@article {pmid39703432,
year = {2024},
author = {Zhao, J and Pierre Both, J and Konstantinidis, KT},
title = {Approximate nearest neighbor graph provides fast and efficient embedding with applications for large-scale biological data.},
journal = {NAR genomics and bioinformatics},
volume = {6},
number = {4},
pages = {lqae172},
pmid = {39703432},
issn = {2631-9268},
abstract = {Dimension reduction (DR or embedding) algorithms such as t-SNE and UMAP have many applications in big data visualization but remain slow for large datasets. Here, we further improve the UMAP-like algorithms by (i) combining several aspects of t-SNE and UMAP to create a new DR algorithm; (ii) replacing its rate-limiting step, the K-nearest neighbor graph (K-NNG), with a Hierarchical Navigable Small World (HNSW) graph; and (iii) extending the functionality to DNA/RNA sequence data by combining HNSW with locality sensitive hashing algorithms (e.g. MinHash) for distance estimations among sequences. We also provide additional features including computation of local intrinsic dimension and hubness, which can reflect structures and properties of the underlying data that strongly affect the K-NNG accuracy, and thus the quality of the resulting embeddings. Our library, called annembed, is implemented, and fully parallelized in Rust and shows competitive accuracy compared to the popular UMAP-like algorithms. Additionally, we showcase the usefulness and scalability of our library with three real-world examples: visualizing a large-scale microbial genomic database, visualizing single-cell RNA sequencing data and metagenomic contig (or population) binning. Therefore, annembed can facilitate DR for several tasks for biological data analysis where distance computation is expensive or when there are millions to billions of data points to process.},
}

@article {pmid39703404,
year = {2024},
author = {Huang, K and Zhang, X and Xiong, N and Sun, L and Zhao, X and Zhou, K and Wu, J},
title = {First metagenomic sequencing for the analysis of microbial community populations of adults and pupae of Melophagus ovinus in Xinjiang, China.},
journal = {Frontiers in veterinary science},
volume = {11},
number = {},
pages = {1462772},
pmid = {39703404},
issn = {2297-1769},
abstract = {INTRODUCTION: Melophagus ovinus, a parasite on the body surface of sheep, directly attacks the host through biting and sucking blood and may also transmit pathogens in the process. There are currently only a few studies on the microbial composition of M. ovinus, while there are no such studies on pupae.

METHODS: In this study, samples AT-1 to AT-4 each contained four M. ovinus individuals, while sample AT-5 comprised four M. ovinus pupae, all used for metagenomic sequencing and analysis. Melophagus ovinus adults and pupae were collected from four regions in Xinjiang, China. DNA was extracted from the samples, amplified, and sequenced using the Illumina Novaseq 6000 System; finally, the sequencing data were analyzed using molecular biology software.

RESULTS AND DISCUSSION: From all samples, a total of 32 phyla, comprising 372 genera and 1,037 species, were detected. The highest microbial diversity was observed in Kuqa City (AT-2) and Qira County (AT-4). Pupae exhibited 40 unique microbial genera (AT-5) but did not have the highest microbial diversity. Proteobacteria was the dominant phylum in all samples. The dominant genera included Bartonella, Wolbachia, Pseudomonas, and Arsenophonus. This is the first study to report most of the bacteria (e.g., Pseudomonas versuta and Arsenophonus nasoniae), fungi (e.g., Saitoella complicata), viruses (e.g., Orf virus and Wolbachia phage WO), and protozoa (e.g., Trypanosoma theileri and Babesia bigemina) in M. ovinus. This study has enriched the microbial diversity data of M. ovinus, and the pathogens it carries may pose a threat to public health safety and the economy of related industries, necessitating further research to develop effective biological control strategies.},
}

@article {pmid39702789,
year = {2024},
author = {Kaur, S and Patel, BCK and Collen, A and Malhotra, R},
title = {The microbiome and the eye: a new era in ophthalmology.},
journal = {Eye (London, England)},
volume = {},
number = {},
pages = {},
pmid = {39702789},
issn = {1476-5454},
abstract = {The human microbiome has progressively been recognised for its role in various disease processes. In ophthalmology, complex interactions between the gut and distinct ocular microbiota within each structure and microenvironment of the eye has advanced our knowledge on the multi-directional relationships of these ecosystems. Increasingly, studies have shown that modulation of the microbiome can be achieved through faecal microbiota transplantation and synbiotics producing favourable outcomes for ophthalmic diseases. As ophthalmologists, we are obliged to educate our patients on measures to cultivate a healthy gut microbiome through a range of holistic measures. Further integrative studies combining microbial metagenomics, metatranscriptomics and metabolomics are necessary to fully characterise the human microbiome and enable targeted therapeutic interventions.},
}

@article {pmid39702650,
year = {2024},
author = {Vriend, EMC and Galenkamp, H and Herrema, H and Nieuwdorp, M and van den Born, BH and Verhaar, BJH},
title = {Machine learning analysis of sex and menopausal differences in the gut microbiome in the HELIUS study.},
journal = {NPJ biofilms and microbiomes},
volume = {10},
number = {1},
pages = {152},
pmid = {39702650},
issn = {2055-5008},
support = {189235//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; 09150182010020/ZONMW_/ZonMw/Netherlands ; 101141346/ERC_/European Research Council/International ; },
mesh = {*Gastrointestinal Microbiome ; Humans ; Female ; *Machine Learning ; Male ; Middle Aged ; *Menopause ; Aged ; Sex Factors ; Metagenomics/methods ; Adult ; Cohort Studies ; Bacteria/classification/genetics/isolation & purification ; Feces/microbiology ; },
abstract = {Sex differences in the gut microbiome have been examined previously, but results are inconsistent, often due to small sample sizes. We investigated sex and menopausal differences in the gut microbiome in a large multi-ethnic population cohort study, including 5166 participants. Using machine learning models, we revealed modest associations between sex and menopausal status, and gut microbiota composition (AUC 0.61-0.63). After adjustments for age, cardiovascular risk factors, and diet, a part of the associations of the highest-ranked gut microbes with sex were attenuated, but most associations remained significant. In contrast, most associations with menopausal status were driven by age and lost significance after adjustment. Using pathway analyses on metagenomic data, we identified sex differences in vitamin B6 synthesis and stachyose degradation pathways. Since some of sex differences in gut microbiome composition and function could not be explained by covariates, we recommend sex stratification in future microbiome studies.},
}

*Gastrointestinal Microbiome
Humans
Female
*Machine Learning
Male
Middle Aged
*Menopause
Aged
Sex Factors
Metagenomics/methods
Adult
Cohort Studies
Bacteria/classification/genetics/isolation & purification
Feces/microbiology

@article {pmid39702405,
year = {2024},
author = {Soufi, HH and Porch, R and Korchagina, MV and Abrams, JA and Schnider, JS and Carr, BD and Williams, MA and Louca, S},
title = {Taxonomic variability and functional stability across Oregon coastal subsurface microbiomes.},
journal = {Communications biology},
volume = {7},
number = {1},
pages = {1663},
pmid = {39702405},
issn = {2399-3642},
mesh = {Oregon ; *Microbiota/genetics ; *Geologic Sediments/microbiology ; *RNA, Ribosomal, 16S/genetics ; Bacteria/genetics/classification ; Phylogeny ; Metagenomics/methods ; Biodiversity ; },
abstract = {The factors shaping microbial communities in marine subsurface sediments remain poorly understood. Here, we analyzed the microbiome of subsurface sediments within a depth range of 1.6-1.9 m, at 10 locations along the Oregon coast. We used metagenomics to reconstruct the functional structure and 16S rRNA gene amplicon sequencing to estimate the taxonomic composition of microbial communities, accompanied by physicochemical measurements. Functional community structure, in terms of the proportions of various gene groups, was remarkably stable across samples, despite the latter covering a region spanning over 300 km. In contrast, taxonomic composition was highly variable, especially at the level of amplicon sequence variants (ASVs) and operational taxonomic units (OTUs). Mantel correlation tests between compositional dissimilarities and geographic distances revealed only a moderate influence of distance on composition. Regression models predicting taxonomic dissimilarities and considering up to 20 physicochemical variables as predictors, almost always failed to select a significant predictor, suggesting that variation in local conditions does not explain the high taxonomic variability. Permutation null models of community assembly revealed that taxa tend to strongly segregate, i.e., exclude each other. We conclude that biological interactions are important drivers of taxonomic variation in subsurface sediments, and that this variation can decouple from functional structure.},
}

Oregon
*Microbiota/genetics
*Geologic Sediments/microbiology
*RNA, Ribosomal, 16S/genetics
Bacteria/genetics/classification
Phylogeny
Metagenomics/methods
Biodiversity

@article {pmid39702006,
year = {2024},
author = {Demirkan, A and van Dongen, J and Finnicum, CT and Westra, HJ and Jankipersadsing, S and Willemsen, G and Ijzerman, RG and Boomsma, DI and Ehli, EA and Bonder, MJ and Fu, J and Franke, L and Wijmenga, C and de Geus, EJC and Kurilshikov, A and Zhernakova, A},
title = {Linking the gut microbiome to host DNA methylation by a discovery and replication epigenome-wide association study.},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {1224},
pmid = {39702006},
issn = {1471-2164},
mesh = {*DNA Methylation ; *Gastrointestinal Microbiome/genetics ; Humans ; *Epigenome ; *Genome-Wide Association Study ; Male ; Female ; RNA, Ribosomal, 16S/genetics ; CpG Islands/genetics ; Middle Aged ; Adult ; Netherlands ; },
abstract = {Microbiome influences multiple human systems, but its effects on gene methylation is unknown. We investigated the relations between gene methylation in blood and the abundance of common gut bacteria profiled by 16s rRNA gene sequencing in two population-based Dutch cohorts: LifeLines-Deep (LLD, n = 616, discovery) and the Netherlands Twin Register (NTR, n = 296, replication). In LLD, we also explored microbial pathways using data generated by shotgun metagenomic sequencing (n = 683). Methylation in both cohorts was profiled in blood samples using the Illumina 450K array. Discovery and replication analysis identified two independent CpGs associated with the genus Eggerthella: cg16586104 (Pmeta-analysis = 3.21 × 10[-11]) and cg12234533 (Pmeta-analysis = 4.29 × 10[-10]). We also show that microbiome can mediate the effect of environmental factors on host gene methylation. In this first association study linking epigenome to microbiome, we found and replicated the associations of two CpGs to the abundance of genus Eggerthella and identified microbiome as a mediator of the exposome. These associations are observational and suggest further investigation in larger and longitudinal set-ups.},
}

*DNA Methylation
*Gastrointestinal Microbiome/genetics
Humans
*Epigenome
*Genome-Wide Association Study
Male
Female
RNA, Ribosomal, 16S/genetics
CpG Islands/genetics
Middle Aged
Adult
Netherlands

@article {pmid39701966,
year = {2024},
author = {Oskolkov, N and Sandionigi, A and Götherström, A and Canini, F and Turchetti, B and Zucconi, L and Mimmo, T and Buzzini, P and Borruso, L},
title = {Unraveling the ancient fungal DNA from the Iceman gut.},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {1225},
pmid = {39701966},
issn = {1471-2164},
mesh = {*DNA, Ancient/analysis ; Humans ; *DNA, Fungal/genetics ; Metagenomics/methods ; Gastrointestinal Microbiome/genetics ; Gastrointestinal Tract/microbiology ; Mummies/microbiology ; Computational Biology/methods ; Fungi/genetics/classification ; },
abstract = {BACKGROUND: Fungal DNA is rarely reported in metagenomic studies of ancient samples. Although fungi are essential for their interactions with all kingdoms of life, limited information is available about ancient fungi. Here, we explore the possibility of the presence of ancient fungal species in the gut of Ötzi, the Iceman, a naturally mummified human found in the Tyrolean Alps (border between Italy and Austria).

METHODS: A robust bioinformatic pipeline has been developed to detect and authenticate fungal ancient DNA (aDNA) from muscle, stomach, small intestine, and large intestine samples.

RESULTS: We revealed the presence of ancient DNA associated with Pseudogymnoascus genus, with P. destructans and P. verrucosus as possible species, which were abundant in the stomach and small intestine and absent in the large intestine and muscle samples.

CONCLUSION: We suggest that Ötzi may have consumed these fungi accidentally, likely in association with other elements of his diet, and they persisted in his gut after his death due to their adaptability to harsh and cold environments. This suggests the potential co-occurrence of ancient humans with opportunistic fungal species and proposes and validates a conservative bioinformatic approach for detecting and authenticating fungal aDNA in historical metagenomic samples.},
}

*DNA, Ancient/analysis
Humans
*DNA, Fungal/genetics
Metagenomics/methods
Gastrointestinal Microbiome/genetics
Gastrointestinal Tract/microbiology
Mummies/microbiology
Computational Biology/methods
Fungi/genetics/classification

@article {pmid39701896,
year = {2024},
author = {Haas, AL and Bradley, BT and Hanson, KE},
title = {Recent Developments in Culture-Independent Fungal Diagnostics.},
journal = {Infectious disease clinics of North America},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.idc.2024.11.004},
pmid = {39701896},
issn = {1557-9824},
abstract = {Culture-independent diagnostics for fungi potentially offer increased sensitivity and more rapid results relative to culture. Recent developments include new platforms for fungal cell wall antigen detection, commercially available targeted nucleic acid amplification tests, and the use of sequencing-based technologies for the detection and identification of a broad range of fungal pathogens. Although these tests are not without limitations, many more commercially available platforms now exist, and efforts to increase the standardization of laboratory-developed tests are ongoing. Additionally, implementation studies are beginning to delineate the optimal use cases for molecular diagnostics across a range of fungal diseases and at-risk populations.},
}

@article {pmid39701829,
year = {2024},
author = {McAlister, JS and Blum, MJ and Bromberg, Y and Fefferman, NH and He, Q and Lofgren, E and Miller, DL and Schreiner, C and Candan, KS and Szabo-Rogers, H and Reed, JM},
title = {An interdisciplinary perspective of the built-environment microbiome.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiae166},
pmid = {39701829},
issn = {1574-6941},
abstract = {The built environment provides an excellent setting for interdisciplinary research on the dynamics of microbial communities. The system is simplified compared to many natural settings, and to some extent the entire environment can be manipulated, from architectural design to materials use, air flow, human traffic, and capacity to disrupt microbial communities through cleaning. Here we provide an overview of the ecology of the microbiome in the built environment. We address niche space and refugia, population and community (metagenomic) dynamics, spatial ecology within a building, including the major microbial transmission mechanisms, as well as evolution. We also address landscape ecology, connecting microbiomes between physically separated buildings. At each stage we pay particular attention to the actual and potential interface between disciplines, such as ecology, epidemiology, materials science, and human social behavior. We end by identifying some opportunities for future interdisciplinary research on the microbiome of the built environment.},
}

@article {pmid39701698,
year = {2024},
author = {Bao, YY and Li, MX and Gao, XX and Wei, WJ and Huang, WJ and Lin, LZ and Wang, H and Zheng, NN and Li, HK},
title = {[Astragalus polysaccharides improve adipose tissue aging in naturally aged mice via indole-3-lactic acid].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {49},
number = {22},
pages = {5998-6007},
doi = {10.19540/j.cnki.cjcmm.20240508.401},
pmid = {39701698},
issn = {1001-5302},
mesh = {Animals ; Mice ; *Aging/drug effects ; *Adipose Tissue/drug effects/metabolism ; *Polysaccharides/pharmacology ; *Indoles/pharmacology ; Male ; *Astragalus Plant/chemistry ; 3T3-L1 Cells ; Humans ; Adipocytes/drug effects/metabolism/cytology ; Mice, Inbred C57BL ; Cellular Senescence/drug effects ; Drugs, Chinese Herbal/pharmacology/administration & dosage ; Gastrointestinal Microbiome/drug effects ; },
abstract = {Plant polysaccharides are effective components that widely present in traditional Chinese medicine(TCM), exhibiting rich biological activities. However, as most plant polysaccharides cannot be directly absorbed and utilized by the human digestive system, it is now believed that their mode of action mainly involves interaction with intestinal microbiota, leading to the production of functional small molecules. The efficacy of Astragalus polysaccharide(APS) is extensive, including weight loss, improvement of fatty liver, reduction of blood lipids, and enhancement of insulin sensitivity, which may also be related to the regulation of intestinal microbiota. Adipose tissue senescence is an important characteristic of the physiological aging process in the body, often occurring prior to the aging of other important organs. Its main features include the accumulation of senescent cells and exacerbation of inflammation within the tissue. Therefore, to explore the potential protective effects of APS on aging, the improvement of adipose tissue aging phenotype in naturally aging mice was observed using APS, and combined with metagenomic metabolomics, corresponding microbial metabolic functional molecules were identified. Furthermore, functional tests in cell aging models were conducted. The results showed that APS significantly improved the adipocyte aging characteristics of naturally aging mice: specifically reducing aging-induced adipocyte hypertrophy; decreasing the protein expression of aging markers cyclin-dependent kinase inhibitor p21(P21) and multiple tumor suppressor 1(P16); lowering the tissue inflammation reaction. Metagenomic metabolomic analysis of serum from mice in each group revealed that APS significantly increased the content of indole-3-lactic acid(ILA) in naturally aging mice. Further in vitro studies showed that ILA could improve the aging of 3T3-L1 mouse embryonic fibroblasts induced by bleomycin, reduce the protein expression of the aging marker P21, alleviate inflammation, and enhance the ability of preadipocytes to mature. Therefore, APS had the efficacy of protecting naturally aging mice, and its action may be related to the increase in the intestinal microbiota metabolite ILA. This study suggested that TCM may serve as an important entry point for explaining the mechanism of action of TCM by regulating intestinal microbiota and their functional metabolites.},
}

Animals
Mice
*Aging/drug effects
*Adipose Tissue/drug effects/metabolism
*Polysaccharides/pharmacology
*Indoles/pharmacology
Male
*Astragalus Plant/chemistry
3T3-L1 Cells
Humans
Adipocytes/drug effects/metabolism/cytology
Mice, Inbred C57BL
Cellular Senescence/drug effects
Drugs, Chinese Herbal/pharmacology/administration & dosage
Gastrointestinal Microbiome/drug effects

@article {pmid39701526,
year = {2024},
author = {Sinclair, KD},
title = {Developmental epigenetics: Understanding genetic and sexually dimorphic responses to parental diet and outcomes following assisted reproduction.},
journal = {Journal of dairy science},
volume = {},
number = {},
pages = {},
doi = {10.3168/jds.2024-25811},
pmid = {39701526},
issn = {1525-3198},
abstract = {The developmental integrity and wellbeing of offspring are influenced by events that occur in utero, particularly around the time of conception. While extraneous factors such as environmental temperature and exposure to environmental chemicals can each have a bearing on these events, the epigenetic mechanisms that direct cellular differentiation during early development in ruminants are best described for studies which have investigated the effects of parental nutrition or pregnancy outcomes following assisted reproduction. In this article the case is made that the genetic constitution of an individual directs epigenetic responses to environmental stimuli, and consideration in this regard is also given to the origins of sexual dimorphism and mechanisms of germline intergenerational inheritance. These aspects are considered in the context of epigenetic modifications that take place during the normal course of gametogenesis and embryogenesis, and again following either dietary or procedural interventions such as embryo culture. A recurring feature of such interventions, irrespective of species, is that one carbon metabolic pathways are invariably disrupted, and this affects the provision of methyl groups for chromatin and RNA methylation. Inter-specific variation in how these pathways operate, both within the liver and in germ cells, indicates that ruminants may be particularly sensitive in this regard. Recent advances in genomic technologies should enable rapid progress in these areas. Knowledge gained can be integrated into breed improvement programs and used to tailor management practices to specific breeds and strains (including sexes) within breeds. Ultimately, consideration should be given to integrating metagenomics into analyses of genetic-directed epigenetic programming of animal development.},
}

@article {pmid39701375,
year = {2024},
author = {Corbett, GA and Corcoran, S and Feehily, C and Soldati, B and Rafferty, A and MacIntyre, DM and Cotter, PD and McAuliffe, FM},
title = {Preterm-birth-prevention with Lactobacillus Crispatus oral probiotics: Protocol for a double blinded randomised placebo-controlled trial (the PrePOP study).},
journal = {Contemporary clinical trials},
volume = {},
number = {},
pages = {107776},
doi = {10.1016/j.cct.2024.107776},
pmid = {39701375},
issn = {1559-2030},
abstract = {INTRODUCTION: Effective spontaneous preterm birth (sPTB) prevention is an urgent unmet clinical need. Vaginal depletion of Lactobacillus crispatus is linked to sPTB. This trial will investigate impact of an oral Lactobacillus spp. probiotic product containing an L. crispatus strain with other Lactobacilli spp., on the maternal vaginal and gut microbiome in pregnancies high-risk for sPTB.

METHODS: A double-blind, placebo-controlled, randomised trial will be performed at the National Maternity Hospital Dublin, Ireland. Inclusion criteria are women with history of sPTB or mid-trimester loss, cervical surgery (cone biopsy or two previous large-loop-excision-of-transformation-zone) or uterine anomaly. The intervention is oral supplementation for twelve weeks with probiotic or identical placebo. The probiotic will contains: ◦ 4 billion CFU Lactobacillus crispatus Lbv 88(2x10[9]CFU/Capsule) ◦ 4 billion CFU Lactobacillus rhamnosus Lbv 96(2x10[9]CFU/Capsule) ◦ 0.8 billion CFU Lactobacillus jensenii Lbv 116(0.4x10[9]CFU/Capsule) ◦ 1.2 billion CFU Lactobacillus gasseri Lbv 150(0.6x10[9]CFU/Capsule) Investigators and participants will be blinded to assignment.

RESULTS: The primary outcome is detectable L. crispatus in the vaginal microbiome after twelve weeks of treatment, measured using high-throughput DNA sequencing. A total of 126 women are required to detect a 25 % increase in detectable L. crispatus. Secondary outcomes include impact of intervention on the gut microbiome and metabolome, rate of sPTB and mid-trimester loss, neonatal outcomes and maternal morbidity.

CONCLUSIONS: This randomised trial will investigate ability of an oral probiotic containing L. crispatus to increase its abundance in the vaginal microbiome, both directly by horizontal transfer and indirectly via microbiome and metabolome of the gut.},
}

@article {pmid39701354,
year = {2024},
author = {Liu, J and Zhou, M and Zhou, L and Dang, R and Xiao, L and Tan, Y and Li, M and Yu, J and Zhang, P and Hernández, M and Lichtfouse, E},
title = {Methane production related to microbiota in dairy cattle feces.},
journal = {Environmental research},
volume = {},
number = {},
pages = {120642},
doi = {10.1016/j.envres.2024.120642},
pmid = {39701354},
issn = {1096-0953},
abstract = {Methane (CH4) emission from livestock feces, led by ruminants, shows a profound impact on global warming. Despite this, we have almost no information on the syntrophy of the intact microbiome metabolisms, from carbohydrates to the one-carbon units, covering multiple stages of ruminant development. In this study, syntrophic effects of polysaccharide degradation and acetate-producing bacteria, and methanogenic archaea were revealed through metagenome-assembled genomes from water saturated dairy cattle feces. Although CH4 is thought to be produced by archaea, more edges, nodes, and balanced interaction types revealed by network analysis provided a closed bacteria-archaea network. The CH4 production potential and pathways were further evaluated through dynamic, thermodynamic and [13]C stable isotope analysis. The powerful CH4 production potential benefited from the metabolic flux: classical polysaccharides, soluble sugar (glucose, galactose, lactose), acetate, and CH4 produced via typical acetoclastic methanogenesis. In comparison, a cooperative model dominated by hydrogenotrophic methanogenic archaea presented a weak ability to generate CH4. Our findings comprehensively link carbon and CH4 metabolism paradigm to specific microbial lineages which are shaped related to developmental stages of the dairy cattle, directing influencing global warming from livestock and waste treatment.},
}

@article {pmid39700995,
year = {2024},
author = {Xu, X and Hao, Y and Cai, Z and Cao, Y and Jia, W and Zhao, J and White, JC and Ma, C},
title = {Nanoscale‑boron nitride positively alters rhizosphere microbial communities and subsequent cucumber (Cucumis sativa) growth: A metagenomic analysis.},
journal = {The Science of the total environment},
volume = {958},
number = {},
pages = {178115},
doi = {10.1016/j.scitotenv.2024.178115},
pmid = {39700995},
issn = {1879-1026},
abstract = {Boron (B) deficiency affects over 132 crop species globally, making effective B supplement crucial for enhancing agricultural yield and health. This study explores an innovative application of nanoscale boron nitride (nano-BN) as a sustainable solution for addressing B deficiency in crops. Cucumber seedlings were treated with different contents of nano-BN under greenhouse conditions and both B and N ionic treatments were set as comparisons. Results show that soil application of 10 mg/kg nano-BN achieved a remarkable 15.8 % increase in fresh weight compared to the control. Notably, nano-BN exhibited superior efficiency in providing essential micronutrients without inducing toxicity as compared to traditional ionic B sources. Phytohormone correlation analysis reveals that nano-BN application significantly enhances levels of indole-3-acetic acid (IAA) and cytokinins while reducing abscisic acid (ABA), fostering optimal plant growth conditions. Furthermore, increases in dissolved organic matter (DOM) and dissolved organic carbon (DOC) levels in the rhizosphere improve nutrient availability and promote beneficial microbial activity in the soil as affected by nano-BN. Metagenomics techniques were used to investigate the impact of nano-BN on soil carbon and nitrogen cycling, alongside its effects on the soil microbiome. The upregulation of genes associated with fermentation pathways as affected by nano-BN suggests the enhanced carbon cycling. Additionally, nano-BN upregulated a number of functional genes involved in nitrogen-based processes, leading to a significant increase in microorganisms harboring nitrogen-fixing genes, including Phenylobacterium, Novosphingobium, and Reyranella. Overall, these findings provide valuable insight into the application of nano-BN in agriculture to sustainably increase crop productivity and enhance the efficiency of carbon and nitrogen cycling.},
}

@article {pmid39700989,
year = {2024},
author = {Liu, F and Zeng, J and Ding, J and Wang, C and He, Z and Liu, Z and Shu, L},
title = {Microbially-driven phosphorus cycling and its coupling mechanisms with nitrogen cycling in mangrove sediments.},
journal = {The Science of the total environment},
volume = {958},
number = {},
pages = {178118},
doi = {10.1016/j.scitotenv.2024.178118},
pmid = {39700989},
issn = {1879-1026},
abstract = {The phosphorus (P) cycle plays a crucial role in the biogeochemical cycling of mangrove sediments. However, the diversity of microbially-driven P-cycling and its coupling with nitrogen (N)-cycling remain poorly understood. In this study, we used metagenomic approaches to investigate microbial P-cycling and its potential interactions with N-cycling in mangrove sediments. Our results revealed that pH, total carbon, and total nitrogen were key environmental factors influencing the diversity of P-cycling microbial communities. Phosphorus metabolic pathways differed among mangrove sediment depths. In surface sediments (0-5 cm), microbial communities primarily acquired readily available inorganic phosphorus, whereas, in deeper sediments (>60 cm), they hydrolyzed more persistent triphosphates, reabsorbed nucleotides, and sourced free phosphate, reflecting a shift in phosphorus transport modes. We also identified glutamate metabolism as a potential pathway linking P-cycling with N-cycling, with these functions co-occurring in both contigs and genomes. Additionally, the diversity of microbial communities associated with the P-cycling increased with sediment depth, suggesting that microbially-driven P-cycling diversifies as depth increases. This study provides new insights into P-cycling and its potential coupling with N-cycling through glutamate metabolism, its coupling with N-cycling through glutamate metabolism.},
}

@article {pmid39700951,
year = {2024},
author = {Gu, H and Hu, X and Zhang, J and Li, Y and Yu, Z and Liu, J and Sui, Y and Jin, J and Liu, X and Wang, G},
title = {Biogeographic patterns of viral communities, ARG profiles and virus-ARG associations in adjacent paddy and upland soils across black soil region.},
journal = {Journal of hazardous materials},
volume = {485},
number = {},
pages = {136909},
doi = {10.1016/j.jhazmat.2024.136909},
pmid = {39700951},
issn = {1873-3336},
abstract = {Biogeographic distribution of prokaryotic and eukaryotic communities has been extensively studied. Yet, our knowledge of viral biogeographic patterns, the corresponding driving factors and the virus-resistome associations is still limited. Here, using metagenomic analysis, we explored the viral communities and profiles of antibiotic resistance genes (ARGs) in 30 fields of paddy (rice soils, RS) and upland soils (corn soils, CS) at a regional scale across black soil region of Northeast China. Our finding revealed that viral communities displayed significant distance-decay relationships, and environmental variables largely dominated viral community patterns in agricultural soils. Compared to RS, viral community in CS harbored significantly higher viral α-diversity and distinct β-diversity, and exhibited a higher turnover along with environmental gradients and spatial distance. However, no clear latitudinal diversity gradient (LDG) pattern was observed in viral diversity over large-scale sampling for RS and CS, and heterogeneous distribution of soil viruses was well maintained over large-scale sampling. Soil pH was the important influential factor driving viral community, and the high soil nutrient levels negatively affected viral diversity. Uroviricota, Nucleocytoviricota and Artverviricota were the main viral phyla in agricultural soils, and virus-host linkages spanned 17 prokaryotic phyla, including Actinobacteriota and Proteobacteria. Besides, 2578 ARG subtypes were retrieved and conferred resistance to 27 types of antibiotics, in which multidrug was the predominant ARG type in Mollisols. Procrustes analysis showed the significant contribution of viral community to ARG profiles, which was more obvious in CS compared to RS. We identified 9.61 % and 11.4 % of soil viruses carried at least one ARG can infect multi-host in RS and CS. Furthermore, 43 and 77 complete viral metagenome-assembled genome (vMAG) were reconstructed in RS and CS, respectively. Notably, the lysogenic phages in RS contained 29.7 % of ARGs, a higher proportion than the 12.5 % found in CS. Overall, our study underscored the prevalent distribution of viral communities and ARG profiles at a large spatial scale, and the distinct ecological strategies of virus-ARG associations in adjacent paddy and upland soils.},
}

@article {pmid39700725,
year = {2024},
author = {Petersen, JF and Valk, LC and Verhoeven, MD and Nierychlo, MA and Singleton, CM and Dueholm, MKD and Nielsen, PH},
title = {Diversity and physiology of abundant Rhodoferax species in global wastewater treatment systems.},
journal = {Systematic and applied microbiology},
volume = {48},
number = {1},
pages = {126574},
doi = {10.1016/j.syapm.2024.126574},
pmid = {39700725},
issn = {1618-0984},
abstract = {Wastewater treatment plants rely on complex microbial communities for bioconversion and removal of pollutants, but many process-critical species are still poorly investigated. One of these genera is Rhodoferax, an abundant core genus in wastewater treatment plants across the world. The genus has been associated with many metabolic traits such as iron reduction and oxidation and denitrification. We used 16S rRNA gene amplicon data to uncover the diversity and abundance of Rhodoferax species in Danish and global treatment plants. Publicly available metagenome-assembled genomes were analyzed based on phylogenomics to delineate species and assign taxonomies based on the SeqCode. The phylogenetic analysis of "Rhodoferax" revealed that species previously assigned to Rhodoferax in wastewater treatment plants should be considered as at least eight different genera, with five representing previously undescribed genera. Genome annotation showed potential for several key-bioconversions in wastewater treatment, such as nitrate reduction, carbohydrate degradation, and accumulations of various storage compounds. Iron oxidation and reduction capabilities were not predicted for abundant species. Species-resolved FISH-Raman was performed to gain an overview of the morphology and ecophysiology of selected taxa to clarify their potential role in global wastewater treatment systems. Our study provides a first insight into the functional and ecological characteristics of several novel genera abundant in global wastewater treatment plants, previously assigned to the Rhodoferax genus.},
}

@article {pmid39700724,
year = {2024},
author = {Mao, YL and Dong, XY and Tao, CQ and Wu, ZP and Shi, XW and Hou, J and Cui, HL},
title = {Natronorarus salvus gen. nov., sp. nov., Halalkalicoccus ordinarius sp. nov., and Halalkalicoccus salilacus sp. nov., halophilic archaea from a soda lake and two saline lakes, and proposal to classify the genera Halalkalicoccus and Natronorarus into Halalkalicoccaceae fam. nov. in the order Halobacteriales within the class Halobacteria.},
journal = {Systematic and applied microbiology},
volume = {48},
number = {1},
pages = {126577},
doi = {10.1016/j.syapm.2024.126577},
pmid = {39700724},
issn = {1618-0984},
abstract = {Four novel halophilic archaeal strains CGA53[T], CG83[T], FCH27[T], and SEDH24 were isolated from a soda lake and two saline lakes in China, respectively. Strain CGA53[T] showed the highest 16S rRNA gene similarity (92.6%) to Salinilacihabitans rarus AD-4[T], and the other three strains were found to be related to Halalkalicoccus species with similarities of 97.6-98.3%. Metagenomic studies indicated that these four strains are low abundant inhabitants detected in these hypersaline environments, and only one MAG of Chagannuoer Soda Lake (CG) could be assigned to the genus Halalkalicoccus. Their growth occurred at 20-60 °C (optima, 42, 37, 37-42, and 35 °C), 0.9-5.1 M NaCl (optima, 3.9, 2.6, 3.5, and 3 M), and 0-1.0 M MgCl2 (optima, 0.5, 0.7, and 0.1) and pH 5.5-10.5 (optima, 9.0, 7.5, 7.0, and 7.0), respectively. Phylogenetic and phylogenomic analyses revealed that strains CG83[T], FCH27[T], and SEDH24 cluster with the current species of the genus Halalkalicoccus, and strain CGA53[T] forms an independent branch separated from this genus. The average nucleotide identity (ANI), digital DNA-DNA hybridization (dDDH), and average amino acid identity (AAI) values among strains CGA53[T], CG83[T], FCH27[T], SEDH24, and the type species of the current genera within the class Halobacteria were 67.4-81.6%, 16.5-28.6% and 49.7-74.1%, respectively, clearly lower than the cutoff values for species demarcation. Strain CGA53[T] may represent a novel species of a new genus according to the cutoff value for genus demarcation of 65% AAI. Diverse differential phenotypic characteristics, such as nutrition, biochemical activities, antibiotic sensitivity, and H2S formation, were found among these four strains and Halalkalicoccus species. Genome-based classification supported that strains CGA53[T], CG83[T], FCH27[T], SEDH24, and the current species of Halalkalicoccus represent a novel family of the order Halobacteriales within the class Halobacteria.},
}

@article {pmid39700673,
year = {2024},
author = {Zhang, Z and Zhou, L and Li, H and Li, L and Liu, H},
title = {Diagnostic performance of metagenomic next-generation sequencing based on alveolar lavage fluid in unexplained lung shadows.},
journal = {Diagnostic microbiology and infectious disease},
volume = {111},
number = {3},
pages = {116651},
doi = {10.1016/j.diagmicrobio.2024.116651},
pmid = {39700673},
issn = {1879-0070},
abstract = {BACKGROUND: Unexplained lung shadows are challenging in respiratory medicine, with both infectious and non-infectious etiologies. Lung biopsy is definitive but invasive, prompting a need for non-invasive alternatives. Metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid (BALF) is emerging as a promising diagnostic tool.

METHODS: We retrospectively analyzed 105 patients with unexplained lung shadows, collecting general information, mNGS results from BALF, and clinical diagnosis. We evaluated mNGS's diagnostic performance by comparing with final diagnosis.

RESULTS: mNGS showed good diagnostic performance in differentiating infectious from non-infectious causes. The specificity and accuracy for bacteria and fungi exceeded 90%, while the sensitivity and precision for fungi were lower than for bacteria. Atypical pathogens were frequently identified, especially in mixed infections.

CONCLUSIONS: mNGS of BALF is efficient in diagnosing infectious and non-infectious causes of unexplained lung shadows. While effective for bacteria and fungi detection, the sensitivity and precision for fungi are lower.},
}

@article {pmid39700412,
year = {2024},
author = {Duan, HN and Hearne, G and Polikar, R and Rosen, GL},
title = {The Naïve Bayes Classifier ++ for Metagenomic Taxonomic Classification-Query Evaluation.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btae743},
pmid = {39700412},
issn = {1367-4811},
abstract = {MOTIVATION: This study examines the query performance of the NBC ++ (Incremental Naive Bayes Classifier) program for variations in canonicality, k-mer size, databases, and input sample data size. We demonstrate that both NBC ++ and Kraken2 are influenced by database depth, with macro measures improving as depth increases. However, fully capturing the diversity of life, especially viruses, remains a challenge.

RESULTS: NBC ++ can competitively profile the superkingdom content of metagenomic samples using a small training database. NBC ++ spends less time training and can use a fraction of the memory than Kraken2 but at the cost of long querying time. Major NBC ++ enhancements include accommodating canonical k-mer storage (leading to significant storage savings) and adaptable and optimized memory allocation that accelerates query analysis and enables the software to be run on nearly any system. Additionally, the output now includes log-likelihood values for each training genome, providing users with valuable confidence information.

AVAILABILITY: Source code and Dockerfile are available at http://github.com/EESI/Naive_Bayes.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online, and databases are available at Zenodo records #11657719 and #11643985.},
}

@article {pmid39699489,
year = {2024},
author = {Souza, PJ and Fernandes, J and Coelho, TA and Cosentino, M and D'arc, M and Alves, PDG and Guterres, A and Vilar, EM and Lemos, ERS and Cordeiro-Estrela, P and Santos, AFA and Oliveira, RC},
title = {A newly bat-borne hantavirus detected in Seba's short-tailed bats (Carollia perspicillata) in the Brazilian Atlantic Rainforest.},
journal = {Memorias do Instituto Oswaldo Cruz},
volume = {119},
number = {},
pages = {e240132},
doi = {10.1590/0074-02760240132},
pmid = {39699489},
issn = {1678-8060},
mesh = {Animals ; *Chiroptera/virology ; Brazil/epidemiology ; *Orthohantavirus/genetics/classification/isolation & purification ; *Phylogeny ; *Rainforest ; RNA, Viral/genetics/analysis ; Reverse Transcriptase Polymerase Chain Reaction ; Hantavirus Infections/veterinary/epidemiology/virology ; },
abstract = {BACKGROUND: Bat-borne hantaviruses have been identified worldwide but little is known about neotropical bats in the megadiverse biomes of the American continent. Although serological evidence has hinted at hantavirus circulation in Brazil, the scarce number of genomic detection represents a gap to understand viral diversity, prevalence, and ecology of bat-borne hantaviruses.

OBJECTIVE: We aim to investigate and evaluate the presence and prevalence of bat-borne hantavirus in the Brazilian Atlantic Forest.

METHODS: Here in, 97 lung and kidney tissue samples from bats captured in the Brazilian Atlantic Rainforest were submitted to hantavirus-specific nested reverse transcription-polymerase chain reaction (RT-PCR) targeted the hantaviral L segment and metagenomic analysis.

FINDINGS: Hantavirus RNA was detected in five tissue fragments of 20 Seba's short-tailed bats (Carollia perspicillata). Phylogenetic analysis, based on partial L-segment sequence using maximum likelihood method, demonstrated that the identified virus formed a monophyletic clade and a highly divergent bat-borne lineage comprising other recent strains found in the genus Carollia from South America.

MAIN CONCLUSIONS: Our findings suggest the presence of a novel bat-borne hantavirus in Brazil, tentatively named Mamanguape virus (MGPV). Additional genomic data will help to extend our knowledge about the classification of MGPV within the Hantaviridae family and the evolution origins of new world bat-borne hantaviruses.},
}

Animals
*Chiroptera/virology
Brazil/epidemiology
*Orthohantavirus/genetics/classification/isolation & purification
*Phylogeny
*Rainforest
RNA, Viral/genetics/analysis
Reverse Transcriptase Polymerase Chain Reaction
Hantavirus Infections/veterinary/epidemiology/virology

@article {pmid39699221,
year = {2024},
author = {Lustermans, JJM and Sereika, M and Burdorf, LDW and Albertsen, M and Schramm, A and Marshall, IPG},
title = {Extracellular electron transfer genes expressed by candidate flocking bacteria in cable bacteria sediment.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0125924},
doi = {10.1128/msystems.01259-24},
pmid = {39699221},
issn = {2379-5077},
abstract = {UNLABELLED: Cable bacteria, filamentous sulfide oxidizers that live in sulfidic sediments, are at times associated with large flocks of swimming bacteria. It has been proposed that these flocks of bacteria transport electrons extracellularly to cable bacteria via an electron shuttle intermediate, but the identity and activity of these bacteria in freshwater sediment remain mostly uninvestigated. Here, we elucidate the electron exchange capabilities of the bacterial community by coupling metagenomics and metatranscriptomics to 16S rRNA amplicon-based correlations with cable bacteria over 155 days. We identified candidate flocking bacteria as bacteria containing genes for motility and extracellular electron transfer including synthesis genes for potential extracellular electron shuttles: phenazines and flavins. Based on these criteria, 22 MAGs were from candidate flockers, which constituted 21.4% of all 103 MAGs. Of the candidate flocking bacteria, 42.1% expressed extracellular electron transfer genes. The proposed flockers belonged to a large variety of metabolically versatile taxonomic groups: 18 genera spread across nine phyla. Our data suggest that cable bacteria in freshwater sediments engage in electric relationships with diverse exoelectrogenic microbes. This community, found in deeper anoxic sediment layers, is involved in sulfur, carbon, and metal (in particular Fe) cycling and indirectly utilizes oxygen here by extracellularly transferring electrons to cable bacteria.

IMPORTANCE: Cable bacteria are ubiquitous, filamentous bacteria that couple sulfide oxidation to the reduction of oxygen at up to centimeter distances in sediment. Cable bacterial impact extends beyond sulfide oxidation via interactions with other bacteria that flock around cable bacteria and use them as electron acceptor "shortcut" to oxygen. The exact nature of this interspecies electric interaction remained unknown. With metagenomics and metatranscriptomics, we determined what extracellular electron transport processes co-occur with cable bacteria, demonstrating the identity and metabolic capabilities of these potential flockers. In sediments, microbial activities are sharply divided into anaerobic and aerobic processes, with oxygen reaching only millimeters deep. Cable bacteria extend the influence of oxygen to several centimeters, revealing a new class of anaerobic microbial metabolism with cable bacteria as electron acceptors. This fundamentally changes our understanding of sediment microbial ecology with wide-reaching consequences for sulfur, metal (in particular Fe), and carbon cycling in freshwater and marine sediments.},
}

@article {pmid39699218,
year = {2024},
author = {Kalu, CM and Mudau, KL and Ntobeng, LR and Masindi, V and Tekere, M},
title = {Antibiotic resistance genes profile of selected drinking water treatment plants in South Africa as impacted by different treatment stages.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0093424},
doi = {10.1128/mra.00934-24},
pmid = {39699218},
issn = {2576-098X},
abstract = {Water treatment plants treat raw water making it suitable for consumption. Treatment stages are linked to the quality status of the treatment. The classes of antibiotic resistance genes as impacted by treatment stages remain under explored. We report the classes of antibiotic resistance genes (ARGs) from shotgun metagenomes as influenced by treatment stages.},
}

@article {pmid39699190,
year = {2024},
author = {Prattico, C and Gonzalez, E and Dridi, L and Jazestani, S and Low, KE and Abbott, DW and Maurice, CF and Castagner, B},
title = {Identification of novel fructo-oligosaccharide bacterial consumers by pulse metatranscriptomics in a human stool sample.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0066824},
doi = {10.1128/msphere.00668-24},
pmid = {39699190},
issn = {2379-5042},
abstract = {UNLABELLED: Dietary fibers influence the composition of the human gut microbiota and directly contribute to its downstream effects on host health. As more research supports the use of glycans as prebiotics for therapeutic applications, the need to identify the gut bacteria that metabolize glycans of interest increases. Fructo-oligosaccharide (FOS) is a common diet-derived glycan that is fermented by the gut microbiota and has been used as a prebiotic. Despite being well studied, we do not yet have a complete picture of all FOS-consuming gut bacterial taxa. To identify new bacterial consumers, we used a short exposure of microbial communities in a stool sample to FOS or galactomannan as the sole carbon source to induce glycan metabolism genes. We then performed metatranscriptomics, paired with whole metagenomic sequencing, and 16S amplicon sequencing. The short incubation was sufficient to cause induction of genes involved in carbohydrate metabolism, like carbohydrate-active enzymes (CAZymes), including glycoside hydrolase family 32 genes, which hydrolyze fructan polysaccharides like FOS and inulin. Interestingly, FOS metabolism transcripts were notably overexpressed in Blautia species not previously reported to be fructan consumers. We therefore validated the ability of different Blautia species to ferment fructans by monitoring their growth and fermentation in defined media. This pulse metatranscriptomics approach is a useful method to find novel consumers of prebiotics and increase our understanding of prebiotic metabolism by CAZymes in the gut microbiota.

IMPORTANCE: Complex carbohydrates are key contributors to the composition of the human gut microbiota and play an essential role in the microbiota's effects on host health. Understanding which bacteria consume complex carbohydrates, or glycans, provides a mechanistic link between dietary prebiotics and their beneficial health effects, an essential step for their therapeutic application. Here, we used a pulse metatranscriptomics pipeline to identify bacterial consumers based on glycan metabolism induction in a human stool sample. We identified novel consumers of fructo-oligosaccharide among Blautia species, expanding our understanding of this well-known glycan. Our approach can be applied to identify consumers of understudied glycans and expand our prebiotic repertoire. It can also be used to study prebiotic glycans directly in stool samples in distinct patient populations to help delineate the prebiotic mechanism.},
}

@article {pmid39699181,
year = {2024},
author = {Olson, N and Lamar, F and Mucache, H and Fafetine, J and Saíde, J and Milisse, A and Brito, DRA and Jesser, KJ and Levy, K and Freeman, MC and Nadimpalli, ML},
title = {Farm-to-fork changes in poultry microbiomes and resistomes in Maputo City, Mozambique.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0103724},
doi = {10.1128/msystems.01037-24},
pmid = {39699181},
issn = {2379-5077},
abstract = {UNLABELLED: Increasing demand for poultry has spurred poultry production in low- and middle-income countries like Mozambique. Poultry may be an important source of foodborne, antimicrobial-resistant bacteria to consumers in settings with limited water, sanitation, and hygiene infrastructure. The Chicken Exposures and Enteric Pathogens in Children Exposed through Environmental Pathways (ChEEP ChEEP) study was conducted in Maputo City, Mozambique from 2019 to 2021 to quantify enteric pathogen exposures along the supply chain for commercial and local (i.e., scavenger) chicken breeds. Here, we performed metagenomic sequencing of total DNA from banked ChEEP ChEEP samples to characterize fecal and carcass microbiomes and resistome diversity between chicken breeds and along the supply chain. Fecal samples (n = 26) were collected from commercial and local chickens at production sites and markets and carcass (n = 49) and rinse bucket samples (n = 26) from markets. We conducted taxonomic profiling and identified antimicrobial resistance genes (ARGs) from metagenomic sequence data, focusing especially on potential human pathogens and "high-risk" ARGs. We estimated alpha diversity for each sample and compared by site and breed. We estimated Bray-Curtis dissimilarity between samples and examined clustering. We found that commercial and local chickens harbored distinct fecal potential pathogens and resistomes at production and market sites. Many potentially pathogenic bacteria and ARGs present in chicken fecal samples are also present on carcasses sold to consumers. Finally, commercial chicken carcasses contain high-risk ARGs that are not necessarily introduced from chicken feces. These results indicate markets are an important site of exposure to potentially pathogenic bacteria and high-risk ARGs.

IMPORTANCE: While chicken eggs and meat are a critical protein source in low-income settings, antibiotics are routinely fed to chickens with consequences for selection of antimicrobial resistance. Evaluating how poultry gut bacterial communities, including potential human pathogens and high-risk antimicrobial resistance genes, differ from farm to market could help identify where to target interventions to minimize transmission risks to human populations. In this study in Maputo City, Mozambique, we found compositional differences between commercial and local chicken breeds at production and market sites. We also found that while all potentially pathogenic bacteria and many high-risk antimicrobial resistance genes persisted from production and market through processing, some resistance genes were detected on carcass samples only after processing, suggesting human or environmental contamination is occurring within markets. Overall, our findings indicate that open-air markets may represent a critical juncture for human exposures to pathogens and antimicrobial resistance genes from poultry and poultry products.},
}

@article {pmid39698321,
year = {2024},
author = {Lyu, J and Huang, J and Huang, J and Hu, H and Wang, Q and Ding, H and Li, H and Fang, X and Zhang, W},
title = {Rising challenges in periprosthetic joint infections: a focus on rare pathogens and their clinical implications.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1451398},
pmid = {39698321},
issn = {2235-2988},
mesh = {Humans ; *Prosthesis-Related Infections/microbiology ; Male ; Female ; Aged ; Retrospective Studies ; Middle Aged ; *Arthroplasty, Replacement, Knee/adverse effects ; *Anti-Bacterial Agents/therapeutic use ; *Arthroplasty, Replacement, Hip/adverse effects ; Risk Factors ; Treatment Outcome ; Bacteria/isolation & purification/classification/genetics ; Aged, 80 and over ; Coinfection/microbiology ; C-Reactive Protein/analysis ; },
abstract = {OBJECTIVES: The study aimed to evaluate differences in clinical characteristics and treatment outcomes of periprosthetic joint infection (PJI) attributed to rare versus common pathogens.

METHODS: Data on PJI patients who underwent hip or knee arthroplasty at our center from April 2013 to December 2022 were retrospectively collected. Among the 219 enrolled patients, we compared 32 cases of PJI caused by rare pathogens with 187 controls of PJI caused by common pathogens, analyzing demographic information, clinical characteristics, and treatment outcomes.

RESULTS: In demographic data, the Charlson comorbidity index and preoperative invasive procedures were identified as risk factors for rare pathogen PJI. Clinically, the rare pathogen cohort exhibited a significantly higher rate of sinus tract formation compared to those with common bacteria PJI. In terms of laboratory findings, the mean serum C-reactive protein (CRP) was significantly lower in the rare pathogen group. This cohort also had a significantly lower culture positivity rate and a higher rate of polymicrobial co-infections. The median hospital stay was statistically longer for rare pathogen PJI cases than for those with common bacteria PJI. Furthermore, the rare pathogen group required longer antibiotic treatments and had higher rates of antibiotic-related adverse events, although reinfection rates did not significantly differ.

CONCLUSION: PJI caused by rare pathogens exhibits distinct clinical presentations. With advances in diagnostic techniques such as metagenomic next-generation sequencing (mNGS), optimized culture methods, and an interdisciplinary approach facilitating early targeted treatment, rare pathogen PJIs may achieve outcomes comparable to those of typical cases.},
}

Humans
*Prosthesis-Related Infections/microbiology
Male
Female
Aged
Retrospective Studies
Middle Aged
*Arthroplasty, Replacement, Knee/adverse effects
*Anti-Bacterial Agents/therapeutic use
*Arthroplasty, Replacement, Hip/adverse effects
Risk Factors
Treatment Outcome
Bacteria/isolation & purification/classification/genetics
Aged, 80 and over
Coinfection/microbiology
C-Reactive Protein/analysis

@article {pmid39698295,
year = {2024},
author = {Bovio-Winkler, P and Cabezas, A and Etchebehere, C},
title = {Unveiling the hidden diversity and functional role of Chloroflexota in full-scale wastewater treatment plants through genome-centric analyses.},
journal = {ISME communications},
volume = {4},
number = {1},
pages = {ycae050},
pmid = {39698295},
issn = {2730-6151},
abstract = {The phylum Chloroflexota has been found to exhibit high abundance in the microbial communities from wastewater treatment plants (WWTPs) in both aerobic and anaerobic systems. However, its metabolic role has not been fully explored due to the lack of cultured isolates. To address this gap, we use publicly available metagenome datasets from both activated sludge (AS) and methanogenic (MET) full-scale wastewater treatment reactors to assembled genomes. Using this strategy, 264 dereplicated, medium- and high-quality metagenome-assembled genomes (MAGs) classified within Chloroflexota were obtained. Taxonomic classification revealed that AS and MET reactors harbored distinct Chloroflexota families. Nonetheless, the majority of the annotated MAGs (166 MAGs with >85% completeness and < 5% contamination) shared most of the metabolic potential features, including the ability to degrade simple sugars and complex polysaccharides, fatty acids and amino acids, as well as perform fermentation of different products. While Chloroflexota MAGs from MET reactors showed the potential for strict fermentation, MAGs from AS harbored the potential for facultatively aerobic metabolism. Metabolic reconstruction of Chloroflexota members from AS unveiled their versatile metabolism and suggested a primary role in hydrolysis, carbon removal and involvement in nitrogen cycling, thus establishing them as fundamental components of the ecosystem. Microbial reference genomes are essential resources for understanding the potential functional role of uncultured organisms in WWTPs. Our study provides a comprehensive genome catalog of Chloroflexota for future analyses aimed at elucidating their role in these ecosystems.},
}

@article {pmid39697828,
year = {2024},
author = {Guo, Y and Cao, Y and He, B and Dong, X and Bi, M and Wang, X and Gao, T and Liu, X and Wang, K and Wang, Y and Zhang, H and Sun, Y and Gao, W and Zhang, Y and Jia, Z},
title = {The First Case of Serogroup Y Neisseria meningitidis and An Expanded Investigation of Healthy Carriers - Shijiazhuang City, Hebei Province, China, 2023.},
journal = {China CDC weekly},
volume = {6},
number = {47},
pages = {1242-1247},
pmid = {39697828},
issn = {2096-7071},
abstract = {Neisseria meningitidis (Nm) is a bacterial pathogen that causes meningococcal disease. Serogroups A, B, C, W, X, and Y account for the vast majority of cases. However, invasive meningococcal disease (IMD) caused by NmY is rare in China and has been reported only in Tianjin, Guangdong, Shanghai, and Hunan provinces and cities.

WHAT IS ADDED BY THIS REPORT?: This article reports the first case of NmY:cc23 meningococcal disease in Hebei Province, confirmed by metagenomic sequencing. We also present the results of expanded surveillance in the healthy population associated with the case.

NmY has caused multiple case reports across China, especially in southern cities. The first report of a serogroup Y case in Hebei Province, and the carriage rate in the healthy population, reminds us to increase public health attention on Nm. The results of this study suggest that surveillance of the Nm carriage rate among healthy carriers and serogroup changes in Nm should be strengthened.},
}

@article {pmid39697658,
year = {2024},
author = {Yu, J and Yang, S and Zhang, X and Liu, X and Tang, X and Wang, L and Chen, J and Luo, H and Liu, C and Song, C},
title = {Integrating metagenomics and culturomics to uncover the soil bacterial community in Asparagus cochinchinensis cultivation.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1467864},
pmid = {39697658},
issn = {1664-302X},
abstract = {Asparagus cochinchinensis is a medicinal plant in China, which has gained attention owing its protective effect in human health. However, there are seldom studies to systematically reveal the rhizosphere bacterial community of A. cochinchinensis. In this study, we employed metagenomics and culturomics to analyze the bacterial community composition and diversity in continuous rhizosphere soil of A. cochinchinensis. Meanwhile, we assessed the effect of soil physicochemical properties on the bacterial community. Results showed that the most abundant TAXA is a taxon belonging to the family Streptomycetaceae, the genus Mycobacterium and the species Oligotropha carboxidovorans. The bacterial communities across various areas were similar. Significant differences of exchangeable magnesium and available phosphorus level were observed between three groups. Furthermore, bacterial community structure correlated closely with soil physicochemical properties. Additionally, a total of 103 strains were isolated and identified, representing 28 species. Based on this study, the rhizosphere bacterial community of A. cochinchinensis might influence its growth and development. The rhizosphere strains were isolated and their function request further investigation. This study firstly revealed the bacterial community in the A. cochinchinensis rhizosphere soil, providing valuable references for its quality improvement in practical cultivation process.},
}

@article {pmid39697332,
year = {2024},
author = {Guo, Y and Zhang, J and Chai, R and Yang, Y and Tian, K and Shi, G and Zhang, L},
title = {Cerebral schistosomiasis in a 3-year-old girl due to Schistosoma japonicum: a case report.},
journal = {Frontiers in immunology},
volume = {15},
number = {},
pages = {1502627},
pmid = {39697332},
issn = {1664-3224},
mesh = {Humans ; Female ; *Schistosoma japonicum ; Child, Preschool ; Animals ; *Schistosomiasis japonica/diagnosis/drug therapy/parasitology ; *Praziquantel/therapeutic use ; Magnetic Resonance Imaging ; Neuroschistosomiasis/diagnosis/drug therapy ; Brain/parasitology/diagnostic imaging/pathology ; Anthelmintics/therapeutic use ; Treatment Outcome ; },
abstract = {INTRODUCTION: Cerebral schistosomiasis is a rare but severe manifestation of Schistosoma japonicum infection, often leading to significant neurological impairment. This case report details the clinical presentation, diagnostic challenges, and treatment of a 3-year-old girl with cerebral schistosomiasis in Sichuan, China.

CASE DESCRIPTION: A 3-year-old girl from a rural area in Sichuan, China, presented with a 3-month history of unstable walking, left facial paralysis, drowsiness, and intermittent fever. Brain MRI revealed giant polycystic lesions in the right temporal, parietal, and occipital lobes, suggestive of an abscess with ependymitis. Despite no history of travel to endemic areas or known freshwater exposure, the patient was diagnosed with cerebral schistosomiasis due to Schistosoma japonicum based on histological examination and metagenomic next-generation sequencing (mNGS) of brain tissue obtained through surgery. The patient underwent surgical resection of the lesions and received two courses of praziquantel combined with corticosteroids and anticonvulsants. Despite residual left-sided hemiplegia, her cognitive function remained comparable to that of her peers, and no recurrence of the disease was observed over three years of follow-up.

CONCLUSION: This case underscores the diagnostic challenges of cerebral schistosomiasis, particularly in non-endemic areas or in the absence of a clear history of freshwater exposure. Early surgical intervention combined with praziquantel treatment can lead to favorable outcomes, even in severe cases with extensive brain involvement.},
}

Humans
Female
*Schistosoma japonicum
Child, Preschool
Animals
*Schistosomiasis japonica/diagnosis/drug therapy/parasitology
*Praziquantel/therapeutic use
Magnetic Resonance Imaging
Neuroschistosomiasis/diagnosis/drug therapy
Brain/parasitology/diagnostic imaging/pathology
Anthelmintics/therapeutic use
Treatment Outcome

@article {pmid39697208,
year = {2024},
author = {Zhou, Y and Zou, Y and Zhou, L and Wei, H and Zou, YW and Guo, XR and Ye, YQ and Li, N and Lu, Y},
title = {Acute respiratory distress syndrome caused by Chlamydia psittaci: a case report and literature review.},
journal = {Frontiers in medicine},
volume = {11},
number = {},
pages = {1418241},
pmid = {39697208},
issn = {2296-858X},
abstract = {BACKGROUND: Psittacosis is a zoonotic disease with a low incidence rate and a lack of specificity in clinical manifestations, making it prone to be missed, misdiagnosed, and even cause delayed treatment for patients. Metagenomic next-generation sequencing (mNGS) was successfully performed for the diagnosis of a young patient with psittacosis progressing to acute respiratory distress syndrome (ARDS), and precisely targeted antibiotic treatment was promptly administered. Additionally, a comprehensive review was conducted on 68 cases of psittacosis complicated with ARDS, with the goal of improving the clinical awareness of this disease.

CASE PRESENTATION: This study reports a 37-year-old young female who was infected with Chlamydia psittaci (C. psittaci) after contact with parrots and eventually developed ARDS. The patient initially developed fever and sore throat, followed by cough and expectoration. Despite receiving empirical anti-infection treatment, the condition continued to progress rapidly, and severe dyspnea developed within a short period of time. She was subsequently transferred to the intensive care unit (ICU) and underwent tracheal intubation and mechanical ventilation due to acute respiratory failure. After the DNA sequence of C. psittaci in bronchoalveolar lavage fluid (BALF) was detected through mNGS, the patient received targeted antibiotic treatment with doxycycline and moxifloxacin, and her clinical symptoms gradually improved.

CONCLUSION: Epidemiological investigations and the application of mNGS are crucial for the early identification and diagnosis of psittacosis. For suspected psittacosis patients, the application of mNGS technology could promote early identification of pathogens and targeted antimicrobial therapy, which might improve patient prognosis. In addition, young psittacosis patients without underlying disease should also be vigilant about the possibility of developing severe cases.},
}

@article {pmid39696809,
year = {2024},
author = {Dianat, M and Straaten, S and Maritato, A and Wibberg, D and Busche, T and Blank, LM and Ebert, BE},
title = {Exploration of In Situ Extraction for Enhanced Triterpenoid Production by Saccharomyces cerevisiae.},
journal = {Microbial biotechnology},
volume = {17},
number = {12},
pages = {e70061},
doi = {10.1111/1751-7915.70061},
pmid = {39696809},
issn = {1751-7915},
support = {031B0356B//Bundesministerium für Bildung und Forschung/ ; },
mesh = {*Saccharomyces cerevisiae/metabolism/genetics ; *Triterpenes/metabolism ; *Fermentation ; Metabolic Engineering/methods ; Chemical Fractionation/methods ; },
abstract = {Plant-derived triterpenoids are in high demand due to their valuable applications in cosmetic, nutraceutical, and pharmaceutical industries. To meet this demand, microbial production of triterpenoids is being developed for large-scale production. However, a prominent limitation of microbial synthesis is the intracellular accumulation, requiring cell disruption during downstream processing. Destroying the whole-cell catalyst drives up production costs and limits productivity and product yield per cell. Here, in situ product extraction of triterpenoids into a second organic phase was researched to address this limitation. An organic solvent screening identified water-immiscible isopropyl myristate as a suitable in situ extractant, enabling extraction of up to 90% of total triterpenoids from engineered Saccharomyces cerevisiae. Combining isopropyl myristate and β-cyclodextrins improved extraction efficiency. In a first configuration, repeated batch fermentation with sequential product extraction and cell recycling resulted in 1.8 times higher production than a reference fermentation without in situ product extraction. In the second configuration, yeast cells were in contact with the second organic phase throughout a fed-batch fermentation to continuously extract triterpenoids. This resulted in 90% product extraction and an extended production phase. Further improvement of triterpenoid production was not achieved due to microbial host limitations uncovered through omics analyses.},
}

*Saccharomyces cerevisiae/metabolism/genetics
*Triterpenes/metabolism
*Fermentation
Metabolic Engineering/methods
Chemical Fractionation/methods

@article {pmid39696719,
year = {2024},
author = {Herbold, CW and Noell, SE and Lee, CK and Vickers, CJ and Stott, MB and Eisen, JA and McDonald, IR and Cary, SC},
title = {Nutritional niches of potentially endemic, facultatively anaerobic heterotrophs from an isolated Antarctic terrestrial hydrothermal refugium elucidated through metagenomics.},
journal = {Environmental microbiome},
volume = {19},
number = {1},
pages = {104},
pmid = {39696719},
issn = {2524-6372},
support = {UOW0802//Marsden Fund/ ; UOW0802//Marsden Fund/ ; },
abstract = {BACKGROUND: Tramway Ridge, a geothermal Antarctic Specially Protected Area (elevation 3340 m) located near the summit of Mount Erebus, is home to a unique community composed of cosmopolitan surface-associated micro-organisms and abundant, poorly understood subsurface-associated microorganisms. Here, we use shotgun metagenomics to compare the functional capabilities of this community to those found elsewhere on Earth and to infer in situ diversity and metabolic capabilities of abundant subsurface taxa.

RESULTS: We found that the functional potential in this community is most similar to that found in terrestrial hydrothermal environments (hot springs, sediments) and that the two dominant organisms in the subsurface carry high rates of in situ diversity which was taken as evidence of potential endemicity. They were found to be facultative anaerobic heterotrophs that likely share a pool of nitrogenous organic compounds while specializing in different carbon compounds.

CONCLUSIONS: Metagenomic insights have provided a detailed understanding of the microbe-based ecosystem found in geothermally heated fumaroles at Tramway Ridge. This approach enabled us to compare Tramway Ridge with other microbial systems, identify potentially endemic taxa and elucidate the key metabolic pathways that may enable specific organisms to dominate the ecosystem.},
}

@article {pmid39696556,
year = {2024},
author = {Amano, Y and Sachdeva, R and Gittins, D and Anantharaman, K and Lei, S and Valentin-Alvarado, LE and Diamond, S and Beppu, H and Iwatsuki, T and Mochizuki, A and Miyakawa, K and Ishii, E and Murakami, H and Jaffe, AL and Castelle, C and Lavy, A and Suzuki, Y and Banfield, JF},
title = {Diverse microbiome functions, limited temporal variation and substantial genomic conservation within sedimentary and granite rock deep underground research laboratories.},
journal = {Environmental microbiome},
volume = {19},
number = {1},
pages = {105},
pmid = {39696556},
issn = {2524-6372},
support = {JPJ007597//The Ministry of Economy, Trade and Industry of Japan/ ; 19K05342//the Japan Society for the Promotion of Science/ ; OCE2049478//National Science Foundation/ ; DE-AC02-05CH11231//the Watershed Function Scientific Focus Area funded by the U.S. Department of Energy/ ; 2230766//NSF "Four Networks for Geologic Hydrogen Storage"/ ; },
abstract = {BACKGROUND: Underground research laboratories (URLs) provide a window on the deep biosphere and enable investigation of potential microbial impacts on nuclear waste, CO2 and H2 stored in the subsurface. We carried out the first multi-year study of groundwater microbiomes sampled from defined intervals between 140 and 400 m below the surface of the Horonobe and Mizunami URLs, Japan.

RESULTS: We reconstructed draft genomes for > 90% of all organisms detected over a four year period. The Horonobe and Mizunami microbiomes are dissimilar, likely because the Mizunami URL is hosted in granitic rock and the Horonobe URL in sedimentary rock. Despite this, hydrogen metabolism, rubisco-based CO2 fixation, reduction of nitrogen compounds and sulfate reduction are well represented functions in microbiomes from both URLs, although methane metabolism is more prevalent at the organic- and CO2-rich Horonobe URL. High fluid flow zones and proximity to subsurface tunnels select for candidate phyla radiation bacteria in the Mizunami URL. We detected near-identical genotypes for approximately one third of all genomically defined organisms at multiple depths within the Horonobe URL. This cannot be explained by inactivity, as in situ growth was detected for some bacteria, albeit at slow rates. Given the current low hydraulic conductivity and groundwater compositional heterogeneity, ongoing inter-site strain dispersal seems unlikely. Alternatively, the Horonobe URL microbiome homogeneity may be explained by higher groundwater mobility during the last glacial period. Genotypically-defined species closely related to those detected in the URLs were identified in three other subsurface environments in the USA. Thus, dispersal rates between widely separated underground sites may be fast enough relative to mutation rates to have precluded substantial divergence in species composition. Species overlaps between subsurface locations on different continents constrain expectations regarding the scale of global subsurface biodiversity.

CONCLUSIONS: Our analyses reveal microbiome stability in the sedimentary rocks and surprising microbial community compositional and genotypic overlap over sites separated by hundreds of meters of rock, potentially explained by dispersal via slow groundwater flow or during a prior hydrological regime. Overall, microbiome and geochemical stability over the study period has important implications for underground storage applications.},
}

@article {pmid39695983,
year = {2024},
author = {Su, L and Guo, J and Shi, W and Tong, W and Li, X and Yang, B and Xiang, Z and Qin, C},
title = {Metagenomic analysis reveals the community composition of the microbiome in different segments of the digestive tract in donkeys and cows: implications for microbiome research.},
journal = {BMC microbiology},
volume = {24},
number = {1},
pages = {530},
pmid = {39695983},
issn = {1471-2180},
support = {2021YFF0702900//National Key Research and Development Program of China/ ; 2023-PT180-01//Non-profit Central Research Institute Fund of Chinese Academy of Medical Sciences/ ; 2021-I2M-1-039, 2021-I2M-1-034//CAMS initiative for Innovative Medicine of China/ ; },
mesh = {Animals ; *Equidae/microbiology ; Cattle/microbiology ; *Metagenomics/methods ; *Gastrointestinal Microbiome/genetics ; *Feces/microbiology ; *Bacteria/classification/genetics/isolation & purification ; *Gastrointestinal Tract/microbiology ; Sequence Analysis, DNA/methods ; Metagenome ; Bacteroidetes/genetics/isolation & purification/classification ; },
abstract = {INTRODUCTION: The intestinal microbiota plays a crucial role in health and disease. This study aimed to assess the composition and functional diversity of the intestinal microbiota in donkeys and cows by examining samples collected from different segments of the digestive tract using two distinct techniques: direct swab sampling and faecal sampling.

RESULTS: In this study, we investigated and compared the effects of multiple factors on the composition and function of the intestinal microbial community. Approximately 300 GB of metagenomic sequencing data from 91 samples obtained from various segments of the digestive tract were used, including swabs and faecal samples from monogastric animals (donkeys) and polygastric animals (cows). We assembled 4,004,115 contigs for cows and 2,938,653 contigs for donkeys, with a total of 9,060,744 genes. Our analysis revealed that, compared with faecal samples, swab samples presented a greater abundance of Bacteroidetes, whereas faecal samples presented a greater abundance of Firmicutes. Additionally, we observed significant variations in microbial composition among different digestive tract segments in both animals. Our study identified key bacterial species and pathways via different methods and provided evidence that multiple factors can influence the microbial composition. These findings provide new insights for the accurate characterization of the composition and function of the gut microbiota in microbiome research.

CONCLUSIONS: The results obtained by both sampling methods in the present study revealed that the composition and function of the intestinal microbiota in donkeys and cows exhibit species-specific and region-specific differences. These findings highlight the importance of using standardized sampling protocols to ensure accurate and consistent characterization of the intestinal microbiota in various animal species. The implications and underlying mechanisms of these associations provide multiple perspectives for future microbiome research.},
}

Animals
*Equidae/microbiology
Cattle/microbiology
*Metagenomics/methods
*Gastrointestinal Microbiome/genetics
*Feces/microbiology
*Bacteria/classification/genetics/isolation & purification
*Gastrointestinal Tract/microbiology
Sequence Analysis, DNA/methods
Metagenome
Bacteroidetes/genetics/isolation & purification/classification

@article {pmid39695885,
year = {2024},
author = {Galic, I and Bez, C and Bertani, I and Venturi, V and Stankovic, N},
title = {Herbicide-treated soil as a reservoir of beneficial bacteria: microbiome analysis and PGP bioinoculants in maize.},
journal = {Environmental microbiome},
volume = {19},
number = {1},
pages = {107},
pmid = {39695885},
issn = {2524-6372},
support = {451-03-47/2023-01/ 200042//Ministarstvo Prosvete, Nauke i Tehnološkog Razvoja/ ; 451-03-47/2023-01/ 200042//Ministarstvo Prosvete, Nauke i Tehnološkog Razvoja/ ; Research and Training Grant 1818//FEMS/ ; },
abstract = {BACKGROUND: Herbicides are integral to agricultural weed management but can adversely affect non-target organisms, soil health, and microbiome. We investigated the effects of herbicides on the total soil bacterial community composition using 16S rRNA gene amplicon community profiling. Further, we aimed to identify herbicide-tolerant bacteria with plant growth-promoting (PGP) capabilities as a mitigative strategy for these negative effects, thereby promoting sustainable agricultural practices.

RESULTS: A bacterial community analysis explored the effects of long-term S-metolachlor application on soil bacterial diversity, revealing that the herbicide's impact on microbial communities is less significant than the effects of temporal factors (summer vs. winter) or agricultural practices (continuous maize cultivation vs. maize-winter wheat rotation). Although S-metolachlor did not markedly alter the overall bacteriome structure in our environmental context, the application of enrichment techniques enabled the selection of genera such as Pseudomonas, Serratia, and Brucella, which were rare in metagenome analysis of soil samples. Strain isolation revealed a rich source of herbicide-tolerant PGP bacteria within the culturable microbiome fraction, termed the high herbicide concentration tolerant (HHCT) bacterial culture collection. Within the HHCT collection, we isolated 120 strains that demonstrated significant in vitro PGP and biocontrol potential, and soil quality improvement abilities. The most promising HHCT isolates were combined into three consortia, each exhibiting a comprehensive range of plant-beneficial traits. We evaluated the efficacy and persistence of these multi-strain consortia during 4-week in pot experiments on maize using both agronomic parameters and 16S rRNA gene community analysis assessing early-stage plant development, root colonization, and rhizosphere persistence. Notably, 7 out of 10 inoculated consortia partners successfully established themselves and persisted in the maize root microbiome without significantly altering host root biodiversity. Our results further evidenced that all three consortia positively impacted both seed germination and early-stage plant development, increasing shoot biomass by up to 47%.

CONCLUSIONS: Herbicide-treated soil bacterial community analysis revealed that integrative agricultural practices can suppress the effects of continuous S-metolachlor application on soil microbial diversity and stabilize microbiome fluctuations. The HHCT bacterial collection holds promise as a source of beneficial bacteria that promote plant fitness while maintaining herbicide tolerance.},
}

@article {pmid39695840,
year = {2024},
author = {Gomathinayagam, S and Kanagalingam, S and Chandrasekaran, S and Krishnan, T and Kodiveri Muthukaliannan, G},
title = {Millennial-scale microbiome analysis reveals ancient antimicrobial resistance conserved despite modern selection pressures.},
journal = {Environmental microbiome},
volume = {19},
number = {1},
pages = {110},
pmid = {39695840},
issn = {2524-6372},
support = {AMR/Fellowship/20/2022-ECD-lI//Indian Council of Medical Research/ ; },
abstract = {BACKGROUND: Antimicrobial resistance presents a formidable challenge, yet its existence predates the introduction of antibiotics. Our study delves into the presence of antimicrobial resistance genes (ARGs) in ancient permafrost microbiomes, comparing them with contemporary soil and pristine environments. Majority of the samples are from regions around Beringia, encompassing parts of Russia and Alaska, with only one sample originating from the Tien Shan Mountain range in Kyrgyzstan.

RESULTS: From over 2.3 tera basepairs of raw metagenomic data, retrieved from samples ranging in age from approximately 7,000 years to 1.1 million years, we assembled about 1.3 billion metagenomic contigs and explored the prevalence of ARGs within them. Our findings reveal a diverse array of ARGs in ancient microbiomes, akin to contemporary counterparts. On average, we identified 2 ARGs per rRNA gene in ancient samples. Actinomycetota, Bacillota, and several thermophiles were prominent carriers of ARGs in Chukochi and Kamchatkan samples. Conversely, ancient permafrost from the Tien Shan Mountain range exhibited no Thermophiles or Actinomycetota carrying ARGs. Both ancient and contemporary microbiomes showcased numerous divergent ARGs, majority of which have identity between 40 and 60% to genes in antibiotic resistance gene databases. To study the selection pressure on ARGs, we performed dN/dS analysis specifically on antibiotic inactivation-type ARGs, which exhibited purifying selection compared to contemporary genes.

CONCLUSION: Antibiotic resistance has existed throughout microbial evolution and will likely persist, as microbes have the capacity to develop and retain resistance genes through evolutionary processes. The classes of antimicrobial resistance genes profiled and the function of antibiotic-inactivating enzymes from ancient permafrost microbiomes do not seem to be very different from the genes found in the antibiotic era. Additionally, we retrieved 359 putative complete viruses from ancient microbiomes and none of them harboured any ARGs.},
}

@article {pmid39695397,
year = {2024},
author = {Wang, Y and Xiang, Y and Lei, C and Zheng, X and Wu, W and Zhang, Z and Qu, X},
title = {Liver abscess and splenic infarction due to Yersinia pseudotuberculosis bloodstream infection: a case report.},
journal = {BMC infectious diseases},
volume = {24},
number = {1},
pages = {1415},
pmid = {39695397},
issn = {1471-2334},
mesh = {Humans ; Male ; Adult ; *Yersinia pseudotuberculosis/isolation & purification/genetics ; *Yersinia pseudotuberculosis Infections/diagnosis/microbiology/drug therapy ; *Splenic Infarction/microbiology ; *Liver Abscess/microbiology ; Multiple Organ Failure ; Anti-Bacterial Agents/therapeutic use ; Bacteremia/microbiology/diagnosis/drug therapy ; Tomography, X-Ray Computed ; },
abstract = {BACKGROUND: Yersinia pseudotuberculosis is an emerging zoonotic intestinal pathogen primarily transmitted through contaminated food and water. Infections caused by Yersinia pseudotuberculosis are typically self-limiting, often presenting as gastroenteritis or "pseudoappendicitis," which is characterized by fever and abdominal pain. Although bloodstream infections with Yersinia pseudotuberculosis are rare, they can lead to multiple distant sites of infection, including abscesses in the liver, spleen, and kidneys, as well as in the hip and knee joints, particularly in individuals with underlying immunodeficiency.

CASE PRESENTATION: We report the case of a 40-year-old male patient who was admitted to the intensive care unit (ICU) with intermittent fever lasting for five days, followed by exacerbation of abdominal pain and distension one day after ingesting contaminated food. Upon admission, the patient exhibited severe hypotension, which rapidly progressed to signs of liver and kidney failure, ultimately leading to multiple organ dysfunction syndrome (MODS). Notably, abdominal computed tomography (CT) revealed evidence of a liver abscess and splenic infarction. The treatment regimen included fluid resuscitation, broad-spectrum antibiotics, vasopressors, continuous renal replacement therapy (CRRT), and plasma exchange. Blood cultures along with metagenomic next-generation sequencing (mNGS) confirmed an infection caused by Yersinia pseudotuberculosis. After 17 days in the ICU, the patient was transferred to the infectious disease department for an additional 14 days of treatment before being discharged. Three months post-discharge, follow-up visits indicated that the patient was in good health.

CONCLUSIONS: To the best of our knowledge, this case represents a rare instance of multiple organ dysfunction syndrome (MODS), liver abscess, and splenic infarction resulting from Yersinia pseudotuberculosis infection. The identification of the pathogen was facilitated by blood culture and metagenomic next-generation sequencing (mNGS) of blood samples. The administration of broad-spectrum antibiotics, along with active support for organ function, ultimately contributed to the patient's recovery.

CLINICAL TRIAL NUMBER: No applicable.},
}

Humans
Male
Adult
*Yersinia pseudotuberculosis/isolation & purification/genetics
*Yersinia pseudotuberculosis Infections/diagnosis/microbiology/drug therapy
*Splenic Infarction/microbiology
*Liver Abscess/microbiology
Multiple Organ Failure
Anti-Bacterial Agents/therapeutic use
Bacteremia/microbiology/diagnosis/drug therapy
Tomography, X-Ray Computed

@article {pmid39695297,
year = {2024},
author = {Conteville, LC and Silva, JVD and Andrade, BGN and Coutinho, LL and Palhares, JCP and Regitano, LCA},
title = {Recovery of metagenome-assembled genomes from the rumen and fecal microbiomes of Bos indicus beef cattle.},
journal = {Scientific data},
volume = {11},
number = {1},
pages = {1385},
pmid = {39695297},
issn = {2052-4463},
mesh = {Animals ; Cattle/microbiology ; *Feces/microbiology ; *Metagenome ; *Rumen/microbiology ; *Phylogeny ; Gastrointestinal Microbiome ; Brazil ; Male ; Archaea/genetics/classification ; Bacteria/genetics/classification ; Microbiota ; },
abstract = {Nelore is a Bos indicus beef breed that is well-adapted to tropical environments and constitutes most of the world's largest commercial cattle herd: the Brazilian bovine herd. Despite its significance, microbial genome recovery from ruminant microbiomes has largely excluded representatives from Brazilian Nelore cattle. To address this gap, this study presents a comprehensive dataset of microbial genomes recovered from the rumen and feces of 52 Brazilian Nelore bulls. A total of 1,526 non-redundant metagenome-assembled genomes (MAGs) were recovered from their gastrointestinal tract, with 497 ruminal and 486 fecal classified as high-quality. Phylogenetic analysis revealed that the bacterial MAGs fall into 12 phyla, with Firmicutes and Bacteroidota being the most predominant, while all archaeal MAGs belong to the genus Methanobrevibacter. The exploration of these microbial genomes will provide valuable insights into the metabolic potential and functional roles of individual microorganisms within host-microbiome interactions, contributing to a better understanding of the microbiome's roles in bovine performance.},
}

Animals
Cattle/microbiology
*Feces/microbiology
*Metagenome
*Rumen/microbiology
*Phylogeny
Gastrointestinal Microbiome
Brazil
Male
Archaea/genetics/classification
Bacteria/genetics/classification
Microbiota

@article {pmid39695240,
year = {2024},
author = {Shen, Y and An, Z and Xia, S and Ding, Q and Chen, K and Miao, Y and Wang, T and Zhong, J and Li, J and Wang, X and Wang, H},
title = {A multi-omics database of buffaloes from Yangtze valley reveals diversity of water buffalo (Bubalus bubalis).},
journal = {Scientific data},
volume = {11},
number = {1},
pages = {1375},
pmid = {39695240},
issn = {2052-4463},
support = {ZR2023QC252//Natural Science Foundation of Shandong Province (Shandong Provincial Natural Science Foundation)/ ; CARS-36//Earmarked Fund for China Agriculture Research System/ ; },
mesh = {*Buffaloes/genetics ; Animals ; Male ; China ; Transcriptome ; Metabolome ; Metagenome ; Rumen ; Multiomics ; },
abstract = {Asian water buffalo (Bubalus bubalis) is the fundamental livestock resource for local rural populations and holds a promising prospect of their milk and meat. Xuyi mountain (XYM) and Haizi (HZ) buffaloes from Yangtze valley comprises of species diversity of Asian water buffaloes. Current multi-omics enables identification of causal genes and elucidation of genetic regulatory mechanisms underlying complex traits in buffaloes. Here, we conducted the integrated analysis of metabolome and metagenome of rumen fluid, transcriptome and metabolome of blood, and whole genome sequence data from XYM (n = 7) and HZ (n = 10) male buffaloes. Our results revealed the apparent diversity of multi-layer omics profiles between two buffalo species. The built-up multi-omics database supports the discoveries of diversity in Asian water buffalo and potentially serves valuable resources for studying causal regulatory variants and their mechanisms.},
}

*Buffaloes/genetics
Animals
Male
China
Transcriptome
Metabolome
Metagenome
Rumen
Multiomics

@article {pmid39695203,
year = {2024},
author = {Jeon, J and Park, Y and Lee, DH and Kim, JH and Jin, YK and Hong, JK and Lee, YM},
title = {Microbial profiling of the East Siberian Sea sediments using 16S rRNA gene and metagenome sequencing.},
journal = {Scientific data},
volume = {11},
number = {1},
pages = {1350},
pmid = {39695203},
issn = {2052-4463},
mesh = {*Geologic Sediments/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Metagenome ; *Archaea/genetics/classification ; *Bacteria/genetics/classification ; Arctic Regions ; Microbiota ; Oceans and Seas ; Siberia ; },
abstract = {The Arctic Ocean is experiencing significant global warming, leading to reduced sea-ice cover, submarine permafrost thawing, and increased river discharge. The East Siberian Sea (ESS) undergoes more significant terrestrial inflow from coastal erosion and river runoff than other Arctic seas. Despite extensive research on environmental changes, microbial communities and their functions in the ESS, which are closely related to environmental conditions, remain largely unexplored. Here, we investigated microbial communities in ESS surface sediments spanning latitudes from 73°N to 77°N using 16S rRNA amplicon sequencing, and reconstructed 211 metagenome-assembled genomes (MAGs) using shotgun metagenome sequencing. Taxonomic analysis identified 209 bacterial MAGs, with the predominant phyla Pseudomonadota (n = 82), Actinobacteriota (n = 38), Desulfobacterota (n = 23), along with 2 archaeal MAGs of Thermoproteota. Notably, 86% of the MAGs (n = 183) could not be classified into known species, indicating the potential presence of novel and unidentified microorganisms in the ESS. This dataset provides invaluable information on the microbial diversity and ecological functions in the rapidly changing ESS.},
}

*Geologic Sediments/microbiology
*RNA, Ribosomal, 16S/genetics
*Metagenome
*Archaea/genetics/classification
*Bacteria/genetics/classification
Arctic Regions
Microbiota
Oceans and Seas
Siberia

@article {pmid39694980,
year = {2024},
author = {Wang, S and Liu, Y and Li, Y and Gao, Y and Zou, Z and Xu, N and Song, Q and Liu, F and Song, Y and Wang, X and Fan, Z},
title = {Rapid, multiplex and automated detection of bacteria and fungi in endophthalmitis via a microfluidic real-time pcr system.},
journal = {Journal of ophthalmic inflammation and infection},
volume = {14},
number = {1},
pages = {64},
pmid = {39694980},
issn = {1869-5760},
abstract = {BACKGROUND: Endophthalmitis is an ophthalmologic emergency requiring accurate and rapid diagnosis for treatment. Currently, the diagnosis commonly relies on culture and molecular biology, which falls short of clinical rapid diagnosis. The purpose of this study was to evaluate the feasibility of a self-build Microfluidic Real-time Polymerase Chain Reaction (RT-PCR) System for rapidly identifying potential pathogens of endophthalmitis.

METHODS: This study included 22 patients who presented to Shenzhen Eye Hospital and the Ophthalmology Department of the Affiliated Hospital of Guizhou Medical University in China between January 2023 and March 2024. The samples were cultured using conventional methods and underwent Microfluidic RT-PCR and metagenomic next-generation sequencing (mNGS).

RESULTS: The Microfluidic RT-PCR System identified pathogens in 11 of 22 cases (50.00%), compared with 40.91% for microbiology culture. 14 cases (63.64%) had concordant results, and 5 cases were positive for the microfluidic system only. The agreements between culture and microfluidic system, as well as culture and mNGS were 100.00% (6/6) and 50.00% (3/6), respectively. The average waiting time for the microfluidic system was about 30 min if excepting DNA extraction time, which was much shorter than 2.88 days for culture and 1.57 days for mNGS.

CONCLUSION: The microfluidic-based RT-PCR system was preliminarily proved to be a sensitive, easy-to-operate, and rapid in-hospital technology. It is expected to become a rapid diagnostic platform for endophthalmitis.},
}

@article {pmid39694283,
year = {2024},
author = {Parde, D and Behera, M and Dash, RR},
title = {Assessment of Reactor Configurations and Key Factors for Enhanced Anammox-Based Nitrogen Removal.},
journal = {Chemosphere},
volume = {},
number = {},
pages = {143972},
doi = {10.1016/j.chemosphere.2024.143972},
pmid = {39694283},
issn = {1879-1298},
abstract = {Wastewater treatment processes are continually evolving to meet stringent environmental standards while optimizing energy consumption and operational costs. With significant advantages over more traditional approaches, the anammox process has become a hopeful substitute for nitrogen removal. The objective of this work was to evaluate upflow anaerobic sludge blanket reactor (UASBR), moving bed biofilm reactor (MBBR), and sequential batch reactor (SBR) among diverse reactor configurations, in culturing anammox bacteria and achieving nitrogen removal efficiencies. Synthetic wastewater containing NH4[+]-N concentration and NO2[-]-N concentration of 80±5 mg/L was introduced to the reactors, and observations were made for up to 150 days. This study found that the MBBR demonstrated superior anammox activity, achieving a total nitrogen removal efficiency (TNRE) of 94±3%, SBR exhibited a TNRE of approximately 85±3%, while UASB displayed TNRE of 73±3%. The effect of varying carbon-to-nitrogen (C/N) ratios on nitrogen removal efficiencies was investigated, revealing a decrease in TNRE as the C/N ratio increased from 3 to 8. This study demonstrated the enhancing and inhibitory effects of C/N ratio, NO2[-]-N, and Fe concentrations. It revealed that Fe concentrations between 1-5 mg/L increase specific anammox activity (SAA), while concentrations between 5-10 mg/L negatively impact it. Additionally, NO2[-]-N concentrations above 150 mg/L significantly reduce SAA. Furthermore, a 16S rRNA metagenomic analysis of MBBR sludge samples revealed the significant presence of Candidatus Brocadia bacteria, constituting 20.4% of the microbial community. This research highlights the potential of MBBR in fostering anammox reactions and achieving efficient nitrogen removal in wastewater treatment applications.},
}

@article {pmid39694238,
year = {2024},
author = {Vermeersch, AS and Ducatelle, R and Geldhof, P and Opsomer, G},
title = {INVITED REVIEW: Udder cleft dermatitis in dairy cows.},
journal = {Journal of dairy science},
volume = {},
number = {},
pages = {},
doi = {10.3168/jds.2024-25086},
pmid = {39694238},
issn = {1525-3198},
abstract = {Udder cleft dermatitis (UCD) is a common dermatological condition of the udder skin in dairy cows. It is generally considered to be a multifactorial disease, being described in a rather limited amount of literature. Its cow-and within-herd prevalence widely ranges between studies depending on the study characteristics, environment and breed. Known risk factors include husbandry practices and environmental factors such as freestall housing, the use of mattresses as cubicle bases, and footbathing. Cow-related elements such as udder conformation, parity and lactation parameters are well-known risk factors for developing UCD. Despite being associated with a high incidence of veterinary-treated clinical mastitis and culling due to udder disease, the somatic cell count of the milk is not influenced by UCD. Severe UCD lesions are characterized by chronic and persistent, dysregulated inflammation accompanied by hampered skin healing and an impaired skin barrier. There is a decrease in microbial diversity followed by dysbiosis and a concomitant overgrowth of opportunistic bacteria negatively impacting beneficial commensal bacteria. Concurrently, a shift in virulence factors most likely contributes to the creation of an environment favorable to pathogens. Anecdotally, mange mites have been associated with UCD but current literature refutes this. The role of treponemes remains inconclusive. Multi-omics analysis of both transcriptomic and metagenomic severe UCD data sets, revealed the negative interaction of the facultative pathogen Streptococcus pyogenes with microbiome-associated virulence factors and the patient's transcriptome. No efficient curative treatments nor prevention strategies have been identified so far, although alginogel products have been described to have a positive effect on the healing process of severe lesions. All in all, UCD is a painful skin disease for which an array of miscellaneous risk factors have been identified. For the first time we assimilate literature on prevalence and risk factors, and results from recent elementary studies that provide insights into the pathogenesis of this challenging disease.},
}

@article {pmid39694116,
year = {2024},
author = {Zhong, S and Yang, YN and Huo, JX and Sun, YQ and Zhao, H and Dong, XT and Feng, JY and Zhao, J and Wu, CM and Li, YG},
title = {Cyanidin-3-rutinoside from Mori Fructus ameliorates dyslipidemia via modulating gut microbiota and lipid metabolism pathway.},
journal = {The Journal of nutritional biochemistry},
volume = {},
number = {},
pages = {109834},
doi = {10.1016/j.jnutbio.2024.109834},
pmid = {39694116},
issn = {1873-4847},
abstract = {Dyslipidemia is responsible for pathologies of cardiovascular diseases and gut microbiota plays an essential role in lipid metabolism. Dietary supplementation is an important supplement to medicine in management of dyslipidemia. Mori Fructus is a popular Asia medical food with various pharmacological benefits including anti-hyperlipidemia. Cyanidin-3-rutinoside (C3R) is the main anthocyanin component in Mori Fructus, but the lipid-lowering effect and underlying mechanism of Mori Fructus-derived C3R remains unknown. In this study, we assessed the beneficial effect of Mori Fructus-derived C3R in HFD-induced hyperlipidemic mice and investigated its potential mechanism through 16S rRNA-based metagenomics and transcriptomics analysis. Our results showed that C3R from Mori Fructus significantly decreased serum lipid levels and attenuated hepatic damage induced by HFD. Analysis of the gut microbiota revealed that C3R altered the specific gut micorbiota but not changed its diversity. Among changed genera, Family_XIII_UCG-001 was significantly enriched by C3R, and it was positively associated with HDL-c, but negatively related with TC, TG, LDL-c, insulin and body weight. Transcriptomic analysis showed that C3R activates the lipid metabolism related pathways including MAPK signaling pathway, Rap1 signaling pathway, Ras signaling pathway and PI3K-Akt signaling pathway. Additionally, correlation analysis unraveled that C3R-enriched Family_XIII_UCG-001 was negatively associated with C3R-inhibited genes of Camk2a, Eef1a2, Gad1, Kif5a and Sv2b, which further positively related with TC, TG, LDL-c, insulin and body weight, but negatively associated with HDL-c. In sum, C3R may inhibit expression of immune-related genes by enriching the Family_XIII_UCG-001 genus, further ameliorating lipid metabolism disorders in HFD-challenged mice. This study provides an optional strategy for the daily management of dyslipidemia.},
}

@article {pmid39693984,
year = {2024},
author = {Wang, Y and Wu, SL and Wei, W and Wu, L and Huang, S and Dai, X and Ni, BJ},
title = {pH-dependent medium-chain fatty acid synthesis in waste activated sludge fermentation: Metabolic pathway regulation.},
journal = {Journal of environmental management},
volume = {373},
number = {},
pages = {123722},
doi = {10.1016/j.jenvman.2024.123722},
pmid = {39693984},
issn = {1095-8630},
abstract = {Transforming waste activated sludge (WAS) into medium-chain fatty acids (MCFAs) via chain elongation (CE) technology is sustainable, yet pH effects on this process are poorly understood. In this study, semi-continuous flow experiments demonstrated that WAS degradation was highest under alkaline pH (10) but unsuitable for CE. Continuous output of MCFAs indicated that CE could be successfully performed under acidic pH (5) and neutral pH (7). Moreover, neutral pH optimized MCFAs production, achieving higher MCFAs yield (8.9 ± 1.2 g COD/L), MCFAs selectivity (51.2 ± 7.3%), and WAS degradation (25.4 ± 0.4%) than acidic pH. Further metagenomic and metatranscriptomic analysis revealed that the reverse β-oxidation cycle was the primary CE pathway. The absence of CE-related microorganisms and enzymes under alkaline pH hindered MCFAs synthesis, while under acidic pH, carboxylate accumulation may reduce cellular protection capabilities and affect energy metabolism, thereby inhibiting anaerobic fermentation. Conversely, neutral pH enhanced amino acid and butyrate metabolic pathways, facilitating WAS degradation and SCFAs production, providing precursor substrates for MCFAs production. Additionally, neutral pH promoted the enrichment and activity of CE-related microorganisms and enzymes, contributing to the accumulation of high-concentration MCFAs. Notably, Clostridium_kluyveri and Sporanaerobacter_acetigenes were key CE-functional bacteria at neutral pH.},
}

@article {pmid39693975,
year = {2024},
author = {Bharti, S and Raj, A and Saratale, GD and Romanholo Ferreira, LF and Lucena de Souza, R and Mulla, SI and Bharagava, RN},
title = {A critical review on the symbiotic effect of bacteria and microalgae on treatment of sewage with biofertilizer production.},
journal = {Journal of environmental management},
volume = {373},
number = {},
pages = {123704},
doi = {10.1016/j.jenvman.2024.123704},
pmid = {39693975},
issn = {1095-8630},
abstract = {Wastes like sewage, kitchen and industrial are the major sources of environmental pollution and health hazards. Sewage contains 99.9% water and 0.1% solid waste including urinal waste and faecal matter alongwith large amounts of nitrate, nitrite, ammonium and phosphate ions. Sewage may also contain a variety of harmful contaminants like analgesics, antihypertensive drugs, antibiotics, dioxin, furans, polychlorinated biphenyls, chlorinated hydrocarbon pesticides, chlorine derivatives and plasticizers etc. making it more harmfull to environment and public health. Hence, sewage must be adequately treated by an effective process before its final discharge into the environment. Biological treatment of sewage is an emerging idea in recent years, which has diverse economic and environmental advantages. Sewage treatment by bacteria and microalgae has numerous advantages as it removes various excessive nutrients from waste with large biomass production and also prevents the utilization of toxic chemicals in conventional treatment process. Microalgae-bacterial biomass have potential to be used as biofertilizers, bio-stimulants and bio-seed primers in agricultural field as these contain various biologically active substances like polysaccharides, carotenoids, free fatty acids, phenols, and terpenoids. This review paper mainly discussing the sewage characteristics and different kinds of organic and inorganic pollutants it contained alongwith its harmfull impacts on environment and public health. It also deals the different conventional as well as emerging treatment technologies and different factors affecting the treatment efficiency. In addition, the utilization of developed microalgal and bacterial biomass as biofertilizer and its effects on crop plant alongwith future prospects has been also discussed in detail.},
}

@article {pmid39693966,
year = {2024},
author = {Li, T and Wang, P and Zhi, Z and Guo, T and Zhou, J and Zhang, H and Cao, C and Cai, Y and Li, Y and Zhang, J},
title = {Free-caged rearing modes regulate chicken intestinal metabolism by influencing gut microbial homeostasis.},
journal = {Poultry science},
volume = {104},
number = {1},
pages = {104381},
doi = {10.1016/j.psj.2024.104381},
pmid = {39693966},
issn = {1525-3171},
abstract = {Free-caged rearing modes, which prioritize animal welfare, are believed to enhance the quality of animal products. The impact of rearing modes on meat quality may play a key role in the superior quality of local chicken breeds. This study analyzed the cecal contents of free-range and caged black-bone chickens at different ages using metagenomic and metabolomic sequencing. We identified 32 metabolites and 367 microbial species significantly affected by the rearing mode. Linear discriminant analysis Effect Size (LefSe) highlighted five key microorganisms, Gemmiger formicilis, Bacteria unclassified, Bacteroides sp. ET225, Massilistercora timonensis, and Bacteroidales unclassified, that showed distinct abundance patterns across all age points. Among them, Bacteroides sp. ET225 and Massilistercora timonensis were positively associated with certain phospholipids and plant-derived metabolites, while negatively correlated with others like demissidine and acylcarnitine. Functional analysis revealed that rearing modes impact gut metabolites involved in gut metabolism as well as broader processes such as signal transduction, protein digestion, and autophagy. This study offers new insights into how rearing modes influence gut microbiota and metabolites, shedding light on the study of rearing mode-mediated muscle development and fat deposition.},
}

@article {pmid39693717,
year = {2024},
author = {Tan, Q and Zhu, Y and Zhao, Y and Zheng, L and Wang, X and Xing, Y and Wu, H and Tian, Q and Zhang, Y},
title = {Comparative analysis of niche adaptation strategies of AOA, AOB, and comammox along a gate-controlled river-estuary continuum.},
journal = {Water research},
volume = {273},
number = {},
pages = {122964},
doi = {10.1016/j.watres.2024.122964},
pmid = {39693717},
issn = {1879-2448},
abstract = {Ammonia oxidizers are key players in the biogeochemical nitrogen cycle. However, in critical ecological zones such as estuaries, especially those affected by widespread anthropogenic dam control, our understanding of their occurrence, ecological performance, and survival strategies remains elusive. Here, we sampled sediments along the Haihe River-Estuary continuum in China, controlled by the Haihe Tidal Gate, and employed a combination of biochemical and metagenomic approaches to investigate the abundance, activity, and composition of ammonia-oxidizing archaea (AOA), ammonia-oxidizing bacteria (AOB), and complete ammonia oxidizers (comammox). We also conducted an extensive comparison of the salinity adaptation mechanisms of different ammonia oxidizers. We found that AOB (57.55 ± 11.46 %) dominated the nitrification process upstream of the tidal gate, while comammox (68.22 ± 14.42 %) played the major role downstream. Redundancy analysis results showed that total nitrogen, ammonium, and salinity were the primary factors influencing the abundance, activity, and contribution of ammonia oxidizers. The abundance and activity of AOB were significantly positively correlated with ammonium. KEGG annotation results showed that AOA Nitrososphaera, AOB Nitrosomonas, and comammox Nitrospira had 7, 31, and 22 genes associated to salinity adaptation, respectively, and were capable of employing both the "salt-in" and "salt-out" strategies. Metagenome assembly results indicated that comammox outperformed AOA primarily in compatible solute accumulation; AOA can synthesize glutamate, whereas comammox Nitrospira can additionally synthesize glycine betaine, choline, and trehalose. The tidal gate caused sharp shifts in ammonium (from 4.10 ± 3.28 mg·kg[-1] to 0.45 ± 0.10 mg·kg[-1]) and salinity (from 1.64 ± 0.48 ppt to 3.26 ± 0.89 ppt), playing a dominant role in driving niche differentiation of ammonia oxidizers along the Haihe River-Estuary continuum. These findings provide profound insights into the nitrogen cycle in freshwater-saltwater transition zones, especially in today's world where estuaries are widely controlled by tidal gates.},
}

@article {pmid39694112,
year = {2024},
author = {Li, D and Liang, W and Sun, X and Sun, W and Liu, G and Zeng, EY},
title = {Long-term stability of comammox Nitrospira under weakly acidic conditions and their acid-adaptive mechanisms revealed by genome-centric metatranscriptomics.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {131986},
doi = {10.1016/j.biortech.2024.131986},
pmid = {39694112},
issn = {1873-2976},
abstract = {Despite their widespread presence in acidic environments, the stability and adaptative mechanisms of complete ammonia oxidization (comammox) bacteria remain poorly understood. In this three-year study, comammox Nitrospira consistently dominated both abundance and activity in an acidic nitrifying reactor (pH = 6.3-6.8), as revealed by metagenomic and cDNA-based 16S rRNA sequencing. Batch tests demonstrated their decent nitrification down to pH 4.7, while ceasing at pH 4.2. Genome-centric metatranscriptomics revealed that comammox Nitrospira upregulated a Rh-type ammonium transporter to enhance substrate uptake under acidic conditions. Active proton transport, mediated by NADH dehydrogenases and F-type ATPase, was identified as a primary strategy for maintaining pH homeostasis in comammox Nitrospira. Genes associated with carbon acquisition, chemotaxis, and DNA repair were upregulated at low pH, suggesting these processes play roles in acid adaptation. These findings enhance the understanding of ecological roles and adaptive mechanisms of comammox bacteria in acidic environments.},
}

@article {pmid39694110,
year = {2024},
author = {Vinh, NT and Trinh, HP and Park, HD},
title = {Genome-based analysis reveals niche differentiation among Firmicutes in full-scale anaerobic digestion systems.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {131993},
doi = {10.1016/j.biortech.2024.131993},
pmid = {39694110},
issn = {1873-2976},
abstract = {Fermentative Firmicutes species are key players in anaerobic digestion (AD); however, their niche differentiation based on carbohydrate utilization in full-scale systems remains unclear. In this study, we investigated niche differentiation among four major Firmicutes classes using a genome-centric approach by reconstructing 39 high-quality metagenome-assembled genomes (MAGs). Limnochordia and Clostridia exhibited the broadest substrate versatility, utilizing 24% and 18% of the predicted substrates, respectively. Although common substrates were shared, each class demonstrated unique substrate preferences driven by distinct functional and metabolic differences. Limnochordia and Clostridia possess unique carbohydrate-active enzymes (CAZymes) families, such as GH177 and CBM91, which enable xylan and arabinan degradation. Bacilli were abundant with the GH1 and GH3 families, which are critical for cellulose degradation. Overall, the Firmicutes classes showed low overlap in substrate use and functional profiles, confirming significant niche differentiation. Our results demonstrate that Firmicutes occupy distinct dietary niches supporting insights into bacterial coexistence in AD systems.},
}

@article {pmid39694109,
year = {2024},
author = {Dai, B and Zhou, J and Wang, Z and Yang, Y and Wang, Z and He, J and Xia, S and Rittmann, BE},
title = {Hydrazine promoted nitrite reduction in partial-denitrification by enhancing organic-substrate uptake and electron transport.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {131991},
doi = {10.1016/j.biortech.2024.131991},
pmid = {39694109},
issn = {1873-2976},
abstract = {Partial denitrification coupled with anammox is a promising approach for sustainable nitrogen removal from wastewater. However, this coupling can be influenced by hydrazine (N2H4) released by anammox bacteria. This study aimed to reveal how N2H4 regulates partial denitrification. Short-term batch experiments showed that 0.5 to 10 mg N/L of N2H4 promoted nitrite (NO2[-]) accumulation, likely by inhibiting the electron transfer from cyt c to nitrite reductase. However, long-term exposure to N2H4 (0.5 and 1 mg N/L) shifted the microbial community and increased NO2[-] reduction. This exposure enriched the genera OLB8, Thauera, and f_Rhodocyclaceae, and increased the abundance of genes involved in EPS formation, substrate transport and electron transport. The long-term outcome was more NO2[-] reduction to N2 and more substrate (COD) oxidation. While N2H4 benefits NO2[-] accumulation in short-term, the mechanism is not sustainable, highlighting the importance of minimizing N2H4 release for successful in such coupled nitrogen removal systems.},
}

@article {pmid39693773,
year = {2024},
author = {Shen, D and Li, C and Guo, Z},
title = {Dynamics of antibiotic resistance in poultry farms via multivector analysis.},
journal = {Poultry science},
volume = {104},
number = {2},
pages = {104673},
doi = {10.1016/j.psj.2024.104673},
pmid = {39693773},
issn = {1525-3171},
abstract = {This study examines the distribution of microbial communities and antibiotic resistance genes (ARGs) across various vectors in poultry farm environments. The results show that airborne particulate matter (PM) and soil harbor the highest counts of microbial genes, exceeding those found in poultry visceral samples, which display lower microbial diversity and ARG levels. This highlights environmental vectors, particularly soil and PM, as major reservoirs for ARGs. Proteobacteria, predominantly present in feces and feed, are identified as key carriers of ARGs, with resistance mechanisms primarily involving efflux and target modification. Notably, Chlamydia spp. in visceral samples, despite lower overall abundance, show a high proportion of ARGs, raising concerns about ARG persistence in poultry microbiota. Furthermore, a significant correlation between different ARGs was detected, indicating the possibility of cooperative transmission processes. The findings underline the role of PM in ARG transmission due to its mobility and capacity to retain ARGs across distances. Additionally, therapeutic antibiotics in feed may contribute to ARG proliferation in animal microbiomes, suggesting a need for improved management practices to mitigate ARG spread in poultry farming environments.},
}

@article {pmid39693444,
year = {2024},
author = {Ruff, SE and de Angelis, IH and Mullis, M and Payet, JP and Magnabosco, C and Lloyd, KG and Sheik, CS and Steen, AD and Shipunova, A and Morozov, A and Reese, BK and Bradley, JA and Lemonnier, C and Schrenk, MO and Joye, SB and Huber, JA and Probst, AJ and Morrison, HG and Sogin, ML and Ladau, J and Colwell, F},
title = {A global comparison of surface and subsurface microbiomes reveals large-scale biodiversity gradients, and a marine-terrestrial divide.},
journal = {Science advances},
volume = {10},
number = {51},
pages = {eadq0645},
doi = {10.1126/sciadv.adq0645},
pmid = {39693444},
issn = {2375-2548},
mesh = {*Microbiota/genetics ; *Biodiversity ; *Archaea/genetics/classification ; *Phylogeny ; *Bacteria/genetics/classification ; Metagenome ; Seawater/microbiology ; Ecosystem ; },
abstract = {Subsurface environments are among Earth's largest habitats for microbial life. Yet, until recently, we lacked adequate data to accurately differentiate between globally distributed marine and terrestrial surface and subsurface microbiomes. Here, we analyzed 478 archaeal and 964 bacterial metabarcoding datasets and 147 metagenomes from diverse and widely distributed environments. Microbial diversity is similar in marine and terrestrial microbiomes at local to global scales. However, community composition greatly differs between sea and land, corroborating a phylogenetic divide that mirrors patterns in plant and animal diversity. In contrast, community composition overlaps between surface to subsurface environments supporting a diversity continuum rather than a discrete subsurface biosphere. Differences in microbial life thus seem greater between land and sea than between surface and subsurface. Diversity of terrestrial microbiomes decreases with depth, while marine subsurface diversity and phylogenetic distance to cultured isolates rivals or exceeds that of surface environments. We identify distinct microbial community compositions but similar microbial diversity for Earth's subsurface and surface environments.},
}

*Microbiota/genetics
*Biodiversity
*Archaea/genetics/classification
*Phylogeny
*Bacteria/genetics/classification
Metagenome
Seawater/microbiology
Ecosystem

@article {pmid39693383,
year = {2024},
author = {Arrington, EC and Tarn, J and Kivenson, V and Nunn, BL and Liu, RM and Paul, BG and Valentine, DL},
title = {Hydrocarbon metabolism and petroleum seepage as ecological and evolutionary drivers for Cycloclasticus.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrae247},
pmid = {39693383},
issn = {1751-7370},
abstract = {Aqueous-soluble hydrocarbons dissolve into the ocean's interior and structure deep-sea microbial populations influenced by natural oil seeps and spills. n-Pentane is a seawater-soluble, volatile compound abundant in petroleum products and reservoirs and will partially partition to the deep-water column following release from the seafloor. In this study, we explore the ecology and niche partitioning of two free-living Cycloclasticus strains recovered from seawater incubations with n-pentane and distinguish them as an open ocean variant and a seep-proximal variant, each with distinct capabilities for hydrocarbon catabolism. Comparative metagenomic analysis indicates the variant more frequently observed further from natural seeps encodes more general pathways for hydrocarbon consumption, including short-chain alkanes, aromatics, and long-chain alkanes, and also possesses redox versatility in the form of respiratory nitrate reduction and thiosulfate oxidation; in contrast, the seep variant specializes in short-chain alkanes and relies strictly on oxygen as the terminal electron acceptor. Both variants observed in our work were dominant ecotypes of Cycloclasticus observed during the Deepwater Horizon disaster, a conclusion supported by 16S rRNA gene analysis and read-recruitment of sequences collected from the submerged oil plume during active flow. A comparative genomic analysis of Cycloclasticus across various ecosystems suggests distinct strategies for hydrocarbon transformations among each clade. Our findings suggest Cycloclasticus is a versatile and opportunistic consumer of hydrocarbons and may have a greater role in the cycling of sulfur and nitrogen, thus contributing broad ecological impact to various ecosystems globally.},
}

@article {pmid39693209,
year = {2024},
author = {Yamamoto, A and Kawashima, A and Uemura, T and Nakano, K and Matsushita, M and Ishizuya, Y and Jingushi, K and Hase, H and Katayama, K and Yamaguchi, R and Sassi, N and Motoyama, Y and Nojima, S and Mita, M and Kimura, T and Motooka, D and Horibe, Y and Okuda, Y and Oka, T and Yamamichi, G and Tomiyama, E and Koh, Y and Yamamoto, Y and Kato, T and Hatano, K and Uemura, M and Imoto, S and Wada, H and Morii, E and Tsujikawa, K and Nonomura, N},
title = {A novel mouse model of upper tract urothelial carcinoma highlights the impact of dietary intervention on gut microbiota and carcinogenesis prevention despite carcinogen exposure.},
journal = {International journal of cancer},
volume = {},
number = {},
pages = {},
doi = {10.1002/ijc.35295},
pmid = {39693209},
issn = {1097-0215},
support = {19K09709//Japan Society for the Promotion of Science/ ; 21K20968//Japan Society for the Promotion of Science/ ; 22H03213//Japan Society for the Promotion of Science/ ; 22K09523//Japan Society for the Promotion of Science/ ; 22K18398//Japan Society for the Promotion of Science/ ; JP22ym0126809i0002//Japan Agency for Medical Research and Development/ ; JP23ama121054//Japan Agency for Medical Research and Development/ ; },
abstract = {Animal models of N-butyl-N-(4-hydroxy butyl) nitrosamine (BBN)-induced urothelial carcinoma (UC), particularly bladder cancer (BC), have long been established. However, the rare incidence of BBN-induced upper urinary tract UC (UTUC), which originates from the same urothelium as BC, remains elusive. The scarcity of animal models of UTUC has made it challenging to study the biology of UTUC. To address this problem, we tried to establish a novel mouse model of UTUC by treating multiple mice strains and sexes with BBN. The molecular consistency between the UTUC mouse model and human UTUC was confirmed using multi-omics analyses, including whole-exome, whole-transcriptome, and spatial transcriptome sequencing. 16S ribosomal RNA metagenome sequencing, metabolome analysis, and dietary interventions were employed to assess changes in the gut microbiome, metabolome, and carcinogenesis of UTUC. Of all treated mice, only female BALB/c mice developed UTUC over BC. Multi-omics analyses confirmed that the UTUC model reflected the molecular characteristics and heterogeneity of human UTUC with poor prognosis. Furthermore, the model exhibited increased Tnf-related inflammatory gene expression in the upper urinary tract and a low relative abundance of Parabacteroides distasonis in the gut. Dietary intervention, mainly without alanine, led to P. distasonis upregulation and successfully prevented UTUC, as well as suppressed Tnf-related inflammatory gene expression in the upper urinary tract despite the exposure to BBN. This is the first report to demonstrate a higher incidence of UTUC than BC in a non-engineered mouse model using BBN. Overall, this model could serve as a useful tool for comprehensively investigating UTUC in future studies.},
}

@article {pmid39692728,
year = {2024},
author = {Fiorito, G and Tosti, V and Polidoro, S and Bertozzi, B and Veronese, N and Cava, E and Spelta, F and Piccio, L and Early, DS and Raftery, D and Vineis, P and Fontana, L},
title = {Multi-omic analysis of biological aging biomarkers in long-term calorie restriction and endurance exercise practitioners: A cross-sectional study.},
journal = {Aging cell},
volume = {},
number = {},
pages = {e14442},
doi = {10.1111/acel.14442},
pmid = {39692728},
issn = {1474-9726},
support = {//Australian Youth and Health Foundation/ ; APP1177797//Australian NHMRC Investigator Grant/ ; //Bakewell Foundation/ ; },
abstract = {Calorie restriction (CR) and physical exercise (EX) are well-established interventions known to extend health span and lifespan in animal models. However, their impact on human biological aging remains unclear. With recent advances in omics technologies and biological age (BioAge) metrics, it is now possible to assess the impact of these lifestyle interventions without the need for long-term follow-up. This study compared BioAge biomarkers in 41 middle-aged and older adult long-term CR practitioners, 41 age- and sex-matched endurance athletes (EX), and 35 sedentary controls consuming Western diets (WD), through PhenoAge: a composite score derived from nine blood-biomarkers. Additionally, a subset of participants (12 CR, 11 EX, and 12 WD) underwent multi-omic profiling, including DNA methylation and RNAseq of colon mucosa, blood metabolomics, and stool metagenomics. A group of six young WD subjects (yWD) served as a reference for BioAge calculation using Mahalanobis distance across six omic layers. The results demonstrated consistently lower BioAge biomarkers in both CR and EX groups compared to WD controls across all layers. CR participants exhibited lower BioAge in gut microbiome and blood-derived omics, while EX participants had lower BioAge in colon mucosa-derived epigenetic and transcriptomic markers, suggesting potential tissue-specific effects. Multi-omic pathway enrichment analyses suggested both shared and intervention-specific mechanisms, including oxidative stress and basal transcription as common pathways, with ether lipid metabolism uniquely enriched in CR. Despite limitations due to sample size, these findings contribute to the broader understanding of the potential anti-aging effects of CR and EX, offering promising directions for further research.},
}

@article {pmid39692706,
year = {2024},
author = {Girão, M and Rego, A and Fonseca, AC and Cao, W and Jia, Z and Urbatzka, R and Leão, PN and Carvalho, MF},
title = {Actinomycetota From Macroalgae as Rich Source for Natural Products Discovery Revealed Through Culture-Dependent and -Independent Approaches.},
journal = {Microbial biotechnology},
volume = {17},
number = {12},
pages = {e70058},
doi = {10.1111/1751-7915.70058},
pmid = {39692706},
issn = {1751-7915},
support = {C644915664-00000026//PRR, The Portuguese Republic and the European Union/ ; UIDB/04423/2020//European Regional Development Fund/ ; CEECIND/02968/2017//Fundação para a Ciência e a Tecnologia/ ; FRH/BD/145646/2019//Fundação para a Ciência e a Tecnologia/ ; },
mesh = {*Seaweed/microbiology ; *Biological Products/metabolism/pharmacology ; *Actinobacteria/genetics/metabolism/classification/isolation & purification ; Animals ; Portugal ; Cell Survival/drug effects ; Bioprospecting ; Zebrafish/microbiology ; Anti-Infective Agents/metabolism/pharmacology ; Humans ; Metagenomics ; },
abstract = {Actinomycetota are unrivalled producers of bioactive natural products, with strains living in association with macroalgae representing a prolific-yet largely unexplored-source of specialised chemicals. In this work, we have investigated the bioactive potential of Actinomycetota from macroalgae through culture-dependent and -independent approaches. A bioprospecting pipeline was applied to a collection of 380 actinobacterial strains, recovered from two macroalgae species collected in the Portuguese northern shore-Codium tomentosum and Chondrus crispus-in order to explore their ability to produce antibacterial, antifungal, anticancer and lipid-reducing compounds. Around 43% of the crude extracts showed activity in at least one of the screenings performed: 111 presented antimicrobial activity at 1 mg/mL, 83 significantly decreased cancer cells viability at 15 μg/mL and 5 reduced lipid content in zebrafish > 60% at 15 ug/mL. Dereplication of active extracts unveiled the presence of compounds that could explain most of the recorded results, but also unknown molecules in the metabolome of several strains, highlighting the opportunity for discovery. The bioactive potential of the actinobacterial community from the same macroalgae specimens, which served as the source for the aforementioned Actinomycetota collection, was also explored through metagenomics analysis, allowing to obtain a broader picture of its functional diversity and novelty. A total of 133 biosynthetic gene clusters recovered from metagenomic contigs and metagenome assembled genomes (MAGs). These were grouped into 91 gene cluster families, 83 of which shared less than 30% of similarity to database entries. Our findings provided by culture-dependent and -independent approaches underscore the potential held by actinomycetes from macroalgae as reservoirs for novel bioactive natural products.},
}

*Seaweed/microbiology
*Biological Products/metabolism/pharmacology
*Actinobacteria/genetics/metabolism/classification/isolation & purification
Animals
Portugal
Cell Survival/drug effects
Bioprospecting
Zebrafish/microbiology
Anti-Infective Agents/metabolism/pharmacology
Humans
Metagenomics

@article {pmid39692191,
year = {2024},
author = {Zou, X and Yan, M and Wang, Y and Ni, Y and Zhao, J and Lu, B and Liu, B and Cao, B},
title = {Accurate Diagnosis of Lower Respiratory Infections Using Host Response and Respiratory Microbiome from a Single Metatranscriptome Test of Bronchoalveolar Lavage Fluid.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e2405087},
doi = {10.1002/advs.202405087},
pmid = {39692191},
issn = {2198-3844},
support = {2022YFA1304300//National Key R&D Program of China grant/ ; ZRJY2023-GG24//China-Japan Friendship Hospital elite program grant/ ; },
abstract = {Lower respiratory tract infections (LRTIs) diagnosis is challenging because noninfectious diseases mimic its clinical features. The altered host response and respiratory microbiome following LRTIs have the potential to differentiate LRTIs from noninfectious respiratory diseases (non-LRTIs). Patients suspected of having LRTIs are retrospectively enrolled and a clinical metatranscriptome test is performed on bronchoalveolar lavage fluid (BALF). Transcriptomic and metagenomic analysis profiled the host response and respiratory microbiome in patients with confirmed LRTI (n = 126) or non-LRTIs (n = 75). Patients with evidenced LRTIs exhibited enhanced pathways on chemokine and cytokine response, neutrophile recruitment and activation, along with specific gene modules linked to LRTIs status and key blood markers. Moreover, LRTIs patients exhibited reduced diversity and evenness in the lower respiratory microbiome, likely driven by an increased abundance of bacterial pathogens. Host marker genes are selected, and classifiers are developed to distinguish patients with LRTIs, non-LRTIs, and indeterminate status, achieving an area under the receiver operating characteristic curve of 0.80 to 0.86 and validated in a subsequently enrolled cohort. Incorporating respiratory microbiome features further enhanced the classifier's performance. In summary, a single metatranscriptome test of BALF proved detailed profiles of host response and respiratory microbiome, enabling accurate LRTIs diagnosis.},
}

@article {pmid39692041,
year = {2024},
author = {Yang, Z and Zhang, Z and Jiang, S and Li, A and Song, H and Zhang, J},
title = {Diet shapes and maintains the personalized native gut microbiomes in mice.},
journal = {Journal of the science of food and agriculture},
volume = {},
number = {},
pages = {},
doi = {10.1002/jsfa.14073},
pmid = {39692041},
issn = {1097-0010},
support = {//National Natural Science Foundation of China (No. 32222066 and No. 32160545)/ ; },
abstract = {BACKGROUND: The gut microbiome plays a critical role in human health and disease. Different dietary backgrounds play an important role in the uniqueness and diversity of the gut microbiota in different individuals, which promotes heterogeneity in disease phenotypes and treatment responses. Here, we explored how diet affects the composition and function of the native gut microbiome of model mice, based on the shotgun metagenomic and metabolomic, by analyzing the gut microbiome of C57B/6J mice in different dietary backgrounds.

RESULTS: The gut microbiomes of mice receiving different diets consistently exhibit distinct compositions across bacterial species, strains, fungi and phages. This implies that native microbial communities cannot 'homogenize' rapidly becaise of priority effects and unchanging diets. Notably, hotspot bacteria such as Limosilactobacillus reuteri, Parabacteroides distasonis and Akkermansia muciniphila were significantly different among the groups. These species harbor diverse adaptive mutations, reflecting genomic evolutionary diversity. The functional profiles of the gut microbiota also exhibit selective differences, involving the capacity for carbohydrate, branched-chain amino acid and fatty acid synthesis, as well as virulence factors, carbohydrate-active enzymes and antibiotic resistance. Furthermore, the differences in the gut microbiota also propagate to the host's serum, where structural and specific metabolite differences were observed. Metabolites that directly impact host health, such as d-glucosamine 6-phosphate and testolic acid, also show significant differences between the different dietary groups.

CONCLUSION: Our findings underscore the profound influence of different dietary the composition and functionality of the gut microbiome, offering valuable insights into optimizing health outcomes through personalized nutritional interventions. © 2024 Society of Chemical Industry.},
}

@article {pmid39691696,
year = {2024},
author = {Klvanova, E and Videnska, P and Barton, V and Bohm, J and Splichalova, P and Koksova, V and Urik, M and Lanickova, B and Prokes, R and Budinska, E and Klanova, J and Borilova Linhartova, P},
title = {Resistome in the indoor dust samples from workplaces and households: a pilot study.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1484100},
doi = {10.3389/fcimb.2024.1484100},
pmid = {39691696},
issn = {2235-2988},
mesh = {*Dust/analysis ; Pilot Projects ; *Workplace ; Humans ; Air Pollution, Indoor ; Bacteria/genetics/isolation & purification/drug effects/classification ; Family Characteristics ; Anti-Bacterial Agents/pharmacology ; Genes, Bacterial/genetics ; Air Microbiology ; Metagenome ; High-Throughput Nucleotide Sequencing ; Drug Resistance, Bacterial/genetics ; Real-Time Polymerase Chain Reaction ; },
abstract = {The antibiotic resistance genes (ARGs) limit the susceptibility of bacteria to antimicrobials, representing a problem of high importance. Current research on the presence of ARGs in microorganisms focuses mainly on humans, livestock, hospitals, or wastewater. However, the spectrum of ARGs in the dust resistome in workplaces and households has gone relatively unexplored. This pilot study aimed to analyze resistome in indoor dust samples from participants' workplaces (a pediatric hospital, a maternity hospital, and a research center) and households and compare two different approaches to the ARGs analysis; high-throughput quantitative PCR (HT-qPCR) and whole metagenome shotgun sequencing (WMGS). In total, 143 ARGs were detected using HT-qPCR, with ARGs associated with the macrolides, lincosamides, and streptogramin B (MLSB) phenotype being the most abundant, followed by MDR (multi-drug resistance) genes, and genes conferring resistance to aminoglycosides. A higher overall relative quantity of ARGs was observed in indoor dust samples from workplaces than from households, with the pediatric hospital being associated with the highest relative quantity of ARGs. WMGS analysis revealed 36 ARGs, of which five were detected by both HT-qPCR and WMGS techniques. Accordingly, the efficacy of the WMGS approach to detect ARGs was lower than that of HT-qPCR. In summary, our pilot data revealed that indoor dust in buildings where people spend most of their time (workplaces, households) can be a significant source of antimicrobial-resistant microorganisms, which may potentially pose a health risk to both humans and animals.},
}

*Dust/analysis
Pilot Projects
*Workplace
Humans
Air Pollution, Indoor
Bacteria/genetics/isolation & purification/drug effects/classification
Family Characteristics
Anti-Bacterial Agents/pharmacology
Genes, Bacterial/genetics
Air Microbiology
Metagenome
High-Throughput Nucleotide Sequencing
Drug Resistance, Bacterial/genetics
Real-Time Polymerase Chain Reaction

@article {pmid39691688,
year = {2024},
author = {Ericson, U and Hellstrand, S and Larsson, A and Miari, M and Sayols-Baixeras, S and Dekkers, KF and Bergström, G and Malinovschi, A and Engström, G and Ärnlöv, J and Fall, T and Orho-Melander, M},
title = {A Swedish dietary guideline index, gut microbial α-diversity and prevalence of metabolic syndrome - observations in the Swedish CArdioPulmonary bioImage Study (SCAPIS).},
journal = {Food & nutrition research},
volume = {68},
number = {},
pages = {},
doi = {10.29219/fnr.v68.10547},
pmid = {39691688},
issn = {1654-661X},
abstract = {BACKGROUND: Metabolic syndrome (MetS) is characterized by coexisting risk factors for type 2 diabetes and cardiovascular disease. Diet is of importance in their aetiology, and gut microbiota (GM) may constitute a link between diet and metabolic health. Understanding the interplay between diet and GM could contribute novel insights for future dietary guidelines, and aid in preventive actions to motivate adherence to dietary guidelines.

OBJECTIVE: We intended to create a Swedish dietary guideline index (SweDGI) measuring adherence to 12 Swedish dietary guidelines and examine whether SweDGI and its components are associated with GM α-diversity (Shannon index) and prevalent MetS, and if the association between the Shannon index and MetS differs depending on SweDGI.

DESIGN: SweDGI was based on food-frequency data assessed 2014-2018 in 10,396 diabetes-free participants from the Malmö and Uppsala-sites of the Swedish CArdioPulmonary bioImage Study (SCAPIS) (50-64 y, 53% women). We estimated the Shannon index from shotgun metagenomic sequencing-data to assess microbial richness and evenness. We used a general linear model to examine cross-sectional SweDGI-Shannon associations and logistic regression for associations with MetS.

RESULTS: Most guidelines were followed by less than half of the participants. Men showed poorer adherence. Higher SweDGI was linked to higher Shannon index (P-trend across five SweDGI-groups = 1.7 × 10[-12]). Most guidelines contributed to this observation. Higher SweDGI and Shannon index were associated with lower MetS-prevalence, where the lowest prevalence was observed among those with both high SweDGI and high Shannon index (odds ratio:0.43; 95% confidence interval:0.35, 0.52). Both the Shannon index and SweDGI were associated with MetS, independently of the level of the other factor (P-interaction = 0.82).

CONCLUSIONS: We created a new index to comprehensively reflect adherence to the Swedish dietary guidelines in sub-cohorts within the large multicentre SCAPIS study. Better adherence was associated with a richer and more even GM and lower prevalence of MetS. The inverse association between the Shannon index and MetS was consistent at different levels of adherence to dietary guidelines.},
}

@article {pmid39691489,
year = {2024},
author = {Maimaiti, Z and Liu, L},
title = {Exploring the Microbial Landscape of Bone and Joint Infections: An Analysis Using 16S rRNA Metagenome Sequencing.},
journal = {Infection and drug resistance},
volume = {17},
number = {},
pages = {5557-5566},
doi = {10.2147/IDR.S482931},
pmid = {39691489},
issn = {1178-6973},
abstract = {BACKGROUND: Bone and joint infections (BJIs) are challenging to diagnose. This study evaluated the utility of 16S rRNA gene sequencing in diagnosing BJIs, comparing it with conventional bacterial culture to explore microbial diversity in orthopedic infections.

METHODS: Thirty patients with BJIs were enrolled from January 2019 to September 2020 at a single orthopedic center. Diagnoses were based on the Musculoskeletal Infection Society standards. DNA extraction, 16S rRNA sequencing, and microbial composition analysis were performed. Conventional bacterial culture results were compared with metagenomics detection, and associations with blood routine and biochemical test factors were analyzed.

RESULTS: The study enrolled 30 patients with BJIs. Traditional bacterial culture successfully identified pathogens in 60% (18/30) of cases, predominantly Staphylococcus aureus. In contrast, 16S rRNA metagenomics sequencing revealed distinct microorganisms in all cases, it unveiled a diverse microbial landscape. The correlation between bacterial culture and metagenomics detection showcased both concordance and discrepancies. Consistency of detection between the two methods showed that metagenomics detection detected the same genus or species in 14 (87.5%) of the 16 samples identified as species by bacterial culture. In nearly half of the patients with negative cultures, pathogenic microorganisms were detected, highlighting the capability of 16S rRNA sequencing to identify microorganisms, even in samples with negative or unidentified culture results. Moreover, no significant correlation was observed between bacterial culture, metagenomics detection and the factors of blood routine and biochemical test.

CONCLUSION: This study deepens our understanding of the microbial complexity in BJIs. While traditional culture methods are cost-effective and practical, 16S rRNA gene sequencing proves valuable for complementary microbial analysis, particularly when traditional methods fail or rapid identification is critical. This emerging diagnostic approach can enhance the accuracy and speed of pathogen identification, enabling more effective interventions in the management of BJIs.},
}

@article {pmid39691431,
year = {2024},
author = {Zhang, J and Tan, S and Lyu, B and Yu, M and Lan, Y and Tang, R and Fan, Z and Guo, P and Shi, L},
title = {Differences in Gut Microbial Composition and Characteristics Among Three Populations of the Bamboo Pitviper (Viridovipera stejnegeri).},
journal = {Ecology and evolution},
volume = {14},
number = {12},
pages = {e70742},
pmid = {39691431},
issn = {2045-7758},
abstract = {The gut microbiota contributes to host health by facilitating nutrient uptake, digestion, energy metabolism, intestinal development, vitamin synthesis, and immunomodulation, and plays an important role in the growth and reproduction of the animal itself. Considering the paucity of research on the gut microbiota of wild snakes, this study focused on bamboo pitviper (Viridovipera stejnegeri) populations from Anhui, Guizhou, and Hunan, with multiple fecal samples collected from each population (six, five, and three, respectively). Total microbial DNA was extracted from the fecal samples using metagenomic next-generation sequencing and differences in gut microbial composition, abundance, and carbohydrate-active enzymes (CAZymes) were analyzed and compared among the three populations. Results showed no significant variance in the α-diversity of the gut microbes across the three populations, while principal coordinate analysis revealed significant differences in gut microbe composition. The four most abundant phyla in the gut microbiota of V. stejnegeri were Pseudomonadota, Bacteroidota, Actinomycetota, and Bacillota, while the four most abundant genera were Salmonella, Citrobacter, Bacteroides, and Yokenella. Linear discriminant analysis effect size demonstrated notable differences in gut microbial abundance among the three populations. Marked differences in CAZyme abundance were also observed across the microbial communities. Future studies should incorporate diverse ecological factors to evaluate their influence on the composition and function of gut microbiota.},
}

@article {pmid39691376,
year = {2024},
author = {Zhang, S and Gao, H and Zhang, G and Fang, M and Kong, Y and Jiang, L and Liu, Q and Wang, P and Liu, Y and Li, Y},
title = {Metavirome analysis of domestic sheep in Shaanxi, Gansu, and Ningxia, China.},
journal = {Frontiers in veterinary science},
volume = {11},
number = {},
pages = {1508617},
doi = {10.3389/fvets.2024.1508617},
pmid = {39691376},
issn = {2297-1769},
abstract = {Sheep play an important role in China's agricultural development, but they are also potential hosts for many viruses, some of which have been identified as zoonotic pathogens, which may pose a serious threat to social public health and animal husbandry. Therefore, clarifying the characteristics of viruses in sheep will provide an important basis for the study of pathogenic ecology and viral evolution of viruses carried by sheep. We collected nasal and anal swabs from 688 sheep in 22 counties in Shaanxi, Gansu, and Ningxia, China, between January 2022 and July 2023, and utilized next-generation sequencing technology and bioinformatics approaches to identify the viruses in the samples. A total of 38 virus families carried by sheep were identified, including 12 ssRNA (+) virus families, 2 dsRNA virus families, 8 ssDNA (+) virus families, and 18 dsDNA virus families. Among them, Astroviridae, Coronaviridae, Picornaviridae, and Tobaniviridae in RNA virus families and Herpesviridae, Adenoviridae, and Circoviridae in DNA virus families are all viruses that are frequently detected in most ruminants. Alpha and beta diversity results showed that there was no difference in the overall richness and diversity of RNA and DNA viruses among the three provinces (p > 0.05). The evolutionary analysis demonstrated a tight link between the viral members carried by sheep and other ruminant viruses, implying that these viruses may spread across different species of ruminants. This study established a library of RNA and DNA viruses carried by sheep in the Shaanxi-Gansu-Ningxia region, providing an overview of the viruses present in this population. The findings offer valuable data for further research on virus evolution and monitoring in sheep.},
}

@article {pmid39691165,
year = {2025},
author = {Bescos, R and du Toit, L and Redondo-Rio, A and Warburton, PJ and Nicholas, TL and Kiernan, M and Burton, RA and Belfield, L and Montagut, G and Benavente, A and Vevers, W and Gabaldón, T and Brookes, Z and Casas-Agustench, P},
title = {The comparative effect of propolis and chlorhexidine mouthwash on oral nitrite-producing bacteria and blood pressure regulation.},
journal = {Journal of oral microbiology},
volume = {17},
number = {1},
pages = {2439636},
doi = {10.1080/20002297.2024.2439636},
pmid = {39691165},
issn = {2000-2297},
abstract = {BACKGROUND: Propolis mouthwash (PROP-M) has demonstrated antibacterial properties like those of chlorhexidine mouthwash (CHX-M). However, its impact on the abundance of oral nitrite-producing species (NPS) and nitrite-producing activity (NPA) remains unexplored.

METHODS: Forty-five healthy individuals were randomised into 2 groups to rinse their mouth twice a day for seven days with either CHX-M (n = 21) or PROP-M (n = 24). Metagenomic sequencing (16S rRNA) was performed on saliva samples collected before and after each treatment. Additionally, salivary biomarkers and blood pressure were measured.

RESULTS: CHX-M increased the relative abundance of NPS (p < 0.001) but significantly impaired the NPA (p < 0.001) compared to baseline and PROP-M. No significant differences in the relative abundance of NPS and NPA were observed in the PROP-M group. However, a significant increase of plasma nitrate (+7 µmol/L, p = 0.047) and a decrease in systolic BP (-2 mmHg, p = 0.022) was observed in this group compared to the baseline.

CONCLUSION: The results indicate that PROP-M had a smaller effect on the abundance of NPS and NPA compared to CHX-M. Additionally, PROP-M reduced blood pressure in healthy individuals, but this effect was not associated with changes in the oral microbiome.},
}

@article {pmid39690531,
year = {2024},
author = {, },
title = {[Expert consensus on the application and practice of targeted next-generation sequencing in infectious diseases].},
journal = {Zhonghua yi xue za zhi},
volume = {104},
number = {48},
pages = {4375-4383},
doi = {10.3760/cma.j.cn112137-20240927-02208},
pmid = {39690531},
issn = {0376-2491},
support = {82341107//National Natural Science Foundation of China/ ; 2022YFA1304300//National Key Research and Development Program of China/ ; },
mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Communicable Diseases/diagnosis ; China ; Consensus ; Metagenomics/methods ; },
abstract = {Targeted next-generation sequencing (tNGS) technology focuses on detecting pathogenic microorganisms and drug-resistant genes in clinical samples by designing specific primers or capture probes, providing evidence for the diagnosis, treatment and surveillance of infectious diseases. However, the current clinical application scenarios of tNGS and metagenomic next-generation sequencing (mNGS) are not clearly defined, and the tNGS systems from different manufacturers vary significantly in quality and results. There is an urgent need for consensus and standards regarding the clinical indications, laboratory processes, quality control, performance validation and interpretation of reports for this technology. In order to standardize the application and practice of tNGS in infectious diseases, experts in the fields of microbiology, infectious disease, respiratory disease, epidemiology and other fields from the Society of Clinical Microbiology of China International Exchange and Promotion Association for Medical and Healthcare discussed the above problems, wrote the expert consensus on the application and practice of tNGS in infectious diseases. This consensus summarizes the research on tNGS in infectious diseases, and proposes recommendations that are in line with clinical practice in China, so as to standardize the application and practice of tNGS in infectious diseases. The main contents include: consensus formulation process, clinical indications, technical points, wet and dry experiments, report and interpretation, and report template.},
}

Humans
*High-Throughput Nucleotide Sequencing/methods
*Communicable Diseases/diagnosis
China
Consensus
Metagenomics/methods

@article {pmid39690119,
year = {2024},
author = {Di Gloria, L and Baldi, S and Curini, L and Bertorello, S and Nannini, G and Cei, F and Niccolai, E and Ramazzotti, M and Amedei, A},
title = {Experimental tests challenge the evidence of a healthy human blood microbiome.},
journal = {The FEBS journal},
volume = {},
number = {},
pages = {},
doi = {10.1111/febs.17362},
pmid = {39690119},
issn = {1742-4658},
support = {//Ministry of University and Research (MUR)/ ; //FONZIE project (CUP B55F21007810001)/ ; //National Recovery and Resilience Plan (NRRP)/ ; },
abstract = {The advent of next-generation sequencing (NGS) technologies has made it possible to investigate microbial communities in various environments, including different sites within the human body. Therefore, the previously established belief of the sterile nature of several body sites, including human blood, has now been challenged. However, metagenomics investigation of areas with an anticipated low microbial biomass may be susceptible to misinterpretation. Here, we critically evaluate the results of 16S targeted amplicon sequencing performed on total DNA collected from healthy donors' blood samples while incorporating specific negative controls aimed at addressing potential bias to supplement and strengthen the research in this area. We prepared negative controls by increasing the initial DNA quantity through sequences that can be recognized and subsequently discarded. We found that only three organisms were sporadically present among the samples, and this was mostly attributable to bacteria ubiquitously present in laboratory reagents. Despite not fully confirming or denying the existence of healthy blood microbiota, our results suggest that living bacteria, or at least their residual DNA sequences, are not a common feature of human blood in healthy people. Finally, our study poses relevant questions on the design of controls in this research area that must be considered in order to avoid misinterpreted results that appear to contaminate current high-throughput research.},
}

@article {pmid39689562,
year = {2024},
author = {Liu, W and Wang, W and Jing, C and Yin, Z and Cai, Y},
title = {Novel arsenate-respiring bacteria drive arsenic biogeochemical cycling in Tibetan geothermal springs revealed by DNA-SIP based metagenomics.},
journal = {Journal of hazardous materials},
volume = {485},
number = {},
pages = {136899},
doi = {10.1016/j.jhazmat.2024.136899},
pmid = {39689562},
issn = {1873-3336},
abstract = {Arsenic (As) is a toxic element posing health risks globally, with geothermal environment as one of the hotspots. Arsenic biotransformation is mainly mediated by microorganisms which often employ diverse metabolic strategies for survival. However, the microorganisms responsible for As cycling and their survival strategies in geothermal environment in Tibet, the Third Pole, remain unclear. To address this knowledge gap, we investigated As biotransformation in representative geothermal springs using DNA-stable isotope probing (DNA-SIP) combined with metagenomic sequencing. As(V) reduction to the more toxic As(III) was found to be prevalent. Pseudomonas and Thermincola were identified as the dominant As(V)-reducing bacteria (AsRB). Metagenome-assembled genomes (MAGs) affiliated with AsRB contained abundant genes encoding As(V)-respiratory reductase (arrA, 1044.34 transcripts per million (TPM)), nitrate reduction pathway (e.g., narG), and Wood-Ljungdahl pathway (e.g., acsA), indicating their role as dissimilatory As(V)-reducing prokaryotes (DARPs) with diverse metabolic strategies. Here, Thermincola's potential of As(V) reduction via arrA and carbon fixation via Wood-Ljungdahl pathway was observed for the first time, which was found to be widespread in various ecosystems. Our study unravels the key players driving As biogeochemical cycle in Tibetan geothermal springs and provides insights into the genetic mechanisms enabling their survival in extreme environments.},
}

@article {pmid39689559,
year = {2024},
author = {Zhang, W and Zong, Y and Zhang, J and Ai, J and He, H and Li, L and Peng, S and Zhou, H and Wang, D and Wang, Q},
title = {Mechanistic insights into the viral microorganism inactivation during lime stabilization for wastewater sludges.},
journal = {Journal of hazardous materials},
volume = {485},
number = {},
pages = {136884},
doi = {10.1016/j.jhazmat.2024.136884},
pmid = {39689559},
issn = {1873-3336},
abstract = {The pathogens inactivation in wastewater sludges is vitally important for safely managing solid wastes and protecting public and environmental health especially in the emergency. Reports have shown the effectiveness of lime to kill virus pathogens in sludges, but mechanism of virus inactivation and related human diseases is unclear. This study evaluated representative limes of CaO/CaO2 on actual viral microorganism inactivation by viral metagenomic sequencing technology. As results, the CaO2 treatment enhanced the sludge hydrolysis and enveloped viral pathogens suppression via EPS structure destruction by oxidative radical generations; while CaO suppressed most of none-enveloped plant related viral pathogens. Most of the viromes of plant virus including Virgaviridae and Nodaviridae were inactivated by CaO, but the human virus-Feirsviridae and plant virus-Solemoviridae were occurred after lime stabilization compared to untreated sludge, with abundances of 1 %-37 % and 21 %-32 % in CaO-treated (CaO-T) and CaO2-treated (CaO2-T) samples, respectively. In addition, metatranscriptome analysis revealed distinct gene expression patterns between the CaO-T and CaO2-T sludges, in which lipopolysaccharide biosynthesis (LPS) and aminoacyl-tRNA synthetases (ARSs) in CaO-T, the formation of ribosome in CaO2-T were crucial to RNA virus regrowth in sludge. These findings suggested neither of CaO and CaO2 could completely suppress pathogens in sludge, and the effect of representative limes of CaO and CaO2 on the viral pathogen diversity, abundance, and metabolic function of the core microbiome on virus suppression and regrowth were ignored. Therefore, combined processes were recommended to provide possible alternatives for sludge safe management in pandemic emergencies.},
}

@article {pmid39689421,
year = {2024},
author = {Tang, XF and Guo, XP and Kuang, L and Chen, XJ and Sidikjan, N and Xu, TT and Jiang, S and Liu, M and Hou, LJ and Yang, Y},
title = {Comammox Nitrospira are the dominant ammonia oxidizers in the Yangtze estuarine biofilms.},
journal = {Water research},
volume = {273},
number = {},
pages = {122969},
doi = {10.1016/j.watres.2024.122969},
pmid = {39689421},
issn = {1879-2448},
abstract = {Biofilms are indispensable ecological habitats for microbes that have garnered global attention and play a potential role in influencing the biogeochemical cycling of nitrogen. However, the biogeochemical significance of biofilms and the mechanisms by which they regulate nitrogen cycling remain elusive. In this study, we utilized DNA-stable isotope probing (DNA-SIP) labelling techniques in conjunction with metagenomics to reveal a nitrifying ecological niche in biofilms taken from the Yangtze Estuary, with those from sediment and water samples for comparison. Quantitative analysis showed that the amoA gene abundance of comammox Nitrospira (2.3 × 10[3] copies ng[-1] DNA) was significantly higher than that of ammonia-oxidizing archaea (AOA-amoA, 62.4 copies ng[-1] DNA) and ammonia-oxidizing bacteria (AOB-amoA, 218.1 copies ng[-1] DNA) in biofilms, and the average abundance of comammox Nitrospira showed the following order: water > biofilm > sediment. Moreover, the NOB nxrB gene was more abundant than the amoA gene of ammonia oxidizers in all three media. DNA-SIP further revealed that the active comammox Nitrospira clade A mediates the nitrification process in biofilms with peak abundance at a buoyant density of 1.715 g mL[-1]. Active nitrifying bacteria exhibit metabolic diversity in both biofilms and sediments, and occupy unique nitrifying ecological niches. Additionally, the co-occurrence network showed that chlorophyll a, NO3[-] and salinity emerged as the predominant physicochemical factors affecting the nitrogen transformation genes in biofilms. Taken together, this study indicates that biofilms constitute an emerging nitrifying ecological niche in estuarine environments and deepens our understanding of the mechanisms by which biofilms function in marine biogeochemistry.},
}

@article {pmid39689125,
year = {2024},
author = {McGowan, J and Richards, TA and Hall, N and Swarbreck, D},
title = {Multiple independent genetic code reassignments of the UAG stop codon in phyllopharyngean ciliates.},
journal = {PLoS genetics},
volume = {20},
number = {12},
pages = {e1011512},
doi = {10.1371/journal.pgen.1011512},
pmid = {39689125},
issn = {1553-7404},
abstract = {The translation of nucleotide sequences into amino acid sequences, governed by the genetic code, is one of the most conserved features of molecular biology. The standard genetic code, which uses 61 sense codons to encode one of the 20 standard amino acids and 3 stop codons (UAA, UAG, and UGA) to terminate translation, is used by most extant organisms. The protistan phylum Ciliophora (the 'ciliates') are the most prominent exception to this norm, exhibiting the grfeatest diversity of nuclear genetic code variants and evidence of repeated changes in the code. In this study, we report the discovery of multiple independent genetic code changes within the Phyllopharyngea class of ciliates. By mining publicly available ciliate genome datasets, we discovered that three ciliate species from the TARA Oceans eukaryotic metagenome dataset use the UAG codon to putatively encode leucine. We identified novel suppressor tRNA genes in two of these genomes which are predicted to decode the reassigned UAG codon to leucine. Phylogenomics analysis revealed that these three uncultivated taxa form a monophyletic lineage within the Phyllopharyngea class. Expanding our analysis by reassembling published phyllopharyngean genome datasets led to the discovery that the UAG codon had also been reassigned to putatively code for glutamine in Hartmannula sinica and Trochilia petrani. Phylogenomics analysis suggests that this occurred via two independent genetic code change events. These data demonstrate that the reassigned UAG codons have widespread usage as sense codons within the phyllopharyngean ciliates. Furthermore, we show that the function of UAA is firmly fixed as the preferred stop codon. These findings shed light on the evolvability of the genetic code in understudied microbial eukaryotes.},
}

@article {pmid39647796,
year = {2024},
author = {Zhu, Y and Zhao, S and Qi, S and Zhang, H and Zhang, X and Li, S and Wang, X and Gu, J and Zhang, T and Xi, H and Liu, X},
title = {Effects of energetic compounds on soil microbial communities and functional genes at a typical ammunition demolition site.},
journal = {Chemosphere},
volume = {370},
number = {},
pages = {143913},
doi = {10.1016/j.chemosphere.2024.143913},
pmid = {39647796},
issn = {1879-1298},
abstract = {High concentrations of energetic compounds such as 2,4,6-trinitrotoluene (TNT), hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX), and octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX) in military-contaminated sites pose a serious threat to human health and ecosystems. Better understanding about their effects on microbial diversity and functional genes in soil of ammunition demolition sites is required. In this study, the information of soil microbial community composition was obtained by metagenomic sequencing, and the impacts of energetic compounds on microbial community structure at the level of functional genes and enzymes based on Nr (Non-Redundant Protein Sequence Database), KEGG (Kyoto Encyclopedia of Genes and Genomes), CAZy (Carbohydrate-Active enZymes Database) and other databases were discussed. The results showed that soil microbial diversity and functional gene abundance decreased significantly with the increase of the concentrations of energetic compounds. Conversely, the relative abundance of Proteobacteria increased significantly, reaching over 80% in the heavily TNT-contaminated area near explosive-wastewater pool. Furthermore, functional gene analysis indicated that Proteobacteria had an advantage in degrading energetic compounds, and thus had the potential to improve the soil quality at ammunition demolition sites. This study provides a scientific basis for the future remediation and management of contaminated soils at ammunition demolition sites, as well as for the selection of efficient degraders of energetic compounds.},
}

@article {pmid39688845,
year = {2024},
author = {Oteo-García, G and Mutti, G and Caldon, M and Oosthuitzen, O and ManfrediniK, M and Capelli, C},
title = {Reconstructing micro-evolutionary dynamics shaping local variation in southern African populations using genomics, metagenomics and personal metadata.},
journal = {Journal of anthropological sciences = Rivista di antropologia : JASS},
volume = {102},
number = {},
pages = {},
doi = {10.4436/JASS.10204},
pmid = {39688845},
issn = {2037-0644},
abstract = {Geography is a well-known factor shaping genetic variation in human populations. However, the potential role played by cultural variables remains much understudied. This study investigates the impact of socio-cultural variables on genomic similarity and the saliva microbiome, using data from populations in Lesotho and Namibia. Geographic distance within Lesotho increases genetic differentiation, while shared clan affiliation surprisingly increases it. In Namibia, ethnicity is the predominant factor influencing genetic affinity. Saliva metagenomic data shows a negative correlation between age and alpha diversity, with notable differences in host-interacting taxa and viral load. These findings highlight the role of geography in shaping genetic affinity even at small scales and the complex influences of cultural factors. The saliva microbiome appears primarily affected by unrecorded individual behaviors rather than geographic or cultural variables. At population-level these oral microbiomes reveal insights into some dietary habits, oral health, and also the communal viral load, which appears to have greater incidence in Lesotho possibly related to the long-term effects of the HIV epidemic in the country.},
}

@article {pmid39688758,
year = {2024},
author = {Řezanka, P and Řezanka, M and Kyselová, L and Řezanka, T},
title = {Characterization of Archaea membrane lipids in radioactive springs using shotgun lipidomics.},
journal = {Folia microbiologica},
volume = {},
number = {},
pages = {},
pmid = {39688758},
issn = {1874-9356},
support = {MZE-RO1923//Ministerstvo Zemědělství/ ; RVO61388971//Mikrobiologický Ústav, Akademie Věd České Republiky/ ; },
abstract = {Lipids from microorganisms, and especially lipids from Archaea, are used as taxonomic markers. Unfortunately, knowledge is very limited due to the uncultivability of most Archaea, which greatly reduces the importance of the diversity of lipids and their ecological role. One possible solution is to use lipidomic analysis. Six radioactive sources were investigated, two of which are surface (Wettinquelle and Radonka) and four deep from the Svornost mine (Agricola, Behounek, C1, and Curie). A total of 15 core lipids and 82 intact polar lipids were identified from the membranes of microorganisms in six radioactive springs. Using shotgun lipidomics, typical Archaea lipids were identified in spring water, namely dialkyl glycerol tetraethers, archaeol, hydroxyarchaeol and dihydroxyarchaeol. Diverse groups of polar heads were formed in archaeal IPLs, whose polar heads are formed mainly by hexose, deoxyhexose, and phosphoglycerol. The analysis was performed using shotgun lipidomics and the structure of all molecular species was confirmed by tandem mass spectrometry. After acid hydrolysis, a mixture of polar compounds was obtained from the polar head. Further analysis by GC-MS confirmed that the carbohydrates were glucose and rhamnose. Analysis by HPLC-MS of diastereoisomers of 2-(polyhydroxyalkyl)-3-(O-tolylthiocarbamoyl)thiazolidine-4(R)-carboxylates revealed that both L-rhamnose and D-glucose are present in spring samples only in varying amounts. The glycoside composition depends on the type of spring, that is, Wettinquelle and Radonka springs are basically shallow groundwater, while the samples from the Svornost mine are deep groundwater and do not contain glycosides with rhamnose. This method enables quick screening for characteristic Archaea lipids, allowing decisions on whether to pursue further analyses, such as metagenomic analysis, to directly confirm the presence of Archaea.},
}

@article {pmid39688617,
year = {2024},
author = {Zhao, Y and Mao, R and Zhong, Y and Lu, J and Gong, B and Yi, W and Zeng, Z},
title = {Application of metagenomic next-generation sequencing in pathogen detection for patients with lower respiratory tract infections caused by multidrug-resistant organisms and analysis of related factors.},
journal = {Acta microbiologica et immunologica Hungarica},
volume = {},
number = {},
pages = {},
doi = {10.1556/030.2024.02463},
pmid = {39688617},
issn = {1588-2640},
abstract = {The incidence of lower respiratory tract infections (LRTIs) caused by multidrug-resistant organisms (MDRO) has been high in recent years. However, traditional etiological detection methods have not been able to meet the needs for clinical diagnosis and prognosis of LRTIs. The rapid development of metagenomic next-generation sequencing (mNGS) provides new insights for diagnosis and treatment of LRTIs. We conducted a retrospective study on 95 patients with lower respiratory tract infections caused by MDRO admitted to our respiratory department from January 2022 to December 2023. These patients underwent mNGS testing and conventional culture testing. Additionally, 150 patients without lower respiratory tract infections caused by MDRO during the same period were included as the non-MDRO group. General information was collected, and Logistic regression analysis was performed to identify risk factors for MDRO infections in patients with lower respiratory tract infections. Our results show that the time to pathogen detection by mNGS was 50.76 ± 1.730 h, that is significantly shorter than 55.53 ± 2.782 h required for conventional culture testing. The pathogen detection rate by mNGS was 89.47% (85/95), higher than the 67.37% (64/95) identified by conventional testing. In terms of pathogen genus distribution, mNGS detected a total of 279 pathogens, while conventional testing detected 121 pathogens. Logistic multivariate regression analysis identified that the use of more than two antibiotics, invasive procedures, invasive mechanical ventilation for ≥7 days, and stay in the respiratory intensive care unit (RICU) for ≥7 days were the main influencing factors for lower respiratory tract infections caused by MDRO (P < 0.05).},
}

@article {pmid39687173,
year = {2024},
author = {Yang, Q and Zhou, K and Shen, Y and Huang, R and Liu, L and Liao, S},
title = {A case report of successful treatment of pulmonary mucormycosis caused by Cunninghamella bertholletiae infection in a patient with T-lymphoblastic lymphoma.},
journal = {Heliyon},
volume = {10},
number = {23},
pages = {e36244},
doi = {10.1016/j.heliyon.2024.e36244},
pmid = {39687173},
issn = {2405-8440},
abstract = {Mucormycosis caused by Cunninghamella bertholletiae (C. bertholletiae) is a rare opportunistic infection in patients with hematological malignancies (HM), with high mortality rates. Herein, we first report a case of pulmonary mucormycosis (PM) with C. bertholletiae in a 25-year-old male recently diagnosed with T-lymphoblastic lymphoma (T-LBL). The diagnosis was established through chest computed tomography (CT), metagenomic next-generation sequencing (mNGS) of blood and bronchoalveolar lavage fluid (BALF), as well as histopathological examination. Hematoxylin and eosin (HE) staining of the surgical specimen revealed the presence of fungal hyphae. He was effectively treated with liposomal amphotericin B (L-AmB) and posaconazole enteric-coated tablets, followed by aggressive surgical debridement. In our case, the fungal infection was initially identified as C. bertholletiae using mNGS, which facilitated rapid and accurate diagnosis, enabling clinicians to initiate early intensive treatment. The case also emphasizes the importance of surgical debridement in addressing affected tissues and underscores the significance of a multidisciplinary approach in implementing this treatment strategy.},
}

@article {pmid39686449,
year = {2024},
author = {Luo, A and Li, C and Zhao, J and Wu, Y and Fu, R},
title = {Severe Epstein-Barr virus encephalitis with peripheral nerve damage: A case report.},
journal = {Medicine},
volume = {103},
number = {50},
pages = {e40804},
doi = {10.1097/MD.0000000000040804},
pmid = {39686449},
issn = {1536-5964},
mesh = {Humans ; Female ; Middle Aged ; *Epstein-Barr Virus Infections/complications/diagnosis ; *Encephalitis, Viral/diagnosis/virology ; Antiviral Agents/therapeutic use ; Herpesvirus 4, Human/genetics ; Peripheral Nervous System Diseases/virology/etiology/diagnosis ; Magnetic Resonance Imaging ; },
abstract = {RATIONALE: Epstein-Barr virus (EBV) is a B-lymphotropic double-stranded DNA virus. Most people infected with EBV are asymptomatic infection. Its clinical symptoms are rarely manifested as EBV encephalitis, and peripheral nerve damage is even rarer.

PATIENT CONCERNS: We report a case of a 49-year-old woman with a history of fever. The initial symptoms were numbness and weakness in the right hand, followed by slurred speech. Electromyography showed severe damage to the median nerve of the right wrist (involving sensory and motor fibers). Magnetic resonance imaging revealed multiple lesions in the bilateral cerebral hemispheres on T2 FLAIR images, and T1-enhanced images showed abnormal enhancement of the adjacent leptomeninges. Human herpesvirus 4 (EBV) has been detected in the cerebrospinal fluid using metagenomic next-generation sequencing (NGS). After antiviral treatment, the patient's symptoms continued to worsen.

DIAGNOSIS: Severe EBV encephalitis complicated with peripheral nerve damage.

INTERVENTIONS: Antiviral, hormone therapy.

OUTCOMES: At the patient's condition progressed, a new infarction occurred in the right frontal lobe lesion, with repeated high fever, rapid deterioration of multiple organ function, sudden respiratory failure, cardiac arrest, and death.

LESSONS: In patients with signs of encephalitis, cerebrospinal fluid NGS should be used as early as possible to confirm the diagnosis of EBV encephalitis. Timely and accurate treatment of central nervous system infections is expected to reduce the mortality rate and improve the quality of life of patients in later stages.},
}

Humans
Female
Middle Aged
*Epstein-Barr Virus Infections/complications/diagnosis
*Encephalitis, Viral/diagnosis/virology
Antiviral Agents/therapeutic use
Herpesvirus 4, Human/genetics
Peripheral Nervous System Diseases/virology/etiology/diagnosis
Magnetic Resonance Imaging

@article {pmid39684893,
year = {2024},
author = {Parkar, N and Young, W and Olson, T and Hurst, C and Janssen, P and Spencer, NJ and McNabb, WC and Dalziel, JE},
title = {Peripherally Restricted Activation of Opioid Receptors Influences Anxiety-Related Behaviour and Alters Brain Gene Expression in a Sex-Specific Manner.},
journal = {International journal of molecular sciences},
volume = {25},
number = {23},
pages = {},
doi = {10.3390/ijms252313183},
pmid = {39684893},
issn = {1422-0067},
support = {C10X1706//Ministry of Business, Innovation and Employment/ ; },
mesh = {Animals ; Male ; Female ; *Anxiety/metabolism ; Rats ; *Loperamide/pharmacology ; *Brain/metabolism/drug effects ; *Rats, Sprague-Dawley ; *Receptors, Opioid/metabolism/genetics ; Behavior, Animal/drug effects ; Gastrointestinal Microbiome/drug effects ; Hippocampus/metabolism/drug effects ; Enteric Nervous System/metabolism ; Gene Expression Regulation/drug effects ; Sex Factors ; Sex Characteristics ; },
abstract = {Although effects of stress-induced anxiety on the gastrointestinal tract and enteric nervous system (ENS) are well studied, how ENS dysfunction impacts behaviour is not well understood. We investigated whether ENS modulation alters anxiety-related behaviour in rats. We used loperamide, a potent μ-opioid receptor agonist that does not cross the blood-brain barrier, to manipulate ENS function and assess changes in behaviour, gut and brain gene expression, and microbiota profile. Sprague Dawley (male/female) rats were acutely dosed with loperamide (subcutaneous) or control solution, and their behavioural phenotype was examined using open field and elevated plus maze tests. Gene expression in the proximal colon, prefrontal cortex, hippocampus, and amygdala was assessed by RNA-seq and caecal microbiota composition determined by shotgun metagenome sequencing. In female rats, loperamide treatment decreased distance moved and frequency of supported rearing, indicating decreased exploratory behaviour and increased anxiety, which was associated with altered hippocampal gene expression. Loperamide altered proximal colon gene expression and microbiome composition in both male and female rats. Our results demonstrate the importance of the ENS for communication between gut and brain for normo-anxious states in female rats and implicate corticotropin-releasing hormone and gamma-aminobutyric acid gene signalling pathways in the hippocampus. This study also sheds light on sexually dimorphic communication between the gut and the brain. Microbiome and colonic gene expression changes likely reflect localised effects of loperamide related to gut dysmotility. These results suggest possible ENS pharmacological targets to alter gut to brain signalling for modulating mood.},
}

Animals
Male
Female
*Anxiety/metabolism
Rats
*Loperamide/pharmacology
*Brain/metabolism/drug effects
*Rats, Sprague-Dawley
*Receptors, Opioid/metabolism/genetics
Behavior, Animal/drug effects
Gastrointestinal Microbiome/drug effects
Hippocampus/metabolism/drug effects
Enteric Nervous System/metabolism
Gene Expression Regulation/drug effects
Sex Factors
Sex Characteristics

@article {pmid39684853,
year = {2024},
author = {Tynior, W and Kłósek, M and Salatino, S and Cuber, P and Hudy, D and Nałęcz, D and Chan, YT and Gustave, C and Strzelczyk, JK},
title = {Metagenomic Analysis of the Buccal Microbiome by Nanopore Sequencing Reveals Structural Differences in the Microbiome of a Patient with Molar Incisor Hypomineralization (MIH) Compared to a Healthy Child-Case Study.},
journal = {International journal of molecular sciences},
volume = {25},
number = {23},
pages = {},
doi = {10.3390/ijms252313143},
pmid = {39684853},
issn = {1422-0067},
support = {PCN-1-111/N/2/O//Medical University of Silesia/ ; },
mesh = {Humans ; *Microbiota/genetics ; *Metagenomics/methods ; *Nanopore Sequencing/methods ; *Dental Enamel Hypoplasia/microbiology/genetics ; Child ; Mouth Mucosa/microbiology/pathology ; Male ; Female ; Bacteria/genetics/classification/isolation & purification ; Case-Control Studies ; Metagenome ; Incisor/microbiology ; Molar Hypomineralization ; },
abstract = {Molar incisor hypomineralization (MIH) is a qualitative developmental defect that affects the enamel tissue of permanent molars and can also occur in permanent incisors. Enamel affected by MIH has reduced hardness, increased porosity, and a higher organic content than unaffected enamel. These characteristics predispose the enamel to accumulation of bacteria and a higher prevalence of caries lesions. Through a groundbreaking metagenomic analysis of the buccal mucosal sample from a patient with MIH, we explored the intricacies of its microbiome compared to a healthy control using state-of-the-art nanopore long-read sequencing. Out of the 210 bacterial taxa identified in the MIH microbiome, we found Streptococcus and Haemophilus to be the most abundant genera. The bacteria with the highest read counts in the patient with MIH included Streptococcus mitis, Haemophilus parainfluenzae, Streptococcus pneumoniae, Rothia dentocariosa, and Gemella haemolysans. Our results revealed a striking contrast between healthy and MIH affected children, with a higher dominance and number of pathogenic species (S. pneumoniae, H. influenzae, and N. meningitidis) and reduced diversity in the MIH-affected patient. This distinct microbial profile not only sheds light on MIH-affected patients, but paves the way for future research, inspiring deeper understanding and larger scale studies.},
}

Humans
*Microbiota/genetics
*Metagenomics/methods
*Nanopore Sequencing/methods
*Dental Enamel Hypoplasia/microbiology/genetics
Child
Mouth Mucosa/microbiology/pathology
Male
Female
Bacteria/genetics/classification/isolation & purification
Case-Control Studies
Metagenome
Incisor/microbiology
Molar Hypomineralization

@article {pmid39684830,
year = {2024},
author = {Mansour, O and Fadeev, AV and Perederiy, AA and Danilenko, DM and Lioznov, DA and Komissarov, AB},
title = {Development of Primer Panels for Amplicon Sequencing of Human Parainfluenza Viruses Type 1 and 2.},
journal = {International journal of molecular sciences},
volume = {25},
number = {23},
pages = {},
doi = {10.3390/ijms252313119},
pmid = {39684830},
issn = {1422-0067},
support = {TVKQ-2024-0003 "Complex approach to genetic characterization and early identifications of pathogens with epidemic and pandemic potential using metagenomic sequencing"//Ministry of Health of the Russian Federation/ ; },
mesh = {Humans ; *Parainfluenza Virus 1, Human/genetics/isolation & purification ; *Phylogeny ; *Genome, Viral ; *Parainfluenza Virus 2, Human/genetics/isolation & purification ; Russia ; DNA Primers/genetics ; RNA, Viral/genetics ; },
abstract = {Human parainfluenza viruses (hPIVs) are major contributors to respiratory tract infections in young children worldwide. Despite their global significance, genomic surveillance of hPIV1 and hPIV2 had not previously been conducted in Russia. This study aimed to develop a robust amplicon-based sequencing protocol for these viruses. The designed primer sets were tested on clinical samples containing hPIV RNA to evaluate their performance and efficiency. Sequencing results demonstrated high-quality genome data and efficient amplification across various Ct values. As a result, 41 hPIV1 and 13 hPIV2 near-complete genome sequences were successfully obtained from clinical specimens collected in Saint Petersburg (Russia). Phylogenetic analysis of the HN gene sequences showed that Russian hPIV1 strains clustered into clades II and III, while hPIV2 strains were distributed between clusters G1a and G3. The whole-genome-based trees confirmed the same distribution of the strains. These findings highlight the potential of our primer panels and contribute to a better understanding of the molecular characteristics and phylogenetic diversity of circulating hPIV strains. Notably, this study presents the first evolutionary analysis of hPIVs in Russia.},
}

Humans
*Parainfluenza Virus 1, Human/genetics/isolation & purification
*Phylogeny
*Genome, Viral
*Parainfluenza Virus 2, Human/genetics/isolation & purification
Russia
DNA Primers/genetics
RNA, Viral/genetics

@article {pmid39684458,
year = {2024},
author = {Salini, A and Zuliani, L and Gonnelli, PM and Orlando, M and Odoardo, A and Ragno, D and Aulitto, M and Zaccone, C and Fusco, S},
title = {Plastic-Degrading Microbial Consortia from a Wastewater Treatment Plant.},
journal = {International journal of molecular sciences},
volume = {25},
number = {23},
pages = {},
doi = {10.3390/ijms252312747},
pmid = {39684458},
issn = {1422-0067},
support = {CUP B53D23015130001//MUR - Italian Ministry of University and Research in the framework of the Next Generation EU action/ ; },
mesh = {*Microbial Consortia ; *Wastewater/microbiology ; *Biodegradation, Environmental ; Sewage/microbiology ; Plastics/metabolism ; Bacteria/metabolism/classification/genetics/isolation & purification ; Microbiota ; },
abstract = {Plastic waste pollution has become a global crisis, with millions of tons of plastic expected to accumulate in landfills and in natural environments, posing a serious threat to wildlife and human health. As current recycling methods remain inefficient, there is an urgent need for innovative enzymatic solutions to break down plastics and enable a circular economy approach. In this study, we explore the plastic-degrading potential of microorganisms enriched from activated sludge (AS) sourced from a municipal wastewater treatment plant (WWTP)-a known microplastic-contaminated industrial niche. Five microbial consortia (i.e., microbiomes) were enriched under selective pressure using low-carbon conditions and high concentrations of polyester polymers, including post-consumer PET, post-consumer PLA, and virgin PLA. Enrichment was performed for 100 days at 37 °C and 50 °C, followed by microbiomes isolation and metagenomic analysis to identify plastic-active bacteria and their enzymes. The results revealed that PLA polymers, but not post-consumer PET, were effectively degraded by the microbiomes, as confirmed by nuclear magnetic resonance (NMR) and gel permeation chromatography (GPC), showing significant molecular weight reduction compared to the abiotic controls. Microbial community analysis highlighted a distinct enrichment profile driven by the polymer composition and the temperature. At 50 °C, the Bacillales order became the predominant population, whereas at 37 °C, a more diverse community within the Proteobacteria and Actinobacteria phyla were selected. Nonetheless, the enriched microbial communities at both temperatures included phyla with members known for polyester degradation. Moreover, at 50 °C, enrichment of putative PET/PLA hydrolases was also observed. These findings suggest that AS microorganisms are a reservoir of polyester-active enzymes, particularly PLA-depolymerases, and hold promise for advancing biotechnological strategies to mitigate plastic pollution through re- and up-cycling.},
}

*Microbial Consortia
*Wastewater/microbiology
*Biodegradation, Environmental
Sewage/microbiology
Plastics/metabolism
Bacteria/metabolism/classification/genetics/isolation & purification
Microbiota

@article {pmid39684246,
year = {2024},
author = {Domínguez-Pino, M and Mellado, S and Cuesta, CM and Grillo-Risco, R and García-García, F and Pascual, M},
title = {Metagenomics Reveals Sex-Based Differences in Murine Fecal Microbiota Profiles Induced by Chronic Alcohol Consumption.},
journal = {International journal of molecular sciences},
volume = {25},
number = {23},
pages = {},
doi = {10.3390/ijms252312534},
pmid = {39684246},
issn = {1422-0067},
support = {2023-I024//the Spanish Ministry of Health-PNSD/ ; CIAICO/2021/203//GVA/ ; RD21/0009/0005//the Primary Addiction Care Research Network/ ; pro-ject IMPaCT-Data, exp. IMP/00019//FGG and RGR were supported by and partially funded by the Institute of Health Carlos III/ ; PID2023-146865OB-I00 and PID2021-124430OA-I00//MCIN/AEI/10.13039/501100011033/ FEDER/ ; },
mesh = {Animals ; Female ; Male ; *Feces/microbiology ; Mice ; *Gastrointestinal Microbiome/drug effects ; *Toll-Like Receptor 4/genetics/metabolism ; *Metagenomics/methods ; *Mice, Knockout ; *RNA, Ribosomal, 16S/genetics ; *Ethanol/adverse effects ; Alcohol Drinking/adverse effects ; Mice, Inbred C57BL ; Sex Factors ; Dysbiosis/microbiology/chemically induced ; Sex Characteristics ; },
abstract = {Chronic ethanol exposure induces an inflammatory response within the intestinal tract, compromising mucosal and epithelial integrity and leading to dysbiosis of the gut microbiome. However, the specific roles of the gut microbiota in mediating ethanol-induced effects, as well as their interactions with the immune system, remain poorly characterized. This study aimed to evaluate sex-based differences in fecal microbiota profiles induced by chronic alcohol consumption and to assess whether TLR4 is involved in these effects. We analyzed the 16S rRNA gene sequencing of fecal samples from male and female wild-type (WT) and TLR4-knockout (TLR4-KO) mice with and without chronic ethanol exposure over a three-month period. Our findings provide evidence, for the first time, that male mice are more susceptible to the effects of ethanol on the fecal microbiota, since ethanol exposure induced greater alterations in the Gram-negative and -positive bacteria with immunogenic capacity in the WT male mice than in the female mice. We also demonstrate that the absence of immune receptor TLR4 leads to different microbiota in both sexes, showing anti-inflammatory and protective properties for intestinal barrier function and resulting in a phenotype more resistant to ethanol's effects. These findings may open new avenues for understanding the relationship between gut microbiota profiles and inflammation in the digestive system induced by chronic alcohol consumption.},
}

Animals
Female
Male
*Feces/microbiology
Mice
*Gastrointestinal Microbiome/drug effects
*Toll-Like Receptor 4/genetics/metabolism
*Metagenomics/methods
*Mice, Knockout
*RNA, Ribosomal, 16S/genetics
*Ethanol/adverse effects
Alcohol Drinking/adverse effects
Mice, Inbred C57BL
Sex Factors
Dysbiosis/microbiology/chemically induced
Sex Characteristics

@article {pmid39683635,
year = {2024},
author = {Ouédraogo, LO and Deng, L and Ouattara, CA and Compaoré, A and Ouédraogo, M and Argaw, A and Lachat, C and Houpt, ER and Saidi, Q and Haerynck, F and Sonnenburg, J and Azad, MB and Tavernier, SJ and Bastos-Moreira, Y and Toe, LC and Dailey-Chwalibóg, T},
title = {Describing Biological Vulnerability in Small, Vulnerable Newborns in Urban Burkina Faso (DenBalo): Gut Microbiota, Immune System, and Breastmilk Assembly.},
journal = {Nutrients},
volume = {16},
number = {23},
pages = {},
doi = {10.3390/nu16234242},
pmid = {39683635},
issn = {2072-6643},
support = {INV-035474 & INV-036154/GATES/Bill & Melinda Gates Foundation/United States ; },
mesh = {Humans ; Burkina Faso ; Female ; Infant, Newborn ; *Gastrointestinal Microbiome ; *Milk, Human/immunology ; Prospective Studies ; *Vagina/microbiology/immunology ; *Immune System ; Pregnancy ; Breast Feeding ; Infant, Small for Gestational Age ; Adult ; },
abstract = {Background: Small vulnerable newborns (SVNs), including those born preterm, small for gestational age, or with low birth weight, are at higher risk of neonatal mortality and long-term health complications. Early exposure to maternal vaginal microbiota and breastfeeding plays a critical role in the development of the neonatal microbiota and immune system, especially in low-resource settings like Burkina Faso, where neonatal mortality rates remain high. Objectives: The DenBalo study aims to investigate the role of maternal and neonatal factors, such as vaginal and gut microbiota, immune development, and early nutrition, in shaping health outcomes in SVNs and healthy infants. Methods: This prospective cohort observational study will recruit 141 mother-infant pairs (70 SVNs and 71 healthy controls) from four health centers in Bobo-Dioulasso, Burkina Faso. The mother-infant pairs will be followed for six months with anthropometric measurements and biospecimen collections, including blood, breast milk, saliva, stool, vaginal swabs, and placental biopsies. Multi-omics approaches, encompassing metagenomics, metabolomics, proteomics, and immune profiling, will be used to assess vaginal and gut microbiota composition and functionality, immune cell maturation, and cytokine levels at critical developmental stages. Conclusions: This study will generate comprehensive data on how microbiota, metabolomic, and proteomic profiles, along with immune system development, differ between SVNs and healthy infants. These findings will guide targeted interventions to improve neonatal health outcomes and reduce mortality, particularly in vulnerable populations.},
}

Humans
Burkina Faso
Female
Infant, Newborn
*Gastrointestinal Microbiome
*Milk, Human/immunology
Prospective Studies
*Vagina/microbiology/immunology
*Immune System
Pregnancy
Breast Feeding
Infant, Small for Gestational Age
Adult

@article {pmid39682735,
year = {2024},
author = {Hemmati, MA and Monemi, M and Asli, S and Mohammadi, S and Foroozanmehr, B and Haghmorad, D and Oksenych, V and Eslami, M},
title = {Using New Technologies to Analyze Gut Microbiota and Predict Cancer Risk.},
journal = {Cells},
volume = {13},
number = {23},
pages = {},
doi = {10.3390/cells13231987},
pmid = {39682735},
issn = {2073-4409},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Neoplasms/microbiology ; Machine Learning ; High-Throughput Nucleotide Sequencing/methods ; Metagenomics/methods ; },
abstract = {The gut microbiota significantly impacts human health, influencing metabolism, immunological responses, and disease prevention. Dysbiosis, or microbial imbalance, is linked to various diseases, including cancer. It is crucial to preserve a healthy microbiome since pathogenic bacteria, such as Escherichia coli and Fusobacterium nucleatum, can cause inflammation and cancer. These pathways can lead to the formation of tumors. Recent advancements in high-throughput sequencing, metagenomics, and machine learning have revolutionized our understanding of the role of gut microbiota in cancer risk prediction. Early detection is made easier by machine learning algorithms that improve the categorization of cancer kinds based on microbiological data. Additionally, the investigation of the microbiome has been transformed by next-generation sequencing (NGS), which has made it possible to fully profile both cultivable and non-cultivable bacteria and to understand their roles in connection with cancer. Among the uses of NGS are the detection of microbial fingerprints connected to treatment results and the investigation of metabolic pathways implicated in the development of cancer. The combination of NGS with machine learning opens up new possibilities for creating customized medicine by enabling the development of diagnostic tools and treatments that are specific to each patient's microbiome profile, even in the face of obstacles like data complexity. Multi-omics studies reveal microbial interactions, biomarkers for cancer detection, and gut microbiota's impact on cancer progression, underscoring the need for further research on microbiome-based cancer prevention and therapy.},
}

Humans
*Gastrointestinal Microbiome
*Neoplasms/microbiology
Machine Learning
High-Throughput Nucleotide Sequencing/methods
Metagenomics/methods

@article {pmid39682313,
year = {2024},
author = {Mazzei, M and Sorvillo, B and Sgorbini, M and Bindi, F and Perelli, A and Laus, F},
title = {The Role of Viral Pathogens in Horse Respiratory Diseases: A Cytological and Molecular Approach Using Next-Generation Sequencing.},
journal = {Animals : an open access journal from MDPI},
volume = {14},
number = {23},
pages = {},
doi = {10.3390/ani14233347},
pmid = {39682313},
issn = {2076-2615},
abstract = {(1) Background: Respiratory problems may be associated with pathogens among which viruses may play an important role in causing or promoting clinical signs. However, traditional diagnostic methods for equine infectious diseases, such as PCR, are limited to known pathogens and often miss rare or novel viruses. Metagenomic next-generation sequencing is a transformative method that allows the sequencing of all genomes present in a sample. Recent studies have used next-generation sequences to identify viral sequences in horses with unexplained respiratory symptoms, revealing potential links between viruses and respiratory problems. The aim of the study was to verify a relationship between respiratory diseases and the presence of viral agents through molecular analyses, applied to bronchoalveolar lavage fluid obtained from horses with history or presence of clinical signs of respiratory diseases. (2) Methods: A cohort of 14 horses was enrolled. All the subjects were submitted to a clinical assessment of the respiratory tract, thoracic ultrasound evaluation, respiratory tract endoscopy, and bronchoalveolar lavage. The latter one was used for cytological analysis, DNA and RNA extraction, and molecular biology analysis. (3) Results: No positive results were obtained in the molecular studies except for a sequence of 753 bp obtained by next-generation sequences, with complete homology to Equid gammaherpesvirus 2 strains. The samples were taken from a thoroughbred female horse aged 2 years old and referred for poor performance and sporadic cough at the beginning of the training session. (4) Conclusions: viral involvement may be not common in horses with respiratory diseases. We cannot exclude that the lack of virus detection may be due to the small sample size of the population included.},
}

@article {pmid39681550,
year = {2024},
author = {Baddouri, L and Hannig, M},
title = {Probiotics as an adjunctive therapy in periodontitis treatment-reality or illusion-a clinical perspective.},
journal = {NPJ biofilms and microbiomes},
volume = {10},
number = {1},
pages = {148},
pmid = {39681550},
issn = {2055-5008},
mesh = {*Probiotics/therapeutic use/administration & dosage ; Humans ; *Periodontitis/therapy/microbiology ; Treatment Outcome ; },
abstract = {Periodontitis, a prevalent oral health issue, involves various microorganisms and clinical effects. This review examines probiotics as adjunctive therapy for periodontitis by analyzing forty clinical studies. Findings showed mixed results due to differences in study design, probiotic types, and clinical parameters; however, probiotics improved outcomes in severe cases. Caution is advised when interpreting these results, as longer follow-up periods reveal variability and potential regression in effects.},
}

*Probiotics/therapeutic use/administration & dosage
Humans
*Periodontitis/therapy/microbiology
Treatment Outcome

@article {pmid39681310,
year = {2024},
author = {Tobar, Z and Lee, KY and Gaa, ME and Moore, BP and Li, X and Pitesky, ME},
title = {Evaluation of 16s Long Read Metabarcoding for Characterizing the Microbiome and Salmonella Contamination of Retail Poultry Meat.},
journal = {Journal of food protection},
volume = {},
number = {},
pages = {100434},
doi = {10.1016/j.jfp.2024.100434},
pmid = {39681310},
issn = {1944-9097},
abstract = {The traditional gold standard for detection of Salmonella in meat products is bacterial culture with enrichment. While this method is highly sensitive, it is slow and provides an incomplete assessment of isolate taxonomy in positive samples. This study presents a novel PCR based detection assay which amplifies the 16s-ITS-23s region which is an approximately 2500 base pair region of the larger ribosomal rrn operon. Intra-assay variation was assessed by splitting each biological sample into 3 technical replicates. Limits of detection (LOD) were assessed by utilizing a serial dilution of a pure culture of Salmonella enterica subsp. enterica serovar Heidelberg spiked into either sterile 1× PBS or 1× PBS rinsate of a Salmonella culture-negative chicken meat sample. Results indicate the 16s metabarcoding assay evaluated here could not be reliably used for the detection of Salmonella in adulterated retail meat samples as the LOD observed, 4.70 log colony forming units (CFU)/ml, is above the expected concentration of Salmonella in retail poultry meat samples which previous studies have shown range from under 1 to 2 log CFU/ml. However, due to greater taxonomic resolution afforded by using 16s long reads, the assay allowed alpha diversity assessment of the microbiome of raw poultry meat with the ability to assign taxonomy to the species and strain level for some amplicon sequence variants (ASV). This indicates this process may have value characterizing biodiversity and pathogen contamination of poultry samples in earlier steps of the poultry meat production process where bacterial contamination concentrations are likely to be higher.},
}

@article {pmid39680298,
year = {2024},
author = {Han, L and Lin, C and Lan, Y and Hua, Y and Wu, J and Fan, Z and Li, Y},
title = {Metagenomic Analysis of Gut Microbiome of Persistent Pulmonary Hypertension of the Newborn.},
journal = {Cardiovascular toxicology},
volume = {},
number = {},
pages = {},
pmid = {39680298},
issn = {1559-0259},
support = {2021YFQ0061//Technology Project of Sichuan Province of China/ ; 2021YFQ0061//Technology Project of Sichuan Province of China/ ; 82270249//National Natural Science Foundation of China/ ; },
abstract = {Persistent pulmonary hypertension of the newborn (PPHN) is one of the most common diseases in the neonatal intensive care unit which severely affects neonatal survival. Gut microbes play an increasingly important role in human health, but there are rarely reported how gut microbiota contribute to PPHN. In our study, the metagenomic sequencing of feces from 12 PPHN's neonates and 8 controls were performed to expose the relation between neonatal gut microbes and PPHN disease. Firstly, we found that the abundance of Actinobacteria, Proteobacteria, Bacteroidetes were significantly increased in PPHN compared with controls, but the Firmicutes components was reduced. And some pathogenic strains (like Vibrio metschnikovii) were significantly enriched in the PPHN compared with controls. Secondly, functional annotation of genes found that PPHN up-regulated transmembrane transport, but down-regulated ribosome and ATP binding. Lastly, microbial metabolic pathway enrichment analysis indicated that some metabolic pathway in PPHN were conflicting and contradictory, showed that an abnormally increased metabolism, disturbed protein synthesis and genomic instability in the PPHN neonate. Our results contribute to understanding the changes in the species and function of gut microbiota in PPHN, thus providing a theoretical basis for the explanation and treatment of PPHN.},
}

@article {pmid39679737,
year = {2024},
author = {Zhao, H and Wang, T},
title = {Debiased high-dimensional regression calibration for errors-in-variables log-contrast models.},
journal = {Biometrics},
volume = {80},
number = {4},
pages = {},
doi = {10.1093/biomtc/ujae153},
pmid = {39679737},
issn = {1541-0420},
mesh = {Humans ; Calibration ; *Models, Statistical ; Gastrointestinal Microbiome ; Computer Simulation ; Regression Analysis ; Bias ; Linear Models ; Biometry/methods ; Data Interpretation, Statistical ; Metagenomics/methods/statistics & numerical data ; },
abstract = {Motivated by the challenges in analyzing gut microbiome and metagenomic data, this work aims to tackle the issue of measurement errors in high-dimensional regression models that involve compositional covariates. This paper marks a pioneering effort in conducting statistical inference on high-dimensional compositional data affected by mismeasured or contaminated data. We introduce a calibration approach tailored for the linear log-contrast model. Under relatively lenient conditions regarding the sparsity level of the parameter, we have established the asymptotic normality of the estimator for inference. Numerical experiments and an application in microbiome study have demonstrated the efficacy of our high-dimensional calibration strategy in minimizing bias and achieving the expected coverage rates for confidence intervals. Moreover, the potential application of our proposed methodology extends well beyond compositional data, suggesting its adaptability for a wide range of research contexts.},
}

Humans
Calibration
*Models, Statistical
Gastrointestinal Microbiome
Computer Simulation
Regression Analysis
Bias
Linear Models
Biometry/methods
Data Interpretation, Statistical
Metagenomics/methods/statistics & numerical data

@article {pmid39679708,
year = {2024},
author = {Liu, Z and Jiang, C and Yin, Z and Ibrahim, IA and Zhang, T and Wen, J and Zhou, L and Jiang, G and Li, L and Yang, Z and Huang, Y and Yang, Z and Gu, Y and Meng, D and Yin, H},
title = {Ecological features of microbial community linked to stochastic and deterministic assembly processes in acid mine drainage.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0102824},
doi = {10.1128/aem.01028-24},
pmid = {39679708},
issn = {1098-5336},
abstract = {UNLABELLED: Ecological processes greatly shape microbial community assembly, but the driving factors remain unclear. Here, we compiled a metagenomic data set of microbial communities from global acid mine drainage (AMD) and explored the ecological features of microbial community linked to stochastic and deterministic processes from the perspective of species niche position, interaction patterns, gene functions, and viral infection. Our results showed that dispersal limitation (DL) (48.5%~93.5%) dominated the assembly of phylogenetic bin in AMD microbial community, followed by homogeneous selection (HoS) (3.1%~39.2%), heterogeneous selection (HeS) (1.4%~22.2%), and drift (DR) (0.2%~2.7%). The dominant process of dispersal limitation was significantly influenced by niche position in temperature (r = -0.518, P = 0.007) and dissolved oxygen (r = 0.471, P = 0.015). Network stability had a significantly negative correlation with the relative importance of dispersal limitation, while it had a positive correlation with selection processes, implying changes in network properties could be mediated by ecological processes. Furthermore, we found that ecological processes were mostly related to the gene functions of energy production and conversion (C), and amino acid transport and metabolism (E). Meanwhile, our results showed that the number of proviruses and viral genes involved in arsenic (As) resistance is negatively associated with the relative importance of ecological drift in phylogenetic bin assembly, implying viral infection might weaken ecological drift. Taken together, these results highlight that ecological processes are associated with ecological features at multiple levels, providing a novel insight into microbial community assembly in extremely acidic environments.

IMPORTANCE: Unraveling the forces driving community assemblage is a core issue in microbial ecology, but how ecological constraints impose stochasticity and determinism remains unknown. This study presents a comprehensive investigation to uncover the association of ecological processes with species niche position, interaction patterns, microbial metabolisms, and viral infections, which provides novel insights into community assembly in extreme environments.},
}

@article {pmid39679619,
year = {2024},
author = {Steinbach, E and Belda, E and Alili, R and Adriouch, S and Dauriat, CJG and Donatelli, G and Dumont, JL and Pacini, F and Tuszynski, T and Pelloux, V and Jacques, F and Creusot, L and Coles, E and Taillandier, P and Vazquez Gomez, M and Masi, D and Mateo, V and André, S and Kordahi, M and Rouault, C and Zucker, JD and Sokol, H and Genser, L and Chassaing, B and Le Roy, T and Clément, K},
title = {Comparative analysis of the duodenojejunal microbiome with the oral and fecal microbiomes reveals its stronger association with obesity and nutrition.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2405547},
doi = {10.1080/19490976.2024.2405547},
pmid = {39679619},
issn = {1949-0984},
mesh = {Humans ; *Obesity/microbiology ; *Feces/microbiology ; Female ; Male ; Middle Aged ; *Gastrointestinal Microbiome ; Adult ; *Duodenum/microbiology ; *Bacteria/classification/isolation & purification/genetics/metabolism ; Jejunum/microbiology ; Mouth/microbiology ; Nutritional Status ; },
abstract = {The intestinal microbiota is increasingly recognized as a crucial player in the development and maintenance of various chronic conditions, including obesity and associated metabolic diseases. While most research focuses on the fecal microbiota due to its easier accessibility, the small intestine, as a major site for nutrient sensing and absorption, warrants further investigation to determine its microbiota composition and functions. Here, we conducted a clinical research project in 30 age- and sex-matched participants with (n = 15) and without (n = 15) obesity. Duodenojejunal fluid was obtained by aspiration during endoscopy. Phenotyping included clinical variables related to metabolic status, lifestyle, and psychosocial factors using validated questionnaires. We performed metagenomic analyses of the oral, duodenojejunal, and fecal microbiome, alongside metabolomic data from duodenojejunal fluid and feces, integrating these data with clinical and lifestyle information. Our results highlight significant associations between duodenojejunal microbiota composition and usual dietary intake, as well as clinical phenotypes, with larger effect sizes than the associations between these variables and fecal microbiota. Notably, we found that the duodenojejunal microbiota of patients with obesity exhibited higher diversity and showed distinct differences in the abundance of several duodenojejunal microbiota species compared with individuals without obesity. Our findings support the relevance of studying the role of the small intestinal microbiota in the pathogenesis of nutrition-related diseases.},
}

Humans
*Obesity/microbiology
*Feces/microbiology
Female
Male
Middle Aged
*Gastrointestinal Microbiome
Adult
*Duodenum/microbiology
*Bacteria/classification/isolation & purification/genetics/metabolism
Jejunum/microbiology
Mouth/microbiology
Nutritional Status

@article {pmid39679617,
year = {2024},
author = {McAdams, ZL and Gustafson, KL and Russell, AL and Self, R and Petry, AL and Lever, TE and Ericsson, AC},
title = {Supplier-origin gut microbiomes affect host body weight and select autism-related behaviors.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2385524},
doi = {10.1080/19490976.2024.2385524},
pmid = {39679617},
issn = {1949-0984},
mesh = {*Gastrointestinal Microbiome ; Animals ; Mice ; Male ; *Autism Spectrum Disorder/microbiology ; *Body Weight ; Female ; *Behavior, Animal ; Disease Models, Animal ; Humans ; Brain-Gut Axis/physiology ; Bacteria/classification/isolation & purification/genetics ; Autistic Disorder/microbiology/psychology ; },
abstract = {Autism spectrum disorders (ASD) are complex human neurodiversities increasing in prevalence within the human population. In search of therapeutics to improve quality-of-life for ASD patients, the gut microbiome (GM) has become a promising target as a growing body of work supports roles for the complex community of microorganisms in influencing host behavior via the gut-brain-axis. However, whether naturally-occurring microbial diversity within the host GM affects these behaviors is often overlooked. Here, we applied a model of population-level differences in the GM to a classic ASD model - the BTBR T[+] Itpr3[tf]/J mouse - to assess how complex GMs affect host behavior. Leveraging the naturally occurring differences between supplier-origin GMs, our data demonstrate that differing, complex GMs selectively effect host ASD-related behavior - especially neonatal ultrasonic communication - and reveal a male-specific effect on behavior not typically observed in this strain. We then identified that the body weight of BTBR mice is influenced by the postnatal GM which was potentially mediated by microbiome-dependent effects on energy harvest in the gut. These data provide insight into how variability within the GM affects host behavior and growth, thereby emphasizing the need to incorporate microbial diversity within the host GM as an experimental factor in biomedical research.},
}

*Gastrointestinal Microbiome
Animals
Mice
Male
*Autism Spectrum Disorder/microbiology
*Body Weight
Female
*Behavior, Animal
Disease Models, Animal
Humans
Brain-Gut Axis/physiology
Bacteria/classification/isolation & purification/genetics
Autistic Disorder/microbiology/psychology

@article {pmid39679616,
year = {2024},
author = {Seki, D and Kirkegaard, R and Osvatic, J and Hausmann, B and Séneca, J and Pjevac, P and Berger, A and J Hall, L and Wisgrill, L and Berry, D},
title = {Gut microbiota genome features associated with brain injury in extremely premature infants.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2410479},
doi = {10.1080/19490976.2024.2410479},
pmid = {39679616},
issn = {1949-0984},
mesh = {*Gastrointestinal Microbiome ; Humans ; Infant, Newborn ; *Infant, Extremely Premature ; *Brain Injuries/microbiology/genetics ; *Feces/microbiology ; Female ; Male ; Bacteria/genetics/classification/isolation & purification/metabolism ; Genome, Bacterial ; Cohort Studies ; },
abstract = {Severe brain damage is common among premature infants, and the gut microbiota has been implicated in its pathology. Although the order of colonizing bacteria is well described, the mechanisms underlying aberrant assembly of the gut microbiota remain elusive. Here, we employed long-read nanopore sequencing to assess abundances of microbial species and their functional genomic potential in stool samples from a cohort of 30 extremely premature infants. We identify several key microbial traits significantly associated with severe brain damage, such as the genomic potential for nitrate respiration and iron scavenging. Members of the Enterobacteriaceae were prevalent across the cohort and displayed a versatile metabolic potential, including pathogenic and nonpathogenic traits. Predominance of Enterobacter hormaechei and Klebsiella pneumoniae were associated with an overall loss of genomic functional redundancy as well as poor neurophysiological outcome. These findings reveal microbial traits that may be involved in exacerbating brain injury in extremely premature infants and provide suitable targets for therapeutic interventions.},
}

*Gastrointestinal Microbiome
Humans
Infant, Newborn
*Infant, Extremely Premature
*Brain Injuries/microbiology/genetics
*Feces/microbiology
Female
Male
Bacteria/genetics/classification/isolation & purification/metabolism
Genome, Bacterial
Cohort Studies

@article {pmid39679007,
year = {2025},
author = {Wen, HQ and Chen, GL and Li, YS and Tian, T and Pan, Y and Yu, HQ},
title = {An inconvenient impact: Unveiling the overlooked differences in crystalline forms of iron (hydro)oxides on anaerobic digestion.},
journal = {Water research X},
volume = {26},
number = {},
pages = {100286},
pmid = {39679007},
issn = {2589-9147},
abstract = {Iron (hydro)oxides are commonly used to enhance anaerobic digestion due to their cost-effectiveness and versatility. However, the influence of crystalline structure on digestion performance is often overlooked despite their unique characteristics. In this study, we investigated how different crystalline forms of FeOOH affect substrate utilization, sludge activity, and the microbiomes in up-flow anaerobic sludge blanket (UASB) reactors. The crystalline structure of FeOOH impacted reactor performance, with γ-FeOOH, β-FeOOH, and α-FeOOH showing decreasing effectiveness, as reflected in chemical oxygen demand (COD) removal efficiencies of 99.0 %, 98.3 % and 97.1 %, respectively. FeOOH crystals influenced the secretion of extracellular polymeric substances (EPS) and sludge activity by releasing Fe ions at varying rates, leading to Fe accumulation in EPS in the order of β-FeOOH > γ-FeOOH > α-FeOOH. Additionally, γ-FeOOH supported the most stable microbial community structure, as indicated by the highest Alpha diversity index. This stability was associated with increased levels of Mesotoga and Syntrophus, along with the highest coenzyme F420 activity, which was approximately twice as high as in other groups. These findings underscore the crucial role of the crystalline structure of iron oxides in enhancing anaerobic digestion, emphasizing that biocompatibility should be a priority when optimizing digestion performance.},
}

@article {pmid39678985,
year = {2024},
author = {Sahoo, S and Behera, MR and Mishra, B and Kar, S and Sahoo, P and Sahoo, N and Biswal, S},
title = {Microbial Diversity and Resistome in Milk of Cows with Subclinical Mastitis in a Coastal District of Odisha, India.},
journal = {Indian journal of microbiology},
volume = {64},
number = {4},
pages = {1627-1636},
pmid = {39678985},
issn = {0046-8991},
abstract = {Mastitis is a globally prevalent bacterial disease of lactating cows. Prevention and control of this multi-etiological complex disease relies upon administration of antibiotics. This has led to the emergence of newer multi-drug resistant strains. In the current study, milk samples from subclinical mastitis cows and their healthy counterparts were subjected to Illumina-based whole genome metagenome sequencing to explore bacterial communities and antibiotic resistance genes associated with mastitis-affected and healthy udder. Bovine milk microbiome in subclinical mastitis-affected cows were dominated by pathogenic bacteria such as Acinetobacter baylyi, Acinetobacter pittii, Streptococcus agalactiae, Streptococcus suis, Streptococcus uberis, Aeromonas hydrophila, Aeromonas enteropelogenes, Lactococcus lactis, Corynebacterium resistens and Kocuria rhizophila. We observed higher bacterial abundance and diversity in milk of cows suffering from subclinical mastitis as compared to apparently healthy cows. Resistant genes against fluoroquinolones, peptides, β-lactams, tetracyclines and macrolides were detected in the subclinical group. In contrast, genes resistant to aminoglycosides, penams and β-lactams were found in healthy cow milk. The findings of the study expand our knowledge of bacterial diversity and associated resistant genes found in the milk of mastitis-affected and healthy cow milk.},
}

@article {pmid39678952,
year = {2024},
author = {Sinha, T and Talukdar, NC},
title = {Phylum Level Diversity of Plant Interior Bacteria in Seeds, Supernatant and Pellet Phases of Seed Suspension of Mustard Plant.},
journal = {Indian journal of microbiology},
volume = {64},
number = {4},
pages = {1587-1597},
pmid = {39678952},
issn = {0046-8991},
abstract = {Our previous study explored the bacterial endophytic diversity in a certain quantity of mustard seeds using culture dependent method by development of new isolation strategies. No bacterial colony was initially observed in supernatant obtained after centrifugation of mustard seed suspension. This was later overcome by usage of surfactant whereas pellet part showed presence of bacterial colonies on media. In our present study, presence of bacteria was examined in supernatant and whether the diversity was similar to that of pellet and seeds by culture independent approach. In addition, growth of bacterial colonies on media is explained using GC-MS. In this study, Proteobacteria was the dominant bacterial phyla followed by Firmicutes in pellet, supernatant and seed. This indicated that bacteria were present in supernatant but may not be viable when plated on media. This is either due to antimicrobial compounds or oil-imposed difficulty during their isolation which might have hindered their survival. GC-MS study revealed the presence of compounds with antimicrobial property as suggested by previous literature. Our research conducts fundamental investigations to address the primary objective of understanding the bacterial diversity in mustard seed, pellet, and supernatant. Further research using workflows of metagenomics and metabolomics approaches can enrich our understanding ofthe diversity of microorganisms in seeds.},
}

@article {pmid39678942,
year = {2024},
author = {Anjaria, P and Koringa, P and Bhavsar, P and Soni, M and Desai, M and Nayak, J and Chowdhury, S and Jangid, K and Brahmbhatt, MN},
title = {Metagenomic Analysis Reveals the Complex Microbial Landscape of Market Chicken Meat.},
journal = {Indian journal of microbiology},
volume = {64},
number = {4},
pages = {1846-1855},
pmid = {39678942},
issn = {0046-8991},
abstract = {UNLABELLED: The safety of meat from a microbiological standpoint is of paramount concern to public health, given the potential for bacterial contaminants to grow and persist during processing and storage. To address this issue, a culture-independent approach targeting the V3-V4 region of the 16S rRNA gene was utilized to investigate the inherent bacterial communities present in 10 chicken meat samples obtained from retail markets. Amplicons were sequenced using the Illumina MiSeq platform, and unique amplicon sequence variants (ASVs) were identified using the DADA2 pipeline. Results indicated the presence of 5 phyla, 7 classes, 16 orders, 33 families, 59 genera, and 273 unique ASVs. The dominant families were Flavobacteriaceae, Moraxellaceae, Enterobacteriaceae, Wohlfahrtiimonadaceae, Morganellaceae, and Pseudomonadaceae, comprising 27.03, 22.04, 15.67, 9.40, 7.92, and 5.02% of the identified families, respectively. Functional analysis using PICRUSt showed a diverse range of functional pathways. These findings have significant implications for policymaking regarding food safety and public health. Regular monitoring of bacterial communities in meat products is crucial to ensure their safety for consumption. This study demonstrates the utility of culture-independent approaches in characterizing microbial communities, which can provide valuable information for ensuring food safety and safeguarding public health.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12088-024-01249-y.},
}

@article {pmid39678577,
year = {2024},
author = {Cheng, W and Zhou, J and Li, C and Yao, J and Zhang, X and Mao, F and Gao, Z and Jiang, L and Xu, H},
title = {Severe pneumonia caused by Elizabethkingia anophelis combined with Acinetobacter baumannii infection: a case report.},
journal = {American journal of translational research},
volume = {16},
number = {11},
pages = {6821-6827},
pmid = {39678577},
issn = {1943-8141},
abstract = {Elizabethkingia anophelis is an obligate aerobic, Gram-negative bacillus belonging to the family of Weeksellacease. In recent years, there has been a gradual increase in E. anophelis related infections, especially in chronically hospitalized, immunocompromised populations that often develop severe pneumonia. Severe pneumonia is one of the common critical illnesses. Next-generation sequencing technologies developed based on PCR and gene chip technologies play an important role in the identification of pathogenic microorganisms and in molecular diagnosis. In this case, we report an elderly male patient diagnosed with severe pneumonia during the COVID-19 pandemic. The causative organisms were clearly identified as Elizabethkingia anophelis combined with Acinetobacter baumannii by next-generation sequencing. He was discharged from the hospital after being given cefoperazone sulbactam sodium and minocycline, as well as nebulized inhalation of chymotrypsin, salbutamol, and budesonide to assist ventilation. This article summarizes the diagnosis and treatment of this patient in order to share the experience of the subsequent treatments.},
}

@article {pmid39678030,
year = {2024},
author = {Szklenarik, G and Kiraly, P and Szegvari, G and Dora, D and Lohinai, Z},
title = {Predicting cancer-related mycobiome aspects in gastrointestinal cancers: a systematic review.},
journal = {Frontiers in medicine},
volume = {11},
number = {},
pages = {1488377},
pmid = {39678030},
issn = {2296-858X},
abstract = {BACKGROUND: Colonization of the human gut and tumor tissue by non-pathogenic fungi has emerged as a potential risk factor associated with cancer epidemics. Therefore, we aimed to conduct a systematic review to assess the role of fungal colonization in gastrointestinal (GI) tumors in increasing diagnostic efficiency.

METHODS: A PubMed citation search was conducted for publications up to and including March 2023, followed by full-text screening. Results were reported according to Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) 2020 guidelines. According to the Patient, Intervention, Comparison, Outcome (PICO) framework, patients diagnosed with early-and advanced-stage GI cancers, GI adenoma patients, and healthy subjects were included with metagenomic (MG) or internal transcribed spacer (ITS) sequencing on tumor tissue, adjacent normal tissue, stool, and blood samples.

RESULTS: Fourteen studies were eligible based on the inclusion criteria and methodological quality. Studies were conducted in stool (n = 8) or tissue (n = 7) as the most common specimens to be used for molecular analysis. In the collected data, ITS was used in n = 10 cases and metagenomic analyses in n = 3 cases. Observing the interindividual variability, we found that the Ascomycota/Basidiomycota (A/B) ratio from healthy to cancer state decreased in n = 2, increased in n = 1 cases, and did not change significantly in n = 2 studies. An increase in the relative abundance of Malassezia was identified in n = 4, of Candida in n = 5, of Saccharomyces in n = 2, and of Aspergillus in n = 2 cases. Intraindividual differences in the A/B ratio were identified in cancer and adjacent tissue (n = 4) and cancer vs. stool (n = 1) studies. Intraindividual variability of the A/B ratio showed an increase in n = 2 and no change in n = 3 studies for cancer tissue.

CONCLUSION: In conclusion, the advent of highly sensitive sequencing methods may aid in the identification and the differentiation of cancerous from healthy human fungal colonizations with potential future diagnostic applications. Further studies are needed to establish reliable biomarkers for GI cancer screening.},
}