnessing of the functionality of various types of microbiomes. However, mechanistic knowledge regarding the gathering and interpretation of these interactions is limited. Here, we present a framework utilizing genomics and constraint-based modeling approaches, aiming to interpret the hierarchical trophic interactions in the soil environment. 243 genome scale metabolic models of bacteria associated with a specific disease-suppressive vs disease-conducive apple rhizospheres were drafted based on genome-resolved metagenomes, comprising an in silico native microbial community. Iteratively simulating microbial community members' growth in a metabolomics-based apple root-like environment produced novel data on potential trophic successions, used to form a network of communal trophic dependencies. Network-based analyses have characterized interactions associated with beneficial vs non-beneficial microbiome functioning, pinpointing specific compounds and microbial species as potential disease supporting and suppressing agents. This framework provides a means for capturing trophic interactions and formulating a range of testable hypotheses regarding the metabolic capabilities of microbial communities within their natural environment. Essentially, it can be applied to different environments and biological landscapes, elucidating the conditions for the targeted manipulation of various microbiomes, and the execution of countless predefined functions.},
}

*Rhizosphere
*Malus/microbiology/metabolism
*Microbiota
Plant Roots/microbiology/metabolism
Soil Microbiology
Bacteria/metabolism/genetics/classification
Crops, Agricultural/microbiology
Metabolomics/methods
Models, Biological

@article {pmid39417505,
year = {2024},
author = {Kanehisa, M and Furumichi, M and Sato, Y and Matsuura, Y and Ishiguro-Watanabe, M},
title = {KEGG: biological systems database as a model of the real world.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkae909},
pmid = {39417505},
issn = {1362-4962},
support = {JPMJND2203//NBDC Database Integration Coordination Program/ ; //Japan Science and Technology Agency/ ; },
abstract = {KEGG (https://www.kegg.jp/) is a database resource for representation and analysis of biological systems. Pathway maps are the primary dataset in KEGG representing systemic functions of the cell and the organism in terms of molecular interaction and reaction networks. The KEGG Orthology (KO) system is a mechanism for linking genes and proteins to pathway maps and other molecular networks. Each KO is a generic gene identifier and each pathway map is created as a network of KO nodes. This architecture enables KEGG pathway mapping to uncover systemic features from KO assigned genomes and metagenomes. Additional roles of KOs include characterization of conserved genes and conserved units of genes in organism groups, which can be done by taxonomy mapping. A new tool has been developed for identifying conserved gene orders in chromosomes, in which gene orders are treated as sequences of KOs. Furthermore, a new dataset called VOG (virus ortholog group) is computationally generated from virus proteins and expanded to proteins of cellular organisms, allowing gene orders to be compared as VOG sequences as well. Together with these datasets and analysis tools, new types of pathway maps are being developed to present a global view of biological processes involving multiple organism groups.},
}

@article {pmid39417302,
year = {2024},
author = {Li, J and Fang, W and Li, C and Cui, M and Qian, L and Jiang, Z and Jiang, Y and Shi, L and Xie, X and Guo, H and Li, P and Dong, Y and Xiu, W and Wang, Y and Wang, Y},
title = {Dissimilatory Iodate-Reducing Microorganisms Contribute to the Enrichment of Iodine in Groundwater.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.4c04455},
pmid = {39417302},
issn = {1520-5851},
abstract = {Iodate reduction by dissimilatory iodate-reducing microorganisms (DIRMs) plays a crucial role in the biogeochemical cycling of iodine on Earth. However, the occurrence and distribution of DIRMs in iodine-rich groundwater remain unclear. In this study, we isolated the dissimilatory iodate-reducing bacteriumAzonexus hydrophilusstrain NCP973 from a geogenic high-iodine groundwater of China for the first time. The analysis of genome, transcriptome, and heterologous expression revealed that strain NCP973 uses the dissimilatory iodate-reducing enzyme IdrABP1P2 to reduce dissolved or in situ sediment-bound iodate to iodide. The location of IdrABP1P2 in the conjugative plasmid of strain NCP973 implies that IdrABP1P2 could be spread by horizontal gene transfer and allow the recipient microorganisms to participate in the enrichment of iodide in aquifers. Based on the global iodine-rich groundwater metagenomes and genomes, the identification of idrA showed that phylogenetically diverse DIRMs are widely distributed not only in geogenic high-iodine groundwater of China but also in radionuclide-contaminated groundwater of USA as well as in subsurface cavern waters in Germany and Italy. Moreover, the abundance of idrA was found to be higher in groundwater with a relatively high iodine content. Collectively, these results suggest that terrestrial iodine-affected groundwater systems are another important habitat for DIRMs in addition to marine environments, and their activity in aquifers triggers the mobilization and enrichment of iodine in groundwater worldwide.},
}

@article {pmid39417122,
year = {2024},
author = {Atugonza, C and Muwonge, A and Najjuka, CF and Kateete, DP and Katagirya, E and Mwesigwa, S and Asiimwe, B},
title = {Early changes in the gut microbiome among HIV-infected Individuals in Uganda initiating daily TMP/SMX.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.10.07.24315002},
pmid = {39417122},
abstract = {Daily cotrimoxazole (TMP/SXT) prophylaxis is part of the HIV treatment package for all new HIV-infected individuals in Uganda. Although this treatment has shown reduced morbidity and mortality in HIV, it remains controversial due to its contribution to developing antibiotic-resistant bacteria. Moreover, the effects of daily use of a broad-spectrum antibiotic on the gut microbiome remain unknown. To study the early effects, we analysed shotgun metagenome sequence data from stool samples of five newly HIV-infected individuals initiating TMP/SXT prophylaxis longitudinally for the first 30 days of treatment. Using shotgun metagenomics sequencing, we generated both taxonomic and functional profiles from each patient and compared gut microbial changes Pre-TMP/SXT and post-TMP/SXT on Day 5, Day 14, and Day 30. Daily TMP/SXT prophylaxis resulted in a shift characterised by an enrichment of Prevetollea and Ruminococcus genera members and the depletion of Lactococcus and Bacteroides genera members. Furthermore, these microbial shifts were associated with changes in the functional profile revealed by a differential abundance of pathways of amino acid metabolism, carbohydrate metabolism, and nucleotide biosynthesis linked to members of the Bacteroidaceae and Enterobacteriaceae families. TMP/SXT daily prophylaxis in HIV-infected individuals is associated with dramatic changes in microbial composition and functional profiles; however, other factors such as Age, Gender, HIV clinical stage, and ART regiment are at play. Further investigation is needed to examine the implication of these shifts on clinical management and outcomes among HIV patients.},
}

@article {pmid39417080,
year = {2024},
author = {You, R and Yu, Y and Shen, M and Zhang, Y and Hong, J and Kang, Y},
title = {Applications of different forms of nitrogen fertilizers affect soil bacterial community but not core ARGs profile.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1447782},
doi = {10.3389/fmicb.2024.1447782},
pmid = {39417080},
issn = {1664-302X},
abstract = {The objective of this study was to investigate the impact of various chemical nitrogen fertilizers on the profile of antibiotic resistance genes (ARGs) in soil. A microcosm experiment was conducted with four treatments, including CK (control with no nitrogen), AN (ammonium nitrogen), NN (nitrate nitrogen), and ON (urea nitrogen), and the abundance of ARGs was assessed over a 30-day period using a metagenomic sequencing approach. The levels of core ARGs varied between 0.16 and 0.22 copies per cell across different treatments over time. The abundance of core ARGs in the ON treatment closely resembled that of the CK treatment, suggesting that environmentally friendly nitrogen fertilizers, particularly those in controlled release formulations, may be preferable. The core ARG abundance in the AN and NN treatments exhibited noticeable fluctuations over time. Overall, chemical nitrogen fertilizers had minimal effects on the core ARG profile as determined by principal component analysis and clustering analyses. Conversely, distinct and significant changes in bacterial communities were observed with the use of different nitrogen fertilizers. However, the influence of nitrogen fertilizers on the core ARGs is limited due to the unaffected potential bacterial hosts. Nitrogen-cycling-related genes (NCRGs), such as those involved in nitrogen-fixing (nifK, nifD, nifH) and denitrification (narG, napA, nirK, norB, nosZ) processes, exhibit a positive correlation with ARGs (rosA, mexF, bacA, vanS), indicating a potential risk of ARG proliferation during intense denitrification activities. This study indicates that the application of chemical nitrogen has a minimal effect on the abundance of ARGs in soil, thereby alleviating concerns regarding the potential accumulation of ARGs due to the use of chemical nitrogen fertilizers.},
}

@article {pmid39416816,
year = {2024},
author = {Shamim, U and Yadav, A and Maurya, R and Devi, P and Kumari, P and Kanika, and Khare, K and Tarai, B and Pandey, R},
title = {Functional metagenomics highlights varied infection states with dynamics of pathogens and antibiotic resistance in lower respiratory tract infections.},
journal = {Heliyon},
volume = {10},
number = {19},
pages = {e38380},
doi = {10.1016/j.heliyon.2024.e38380},
pmid = {39416816},
issn = {2405-8440},
abstract = {BACKGROUND: Antimicrobial resistance (AMR) amongst pathogenic bacterial species poses significant challenges in treating infections of the lower respiratory tract (LRT), leading to higher hospitalization and mortality rates.

METHODS: Bronchoalveolar lavage fluid (BALF) from 84 clinically adjudicated LRTI patients were subjected to respiratory pathogen ID/AMR (RPIP) enrichment and sequencing followed by Explify and CZID seq data analysis to identify potential LRTI pathogens and associated AMR genes. Patients were categorized as LRTI-WP (with pneumonia) and LRTI-WoP (without pneumonia).

FINDINGS: mNGS achieved 100 % pathogen detection compared to 73 % through clinician-used BioFire panel. Predominant pathogens included Acinetobacter baumannii, Klebsiella pneumoniae along with detection of Aspergillus versicolor and Herpes simplex virus. Double and polymicrobial infections were captured, involving non-respiratory pathogens like Rothia mucilaginosa, Escherichia coli, and Moraxella osloensis. AMR detection highlighted macrolide (MPH; ERM) and Sulfonamide (SUL) rich resistome in 60 % of patients followed by extended spectrum beta lactamase (OXA) and tetracycline (TET). LRTI-WP showed high abundance of A. baumannii, majorly associated with MPH whereas K. pneumoniae with beta-lactams was comparable in both groups. Differences in clinical severity may stem from non-respiratory pathogens, newly recognized via mNGS. CZID seq pipeline validated and revealed additional microbes and AMR genes in the cohort.

INTERPRETATION: The prevalence of common pathogens like A. baumannii and K. pneumoniae along with the non-respiratory pathogens identified by RPIP-Explify and CZID seq provided an understanding to evaluate the LRTI. mNGS is crucial for precise pathogen and antibiotic resistance detection, vital for combating antibiotic resistance.},
}

@article {pmid39416140,
year = {2024},
author = {Majernik, SN and Beaver, L and Bradley, PH},
title = {Small amounts of misassembly can have disproportionate effects on pangenome-based metagenomic analyses.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.10.11.617902},
pmid = {39416140},
issn = {2692-8205},
abstract = {Individual genes from microbiomes can drive host-level phenotypes. To help identify such candidate genes, several recent tools estimate microbial gene copy numbers directly from metagenomes. These tools rely on alignments to pangenomes, which in turn are derived from the set of all individual genomes from one species. While large-scale metagenomic assembly efforts have made pangenome estimates more complete, mixed communities can also introduce contamination into assemblies, and it is unknown how robust pangenome-based metagenomic analyses are to these errors. To gain insight into this problem, we re-analyzed a case-control study of the gut microbiome in cirrhosis, focusing on commensal Clostridia previously implicated in this disease. We tested for differentially prevalent genes in the Lachnospiraceae , then investigated which were likely to be contaminants using sequence similarity searches. Out of 86 differentially prevalent genes, we found that 33 (38%) were probably contaminants originating in taxa such as Veillonella and Haemophilus , unrelated genera that were independently correlated with disease status. Our results demonstrate that even small amounts of contamination in metagenome assemblies, below typical quality thresholds, can threaten to overwhelm gene-level metagenomic analyses. However, we also show that such contaminants can be accurately identified using a method based on gene-to-species correlation. After removing these contaminants, we observe that several flagellar motility gene clusters in the Lachnospira eligens pangenome are associated with cirrhosis status. We have integrated our analyses into an analysis and visualization pipeline, PanSweep, that can automatically identify cases where pangenome contamination may bias the results of gene-resolved analyses.},
}

@article {pmid39416120,
year = {2024},
author = {Richardson, M and Zhao, S and Sheth, RU and Lin, L and Qu, Y and Lee, J and Moody, T and Ricaurte, D and Huang, Y and Velez-Cortes, F and Urtecho, G and Wang, HH},
title = {SAMPL-seq reveals micron-scale spatial hubs in the human gut microbiome.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.10.08.617108},
pmid = {39416120},
issn = {2692-8205},
abstract = {UNLABELLED: The local arrangement of microbes can profoundly impact community assembly, function, and stability. To date, little is known about the spatial organization of the human gut microbiome. Here, we describe a high-throughput and streamlined method, dubbed SAMPL-seq, that samples microbial composition of micron-scale sub-communities with split-and-pool barcoding to capture spatial colocalization in a complex consortium. SAMPL-seq analysis of the gut microbiome of healthy humans identified bacterial taxa pairs that consistently co-occurred both over time and across multiple individuals. These colocalized microbes organize into spatially distinct groups or "spatial hubs" dominated by Bacteroideceae , Ruminococceae , and Lachnospiraceae families. From a dietary perturbation using inulin, we observed reversible spatial rearrangement of the gut microbiome, where specific taxa form new local partnerships. Spatial metagenomics using SAMPL-seq can unlock new insights to improve the study of microbial communities.

ONE SENTENCE SUMMARY: High throughput micron-scale subcommunity sampling and sequencing identifies distinct spatial associations of gut bacteria within and across individuals.},
}

@article {pmid39416080,
year = {2024},
author = {Wang, Q and Wang, BY and Williams, S and Xie, H},
title = {Diversity and characteristics of the oral microbiome influenced by race and ethnicity.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.10.07.617037},
pmid = {39416080},
issn = {2692-8205},
abstract = {UNLABELLED: Periodontitis disproportionately affects racial/ethnic populations. Besides social determinants contributing to disparities in periodontal health, variations of oral microbial communities may also be a key factor influencing oral immune responses. To characterize the oral microbiome from different racial/ethnic populations, we collected 161 dental plaque samples from African Americans (AAs), Caucasian Americans (CAs), and Hispanic Americans (HAs) with clinical gingival health or biofilm-induced gingivitis on an intact periodontium. Using metagenomic sequencing, we found significant difference in diversity and abundance of microbial taxa in the dental plaque samples from AA, CA, and HA groups and unique microbial species that can only be detected in a particular racial/ethnic group. Moreover, we revealed racial/ethnic associated variations in functional potential of the oral microbiome, showing that diversity and abundance of antibiotic resistant genes were greater in the oral microbiome of the AAs than those in CAs or HAs, and that the AAs exhibited higher levels of genes involving in modification of glycoconjugates, oligo- and polysaccharides. These findings indicate more complex and higher virulence potential oral microbiome in AA and HA populations, which likely contributes to higher prevalence of periodontitis in AAs and HAs.

IMPORTANCE: Recognizing the variations in the oral microbiome among racial/ethnic populations offers insight into the microbial determinants contributing to oral health disparities. In the study presented here, we found a higher level of bleeding on probing (BOP), an indicator of tissue inflammatory response, in the AA group, which is correspondence with a more complex oral microbiome detected in this group. Our observations suggest that the variations of the oral microbiome associated with racial/ethnic backgrounds may directly relate to their virulence potential including their abilities to induce host immune responses and to resist antibiotic treatment. Therefore, these finding can be a stepping stone for developing precision medicine and personalized periodontal prevention/treatment and for reducing oral health disparities.},
}

@article {pmid39416003,
year = {2024},
author = {Jacoby, C and Scorza, K and Ecker, L and McMillin, M and Ramaswamy, R and Sundararajan, A and Sidebottom, AM and Lin, H and Dufault-Thompson, K and Hall, B and Jiang, X and Light, SH},
title = {Gut Bacteria Metabolize Natural and Synthetic Steroid Hormones via the Reductive OsrABC Pathway.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.10.08.617280},
pmid = {39416003},
issn = {2692-8205},
abstract = {Steroid hormone metabolism by the gut microbiome has multiple implications for mammalian physiology, but the underlying mechanisms and broader significance of this activity remains largely unknown. Here, we isolate a novel human gut bacterium, Clostridium steroidoreducens [T] strain HCS.1, that reduces cortisol, progesterone, testosterone, and related steroid hormones to 3β,5β-tetrahydrosteroid products. Through transcriptomics and heterologous enzyme profiling, we identify and biochemically characterize the C. steroidoreducens OsrABC reductive steroid hormone pathway. OsrA is a 3-oxo-Δ [1] -steroid hormone reductase that selectively targets the Δ [1] -bond present in synthetic steroid hormones, including the anti-inflammatory corticosteroids prednisolone and dexamethasone. OsrB is a promiscuous 3-oxo-Δ [4] -steroid hormone reductase that converts steroid hormones to 5β-dihydrosteroid intermediates. OsrC is a 3-oxo-5β-steroid hormone oxidoreductase that reduces 5β-intermediates to 3β,5β-tetrahydro products. We find that osrA and osrB homologs predict steroid hormone reductase activity in diverse gut bacteria and are enriched in Crohn's disease fecal metagenomes. These studies thus identify the basis of reductive steroid hormone metabolism in the gut and establish a link between inflammatory disease and microbial enzymes that deplete anti-inflammatory corticosteroids.},
}

@article {pmid39415203,
year = {2024},
author = {Tong, X and Luo, D and Leung, MHY and Lee, JYY and Shen, Z and Jiang, W and Mason, CE and Lee, PKH},
title = {Diverse and specialized metabolic capabilities of microbes in oligotrophic built environments.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {198},
pmid = {39415203},
issn = {2049-2618},
support = {BK20230230//Jiangsu Science and Technology Programme/ ; 11214721//Hong Kong Research Grants Council, General Research Fund/ ; R1016-20F//Hong Kong Research Grants Council, Research Impact Fund/ ; },
mesh = {Humans ; Hong Kong ; *Microbiota ; *Built Environment ; *Metagenome ; *Phylogeny ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Skin/microbiology ; Micrococcus luteus/genetics/metabolism ; Genome, Bacterial ; },
abstract = {BACKGROUND: Built environments (BEs) are typically considered to be oligotrophic and harsh environments for microbial communities under normal, non-damp conditions. However, the metabolic functions of microbial inhabitants in BEs remain poorly understood. This study aimed to shed light on the functional capabilities of microbes in BEs by analyzing 860 representative metagenome-assembled genomes (rMAGs) reconstructed from 738 samples collected from BEs across the city of Hong Kong and from the skin surfaces of human occupants. The study specifically focused on the metabolic functions of rMAGs that are either phylogenetically novel or prevalent in BEs.

RESULTS: The diversity and composition of BE microbiomes were primarily shaped by the sample type, with Micrococcus luteus and Cutibacterium acnes being prevalent. The metabolic functions of rMAGs varied significantly based on taxonomy, even at the strain level. A novel strain affiliated with the Candidatus class Xenobia in the Candidatus phylum Eremiobacterota and two novel strains affiliated with the superphylum Patescibacteria exhibited unique functions compared with their close relatives, potentially aiding their survival in BEs and on human skins. The novel strains in the class Xenobia possessed genes for transporting nitrate and nitrite as nitrogen sources and nitrosative stress mitigation induced by nitric oxide during denitrification. The two novel Patescibacteria strains both possessed a broad array of genes for amino acid and trace element transport, while one of them carried genes for carotenoid and ubiquinone biosynthesis. The globally prevalent M. luteus in BEs displayed a large and open pangenome, with high infraspecific genomic diversity contributed by 11 conspecific strains recovered from BEs in a single geographic region. The versatile metabolic functions encoded in the large accessory genomes of M. luteus may contribute to its global ubiquity and specialization in BEs.

CONCLUSIONS: This study illustrates that the microbial inhabitants of BEs possess metabolic potentials that enable them to tolerate and counter different biotic and abiotic conditions. Additionally, these microbes can efficiently utilize various limited residual resources from occupant activities, potentially enhancing their survival and persistence within BEs. A better understanding of the metabolic functions of BE microbes will ultimately facilitate the development of strategies to create a healthy indoor microbiome. Video Abstract.},
}

Humans
Hong Kong
*Microbiota
*Built Environment
*Metagenome
*Phylogeny
*Bacteria/classification/genetics/metabolism/isolation & purification
Skin/microbiology
Micrococcus luteus/genetics/metabolism
Genome, Bacterial

@article {pmid39414630,
year = {2024},
author = {Córdoba-Agudelo, M and Arboleda-Rivera, JC and Borrego-Muñoz, DA and Ramírez-Cuartas, CA and Pérez-Jaramillo, JE},
title = {Key Chemical Soil Parameters for the Assembly of Rhizosphere Bacteria Associated with Avocado Cv Hass Grafted on Landrace Rootstocks.},
journal = {Current microbiology},
volume = {81},
number = {12},
pages = {412},
pmid = {39414630},
issn = {1432-0991},
mesh = {*Persea/microbiology ; *Rhizosphere ; *Soil Microbiology ; *Bacteria/classification/genetics/isolation & purification/metabolism ; *Soil/chemistry ; *Microbiota ; *RNA, Ribosomal, 16S/genetics ; *Plant Roots/microbiology ; Colombia ; Phylogeny ; },
abstract = {Avocado cultivation holds significant economic importance in many countries, ranking Colombia as the fifth largest global producer. Particularly, the Hass cultivar plays a pivotal role in Colombia's avocado industry, especially in the Department of Antioquia, the primary export region. This cultivar is grown under diverse soil and climate conditions and exhibits considerable genetic polymorphism due to the hybridization of varieties of agronomic significance, leading to a diverse array of landrace rootstocks. However, the role of soil conditions and rootstock genotype in structuring rhizosphere bacterial communities is still lacking. In addressing this knowledge gap, we investigated the influence of two soil conditions on the structure of rhizosphere bacterial communities associated with two landrace genotypes of Persea americana cv. Hass, utilizing 16S rRNA sequencing. Notably, no significant differences related to genotypes were observed. This study reports that the rhizosphere bacterial microbiome remains consistent across avocado landrace rootstocks, while variations in key parameters such as phosphorus, pH, Mg, and Ca drive distinct rhizosphere effects. Our results reveal that despite the soils having similar management, increases in these crucial parameters can lead to bacterial communities with lower alpha diversity and a more complex co-occurrence network. In addition, we found substantial variations in beta diversity, bacterial composition, and metagenome predictions between the two farms, underscoring the role of soil variables in shaping the bacterial microbiome. These findings provide valuable insights into the factors influencing the bacterial communities that may play a role in the health and productivity of crops with agro-industrial potential, such as Hass avocado.},
}

*Persea/microbiology
*Rhizosphere
*Soil Microbiology
*Bacteria/classification/genetics/isolation & purification/metabolism
*Soil/chemistry
*Microbiota
*RNA, Ribosomal, 16S/genetics
*Plant Roots/microbiology
Colombia
Phylogeny

@article {pmid39414169,
year = {2024},
author = {Zhang, B and Zhang, N and Sui, H and Xue, R and Qiao, S},
title = {Unique ecology of biofilms and flocs: Bacterial composition, assembly, interaction, and nitrogen metabolism within deteriorated bioreactor inoculated with mature partial nitrification-anammox sludge.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {131643},
doi = {10.1016/j.biortech.2024.131643},
pmid = {39414169},
issn = {1873-2976},
abstract = {This work unraveled discrepant ecological patterns between biofilms and flocs in a deteriorated bioreactor inoculated with mature partial nitrification-anammox (PN/A) sludge. Based on 16S rRNA analysis, a comprehensive evaluation of neutral and null models, along with niche width, delineated that the bacterial community assembly in biofilms and flocs was dominantly driven by the stochastic process, and dispersal limitation critically shaped the community assembly. Co-occurrence network analysis revealed that environmental stress caused decentralized and fragmented bacterial colonies, and anammox bacteria were mainly peripheral in biofilms network and less involved in interspecific interactions. Simultaneous PN/A and partial denitrification-anammox (PD/A) processes were identified, whereas PN and PD process primarily occurred in the biofilms and flocs, respectively, as evidenced by metagenomics. Collectively, these outcomes are expected to deepen the basic understanding of complex microbial community and nitrogen metabolism under environmental disturbance, thereby better characterizing and serving the artificial ecosystems.},
}

@article {pmid39414063,
year = {2024},
author = {Yu, Y and Li, Y and Sun, B and Cui, J and Liu, H and Sun, Y and Xu, Q and Boisse, N and Voelker, F and Matioszek, D and Fvero, C and Kieffer, J and Li, Y and Lu, J and Li, H and Bao, M},
title = {Characterization and Degradation Mechanism of a Newly Isolated Hydrolyzed Polyacrylamide-degrading Bacterium Alcaligenes faecalis EPDB-5 from the Oilfield Sludge.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {125124},
doi = {10.1016/j.envpol.2024.125124},
pmid = {39414063},
issn = {1873-6424},
abstract = {Hydrolyzed polyacrylamide (HPAM) is posing serious threats to ecosystems. However, biodegradation is an effective method to remove HPAM owing to its low cost and environmental friendliness. In this study, Alcaligenes faecalis EPDB-5 was isolated as a highly efficient HPAM degrading strain from sludge contaminated with polymerized produced water from Daqing oilfield. Under the optimal conditions, the strain EPDB-5 demonstrated an impressive HPAM degradation rate of 86.05%, the total nitrogen (TN) removal of 71.96% and chemical oxygen demand (COD) removal of 67.98%. Meanwhile, it can maintain a stable degradation rate higher than 75% under different pH and temperature conditions. 27 genes that play a key role in HPAM degradation were annotated by metagenomics sequencing. The key genes were involved in multiple KEGG pathways, including biofilm formation, biosynthesis secondary metabolites, and metabolic pathways. SEM, GPC, and FTIR analyses revealed that the structure of HPAM after biodegradation showed pores, a significant decrease in molecular weight, -NH2 detachment, and carbon chain breakage. Particularly, we propose a possible mechanism of biofilm formation - HPAM degradation - biofilm disappearance and reorganization. Moreover, the degradation rate of strain EPDB-5 on real wastewater containing HPAM was 29.97% in only three days. This work expands our knowledge boundary about the HPAM degradation mechanism at the functional gene level, and supports the potential of strain EPDB-5 as a novel auxiliary microbial resource for the practical application of HPAM.},
}

@article {pmid39413681,
year = {2024},
author = {Wu, X and Qin, L and Song, M and Zhang, C and Guo, J and Yang, Z and Gao, Z and Qiu, M},
title = {Metagenomics combined with untargeted metabolomics to study the mechanism of miRNA-150-5p on SiO2 -induced acute lung injury.},
journal = {Journal of pharmaceutical and biomedical analysis},
volume = {252},
number = {},
pages = {116515},
doi = {10.1016/j.jpba.2024.116515},
pmid = {39413681},
issn = {1873-264X},
abstract = {Acute lung injury is a significant global health issue, and its treatment is becoming a hot topic of the researchers. To investigate the feasibility of miRNA-150-5p tail vein injection in the treatment of SiO2-induced acute lung injury through the regulation of gut microbiota and serum metabolites based on multiomics technology. Twenty-four mice were randomly divided into the control, SiO2 and miRNA-150-5p intervention groups. The SiO2 and miRNA-150-5p intervention groups received a single intranasal dose of 100 µL 4 % SiO2 suspension. Meanwhile, the miRNA-150-5p intervention group was administered with two tail vein injections of miRNA-150-5p (15 nmol each per mouse) on the day of successful modelling and on the third day post modelling. Metagenomics and metabolomics techniques were used to measure gut microbiota and serum metabolites, respectively. Tail vein injection of miRNA-150-5p improved SiO2-induced acute lung injury and reduced the secretion of inflammatory factors interleukin (IL)-6, tumour necrosis factor-α and IL-1β. These conditions altered the structure of gut microbiota, which resulted in the notable modulation of eight species at the species level. In addition, tail vein injection of miRNA-150-5p considerably reduced the levels of substances, such as phosphatidylethanolamine, phosphatidylcholine and phosphatidylinositol, in the glycerophospholipid metabolism and glycosylphosphatidylinositol-anchor biosynthesis pathways. Tail vein injection of miRNA-150-5p can alleviate acute lung injury. Combined metagenomics and untargeted metabolomics revealed the miRNA-150-5p-mitigated SiO2-induced acute lung injury that occurred through the regulation of gut microbiota and serum metabolites.},
}

@article {pmid39413245,
year = {2024},
author = {Wang, L and Yin, Z and Yan, W and Hao, J and Tian, F and Shi, J},
title = {Nitrate-dependent antimony oxidase in an uncultured Symbiobacteriaceae member.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrae204},
pmid = {39413245},
issn = {1751-7370},
abstract = {Autotrophic antimony (Sb) oxidation coupled to nitrate reduction plays an important role in the transformation and detoxification of Sb. However, the specific oxidase involved in this process has yet to be identified. Herein, we enriched the microbiota capable of nitrate-dependent Sb(III) oxidation and identified a new Sb(III) oxidase in an uncultured member of Symbiobacteriaceae. Incubation experiments demonstrated that nitrate-dependent Sb(III) oxidation occurred in the microcosm supplemented with Sb(III) and nitrate. Both the 16S rRNA gene and metagenomic analyses indicated that a species within Symbiobacteriaceae played a crucial role in this process. Furthermore, carbon-13 isotope labelling with carbon dioxide-fixing Rhodopseudomonas palustris in combination with nanoscale secondary ion mass spectrometry revealed that a newly characterized oxidase from the dimethylsulfoxide reductase family, designated as NaoABC, was responsible for autotrophic Sb(III) oxidation coupled with nitrate reduction. The NaoABC complex functions in conjunction with the nitrate reductase NarGHI, forming a redox loop that transfers electrons from Sb(III) to nitrate, thereby generating the energy necessary for autotrophic growth. This research offers new insights into the understanding of how microbes link Sb and nitrogen biogeochemical cycles in the environment.},
}

@article {pmid39413127,
year = {2024},
author = {Balinandi, S and Mulei, S and Whitmer, S and Nyakarahuka, L and Cossaboom, CM and Shedroff, E and Morales-Betoulle, M and Krapiunaya, I and Tumusiime, A and Kyondo, J and Baluku, J and Namanya, D and Torach, CR and Mutesi, J and Kiconco, J and Pimundu, G and Muyigi, T and Rowland, J and Nsawotebba, A and Ssewanyana, I and Muwanguzi, D and Kadobera, D and Harris, JR and Ario, AR and Atek, K and Kyobe, HB and Nabadda, S and Kaleebu, P and Mwebesa, HG and Montgomery, JM and Shoemaker, TR and Lutwama, JJ and Klena, JD},
title = {Crimean-Congo hemorrhagic fever cases diagnosed during an outbreak of Sudan virus disease in Uganda, 2022-23.},
journal = {PLoS neglected tropical diseases},
volume = {18},
number = {10},
pages = {e0012595},
doi = {10.1371/journal.pntd.0012595},
pmid = {39413127},
issn = {1935-2735},
abstract = {BACKGROUND: In September 2022, Uganda experienced an outbreak of Sudan virus disease (SVD), mainly in central Uganda. As a result of enhanced surveillance activities for Ebola disease, samples from several patients with suspected viral hemorrhagic fever (VHF) were sent to the VHF Program at Uganda Virus Research Institute (UVRI), Entebbe, Uganda, and identified with infections caused by other viral etiologies. Herein, we report the epidemiologic and laboratory findings of Crimean-Congo hemorrhagic fever (CCHF) cases that were detected during the SVD outbreak response.

METHODOLOGY: Whole blood samples from VHF suspected cases were tested for Sudan virus (SUDV) by real-time reverse transcription-polymerase chain reaction (RT-PCR); and if negative, were tested for CCHF virus (CCHFV) by RT-PCR. CCHFV genomic sequences generated by metagenomic next generation sequencing were analyzed to ascertain strain relationships.

PRINCIPAL FINDINGS: Between September 2022 and January 2023, a total of 2,626 samples were submitted for VHF testing at UVRI. Overall, 13 CCHF cases (including 7 deaths; case fatality rate of 53.8%), aged 4 to 60 years, were identified from 10 districts, including several districts affected by the SVD outbreak. Four cases were identified within the Ebola Treatment Unit (ETU) at Mubende Hospital. Most CCHF cases were males engaged in livestock farming or had exposure to wildlife (n = 8; 61.5%). Among confirmed cases, the most common clinical symptoms were hemorrhage (n = 12; 92.3%), fever (n = 11; 84.6%), anorexia (n = 10; 76.9%), fatigue (n = 9; 69.2%), abdominal pain (n = 9; 69.2%) and vomiting (n = 9; 69.2%). Sequencing analysis showed that the majority of identified CCHFV strains belonged to the Africa II clade previously identified in Uganda. Two samples, however, were identified with greater similarity to a CCHFV strain that was last reported in Uganda in 1958, suggesting possible reemergence.

CONCLUSIONS/SIGNIFICANCE: Identifying CCHFV from individuals initially suspected to be infected with SUDV emphasizes the need for comprehensive VHF testing during filovirus outbreak responses in VHF endemic countries. Without expanded testing, CCHFV-infected patients would have posed a risk to health care workers and others while receiving treatment after a negative filovirus diagnosis, thereby complicating response dynamics. Additionally, CCHFV-infected cases could acquire an Ebola infection while in the ETU, and upon release because of a negative Ebola virus result, have the potential to spread these infections in the community.},
}

@article {pmid39411387,
year = {2024},
author = {Zhao, J and Wang, C and Hu, J and Ma, R and Yu, B and Zhao, W and Wang, H and Gu, Y and Zhang, J},
title = {Integrated metagenomics and metabolomics analyses revealed biomarkers in β-casein A2A2-type cows.},
journal = {Frontiers in veterinary science},
volume = {11},
number = {},
pages = {1438717},
pmid = {39411387},
issn = {2297-1769},
abstract = {In Holstein cows, β-casein, one of the most critical proteins in milk, exists in two main genotypes, A1 and A2. Herein, 45 Holstein cows [categorized into three groups based on β-casein A1A1, A1A2, and A2A2 genotypes (N = 15)] with the same feeding management and litter size were enrolled to explore differences in rumen microflora and metabolites across various β-casein genotypes. Rumen fluids were collected for metagenomics and metabolomics analyses. Metabolomics and weighted gene co-expression network analysis (WGCNA) revealed that arachidonic acid (AA), adrenic acid (AdA), glycocholic acid (GCA), and taurocholic acid (TCA) were significantly and positively correlated with milk fat % in dairy cows (p < 0.05). Furthermore, macro-genomics and Spearman's correlation analysis revealed significant positive correlations (p < 0.05) between the characteristic flora (g_Acetobacter, g_Pseudoxanthomonas, g_Streptococcus, and g_Pediococcus) and the five characteristic metabolites in the rumen of A2A2 dairy cows. Moreover, functional enrichment analysis revealed more genes enriched to the TRP channel's inflammatory mediator-regulated pathway and the mTOR signaling pathway in A2A2 genotyped cows. Additionally, the regulatory effects of AA on bovine mammary epithelial cells (BMECs) were examined using CCK-8, EdU, and qRT-PCR assays, revealing that AA promoted triglyceride (TG) synthesis and upregulated the milk fat marker genes including SREBF1, ACSS2, AGPAT6, and FASN. Overall, we identified characteristic microorganisms and metabolites in A2A2 Holstein cows and established that AA could be a biomarker for higher milk fat %.},
}

@article {pmid39411197,
year = {2024},
author = {Baumann, KBL and Mazzoli, A and Salazar, G and Ruscheweyh, HJ and Müller, B and Niederdorfer, R and Sunagawa, S and Lever, MA and Lehmann, MF and Bürgmann, H},
title = {Metagenomic and -transcriptomic analyses of microbial nitrogen transformation potential, and gene expression in Swiss lake sediments.},
journal = {ISME communications},
volume = {4},
number = {1},
pages = {ycae110},
pmid = {39411197},
issn = {2730-6151},
abstract = {The global nitrogen (N) cycle has been strongly altered by anthropogenic activities, including increased input of bioavailable N into aquatic ecosystems. Freshwater sediments are hotspots with regards to the turnover and elimination of fixed N, yet the environmental controls on the microbial pathways involved in benthic N removal are not fully understood. Here, we analyze the abundance and expression of microbial genes involved in N transformations using metagenomics and -transcriptomics across sediments of 12 Swiss lakes that differ in sedimentation rates and trophic regimes. Our results indicate that microbial N loss in these sediments is primarily driven by nitrification coupled to denitrification. N-transformation gene compositions indicated three groups of lakes: agriculture-influenced lakes characterized by rapid depletion of oxidants in the sediment porewater, pristine-alpine lakes with relatively deep sedimentary penetration of oxygen and nitrate, and large, deep lakes with intermediate porewater hydrochemical properties. Sedimentary organic matter (OM) characteristics showed the strongest correlations with the community structure of microbial N-cycling communities. Most transformation pathways were expressed, but expression deviated from gene abundance and did not correlate with benthic geochemistry. Cryptic N-cycling may maintain transcriptional activity even when substrate levels are below detection. Sediments of large, deep lakes generally showed lower in-situ N gene expression than agriculture-influenced lakes, and half of the pristine-alpine lakes. This implies that prolonged OM mineralization in the water column can lead to the suppression of benthic N gene expression.},
}

@article {pmid39410870,
year = {2024},
author = {Matsubara, K and Li, J and Enomoto, Y and Takahashi, T and Ma, M and Ninomiya, R and Kazami, D and Miura, K and Hirayama, K},
title = {Beneficial Role of Heat-Treated Lactobacillus sakei HS-1 on Growth Performance, Nutritional Status and Gut Microbiota in Weaned Piglets.},
journal = {Journal of animal physiology and animal nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1111/jpn.14056},
pmid = {39410870},
issn = {1439-0396},
support = {//The authors received no specific funding for this work./ ; },
abstract = {In the swine industry, there is a strong need to replace an antibiotic growth promoter (AGP) used as feed additives in weaned piglets to enhance nutrient utilization in their diets and improve growth performance. Lactobacillus sakei HS-1 strain is a microbial preparation isolated from pickles. The study aim is to investigate the effectiveness of heat-treated L. sakei HS-1 strain (HT-LS) as a growth promoter in weaned piglets compared to colistin (CS), a widely used AGP. Eighteen crossbred weaned piglets (Landrace × Yorkshire × Duroc) of 21 days (average body weight [BW]: 7.06 ± 0.59 kg) were divided into three groups: fed the control diet (CT group), fed a diet supplemented with 30 ppm colistin sulphate (CS group), fed a diet supplemented with HT-LS at a concentration of 2.0 × 10[5] cells/g (LS group) until 49 days. The results indicated that LS group exhibited significantly higher average daily gain (p < 0.05) and higher BW (p < 0.1) compared with CT group, even higher than CS group. CS group showed higher growth performance compared to CT group but the differences were not statistically significant. In addition, LS group had higher (p < 0.05) or tended to higher (p < 0.1) concentrations of several plasma amino acids than the other two groups at 35 and 49 days. Faecal acetate concentration was higher (p < 0.1) in LS group than in CT group at 35 days. Blood immunoglobulin G concentration in LS group was significantly lower (p < 0.05) than in CT group at 35 and 49 days, and blood immunoglobulin A tended to be lower (p < 0.1) at 35 days than in CT group. LS group showed an increased abundance of g_Prevotella 7, g_Streptococcus and g_Lactobacillus (linear discriminant analysis [LDA] score ≥ 2.0). Predictive metagenomic analysis revealed an enrichment of the mixed acid fermentation pathway (LDA score ≥ 2.0). Furthermore, several gut microbes exhibited correlations with plasma amino acids (p < 0.01) and short-chain fatty acids in faeces (p < 0.01). These findings demonstrate that HT-LS improves the growth performance of weaned piglets by enhancing the efficient utilization of nutrients through gut microbiota modification.},
}

@article {pmid39410242,
year = {2024},
author = {Wang, B and Wu, W and Wang, Z and Chen, Z and Wang, X},
title = {Soil-Mulching Treatment Enhances the Content of Stilbene in Grape Berries: A Transcriptomic and Metabolomic Analysis.},
journal = {Foods (Basel, Switzerland)},
volume = {13},
number = {19},
pages = {},
doi = {10.3390/foods13193208},
pmid = {39410242},
issn = {2304-8158},
support = {[CX(21)2027]//Jiangsu Agricultural Science and Technology Innovation Fund/ ; },
abstract = {Soil mulching is a useful agronomic practice that promotes early fruit maturation and affects fruit quality. However, the regulatory mechanism of fruit metabolites under soil-mulching treatments remains unknown. In this study, variations in the gene sets and metabolites of grape berries after mulching (rice straw + felt + plastic film) using transcriptome and metagenomic sequencing were investigated. The results of the cluster analysis and orthogonal projection to latent structures discriminant analysis of the metabolites showed a difference between the mulching and control groups, as did the principal component analysis results for the transcriptome. In total, 36 differentially expressed metabolites were identified, of which 10 (resveratrol, ampelopsin F, piceid, 3,4'-dihydroxy-5-methoxystilbene, ε-viniferin, trans resveratrol, epsilon-viniferin, 3'-hydroxypterostilbene, 1-methyl-resveratrol, and pterostil-bene) were stilbenes. Their content increased after mulching, indicating that stilbene synthase activity increased after mulching. The weighted gene co-expression network analysis revealed that the turquoise and blue modules were positively and negatively related to stilbene compounds. The network analysis identified two seed genes (VIT_09s0054g00610, VIT_13s0156g00260) and two transcription factors (VIT_13s0156g00260, VIT_02s0025g04590). Overall, soil mulching promoted the accumulation of stilbene compounds in grapes, and the results provided key genetic information for further studies.},
}

@article {pmid39410228,
year = {2024},
author = {Kim, S and Kang, JY and Nguyen, QA and Lee, JS},
title = {Effects of Prebiotic Dietary Fibers on the Stimulation of the Mucin Secretion in Host Cells by In Vitro Gut Microbiome Consortia.},
journal = {Foods (Basel, Switzerland)},
volume = {13},
number = {19},
pages = {},
doi = {10.3390/foods13193194},
pmid = {39410228},
issn = {2304-8158},
support = {NRF-2021R1A2C1005811//National Research Foundation of Korea/ ; NRF-2023K2A9A1A01098813, FY2023//National Research Foundation of Korea/ ; KRIBB Research Initiative Program grant (KGM5482423)//Korea Research Institute of Bioscience and Biotechnology/ ; },
abstract = {The gastrointestinal microbiota are important for human health. Dietary intake may modulate the composition and metabolic function of the gut microbiome. We examined how the breakdown of prebiotic dietary fibers by the gut microbiome affects mucin secretion by intestinal epithelial cells. Metagenomic analyses of in vitro gut microbiome consortia revealed taxonomic profiles and genetic diversity of carbohydrate-active enzymes that digest polysaccharides. Two independent consortia exhibited different abilities to produce acetic acid, propionic acid, and butyric acid via the fermentation of polysaccharides derived from dietary fibers of grains and mushrooms. Although acetic acid generally had the highest concentration, the ratios of butyric acid and propionic acid to acetic acid varied depending on the polysaccharide source. These short-chain fatty acids affected morphological differentiation and mucin secretion in HT-29 human intestinal epithelial cells. These results suggest that prebiotic dietary fibers can be digested and metabolized by the gut microbiome to short-chain fatty acids, which can affect gut epithelial cells both directly and indirectly via the modulation of the gut microbiota and their enzymes.},
}

@article {pmid39410210,
year = {2024},
author = {Liang, J and Yuan, H and Fei, Y and Wang, H and Qu, C and Bai, W and Liu, G},
title = {Effects of Saccharomyces cerevisiae and Cyberlindnera fabianii Inoculation on Rice-Flavor Baijiu Fermentation.},
journal = {Foods (Basel, Switzerland)},
volume = {13},
number = {19},
pages = {},
doi = {10.3390/foods13193175},
pmid = {39410210},
issn = {2304-8158},
support = {2021ZDJS005//the Research Capacity Enhancement Project of Key Disciplines in Guangdong Province/ ; 2023KJ101//Guangdong Provincial Agricultural Science and Technology Innovation and Extension Project in 2023/ ; 2021B1212040013//Guangdong Provincial Key Laboratory of Lingnan Specialty Food Science and Technology/ ; },
abstract = {Rice-flavor baijiu is a distilled Chinese spirit prepared from Xiaoqu culture. However, its dull taste may be a market limitation. In order to enhance the flavor profile of rice-flavor baijiu, two ester-producing yeast strains (Saccharomyces cerevisiae and Cyberlindnera fabianii) were inoculated for fermentation. At the end of the fermentation, the total alcohol and ester contents had also increased by 43.3% and 29.8%, respectively, and the number of ester species had increased by eight. Additionally, eleven flavor substances had significant contributions in the inoculated fermentation process, including several different esters and alcohols. A macrogenomic analysis revealed that the majority of the gene abundances associated with the alcohol, acid, and ester pathways were elevated by the third day of inoculated fermentation, and greater abundances of Saccharomyces cerevisiae, Cyberlindnera fabianii, Lichtheimia ramosa, Rhizopus delemar, and Rhizopus oryzaefive, annotated with these genes, were observed from either the pre-fermentation stage or post-fermentation stage. The results demonstrate that two added strains are associated with an increase in the content of the flavor substances. These findings may prove beneficial in enhancing the quality of rice-flavor baijiu through using inoculated fermentation with ester-producing yeast.},
}

@article {pmid39410149,
year = {2024},
author = {Liang, Z and Chen, S and Wang, H and Wu, Q and Guo, W and Ni, L and Lv, X},
title = {Metagenomic and Metabolomic Profiling Reveals the Differences of Flavor Quality between Hongqu Rice Wines Fermented with Gutian Qu and Wuyi Qu.},
journal = {Foods (Basel, Switzerland)},
volume = {13},
number = {19},
pages = {},
doi = {10.3390/foods13193114},
pmid = {39410149},
issn = {2304-8158},
support = {No. 32472296; No. 32472295; No. 32072204//National Natural Science Foundation of China/ ; },
abstract = {Jiuqu (starter) makes an important contribution to the formation of the flavor characteristics of Hongqu rice wine (HQW). Gutian Qu (GTQ) and Wuyi Qu (WYQ) are two kinds of Jiuqu commonly used in HQW brewing, but the comparison of the two kinds of HQW is still insufficient at present. The objective of this study was to compare the dynamic changes of amino acids (AAs), higher alcohols (HAs), bioamines (BAs), volatile flavor compounds (VFCs), and microbial communities in HQW fermentation, with GTQ and WYQ as starter. This study used an automatic amino acid analyzer, GC, HPLC, and GC-MS to detect AAs, HAs, Bas, and VFCs during fermentation; metagenomic sequencing technology was used to elucidate the microbial community and its functional characteristics. The results showed that the contents of AAs and HAs in HQW brewed with WYQ (WYW) were significantly higher than those in HQW brewed with GTQ (GTW). On the contrary, the majority of BAs in GTW were significantly higher than those in WYW. The composition of VFCs in WYW and GTW were obviously different, as most of the VFCs were notably enriched in WYW, while ethyl caproate, isoamyl acetate, ethyl heptanoate, ethyl nonanoate, 1-decanol, citronellol, phenethyl acetate, and hexanoic acid were more abundant in GTW. Burkholderia gladioli, Pantoea dispersa, Weissella cibaria, Monascus purpureus, and Saccharomyces cerevisiae were the predominant microbial populations in GTW brewing at the species level, while Sphingomonas sp., Kosakonia cowanii, Enterobacter asburiae, Leuconostoc lactis, Aspergillus niger, and Saccharomyces cerevisiae were the dominant microbial species in WYW brewing. The abundance of functional genes involved in BAs biosynthesis were much higher in GTW brewing, while the abundance of functional genes related to the metabolism of characteristic VFCs were much higher in WYW brewing. Collectively, these findings provided evidence for elucidating the effects of Jiuqu and microbial communities on HQW flavor quality, and laid a solid foundation for the improvement of HQW flavor quality.},
}

@article {pmid39409842,
year = {2024},
author = {Xie, M and Fei, D and Guang, Y and Xue, F and Xu, J and Zhou, Y},
title = {Role of Metabolomics and Metagenomics in the Replacement of the High-Concentrate Diet with a High-Fiber Diet for Growing Yushan Pigs.},
journal = {Animals : an open access journal from MDPI},
volume = {14},
number = {19},
pages = {},
doi = {10.3390/ani14192893},
pmid = {39409842},
issn = {2076-2615},
support = {2021BDH80013//the Science and Technology Cooperation Program of Jiangxi/ ; 20192ACB60004//the Jiangxi Key Research and Development Program/ ; 2024SSY04211//the safe quality of agricultural products key laboratory of Jiangxi Province/ ; },
abstract = {The objective of this study was to investigate the regulatory effects of a high-fiber content feed on the productive performance, meat quality, and fat acid composition. A total of 18 120-day-old Yushan pigs with similar initial body weight were randomly allotted into high-concentrate diet (high energy, HE) and high-fiber diet (low energy, LE) treatments for the determination of regulatory effects on productive performance, meat quality, and fatty acid content. Further, blood metabolomic, gut microbiota, and liver energy-related gene expression measurements were used to investigate the underlying mechanisms. Results showed that the LE treatment significantly increased ADFI while decreasing carcass weight, fat percentage, and IMF. Metabolomic results showed that the high-fiber treatment significantly down-regulated metabolites that participated in lipid metabolism such as cyclic ADP-ribose and hippuric acid, while up-regulated metabolites were mainly enriched in nitrogen metabolism such as DL-arginine and propionylcarnitine (p < 0.05). Microbial results showed relative abundances of Lactobacillus and Bifidobacterium are significantly proliferated in the high-fiber feeding treatments (p < 0.05). Transcriptomic results showed that genes mainly enriched into the lipid metabolism are significantly up-regulated under the high-fiber dietary treatment (p < 0.05). Conclusion: higher dietary fiber significantly reduced dietary energy provision, effectively decreased the backfat and abdominal fat content of Yushan pigs through proliferating intestinal fiber-degradable bacteria, and up-regulating the hepatic lipolysis-related gene expression.},
}

@article {pmid39409167,
year = {2024},
author = {Evseev, P and Gutnik, D and Evpak, A and Kasimova, A and Miroshnikov, K},
title = {Origin, Evolution and Diversity of φ29-like Phages-Review and Bioinformatic Analysis.},
journal = {International journal of molecular sciences},
volume = {25},
number = {19},
pages = {},
doi = {10.3390/ijms251910838},
pmid = {39409167},
issn = {1422-0067},
mesh = {*Bacteriophages/genetics/classification ; *Computational Biology/methods ; *Genome, Viral ; Evolution, Molecular ; Phylogeny ; Archaea/virology/genetics ; Capsid Proteins/genetics ; },
abstract = {Phage φ29 and related bacteriophages are currently the smallest known tailed viruses infecting various representatives of both Gram-positive and Gram-negative bacteria. They are characterised by genomic content features and distinctive properties that are unique among known tailed phages; their characteristics include protein primer-driven replication and a packaging process characteristic of this group. Searches conducted using public genomic databases revealed in excess of 2000 entries, including bacteriophages, phage plasmids and sequences identified as being archaeal that share the characteristic features of phage φ29. An analysis of predicted proteins, however, indicated that the metagenomic sequences attributed as archaeal appear to be misclassified and belong to bacteriophages. An analysis of the translated polypeptides of major capsid proteins (MCPs) of φ29-related phages indicated the dissimilarity of MCP sequences to those of almost all other known Caudoviricetes groups and a possible distant relationship to MCPs of T7-like (Autographiviridae) phages. Sequence searches conducted using HMM revealed the relatedness between the main structural proteins of φ29-like phages and an unusual lactococcal phage, KSY1 (Chopinvirus KSY1), whose genome contains two genes of RNA polymerase that are similar to the RNA polymerases of phages of the Autographiviridae and Schitoviridae (N4-like) families. An analysis of the tail tube proteins of φ29-like phages indicated their dissimilarity of the lower collar protein to tail proteins of all other viral groups, but revealed its possible distant relatedness with proteins of toxin translocation complexes. The combination of the unique features and distinctive origin of φ29-related phages suggests the categorisation of this vast group in a new order or as a new taxon of a higher rank.},
}

*Bacteriophages/genetics/classification
*Computational Biology/methods
*Genome, Viral
Evolution, Molecular
Phylogeny
Archaea/virology/genetics
Capsid Proteins/genetics

@article {pmid39409144,
year = {2024},
author = {Donchev, D and Stoikov, I and Diukendjieva, A and Ivanov, IN},
title = {Assessment of Skimmed Milk Flocculation for Bacterial Enrichment from Water Samples, and Benchmarking of DNA Extraction and 16S rRNA Databases for Metagenomics.},
journal = {International journal of molecular sciences},
volume = {25},
number = {19},
pages = {},
doi = {10.3390/ijms251910817},
pmid = {39409144},
issn = {1422-0067},
support = {BG05M2OP001-1.002-0001-C04//European Regional Development Fund through the Operational Program Science and Education for Smart Growth 2014-2020/ ; not applicable//Biocampus Sofia Association/ ; },
mesh = {*RNA, Ribosomal, 16S/genetics ; *Milk/microbiology ; *Metagenomics/methods ; Animals ; *DNA, Bacterial/genetics/isolation & purification ; *Bacteria/genetics/classification/isolation & purification ; Flocculation ; Benchmarking ; Microbiota/genetics ; Water Microbiology ; },
abstract = {Water samples for bacterial microbiome studies undergo biomass concentration, DNA extraction, and taxonomic identification steps. Through benchmarking, we studied the applicability of skimmed milk flocculation (SMF) for bacterial enrichment, an adapted in-house DNA extraction protocol, and six 16S rRNA databases (16S-DBs). Surface water samples from two rivers were treated with SMF and vacuum filtration (VF) and subjected to amplicon or shotgun metagenomics. A microbial community standard underwent five DNA extraction protocols, taxonomical identification with six different 16S-DBs, and evaluation by the Measurement Integrity Quotient (MIQ) score. In SMF samples, the skimmed milk was metabolized by members of lactic acid bacteria or genera such as Polaromonas, Macrococcus, and Agitococcus, resulting in increased relative abundance (p < 0.5) up to 5.0 log fold change compared to VF, rendering SMF inapplicable for bacterial microbiome studies. The best-performing DNA extraction protocols were FastSpin Soil, the in-house method, and EurX. All 16S-DBs yielded comparable MIQ scores within each DNA extraction kit, ranging from 61-66 (ZymoBIOMICs) up to 80-82 (FastSpin). DNA extraction kits exert more bias toward the composition than 16S-DBs. This benchmarking study provided valuable information to inform future water metagenomic study designs.},
}

*RNA, Ribosomal, 16S/genetics
*Milk/microbiology
*Metagenomics/methods
Animals
*DNA, Bacterial/genetics/isolation & purification
*Bacteria/genetics/classification/isolation & purification
Flocculation
Benchmarking
Microbiota/genetics
Water Microbiology

@article {pmid39409119,
year = {2024},
author = {Xiang, J and Zhang, N and Li, J and Zhu, Y and Cao, T and Wang, Y},
title = {Unveiling the Hidden Responses: Metagenomic Insights into Dwarf Bamboo (Fargesia denudata) Rhizosphere under Drought and Nitrogen Challenges.},
journal = {International journal of molecular sciences},
volume = {25},
number = {19},
pages = {},
doi = {10.3390/ijms251910790},
pmid = {39409119},
issn = {1422-0067},
support = {2019QZKK0303//the Second Tibetan Plateau Scientific Expedition and Research Program (STEP)/ ; 31470621//National Natural Science Foundation of China/ ; },
mesh = {*Rhizosphere ; *Nitrogen/metabolism ; *Droughts ; *Metagenomics/methods ; Soil Microbiology ; Metagenome ; Stress, Physiological/genetics ; Poaceae/genetics/microbiology ; Plant Roots/microbiology/genetics ; Soil/chemistry ; },
abstract = {Dwarf bamboo (Fargesia denudata) is a crucial food source for the giant pandas. With its shallow root system and rapid growth, dwarf bamboo is highly sensitive to drought stress and nitrogen deposition, both major concerns of global climate change affecting plant growth and rhizosphere environments. However, few reports address the response mechanisms of the dwarf bamboo rhizosphere environment to these two factors. Therefore, this study investigated the effects of drought stress and nitrogen deposition on the physicochemical properties and microbial community composition of the arrow bamboo rhizosphere soil, using metagenomic sequencing to analyze functional genes involved in carbon and nitrogen cycles. Both drought stress and nitrogen deposition significantly altered the soil nutrient content, but their combination had no significant impact on these indicators. Nitrogen deposition increased the relative abundance of the microbial functional gene nrfA, while decreasing the abundances of nirK, nosZ, norB, and nifH. Drought stress inhibited the functional genes of key microbial enzymes involved in starch and sucrose metabolism, but promoted those involved in galactose metabolism, inositol phosphate metabolism, and hemicellulose degradation. NO3[-]-N showed the highest correlation with N-cycling functional genes (p < 0.01). Total C and total N had the greatest impact on the relative abundance of key enzyme functional genes involved in carbon degradation. This research provides theoretical and technical references for the sustainable management and conservation of dwarf bamboo forests in giant panda habitats under global climate change.},
}

*Rhizosphere
*Nitrogen/metabolism
*Droughts
*Metagenomics/methods
Soil Microbiology
Metagenome
Stress, Physiological/genetics
Poaceae/genetics/microbiology
Plant Roots/microbiology/genetics
Soil/chemistry

@article {pmid39408280,
year = {2024},
author = {Nguyen, SM and Tran, TDC and Tran, TM and Wang, C and Wu, J and Cai, Q and Ye, F and Shu, XO},
title = {Influence of Peanut Consumption on the Gut Microbiome: A Randomized Clinical Trial.},
journal = {Nutrients},
volume = {16},
number = {19},
pages = {},
doi = {10.3390/nu16193313},
pmid = {39408280},
issn = {2072-6643},
support = {N/A//The Peanut Institute/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; *Arachis ; Male ; Female ; *Feces/microbiology ; Adult ; Bacteria/classification/genetics ; Vietnam ; Diet ; Middle Aged ; },
abstract = {Background: Peanut consumption could impact cardiometabolic health through gut microbiota, a hypothesis that remains to be investigated. A randomized clinical trial in Vietnam evaluated whether peanut consumption alters gut microbiome communities. Methods: One hundred individuals were included and randomly assigned to the peanut intervention and control groups. A total of 51 participants were provided with and asked to consume 50 g of peanuts daily, while 49 controls maintained their usual dietary intake for 16 weeks. Stool samples were collected before and on the last day of the trial. After excluding 22 non-compliant participants and those who received antibiotic treatment, 35 participants from the intervention and 43 from the control were included in the analysis. Gut microbiota composition was measured by shotgun metagenomic sequencing. Associations of changes in gut microbial diversity with peanut intervention were evaluated via linear regression analysis. Linear mixed-effects models were used to analyze associations of composition, sub-community structure, and microbial metabolic pathways with peanut intervention. We also performed beta regression analysis to examine the impact of peanut intervention on the overall and individual stability of microbial taxa and metabolic pathways. All associations with false discovery rate (FDR)-corrected p-values of <0.1 were considered statistically significant. Results: No significant changes were found in α- and β-diversities and overall gut microbial stability after peanut intervention. However, the peanut intervention led to lower enrichment of five phyla, five classes, two orders, twenty-four metabolic pathways, and six species-level sub-communities, with a dominant representation of Bifidobacterium pseudocatenulatum, Escherichia coli D, Holdemanella biformis, Ruminococcus D bicirculans, Roseburia inulinivorans, and MGYG-HGUT-00200 (p < 0.05 and FDR < 0.1). The peanut intervention led to the short-term stability of several species, such as Faecalibacterium prausnitzii F and H, and a metabolic pathway involved in nitrate reduction V (p < 0.05; FDR < 0.1), known for their potential roles in human health, especially cardiovascular health. Conclusions: In summary, a 16-week peanut intervention led to significant changes in gut microbial composition, species-level sub-communities, and the short-term stability of several bacteria, but not overall gut microbial diversity and stability. Further research with a larger sample size and a longer intervention period is needed to confirm these findings and investigate the direct impact of gut-microbiome-mediated health effects of peanut consumption. Trial registration: The International Traditional Medicine Clinical Trial Registry (ITMCTR). Registration number: ITMCTR2024000050. Retrospectively Registered 24 April 2024.},
}

Humans
*Gastrointestinal Microbiome
*Arachis
Male
Female
*Feces/microbiology
Adult
Bacteria/classification/genetics
Vietnam
Diet
Middle Aged

@article {pmid39407862,
year = {2024},
author = {Alavi, SMA and Petri, F and Mahmoud, OK and Igwilo-Alaneme, R and El Zein, S and Nassr, AN and Gori, A and Berbari, EF},
title = {Culture-Negative Native Vertebral Osteomyelitis: A Narrative Review of an Underdescribed Condition.},
journal = {Journal of clinical medicine},
volume = {13},
number = {19},
pages = {},
doi = {10.3390/jcm13195802},
pmid = {39407862},
issn = {2077-0383},
abstract = {The incidence of culture-negative NVO (CN-NVO) cases is increasing, presenting significant diagnostic and therapeutic challenges due to the inability to isolate causative organisms with conventional microbiological methods. Factors influencing the diagnosis of CN-NVO include prior antimicrobial therapy, low pathogen burden, fastidious or intracellular organisms, technical issues, and non-infectious mimickers. Diagnosis often relies on imaging modalities like magnetic resonance imaging (MRI) and computed tomography (CT)-guided biopsy, though these methods can sometimes fail to yield positive microbiological results. Advanced diagnostic tools, such as polymerase chain reaction (PCR), metagenomic next-generation sequencing (mNGS), and cell-free DNA analysis, may be necessary to identify the pathogen. The causative pathogen cannot be isolated in some patients, among which an empirical antimicrobial therapy should be initiated. This narrative review discusses the management, monitoring, surgical indications, and outcomes for patients with CN-NVO.},
}

@article {pmid39407853,
year = {2024},
author = {Laryushina, Y and Samoilova-Bedych, N and Turgunova, L and Kozhakhmetov, S and Alina, A and Suieubayev, M and Mukhanbetzhanov, N},
title = {Alterations of the Gut Microbiome and TMAO Levels in Patients with Ulcerative Colitis.},
journal = {Journal of clinical medicine},
volume = {13},
number = {19},
pages = {},
doi = {10.3390/jcm13195794},
pmid = {39407853},
issn = {2077-0383},
support = {AP14871959//Science Committee of the Ministry of Education and Science of the Republic of Kazakhstan/ ; },
abstract = {Background: Ulcerative colitis (UC) is an idiopathic and heterogeneous large intestine disease, characterized by chronic mucosa and submucosa inflammation. Alteration of the intestinal microbiome in UC may be responsible for modifications in metabolite production. Aim: To investigate the microbiota status and trimethylamine-N-oxide (TMAO) metabolite levels in patients with UC according to clinical and endoscopic activity. Methods: As part of a grant project AP14871959 from September 2022 to October 2023, 31 patients with UC and 15 healthy volunteers over 18 years at the Clinic of NCJSC "KMU" were assessed for blood TMAO level and metagenomic sequencing of fecal microbiome. Results: A significant depletion of the main representatives of Bacteroides, Parabacteroides, Prevotella; and an increase in the relative abundance of the genera Actinomyces, Klebsiella, Limosilactobacillus, Streptococcus, Escherichia-Shigella were detected in patients with UC. The number of p_Actinobacteria (g_Collinsella) and p_Eubacterium (g_Xylanophilum) representatives with genes encoding TMA-trimethylamine conversion is significantly reduced in UC patients. TMAO levels were significantly lower in UC patients than in healthy individuals (0.233 µmol/L, p = 0.004). TMAO decreased with disease severity and significantly differed between patients with different activities (p = 0.034). Conclusions: The composition of the intestinal microbiome changes and the level of TMAO decreases in patients with UC at different activities.},
}

@article {pmid39407346,
year = {2024},
author = {Barcenilla, C and Cobo-Díaz, JF and Puente, A and Valentino, V and De Filippis, F and Ercolini, D and Carlino, N and Pinto, F and Segata, N and Prieto, M and López, M and Alvarez-Ordóñez, A},
title = {In-depth characterization of food and environmental microbiomes across different meat processing plants.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {199},
pmid = {39407346},
issn = {2049-2618},
support = {BOCYL-D-07072020-6//Junta de Castilla y León and the European Social Fund/ ; PRE2021-098910//Ministerio de Ciencia e Innovación, Spain/ ; },
mesh = {*Microbiota ; *Food Microbiology ; *Bacteria/classification/genetics/isolation & purification ; *Meat Products/microbiology ; *Food Handling ; Environmental Microbiology ; Meat/microbiology ; RNA, Ribosomal, 16S/genetics ; Animals ; Phylogeny ; },
abstract = {BACKGROUND: Processing environments can be an important source of pathogenic and spoilage microorganisms that cross contaminate meat and meat products. The aim of this study was to characterize the microbiome of raw materials, processing environments and end products from 19 facilities producing different meat products.

RESULTS: The taxonomic profiles of the microbial communities evolved along processing, from raw materials to end products, suggesting that food contact (FC) surfaces play an important role in modulating the microbiome of final products. Some species persisted with the highest relative abundance in raw materials, food processing environments and/or in the final product, including species from the genera Pseudomonas, Staphylococcus, Brochothrix, Acinetobacter and Psychrobacter. Processing environments showed a very diverse core microbiota, partially shared with the products. Pseudomonas fragi and Pseudomonas sp. Lz4W (in all sample and facility types) and Brochothrix thermosphacta, Psychrobacter sp. and Psychrobacter sp. P11F6 (in raw materials, FC surfaces and end products) were prominent members of the core microbiota for all facilities, while Latilactobacillus sakei was found as a dominant species exclusively in end products from the facilities producing fermented sausages. Processing environments showed a higher amount of antimicrobial resistance genes and virulence factors than raw materials and end products. One thousand four hundred twenty-one medium/high-quality metagenome-assembled genomes (MAGs) were reconstructed. Of these, 274 high-quality MAGs (completeness > 90%) corresponded to 210 putative new species, mostly found in processing environments. For two relevant taxa in meat curing and fermentation processes (S. equorum and L. sakei, respectively), phylogenetic variation was observed associated with the specific processing facility under study, which suggests that specific strains of these taxa may be selected in different meat processing plants, likely contributing to the peculiar sensorial traits of the end products produced in them.

CONCLUSIONS: Overall, our findings provide the most detailed metagenomics-based perspective up to now of the microbes that thrive in meat, meat products and associated environments and open avenues for future research activities to better understand the microbiome functionality and potential contribution to meat quality and safety. Video Abstract.},
}

*Microbiota
*Food Microbiology
*Bacteria/classification/genetics/isolation & purification
*Meat Products/microbiology
*Food Handling
Environmental Microbiology
Meat/microbiology
RNA, Ribosomal, 16S/genetics
Animals
Phylogeny