@article {pmid39377779,
year = {2024},
author = {Porreca, A and Ibrahimi, E and Maturo, F and Marcos Zambrano, LJ and Meto, M and Lopes, MB},
title = {Robust prediction of colorectal cancer via gut microbiome 16S rRNA sequencing data.},
journal = {Journal of medical microbiology},
volume = {73},
number = {10},
pages = {},
doi = {10.1099/jmm.0.001903},
pmid = {39377779},
issn = {1473-5644},
mesh = {*RNA, Ribosomal, 16S/genetics ; *Colorectal Neoplasms/microbiology ; Humans ; *Gastrointestinal Microbiome/genetics ; *Machine Learning ; *Feces/microbiology ; Bacteria/genetics/classification/isolation & purification ; },
abstract = {Introduction. The study addresses the challenge of utilizing human gut microbiome data for the early detection of colorectal cancer (CRC). The research emphasizes the potential of using machine learning techniques to analyze complex microbiome datasets, providing a non-invasive approach to identifying CRC-related microbial markers.Hypothesis/Gap Statement. The primary hypothesis is that a robust machine learning-based analysis of 16S rRNA microbiome data can identify specific microbial features that serve as effective biomarkers for CRC detection, overcoming the limitations of classical statistical models in high-dimensional settings.Aim. The primary objective of this study is to explore and validate the potential of the human microbiome, specifically in the colon, as a valuable source of biomarkers for colorectal cancer (CRC) detection and progression. The focus is on developing a classifier that effectively predicts the presence of CRC and normal samples based on the analysis of three previously published faecal 16S rRNA sequencing datasets.Methodology. To achieve the aim, various machine learning techniques are employed, including random forest (RF), recursive feature elimination (RFE) and a robust correlation-based technique known as the fuzzy forest (FF). The study utilizes these methods to analyse the three datasets, comparing their performance in predicting CRC and normal samples. The emphasis is on identifying the most relevant microbial features (taxa) associated with CRC development via partial dependence plots, i.e. a machine learning tool focused on explainability, visualizing how a feature influences the predicted outcome.Results. The analysis of the three faecal 16S rRNA sequencing datasets reveals the consistent and superior predictive performance of the FF compared to the RF and RFE. Notably, FF proves effective in addressing the correlation problem when assessing the importance of microbial taxa in explaining the development of CRC. The results highlight the potential of the human microbiome as a non-invasive means to detect CRC and underscore the significance of employing FF for improved predictive accuracy.Conclusion. In conclusion, this study underscores the limitations of classical statistical techniques in handling high-dimensional information such as human microbiome data. The research demonstrates the potential of the human microbiome, specifically in the colon, as a valuable source of biomarkers for CRC detection. Applying machine learning techniques, particularly the FF, is a promising approach for building a classifier to predict CRC and normal samples. The findings advocate for integrating FF to overcome the challenges associated with correlation when identifying crucial microbial features linked to CRC development.},
}

*RNA, Ribosomal, 16S/genetics
*Colorectal Neoplasms/microbiology
Humans
*Gastrointestinal Microbiome/genetics
*Machine Learning
*Feces/microbiology
Bacteria/genetics/classification/isolation & purification

@article {pmid39375475,
year = {2024},
author = {Turocy, T and Crawford, JM},
title = {Bacterial small molecule metabolites implicated in gastrointestinal cancer development.},
journal = {Nature reviews. Microbiology},
volume = {},
number = {},
pages = {},
pmid = {39375475},
issn = {1740-1534},
abstract = {Numerous associations have been identified between cancer and the composition and function of the human microbiome. As cancer remains the second leading global cause of mortality, investigating the carcinogenic contributions of microbiome members could advance our understanding of cancer risk and support potential therapeutic interventions. Although fluctuations in bacterial species have been associated with cancer progression, studying their small molecule metabolites offers one avenue to establish support for causal relationships and the molecular mechanisms governing host-microorganism interactions. In this Review, we explore the expanding repertoire of small molecule metabolites and their mechanisms implicated in the risk of developing gastrointestinal cancers.},
}

@article {pmid39368472,
year = {2024},
author = {El Mouali, Y and Tawk, C and Huang, KD and Amend, L and Lesker, TR and Ponath, F and Vogel, J and Strowig, T},
title = {The RNA landscape of the human commensal Segatella copri reveals a small RNA essential for gut colonization.},
journal = {Cell host & microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2024.09.008},
pmid = {39368472},
issn = {1934-6069},
abstract = {The bacterium Segatella copri is a prevalent member of the human gut microbiota associated with health and disease states. However, the intrinsic factors that determine its ability to colonize the gut effectively remain largely unknown. By extensive transcriptome mapping of S. copri and examining human-derived samples, we discover a small RNA, which we name Segatella RNA colonization factor (SrcF), and show that SrcF is essential for S. copri gut colonization in gnotobiotic mice. SrcF regulates genes involved in nutrient acquisition, and complex carbohydrates, particularly fructans, control its expression. Furthermore, SrcF expression is strongly influenced by human microbiome composition and by the breakdown of fructans by cohabitating commensals, suggesting that the breakdown of complex carbohydrates mediates interspecies signaling among commensals beyond its established function in generating energy. Together, this study highlights the contribution of a small RNA as a critical regulator in gut colonization.},
}

@article {pmid39365053,
year = {2024},
author = {Silk, ET and Bayer, SB and Foster, M and Roy, NC and Taylor, MW and Vatanen, T and Gearry, RB},
title = {Advancing microbiome research in Māori populations: insights from recent literature exploring the gut microbiomes of underrepresented and Indigenous peoples.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0090924},
doi = {10.1128/msystems.00909-24},
pmid = {39365053},
issn = {2379-5077},
abstract = {The gut microbiome plays vital roles in human health, including mediating metabolism, immunity, and the gut-brain axis. Many ethnicities remain underrepresented in gut microbiome research, with significant variation between Indigenous and non-Indigenous peoples due to dietary, socioeconomic, health, and urbanization differences. Although research regarding the microbiomes of Indigenous peoples is increasing, Māori microbiome literature is lacking despite widespread inequities that Māori populations face. These inequities likely contribute to gut microbiome differences that exacerbate negative health outcomes. Characterizing the gut microbiomes of underrepresented populations is necessary to inform efforts to address health inequities. However, for microbiome research to be culturally responsible and meaningful, study design must improve to better protect the rights and interests of Indigenous peoples. Here, we discuss barriers to Indigenous participation in research and the role disparities may play in shaping the gut microbiomes of Indigenous peoples, with a particular focus on implications for Māori and areas for improvement.},
}

@article {pmid39362115,
year = {2024},
author = {Tian, H and Tang, R},
title = {Prediction of Crohn's disease based on deep feature recognition.},
journal = {Computational biology and chemistry},
volume = {113},
number = {},
pages = {108231},
doi = {10.1016/j.compbiolchem.2024.108231},
pmid = {39362115},
issn = {1476-928X},
abstract = {BACKGROUND: Crohn's disease is a complex genetic disease that involves chronic gastrointestinal inflammation and results from a complex set of genetic, environmental, and immunological factors. By analyzing data from the human microbiome, genetic information can be used to predict Crohn's disease. Recent advances in deep learning have demonstrated its effectiveness in feature extraction and the use of deep learning to decode genetic information for disease prediction.

METHODS: In this paper, we present a deep learning-based model that utilizes a sequential convolutional attention network (SCAN) for feature extraction, incorporates adaptive additive interval losses to enhance these features, and employs support vector machines (SVM) for classification. To address the challenge of unbalanced Crohn's disease samples, we propose a random noise one-hot encoding data augmentation method.

RESULTS: Data augmentation with random noise accelerates training convergence, while SCAN-SVM effectively extracts features with adaptive additive interval loss enhancing differentiation. Our approach outperforms benchmark methods, achieving an average accuracy of 0.80 and a kappa value of 0.76, and we validate the effectiveness of feature enhancement.

CONCLUSIONS: In summary, we use deep feature recognition to effectively analyze the potential information in genes, which has a good application potential for gene analysis and prediction of Crohn's disease.},
}

@article {pmid39359681,
year = {2024},
author = {Tian, S and Ding, T and Li, H},
title = {Oral microbiome in human health and diseases.},
journal = {mLife},
volume = {3},
number = {3},
pages = {367-383},
pmid = {39359681},
issn = {2770-100X},
abstract = {The oral cavity contains the second-largest microbiota in the human body. The cavity's anatomically and physiologically diverse niches facilitate a wide range of symbiotic bacteria living at distinct oral sites. Consequently, the oral microbiota exhibits site specificity, with diverse species, compositions, and structures influenced by specific aspects of their placement. Variations in oral microbiota structure caused by changes in these influencing factors can impact overall health and lead to the development of diseases-not only in the oral cavity but also in organs distal to the mouth-such as cancer, cardiovascular disease, and respiratory disease. Conversely, diseases can exacerbate the imbalance of the oral microbiota, creating a vicious cycle. Understanding the heterogeneity of both the oral microbiome and individual humans is important for investigating the causal links between the oral microbiome and diseases. Additionally, understanding the intricacies of the oral microbiome's composition and regulatory factors will help identify the potential causes of related diseases and develop interventions to prevent and treat illnesses in this domain. Therefore, turning to the extant research in this field, we systematically review the relationship between oral microbiome dynamics and human diseases.},
}

@article {pmid39358771,
year = {2024},
author = {Kawano-Sugaya, T and Arikawa, K and Saeki, T and Endoh, T and Kamata, K and Matsuhashi, A and Hosokawa, M},
title = {A single amplified genome catalog reveals the dynamics of mobilome and resistome in the human microbiome.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {188},
pmid = {39358771},
issn = {2049-2618},
mesh = {Humans ; *Bacteria/genetics/classification ; *Gastrointestinal Microbiome/genetics ; *Metagenome ; *Mouth/microbiology ; *Genome, Bacterial ; Interspersed Repetitive Sequences/genetics ; Microbiota/genetics ; Drug Resistance, Bacterial/genetics ; Metagenomics/methods ; Phylogeny ; },
abstract = {BACKGROUND: The increase in metagenome-assembled genomes (MAGs) has advanced our understanding of the functional characterization and taxonomic assignment within the human microbiome. However, MAGs, as population consensus genomes, often aggregate heterogeneity among species and strains, thereby obfuscating the precise relationships between microbial hosts and mobile genetic elements (MGEs). In contrast, single amplified genomes (SAGs) derived via single-cell genome sequencing can capture individual genomic content, including MGEs.

RESULTS: We introduce the first substantial SAG dataset (bbsag20) from the human oral and gut microbiome, comprising 17,202 SAGs above medium-quality without co-assembly. This collection unveils a diversity of bacterial lineages across 312 oral and 647 gut species, demonstrating different taxonomic compositions from MAGs. Moreover, the SAGs showed cellular-level evidence of the translocation of oral bacteria to the gut. We also identified broad-host-range MGEs harboring antibiotic resistance genes (ARGs), which were not detected in the MAGs.

CONCLUSIONS: The difference in taxonomic composition between SAGs and MAGs indicates that combining both methods would be effective in expanding the genome catalog. By connecting mobilomes and resistomes in individual samples, SAGs could meticulously chart a dynamic network of ARGs on MGEs, pinpointing potential ARG reservoirs and their spreading patterns in the microbial community. Video Abstract.},
}

Humans
*Bacteria/genetics/classification
*Gastrointestinal Microbiome/genetics
*Metagenome
*Mouth/microbiology
*Genome, Bacterial
Interspersed Repetitive Sequences/genetics
Microbiota/genetics
Drug Resistance, Bacterial/genetics
Metagenomics/methods
Phylogeny

@article {pmid39358005,
year = {2024},
author = {Manning, S and Sinha, R and Rees, CJ},
title = {Need for standardised approaches to human microbiome research using the example of colorectal neoplasia research.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2024-333765},
pmid = {39358005},
issn = {1468-3288},
}

@article {pmid39352141,
year = {2024},
author = {Coclet, C and Camargo, AP and Roux, S},
title = {MVP: a modular viromics pipeline to identify, filter, cluster, annotate, and bin viruses from metagenomes.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0088824},
doi = {10.1128/msystems.00888-24},
pmid = {39352141},
issn = {2379-5077},
abstract = {While numerous computational frameworks and workflows are available for recovering prokaryote and eukaryote genomes from metagenome data, only a limited number of pipelines are designed specifically for viromics analysis. With many viromics tools developed in the last few years alone, it can be challenging for scientists with limited bioinformatics experience to easily recover, evaluate quality, annotate genes, dereplicate, assign taxonomy, and calculate relative abundance and coverage of viral genomes using state-of-the-art methods and standards. Here, we describe Modular Viromics Pipeline (MVP) v.1.0, a user-friendly pipeline written in Python and providing a simple framework to perform standard viromics analyses. MVP combines multiple tools to enable viral genome identification, characterization of genome quality, filtering, clustering, taxonomic and functional annotation, genome binning, and comprehensive summaries of results that can be used for downstream ecological analyses. Overall, MVP provides a standardized and reproducible pipeline for both extensive and robust characterization of viruses from large-scale sequencing data including metagenomes, metatranscriptomes, viromes, and isolate genomes. As a typical use case, we show how the entire MVP pipeline can be applied to a set of 20 metagenomes from wetland sediments using only 10 modules executed via command lines, leading to the identification of 11,656 viral contigs and 8,145 viral operational taxonomic units (vOTUs) displaying a clear beta-diversity pattern. Further, acting as a dynamic wrapper, MVP is designed to continuously incorporate updates and integrate new tools, ensuring its ongoing relevance in the rapidly evolving field of viromics. MVP is available at https://gitlab.com/ccoclet/mvp and as versioned packages in PyPi and Conda.IMPORTANCEThe significance of our work lies in the development of Modular Viromics Pipeline (MVP), an integrated and user-friendly pipeline tailored exclusively for viromics analyses. MVP stands out due to its modular design, which ensures easy installation, execution, and integration of new tools and databases. By combining state-of-the-art tools such as geNomad and CheckV, MVP provides high-quality viral genome recovery and taxonomy and host assignment, and functional annotation, addressing the limitations of existing pipelines. MVP's ability to handle diverse sample types, including environmental, human microbiome, and plant-associated samples, makes it a versatile tool for the broader microbiome research community. By standardizing the analysis process and providing easily interpretable results, MVP enables researchers to perform comprehensive studies of viral communities, significantly advancing our understanding of viral ecology and its impact on various ecosystems.},
}

@article {pmid39351241,
year = {2024},
author = {Lu, S and Wang, C and Ma, J and Wang, Y},
title = {Metabolic mediators: microbial-derived metabolites as key regulators of anti-tumor immunity, immunotherapy, and chemotherapy.},
journal = {Frontiers in immunology},
volume = {15},
number = {},
pages = {1456030},
pmid = {39351241},
issn = {1664-3224},
mesh = {Humans ; *Neoplasms/immunology/therapy/metabolism/drug therapy ; *Immunotherapy/methods ; *Gastrointestinal Microbiome/immunology ; *Tumor Microenvironment/immunology ; Animals ; *Fatty Acids, Volatile/metabolism ; *Tryptophan/metabolism ; Methylamines/metabolism/immunology ; Antineoplastic Agents/therapeutic use ; },
abstract = {The human microbiome has recently emerged as a focal point in cancer research, specifically in anti-tumor immunity, immunotherapy, and chemotherapy. This review explores microbial-derived metabolites, emphasizing their crucial roles in shaping fundamental aspects of cancer treatment. Metabolites such as short-chain fatty acids (SCFAs), Trimethylamine N-Oxide (TMAO), and Tryptophan Metabolites take the spotlight, underscoring their diverse origins and functions and their profound impact on the host immune system. The focus is on SCFAs' remarkable ability to modulate immune responses, reduce inflammation, and enhance anti-tumor immunity within the intricate tumor microenvironment (TME). The review critically evaluates TMAO, intricately tied to dietary choices and gut microbiota composition, assessing its implications for cancer susceptibility, progression, and immunosuppression. Additionally, the involvement of tryptophan and other amino acid metabolites in shaping immune responses is discussed, highlighting their influence on immune checkpoints, immunosuppression, and immunotherapy effectiveness. The examination extends to their dynamic interaction with chemotherapy, emphasizing the potential of microbial-derived metabolites to alter treatment protocols and optimize outcomes for cancer patients. A comprehensive understanding of their role in cancer therapy is attained by exploring their impacts on drug metabolism, therapeutic responses, and resistance development. In conclusion, this review underscores the pivotal contributions of microbial-derived metabolites in regulating anti-tumor immunity, immunotherapy responses, and chemotherapy outcomes. By illuminating the intricate interactions between these metabolites and cancer therapy, the article enhances our understanding of cancer biology, paving the way for the development of more effective treatment options in the ongoing battle against cancer.},
}

Humans
*Neoplasms/immunology/therapy/metabolism/drug therapy
*Immunotherapy/methods
*Gastrointestinal Microbiome/immunology
*Tumor Microenvironment/immunology
Animals
*Fatty Acids, Volatile/metabolism
*Tryptophan/metabolism
Methylamines/metabolism/immunology
Antineoplastic Agents/therapeutic use

@article {pmid39349378,
year = {2024},
author = {Palmer, D and Henze, L and Murua Escobar, H and Walter, U and Kowald, A and Fuellen, G},
title = {Multicohort study testing the generalisability of the SASKit-ML stroke and PDAC prognostic model pipeline to other chronic diseases.},
journal = {BMJ open},
volume = {14},
number = {9},
pages = {e088181},
pmid = {39349378},
issn = {2044-6055},
mesh = {Humans ; *Diabetes Mellitus, Type 2/complications ; Prognosis ; Female ; Male ; *Pancreatic Neoplasms ; *Stroke ; Middle Aged ; Arthritis, Rheumatoid ; Machine Learning ; Inflammatory Bowel Diseases ; Aged ; Longitudinal Studies ; Chronic Disease ; Prospective Studies ; Biomarkers/blood ; Cohort Studies ; },
abstract = {OBJECTIVES: To validate and test the generalisability of the SASKit-ML pipeline, a prepublished feature selection and machine learning pipeline for the prediction of health deterioration after a stroke or pancreatic adenocarcinoma event, by using it to identify biomarkers of health deterioration in chronic disease.

DESIGN: This is a validation study using a predefined protocol applied to multiple publicly available datasets, including longitudinal data from cohorts with type 2 diabetes (T2D), inflammatory bowel disease (IBD), rheumatoid arthritis (RA) and various cancers. The datasets were chosen to mimic as closely as possible the SASKit cohort, a prospective, longitudinal cohort study.

DATA SOURCES: Public data were used from the T2D (77 patients with potential pre-diabetes and 18 controls) and IBD (49 patients with IBD and 12 controls) branches of the Human Microbiome Project (HMP), RA Map (RA-MAP, 92 patients with RA, 22 controls) and The Cancer Genome Atlas (TCGA, 16 cancers).

METHODS: Data integration steps were performed in accordance with the prepublished study protocol, generating features to predict disease outcomes using 10-fold cross-validated random survival forests.

OUTCOME MEASURES: Health deterioration was assessed using disease-specific clinical markers and endpoints across different cohorts. In the HMP-T2D cohort, the worsening of glycated haemoglobin (HbA1c) levels (5.7% or more HbA1c in the blood), fasting plasma glucose (at least 100 mg/dL) and oral glucose tolerance test (at least 140) results were considered. For the HMP-IBD cohort, a worsening by at least 3 points of a disease-specific severity measure, the "Simple Clinical Colitis Activity Index" or "Harvey-Bradshaw Index" indicated an event. For the RA-MAP cohort, the outcome was defined as the worsening of the "Disease Activity Score 28" or "Simple Disease Activity Index" by at least five points, or the worsening of the "Health Assessment Questionnaire" score or an increase in the number of swollen/tender joints were evaluated. Finally, the outcome for all TCGA datasets was the progression-free interval.

RESULTS: Models for the prediction of health deterioration in T2D, IBD, RA and 16 cancers were produced. The T2D (C-index of 0.633 and Integrated Brier Score (IBS) of 0.107) and the RA (C-index of 0.654 and IBS of 0.150) models were modestly predictive. The IBD model was uninformative. TCGA models tended towards modest predictive power.

CONCLUSIONS: The SASKit-ML pipeline produces informative and useful features with the power to predict health deterioration in a variety of diseases and cancers; however, this performance is disease-dependent.},
}

Humans
*Diabetes Mellitus, Type 2/complications
Prognosis
Female
Male
*Pancreatic Neoplasms
*Stroke
Middle Aged
Arthritis, Rheumatoid
Machine Learning
Inflammatory Bowel Diseases
Aged
Longitudinal Studies
Chronic Disease
Prospective Studies
Biomarkers/blood
Cohort Studies

@article {pmid39345212,
year = {2024},
author = {Basting, CM and Langat, R and Broedlow, CA and Guerrero, CR and Bold, TD and Bailey, M and Velez, A and Schroeder, T and Short-Miller, J and Cromarty, R and Mayer, ZJ and Southern, PJ and Schacker, TW and Safo, SE and Bramante, CT and Tignanelli, CJ and Schifanella, L and Klatt, NR},
title = {SARS-CoV-2 infection is associated with intestinal permeability, systemic inflammation, and microbial dysbiosis in hospitalized patients.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0068024},
doi = {10.1128/spectrum.00680-24},
pmid = {39345212},
issn = {2165-0497},
abstract = {Coronavirus disease 2019 (COVID-19) and its associated severity have been linked to uncontrolled inflammation and may be associated with changes in the microbiome of mucosal sites including the gastrointestinal tract and oral cavity. These sites play an important role in host-microbe homeostasis, and disruption of epithelial barrier integrity during COVID-19 may potentially lead to exacerbated inflammation and immune dysfunction. Outcomes in COVID-19 are highly disparate, ranging from asymptomatic to fatal, and the impact of microbial dysbiosis on disease severity is unclear. Here, we obtained plasma, rectal swabs, oropharyngeal swabs, and nasal swabs from 86 patients hospitalized with COVID-19 and 12 healthy volunteers. We performed 16S rRNA sequencing to characterize the microbial communities in the mucosal swabs and measured concentrations of circulating cytokines, markers of gut barrier integrity, and fatty acids in the plasma samples. We compared these plasma concentrations and microbiomes between healthy volunteers and COVID-19 patients, some of whom had unfortunately died by the end of the study enrollment, and performed a correlation analysis between plasma variables and bacterial abundances. Rectal swabs of COVID-19 patients had reduced abundances of several commensal bacteria including Faecalibacterium prausnitzii and an increased abundance of the opportunistic pathogens Eggerthella lenta and Hungatella hathewayi. Furthermore, the oral pathogen Scardovia wiggsiae was more abundant in the oropharyngeal swabs of COVID-19 patients who died. The abundance of both H. hathewayi and S. wiggsiae correlated with circulating inflammatory markers including IL-6, highlighting the possible role of the microbiome in COVID-19 severity and providing potential therapeutic targets for managing COVID-19.IMPORTANCEOutcomes in coronavirus disease 2019 (COVID-19) are highly disparate and are associated with uncontrolled inflammation; however, the individual factors that lead to this uncontrolled inflammation are not fully understood. Here, we report that severe COVID-19 is associated with systemic inflammation, microbial translocation, and microbial dysbiosis. The rectal and oropharyngeal microbiomes of COVID-19 patients were characterized by a decreased abundance of commensal bacteria and an increased abundance of opportunistic pathogens, which positively correlated with markers of inflammation and microbial translocation. These microbial perturbations may, therefore, contribute to disease severity in COVID-19 and highlight the potential for microbiome-based interventions in improving COVID-19 outcomes.},
}

@article {pmid39342083,
year = {2024},
author = {Wang, X and Yao, S and Yang, X and Li, Y and Yu, Z and Huang, J and Wang, J},
title = {Peritoneal dialysis promotes microbial-driven biosynthesis pathways of sesquiterpenes and triterpenes compounds in end-stage renal disease patients.},
journal = {BMC microbiology},
volume = {24},
number = {1},
pages = {377},
pmid = {39342083},
issn = {1471-2180},
support = {32170071//National Natural Science Foundation of China/ ; 32300051//National Natural Science Foundation of China/ ; 2022JJ40663//Natural Science Foundation of Hunan Province/ ; C2023045//Hunan Province Traditional Chinese Medicine Research Program Project/ ; },
mesh = {Humans ; *Kidney Failure, Chronic/therapy/metabolism/microbiology ; *Gastrointestinal Microbiome ; *Peritoneal Dialysis ; *Sesquiterpenes/metabolism ; Male ; Female ; *Feces/microbiology ; Middle Aged ; *Triterpenes/metabolism ; Bacteria/metabolism/classification/genetics/isolation & purification ; Biosynthetic Pathways ; Adult ; Metagenomics ; Aged ; },
abstract = {The concept of the gut-kidney axis is gaining significant attention due to the close relationship between gut microbiota and kidney disease. Peritoneal dialysis is recognized as a crucial renal replacement therapy for end-stage renal disease (ESRD). The alterations in gut microbiota and related mechanisms after receiving this dialysis method are not fully understood. This study conducted shotgun metagenomic sequencing on fecal samples from 11 end-stage renal disease patients who did not receive dialysis (ESRD_N) and 7 patients who received peritoneal dialysis (ESRD_P). After quality control and correlation analysis of the data, our study is aimed at exploring the impact of peritoneal dialysis on the gut microbiota and health of ESRD patients. Our research findings indicate that the complexity and aggregation characteristics of gut microbiota interactions increase in ESRD_P. In addition, the gut microbiota drives the biosynthesis pathways of sesquiterpenes and triterpenes in ESRD_P patients, which may contribute to blood purification and improve circulation. Therefore, our research will lay the foundation for the prevention and treatment of ESRD.},
}

Humans
*Kidney Failure, Chronic/therapy/metabolism/microbiology
*Gastrointestinal Microbiome
*Peritoneal Dialysis
*Sesquiterpenes/metabolism
Male
Female
*Feces/microbiology
Middle Aged
*Triterpenes/metabolism
Bacteria/metabolism/classification/genetics/isolation & purification
Biosynthetic Pathways
Adult
Metagenomics
Aged

@article {pmid39341037,
year = {2024},
author = {Vogs, C and Lindqvist, D and Wai Tang, S and Gugescu, L and Alenius, H and Wincent, E},
title = {Transcriptomic and functional effects from a chemical mixture based on the exposure profile in Baltic Sea salmon, on metabolic and immune functions in zebrafish embryo.},
journal = {Environment international},
volume = {192},
number = {},
pages = {109018},
doi = {10.1016/j.envint.2024.109018},
pmid = {39341037},
issn = {1873-6750},
abstract = {The Baltic Sea is one of the world's most contaminated seas with long-standing adverse health status of its wildlife such as the Baltic Sea salmon, resulting in reduced fecundity and increased mortality. While adverse health effects have been reported among wild fish from the Baltic Sea, the toxicity mechanisms underlying these adversities, and the chemical effect drivers mediating them are poorly understood. To address this knowledge gap, we utilized the zebrafish (Danio rerio) embryo model to determine molecular and functional effects brought on by exposure to a technical mixture including 9 organohalogen compounds detected in serum from wild-caught Baltic Sea salmon. To align with the salmon exposure scenario, an internal dose regimen was opted to establish same relative proportions of the compounds in the zebrafish (whole body) as observed in the salmon serum. Through transcriptomic profiling, we identified dose-dependent effects on immune system and metabolism as two critical functions overlapping with adverse effects observed in wild fish from the Baltic Sea. We then determined likely effect drivers by comparing gene responses of the mixture with those of individual mixture components. Aligned with our transcriptome results, the number of total macrophages was reduced and the zebrafish's ability to respond to a tissue damage suppressed in a dose-dependent manner. This study brings forth a key advancement in delineating the impact of chemical pollutants on the health of wild fish in the Baltic Sea.},
}

@article {pmid39340867,
year = {2024},
author = {Moghaddam, HS and Abkar, L and Fowler, SJ},
title = {Making waves: From tap to gut- exploring the impact of drinking water on gut microbiota.},
journal = {Water research},
volume = {267},
number = {},
pages = {122503},
doi = {10.1016/j.watres.2024.122503},
pmid = {39340867},
issn = {1879-2448},
abstract = {Drinking water (DW) harbours diverse microbial species and chemical attributes. Water comprises the greatest portion of our daily diet, ingested both on its own and used in the preparation of food. DW is our major source of liquids, which is vital to maintaining homeostasis, and can also supply essential minerals. Limited evidence suggests that DW plays a role in shaping the gut microbiome, which implies that it may impact human health. Despite its significant contribution to diet, DW is often overlooked in studies examining dietary influences on the gut microbiota. This perspective explores our current understanding of the link between DW and the gut microbiota - an area of human microbiome science that has been surprisingly understudied. Existing studies reveal links between DW source, microbiota composition, and gut health, emphasizing the need for comprehensive investigations. Understanding the interplay between DW and gut microbiota holds potential for tailored interventions to enhance human health.},
}

@article {pmid39339787,
year = {2024},
author = {Fraiz, GM and Bonifácio, DB and Lacerda, UV and Cardoso, RR and Corich, V and Giacomini, A and Martino, HSD and Echeverría, SE and Barros, FAR and Milagro, FI and Bressan, J},
title = {Green Tea Kombucha Impacts Inflammation and Salivary Microbiota in Individuals with Excess Body Weight: A Randomized Controlled Trial.},
journal = {Nutrients},
volume = {16},
number = {18},
pages = {},
pmid = {39339787},
issn = {2072-6643},
support = {CAPE 507/2019 - APQ-00035-20//Fundação de Amparo à Pesquisa do Estado de Minas Gerais/ ; CB12/03/30002//Spanish Biomedical Research Centre in Physiopathology of Obesity and Nutrition/ ; 001//Coordenação de Aperfeicoamento de Pessoal de Nível Superior/ ; },
mesh = {Humans ; *Saliva/microbiology ; Male ; Female ; *Inflammation ; Adult ; *Microbiota ; Kombucha Tea ; Middle Aged ; Weight Loss ; Tea ; Overweight/microbiology ; Body Mass Index ; Caloric Restriction ; Body Composition ; },
abstract = {BACKGROUND: Green tea kombucha (GTK) is a fermented beverage with promising health benefits, but few studies proved its impact on human health. Thus, we aimed to investigate the impact of GTK on weight loss, inflammation, and salivary microbiota in individuals with excess body weight.

METHODS: This is a randomized controlled clinical trial that lasted 10 weeks with two groups of individuals with excess body weight: control (CG; n = 29; caloric restriction) and kombucha (KG; n = 30; caloric restriction + 200 mL GTK). Body composition, anthropometry, saliva, and blood collection were performed in the beginning and end of the intervention. Plasma interleukins were determined by flow cytometry. Salivary microbiota was analyzed by 16S rRNA sequencing.

RESULTS: Both groups decreased weight, BMI, and body fat (p < 0.001) after the intervention, but there were no differences between groups. The KG reduced lipid accumulation product (LAP) (p = 0.029). Both groups decreased IL-1β and IL-8, but IL-6 increased in the CG (p = 0.023) compared to the kombucha group. Alpha and beta diversity of salivary microbiota increased in the KG. Moreover, the KG presented lower Bacillota/Bacteroidota ratio (p = 0.028), and BMI was positively associated with the Bacillota phylum.

CONCLUSIONS: GTK did not enhance weight loss, but it decreased the LAP. GTK helped in the inflammatory profile and induced positive changes in oral microbiota composition.},
}

Humans
*Saliva/microbiology
Male
Female
*Inflammation
Adult
*Microbiota
Kombucha Tea
Middle Aged
Weight Loss
Tea
Overweight/microbiology
Body Mass Index
Caloric Restriction
Body Composition

@article {pmid39337688,
year = {2024},
author = {Fleshner, L and Roster, K and Farabi, B and Hirani, R and Tepper, K and Pitchumoni, CS and Safai, B and Marmon, S},
title = {Follicular Skin Disorders, Inflammatory Bowel Disease, and the Microbiome: A Systematic Review.},
journal = {International journal of molecular sciences},
volume = {25},
number = {18},
pages = {},
pmid = {39337688},
issn = {1422-0067},
mesh = {Humans ; *Inflammatory Bowel Diseases/microbiology ; *Gastrointestinal Microbiome ; *Dysbiosis/microbiology ; Microbiota ; Hidradenitis Suppurativa/microbiology ; Skin/microbiology ; Skin Diseases/microbiology ; },
abstract = {Follicular skin disorders, including hidradenitis suppurativa (HS), frequently coexist with systemic autoinflammatory diseases, such as inflammatory bowel disease (IBD) and its subtypes, Crohn's disease and ulcerative colitis. Previous studies suggest that dysbiosis of the human gut microbiome may serve as a pathogenic link between HS and IBD. However, the role of the microbiome (gut, skin, and blood) in the context of IBD and various follicular disorders remains underexplored. Here, we performed a systematic review to investigate the relationship between follicular skin disorders, IBD, and the microbiome. Of the sixteen included studies, four evaluated the impact of diet on the microbiome in HS patients, highlighting a possible link between gut dysbiosis and yeast-exclusion diets. Ten studies explored bacterial colonization and HS severity with specific gut and skin microbiota, including Enterococcus and Veillonella. Two studies reported on immunological or serological biomarkers in HS patients with autoinflammatory disease, including IBD, and identified common markers including elevated cytokines and T-lymphocytes. Six studies investigated HS and IBD patients concurrently. Our systematic literature review highlights the complex interplay between the human microbiome, IBD, and follicular disorders with a particular focus on HS. The results indicate that dietary modifications hold promise as a therapeutic intervention to mitigate the burden of HS and IBD. Microbiota analyses and the identification of key serological biomarkers are crucial for a deeper understanding of the impact of dysbiosis in these conditions. Future research is needed to more thoroughly delineate the causal versus associative roles of dysbiosis in patients with both follicular disorders and IBD.},
}

Humans
*Inflammatory Bowel Diseases/microbiology
*Gastrointestinal Microbiome
*Dysbiosis/microbiology
Microbiota
Hidradenitis Suppurativa/microbiology
Skin/microbiology
Skin Diseases/microbiology

@article {pmid39337215,
year = {2024},
author = {Falara, E and Metallinou, D and Nanou, C and Vlachou, M and Diamanti, A},
title = {Perinatal Exposure to Tobacco Smoke and Its Association with the Maternal and Offspring Microbiome: A Systematic Review.},
journal = {Healthcare (Basel, Switzerland)},
volume = {12},
number = {18},
pages = {},
doi = {10.3390/healthcare12181874},
pmid = {39337215},
issn = {2227-9032},
support = {The APC was partially funded by the "Special Account for Research Grants" of the University of West Attica, Athens, Greece.//The APC was partially funded by the "Special Account for Research Grants" of the University of West Attica, Athens, Greece./ ; },
abstract = {BACKGROUND: The human microbiome, comprising trillions of microorganisms, significantly influences human health and disease. During critical periods like the perinatal phase, the microbiome undergoes significant changes, impacting lifelong health. Tobacco smoke, a known environmental pollutant, has adverse effects on health, particularly during pregnancy. Despite this, its association with the perinatal microbiome remains understudied.

METHODS: We conducted a systematic review to integrate findings on perinatal tobacco smoke exposure and its association with the maternal and neonatal microbiomes. We conducted a comprehensive literature search in the PubMed, Scopus, and Web of Science databases from January 2000 to February 2024. We selected studies that met predefined inclusion criteria and performed data extraction.

RESULTS: The review included eight studies that revealed diverse associations of perinatal tobacco exposure with the maternal and neonatal microbiome. Active smoking during pregnancy was linked to alterations in microbiome composition and diversity in children. Maternal smoking correlated with increased Firmicutes abundance and decreased Akkermansia muciniphila abundance in offspring. Additionally, exposure to thirdhand smoke in neonatal intensive care units was related to infant microbiome diversity. Infants exposed to tobacco smoke showed various microbial changes, suggesting potential implications for childhood health outcomes, including obesity risk.

CONCLUSIONS: Perinatal exposure to tobacco smoke exerts significant influence on the maternal and neonatal microbiomes, with potential implications for long-term health outcomes. Addressing socioeconomic and psychological barriers to smoking cessation, implementing stricter smoking regulations, and promoting public health campaigns are essential steps towards reducing tobacco-related harm during the perinatal period. Further longitudinal studies and standardized assessment methods are needed to validate these findings and guide the development of effective preventive measures.},
}

@article {pmid39335616,
year = {2024},
author = {Xiang, B and Zhang, Q and Wu, H and Lin, J and Xu, Z and Zhang, M and Zhu, L and Hu, J and Zhi, M},
title = {Impact of Mild COVID-19 History on Oral-Gut Microbiota and Serum Metabolomics in Adult Patients with Crohn's Disease: Potential Beneficial Effects.},
journal = {Biomedicines},
volume = {12},
number = {9},
pages = {},
doi = {10.3390/biomedicines12092103},
pmid = {39335616},
issn = {2227-9059},
support = {2014008 (MZ)//the Sun Yat-sen University Clinical Research 5010 Program/ ; 82270544 (MZ)//the National Natural Science Foundation of China/ ; SL2022B03J00237 (MZ)//the Bureau of Science and Technology of Guangzhou Municipality/ ; 2022JBGS06 (MZ)//"Jie Bang Gua Shuai" project of The Sixth Affiliated Hospital of Sun Yat-sen University/ ; 2019ZT08Y464 (LZ)//Guangdong Province "Pearl River Talent Plan" Innovation and Entrepreneurship Team Project/ ; 2020B1111170004 (MZ)//the program of Guangdong Provincial Clinical Research Center for Digestive Diseases/ ; },
abstract = {The impact of coronavirus disease 2019 (COVID-19) history on Crohn's disease (CD) is unknown. This investigation aimed to examine the effect of COVID-19 history on the disease course, oral-gut microbiota, and serum metabolomics in patients with CD. In this study, oral-gut microbiota and serum metabolomic profiles in 30 patients with CD and a history of mild COVID-19 (positive group, PG), 30 patients with CD without COVID-19 history (negative group, NG), and 60 healthy controls (HC) were assessed using 16S rDNA sequencing and targeted metabolomics. During follow-up, the CD activity index showed a stronger decrease in the PG than in the NG (p = 0.0496). PG patients demonstrated higher α-diversity and distinct β-diversity clustering in both salivary and fecal microbiota compared to NG and HC individuals. Notably, the gut microbiota composition in the PG patients showed a significantly greater similarity to that of HC than NG individuals. The interaction between oral and intestinal microbiota in the PG was reduced. Moreover, serum metabolome analysis revealed significantly increased anti-inflammatory metabolites, including short-chain fatty acids and N-Acetylserotonin, among PG patients; meanwhile, inflammation-related metabolites such as arachidonic acid were significantly reduced in this group. Our data suggest that the gut microbiota mediates a potential beneficial effect of a mild COVID-19 history in CD patients.},
}

@article {pmid39334849,
year = {2024},
author = {Mukherjee, S and Verma, A and Kong, L and Rengan, AK and Cahill, DM},
title = {Advancements in Green Nanoparticle Technology: Focusing on the Treatment of Clinical Phytopathogens.},
journal = {Biomolecules},
volume = {14},
number = {9},
pages = {},
doi = {10.3390/biom14091082},
pmid = {39334849},
issn = {2218-273X},
mesh = {*Nanoparticles/chemistry/therapeutic use ; Humans ; *Anti-Bacterial Agents/pharmacology/chemistry/therapeutic use ; Green Chemistry Technology/methods ; Plant Diseases/microbiology/prevention & control ; },
abstract = {Opportunistic pathogenic microbial infections pose a significant danger to human health, which forces people to use riskier, more expensive, and less effective drugs compared to traditional treatments. These may be attributed to several factors, such as overusing antibiotics in medicine and lack of sanitization in hospital settings. In this context, researchers are looking for new options to combat this worrying condition and find a solution. Nanoparticles are currently being utilized in the pharmaceutical sector; however, there is a persistent worry regarding their potential danger to human health due to the usage of toxic chemicals, which makes the utilization of nanoparticles highly hazardous to eukaryotic cells. Multiple nanoparticle-based techniques are now being developed, offering essential understanding regarding the synthesis of components that play a crucial role in producing anti-microbial nanotherapeutic pharmaceuticals. In this regard, green nanoparticles are considered less hazardous than other forms, providing potential options for avoiding the extensive harm to the human microbiome that is prevalent with existing procedures. This review article aims to comprehensively assess the current state of knowledge on green nanoparticles related to antibiotic activity as well as their potential to assist antibiotics in treating opportunistic clinical phytopathogenic illnesses.},
}

*Nanoparticles/chemistry/therapeutic use
Humans
*Anti-Bacterial Agents/pharmacology/chemistry/therapeutic use
Green Chemistry Technology/methods
Plant Diseases/microbiology/prevention & control

@article {pmid39333709,
year = {2024},
author = {Crunkhorn, S},
title = {Identifying antimicrobials in the human microbiome.},
journal = {Nature reviews. Drug discovery},
volume = {},
number = {},
pages = {},
pmid = {39333709},
issn = {1474-1784},
}

@article {pmid39333588,
year = {2024},
author = {Garcia-Vello, P and Tytgat, HLP and Elzinga, J and Van Hul, M and Plovier, H and Tiemblo-Martin, M and Cani, PD and Nicolardi, S and Fragai, M and De Castro, C and Di Lorenzo, F and Silipo, A and Molinaro, A and de Vos, WM},
title = {The lipooligosaccharide of the gut symbiont Akkermansia muciniphila exhibits a remarkable structure and TLR signaling capacity.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {8411},
pmid = {39333588},
issn = {2041-1723},
support = {AdG 250172//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; },
mesh = {*Lipopolysaccharides ; *Akkermansia ; Animals ; *Signal Transduction ; *Toll-Like Receptor 4/metabolism ; Humans ; *Toll-Like Receptor 2/metabolism ; Mice ; Symbiosis ; Mice, Inbred C57BL ; Lipid A/metabolism/chemistry ; Interleukin-10/metabolism ; Gastrointestinal Microbiome ; Liver/metabolism/microbiology ; Female ; },
abstract = {The cell-envelope of Gram-negative bacteria contains endotoxic lipopolysaccharides (LPS) that are recognized by the innate immune system via Toll-Like Receptors (TLRs). The intestinal mucosal symbiont Akkermansia muciniphila is known to confer beneficial effects on the host and has a Gram-negative architecture. Here we show that A. muciniphila LPS lacks the O-polysaccharide repeating unit, with the resulting lipooligosaccharide (LOS) having unprecedented structural and signaling properties. The LOS consists of a complex glycan chain bearing two distinct undeca- and hexadecasaccharide units each containing three 2-keto-3-deoxy-D-manno-octulosonic acid (Kdo) residues. The lipid A moiety appears as a mixture of differently phosphorylated and acylated species and carries either linear or branched acyl moieties. Peritoneal injection of the LOS in mice increased higher gene expression of liver TLR2 than TLR4 (100-fold) and induced high IL-10 gene expression. A. muciniphila LOS was found to signal both through TLR4 and TLR2, whereas lipid A only induced TLR2 in a human cell line. We propose that the unique structure of the A. muciniphila LOS allows interaction with TLR2, thus generating an anti-inflammatory response as to compensate for the canonical inflammatory signaling associated with LOS and TLR4, rationalizing its beneficial host interaction.},
}

*Lipopolysaccharides
*Akkermansia
Animals
*Signal Transduction
*Toll-Like Receptor 4/metabolism
Humans
*Toll-Like Receptor 2/metabolism
Mice
Symbiosis
Mice, Inbred C57BL
Lipid A/metabolism/chemistry
Interleukin-10/metabolism
Gastrointestinal Microbiome
Liver/metabolism/microbiology
Female

@article {pmid39333143,
year = {2024},
author = {Wang, B and Wang, T and Du, X and Li, J and Wang, J and Wu, P},
title = {Microbe-drug association prediction model based on graph convolution and attention networks.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {22327},
pmid = {39333143},
issn = {2045-2322},
support = {145209125//Basic scientific research operations of universities affiliated with Heilongjiang Province/ ; },
mesh = {Humans ; *Deep Learning ; Microbiota ; Computational Biology/methods ; Neural Networks, Computer ; Drug Discovery/methods ; Pharmaceutical Preparations ; },
abstract = {The human microbiome plays a key role in drug development and precision medicine, but understanding its complex interactions with drugs remains a challenge. Identifying microbe-drug associations not only enhances our understanding of their mechanisms but also aids in drug discovery and repurposing. Traditional experiments are expensive and time-consuming, making computational methods for predicting microbe-drug associations a new trend. Currently, computational methods specifically designed for this task are still scarce. Therefore, to address the shortcomings of traditional experimental methods in predicting potential microbe-drug associations, this paper proposes a new prediction model named GCNATMDA. The model combines two deep learning models, Graph Convolutional Network and Graph Attention Network, and aims to reveal potential relationships between microbes and drugs by learning related features. Thus improve the efficiency and accuracy of prediction. We first integrated the microbe-drug association matrix from the existing dataset, and then combined the calculated microbe-drug characteristic matrix as the model input. The GCN module is used to dig deeper into the potential characterization of microbes and drugs, while the GAT module further learns the more complex interactions between them and generates the corresponding score matrix. The experimental results show that the GCNATMDA model achieves 96.59% and 93.01% in AUC and AUPR evaluation indexes, respectively, which is significantly better than the existing prediction models. In addition, the reliability of the prediction results is verified by a series of experiments.},
}

Humans
*Deep Learning
Microbiota
Computational Biology/methods
Neural Networks, Computer
Drug Discovery/methods
Pharmaceutical Preparations

@article {pmid39333099,
year = {2024},
author = {Hickman, B and Salonen, A and Ponsero, AJ and Jokela, R and Kolho, KL and de Vos, WM and Korpela, K},
title = {Gut microbiota wellbeing index predicts overall health in a cohort of 1000 infants.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {8323},
pmid = {39333099},
issn = {2041-1723},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Infant ; *Feces/microbiology ; Female ; Male ; Infant, Newborn ; Cohort Studies ; Longitudinal Studies ; Child, Preschool ; Bifidobacterium/isolation & purification ; Bacteroides/isolation & purification ; },
abstract = {The human gut microbiota is central in regulating all facets of host physiology, and in early life it is thought to influence the host's immune system and metabolism, affecting long-term health. However, longitudinally monitored cohorts with parallel analysis of faecal samples and health data are scarce. In our observational study we describe the gut microbiota development in the first 2 years of life and create a gut microbiota wellbeing index based on the microbiota development and health data in a cohort of nearly 1000 infants using clustering and trajectory modelling. We show that infants' gut microbiota development is highly predictable, following one of five trajectories, dependent on infant exposures, and predictive of later health outcomes. We characterise the natural healthy gut microbiota trajectory and several different dysbiotic trajectories associated with different health outcomes. Bifidobacterium and Bacteroides appear as early keystone organisms, directing microbiota development and consistently predicting positive health outcomes. A microbiota wellbeing index, based on the healthy development trajectory, is predictive of general health over the first 5 years. The results indicate that gut microbiota succession is part of infant physiological development, predictable, and malleable. This information can be utilised to improve the predictions of individual health risks.},
}

Humans
*Gastrointestinal Microbiome/physiology
Infant
*Feces/microbiology
Female
Male
Infant, Newborn
Cohort Studies
Longitudinal Studies
Child, Preschool
Bifidobacterium/isolation & purification
Bacteroides/isolation & purification

@article {pmid39331660,
year = {2024},
author = {Pasqualini, J and Facchin, S and Rinaldo, A and Maritan, A and Savarino, E and Suweis, S},
title = {Emergent ecological patterns and modelling of gut microbiomes in health and in disease.},
journal = {PLoS computational biology},
volume = {20},
number = {9},
pages = {e1012482},
doi = {10.1371/journal.pcbi.1012482},
pmid = {39331660},
issn = {1553-7358},
abstract = {Recent advancements in next-generation sequencing have revolutionized our understanding of the human microbiome. Despite this progress, challenges persist in comprehending the microbiome's influence on disease, hindered by technical complexities in species classification, abundance estimation, and data compositionality. At the same time, the existence of macroecological laws describing the variation and diversity in microbial communities irrespective of their environment has been recently proposed using 16s data and explained by a simple phenomenological model of population dynamics. We here investigate the relationship between dysbiosis, i.e. in unhealthy individuals there are deviations from the "regular" composition of the gut microbial community, and the existence of macro-ecological emergent law in microbial communities. We first quantitatively reconstruct these patterns at the species level using shotgun data, and addressing the consequences of sampling effects and statistical errors on ecological patterns. We then ask if such patterns can discriminate between healthy and unhealthy cohorts. Concomitantly, we evaluate the efficacy of different statistical generative models, which incorporate sampling and population dynamics, to describe such patterns and distinguish which are expected by chance, versus those that are potentially informative about disease states or other biological drivers. A critical aspect of our analysis is understanding the relationship between model parameters, which have clear ecological interpretations, and the state of the gut microbiome, thereby enabling the generation of synthetic compositional data that distinctively represent healthy and unhealthy individuals. Our approach, grounded in theoretical ecology and statistical physics, allows for a robust comparison of these models with empirical data, enhancing our understanding of the strengths and limitations of simple microbial models of population dynamics.},
}

@article {pmid39327438,
year = {2024},
author = {Schmartz, GP and Rehner, J and Gund, MP and Keller, V and Molano, LG and Rupf, S and Hannig, M and Berger, T and Flockerzi, E and Seitz, B and Fleser, S and Schmitt-Grohé, S and Kalefack, S and Zemlin, M and Kunz, M and Götzinger, F and Gevaerd, C and Vogt, T and Reichrath, J and Diehl, L and Hecksteden, A and Meyer, T and Herr, C and Gurevich, A and Krug, D and Hegemann, J and Bozhueyuek, K and Gulder, TAM and Fu, C and Beemelmanns, C and Schattenberg, JM and Kalinina, OV and Becker, A and Unger, M and Ludwig, N and Seibert, M and Stein, ML and Hanna, NL and Martin, MC and Mahfoud, F and Krawczyk, M and Becker, SL and Müller, R and Bals, R and Keller, A},
title = {Decoding the diagnostic and therapeutic potential of microbiota using pan-body pan-disease microbiomics.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {8261},
pmid = {39327438},
issn = {2041-1723},
mesh = {Humans ; *Microbiota/genetics ; *Metagenome/genetics ; *Metagenomics/methods ; Bacteria/genetics/isolation & purification/classification ; Feces/microbiology ; Male ; Female ; Multigene Family ; Saliva/microbiology ; Adult ; },
abstract = {The human microbiome emerges as a promising reservoir for diagnostic markers and therapeutics. Since host-associated microbiomes at various body sites differ and diseases do not occur in isolation, a comprehensive analysis strategy highlighting the full potential of microbiomes should include diverse specimen types and various diseases. To ensure robust data quality and comparability across specimen types and diseases, we employ standardized protocols to generate sequencing data from 1931 prospectively collected specimens, including from saliva, plaque, skin, throat, eye, and stool, with an average sequencing depth of 5.3 gigabases. Collected from 515 patients, these samples yield an average of 3.7 metagenomes per patient. Our results suggest significant microbial variations across diseases and specimen types, including unexpected anatomical sites. We identify 583 unexplored species-level genome bins (SGBs) of which 189 are significantly disease-associated. Of note, the existence of microbial resistance genes in one specimen was indicative of the same resistance genes in other specimens of the same patient. Annotated and previously undescribed SGBs collectively harbor 28,315 potential biosynthetic gene clusters (BGCs), with 1050 significant correlations to diseases. Our combinatorial approach identifies distinct SGBs and BGCs, emphasizing the value of pan-body pan-disease microbiomics as a source for diagnostic and therapeutic strategies.},
}

Humans
*Microbiota/genetics
*Metagenome/genetics
*Metagenomics/methods
Bacteria/genetics/isolation & purification/classification
Feces/microbiology
Male
Female
Multigene Family
Saliva/microbiology
Adult

@article {pmid39322959,
year = {2024},
author = {Wirbel, J and Essex, M and Forslund, SK and Zeller, G},
title = {A realistic benchmark for differential abundance testing and confounder adjustment in human microbiome studies.},
journal = {Genome biology},
volume = {25},
number = {1},
pages = {247},
pmid = {39322959},
issn = {1474-760X},
mesh = {Humans ; *Microbiota ; *Benchmarking ; RNA, Ribosomal, 16S/genetics ; Computer Simulation ; },
abstract = {BACKGROUND: In microbiome disease association studies, it is a fundamental task to test which microbes differ in their abundance between groups. Yet, consensus on suitable or optimal statistical methods for differential abundance testing is lacking, and it remains unexplored how these cope with confounding. Previous differential abundance benchmarks relying on simulated datasets did not quantitatively evaluate the similarity to real data, which undermines their recommendations.

RESULTS: Our simulation framework implants calibrated signals into real taxonomic profiles, including signals mimicking confounders. Using several whole meta-genome and 16S rRNA gene amplicon datasets, we validate that our simulated data resembles real data from disease association studies much more than in previous benchmarks. With extensively parametrized simulations, we benchmark the performance of nineteen differential abundance methods and further evaluate the best ones on confounded simulations. Only classic statistical methods (linear models, the Wilcoxon test, t-test), limma, and fastANCOM properly control false discoveries at relatively high sensitivity. When additionally considering confounders, these issues are exacerbated, but we find that adjusted differential abundance testing can effectively mitigate them. In a large cardiometabolic disease dataset, we showcase that failure to account for covariates such as medication causes spurious association in real-world applications.

CONCLUSIONS: Tight error control is critical for microbiome association studies. The unsatisfactory performance of many differential abundance methods and the persistent danger of unchecked confounding suggest these contribute to a lack of reproducibility among such studies. We have open-sourced our simulation and benchmarking software to foster a much-needed consolidation of statistical methodology for microbiome research.},
}

Humans
*Microbiota
*Benchmarking
RNA, Ribosomal, 16S/genetics
Computer Simulation

@article {pmid39322314,
year = {2024},
author = {Van Hul, M and Cani, PD and Petifils, C and De Vos, WM and Tilg, H and El Omar, EM},
title = {What defines a healthy gut microbiome?.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2024-333378},
pmid = {39322314},
issn = {1468-3288},
abstract = {The understanding that changes in microbiome composition can influence chronic human diseases and the efficiency of therapies has driven efforts to develop microbiota-centred therapies such as first and next generation probiotics, prebiotics and postbiotics, microbiota editing and faecal microbiota transplantation. Central to microbiome research is understanding how disease impacts microbiome composition and vice versa, yet there is a problematic issue with the term 'dysbiosis', which broadly links microbial imbalances to various chronic illnesses without precision or definition. Another significant issue in microbiome discussions is defining 'healthy individuals' to ascertain what characterises a healthy microbiome. This involves questioning who represents the healthiest segment of our population-whether it is those free from illnesses, athletes at peak performance, individuals living healthily through regular exercise and good nutrition or even elderly adults or centenarians who have been tested by time and achieved remarkable healthy longevity.This review advocates for delineating 'what defines a healthy microbiome?' by considering a broader range of factors related to human health and environmental influences on the microbiota. A healthy microbiome is undoubtedly linked to gut health. Nevertheless, it is very difficult to pinpoint a universally accepted definition of 'gut health' due to the complexities of measuring gut functionality besides the microbiota composition. We must take into account individual variabilities, the influence of diet, lifestyle, host and environmental factors. Moreover, the challenge in distinguishing causation from correlation between gut microbiome and overall health is presented.The review also highlights the resource-heavy nature of comprehensive gut health assessments, which hinders their practicality and broad application. Finally, we call for continued research and a nuanced approach to better understand the intricate and evolving concept of gut health, emphasising the need for more precise and inclusive definitions and methodologies in studying the microbiome.},
}

@article {pmid39320132,
year = {2024},
author = {Bosland, MC and Gordon, T and Solomon, JJ and Shore, RE and Lippmann, M},
title = {Seventy-five years of impactful environmental and occupational health research at the Nelson Institute of Environmental Medicine at New York University.},
journal = {Annals of the New York Academy of Sciences},
volume = {},
number = {},
pages = {},
doi = {10.1111/nyas.15226},
pmid = {39320132},
issn = {1749-6632},
abstract = {Founded in 1947 as the Institute of Industrial Medicine, the Nelson Institute and Department of Environmental Medicine at New York University (NYU) Grossman School of Medicine (NYUGSOM) was supported by a National Institute of Environmental Health Science (NIEHS) Center Grant for over 56 years. Nelson Institute researchers generated 75 years of impactful research in environmental and occupational health, radiation effects, toxicology, and cancer. Environmental health research is continuing at NYUGSOM in its departments of medicine and population health. The objective of this historical commentary is to highlight the major achievements of the Nelson Institute and the department in the context of its history at facilities in Sterling Forest, Tuxedo, NY and Manhattan, NY. Aspects of our discussion include leadership, physical facilities, and research in many areas, including air pollution, health effects of environmental radiation exposures, inhalation toxicology methodology, carcinogenesis by chemicals, metals, and hormones, cancer chemoprevention, human microbiome, ecotoxicology, epidemiology, biostatistics, and community health concerns. The research of the institute and department benefited from unique facilities, strong leadership focused on team-based science, and outstanding investigators, students, and staff. A major lasting contribution has been the training of hundreds of graduate students and postdoctoral fellows, many of whom have been and are training the next generation of environmental and occupational health researchers at various institutions.},
}

@article {pmid39315152,
year = {2024},
author = {Zheng, B and Xu, J and Zhang, Y and Qin, J and Yuan, D and Fan, T and Wu, W and Chen, Y and Jiang, Y},
title = {MBCN: A novel reference database for Effcient Metagenomic analysis of human gut microbiome.},
journal = {Heliyon},
volume = {10},
number = {18},
pages = {e37422},
pmid = {39315152},
issn = {2405-8440},
abstract = {Metagenomic shotgun sequencing data can identify microbes and their proportions. But metagenomic shotgun data profiling results obtained from multiple projects using different reference databases are difficult to compare and apply meta-analysis. Our work aims to create a novel collection of human gut prokaryotic genomes, named Microbiome Collection Navigator (MBCN). 2379 human gut metagenomic samples are screened, and 16,785 metagenome-assembled genomes (MAGs) are assembled using a standardized pipeline. In addition, MAGs are combined with the representative genomes from public prokaryotic genomes collections to cluster, and pan-genomes for each cluster's genomes are constructed to build Kraken2 and Bracken databases. The databases built by MBCN are more comprehensive and accurate for profiling metagenomic reads comparing with other collections on simulated reads and virtual bio-projects. We profile 1082 human gut metagenomic samples with MBCN database and organize profiles and metadata on the web program. Meanwhile, using MBCN as a reference database, we also develop a unified, standardized, and systematic metagenomic analysis pipeline and platform, named MicrobiotaCN (http://www.microbiota.cn) and common statistical and visualization tools for microbiome research are integrated into the web program. Taken together, MBCN and MicrobiotaCN can be a valuable resource and a powerful tool that allows researchers to perform metagenomic analysis by a unified pipeline efficiently.},
}

@article {pmid39313228,
year = {2024},
author = {Kirtipal, N and Seo, Y and Son, J and Lee, S},
title = {Systems Biology of Human Microbiome for the Prediction of Personal Glycaemic Response.},
journal = {Diabetes & metabolism journal},
volume = {48},
number = {5},
pages = {821-836},
doi = {10.4093/dmj.2024.0382},
pmid = {39313228},
issn = {2233-6087},
support = {//Ministry of Science ICT/ ; 2021R1C1C1006336//National Research Foundation of Korea/ ; 2021M3A9G8022959//National Research Foundation of Korea/ ; RS-2024-00419699//National Research Foundation of Korea/ ; //Korea Health Industry Development Institute/ ; HR22C141105//Ministry of Health and Welfare/ ; 2024-ER2108-00//Korea National Institute of Health/ ; 2024-ER0608-00//Korea National Institute of Health/ ; //GIST Research Institute/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Precision Medicine/methods ; *Systems Biology/methods ; Machine Learning ; Dysbiosis ; Blood Glucose/analysis ; Diabetes Mellitus/microbiology ; Diabetes Mellitus, Type 2/microbiology ; Hypoglycemic Agents/therapeutic use ; },
abstract = {The human gut microbiota is increasingly recognized as a pivotal factor in diabetes management, playing a significant role in the body's response to treatment. However, it is important to understand that long-term usage of medicines like metformin and other diabetic treatments can result in problems, gastrointestinal discomfort, and dysbiosis of the gut flora. Advanced sequencing technologies have improved our understanding of the gut microbiome's role in diabetes, uncovering complex interactions between microbial composition and metabolic health. We explore how the gut microbiota affects glucose metabolism and insulin sensitivity by examining a variety of -omics data, including genomics, transcriptomics, epigenomics, proteomics, metabolomics, and metagenomics. Machine learning algorithms and genome-scale modeling are now being applied to find microbiological biomarkers associated with diabetes risk, predicted disease progression, and guide customized therapy. This study holds promise for specialized diabetic therapy. Despite significant advances, some concerns remain unanswered, including understanding the complex relationship between diabetes etiology and gut microbiota, as well as developing user-friendly technological innovations. This mini-review explores the relationship between multiomics, precision medicine, and machine learning to improve our understanding of the gut microbiome's function in diabetes. In the era of precision medicine, the ultimate goal is to improve patient outcomes through personalized treatments.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Precision Medicine/methods
*Systems Biology/methods
Machine Learning
Dysbiosis
Blood Glucose/analysis
Diabetes Mellitus/microbiology
Diabetes Mellitus, Type 2/microbiology
Hypoglycemic Agents/therapeutic use

@article {pmid39307902,
year = {2024},
author = {Ma, Z and Zuo, T and Frey, N and Rangrez, AY},
title = {A systematic framework for understanding the microbiome in human health and disease: from basic principles to clinical translation.},
journal = {Signal transduction and targeted therapy},
volume = {9},
number = {1},
pages = {237},
pmid = {39307902},
issn = {2059-3635},
support = {RA 2717/4-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 1289/17-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; },
mesh = {Humans ; *Microbiota/genetics ; Probiotics/therapeutic use ; Symbiosis/genetics ; },
abstract = {The human microbiome is a complex and dynamic system that plays important roles in human health and disease. However, there remain limitations and theoretical gaps in our current understanding of the intricate relationship between microbes and humans. In this narrative review, we integrate the knowledge and insights from various fields, including anatomy, physiology, immunology, histology, genetics, and evolution, to propose a systematic framework. It introduces key concepts such as the 'innate and adaptive genomes', which enhance genetic and evolutionary comprehension of the human genome. The 'germ-free syndrome' challenges the traditional 'microbes as pathogens' view, advocating for the necessity of microbes for health. The 'slave tissue' concept underscores the symbiotic intricacies between human tissues and their microbial counterparts, highlighting the dynamic health implications of microbial interactions. 'Acquired microbial immunity' positions the microbiome as an adjunct to human immune systems, providing a rationale for probiotic therapies and prudent antibiotic use. The 'homeostatic reprogramming hypothesis' integrates the microbiome into the internal environment theory, potentially explaining the change in homeostatic indicators post-industrialization. The 'cell-microbe co-ecology model' elucidates the symbiotic regulation affecting cellular balance, while the 'meta-host model' broadens the host definition to include symbiotic microbes. The 'health-illness conversion model' encapsulates the innate and adaptive genomes' interplay and dysbiosis patterns. The aim here is to provide a more focused and coherent understanding of microbiome and highlight future research avenues that could lead to a more effective and efficient healthcare system.},
}

Humans
*Microbiota/genetics
Probiotics/therapeutic use
Symbiosis/genetics

@article {pmid39306588,
year = {2024},
author = {Sahin, TK and Sonmezer, MC},
title = {The role of the microbiome in head and neck squamous cell cancers.},
journal = {European archives of oto-rhino-laryngology : official journal of the European Federation of Oto-Rhino-Laryngological Societies (EUFOS) : affiliated with the German Society for Oto-Rhino-Laryngology - Head and Neck Surgery},
volume = {},
number = {},
pages = {},
pmid = {39306588},
issn = {1434-4726},
abstract = {The human microbiome has garnered tremendous interest in the field of oncology, and microbiota studies in head and neck oncology has also flourished. Given the increasing incidence and mortality of HNSCC, as well as the suboptimal outcomes of available treatments, there is an urgent need for innovative approaches involving the microbiome. This review evaluates the intricate relationship between the microbiome and HNSCC, highlighting the potential of the microbiome as a marker for cancer detection, its role in malignancy, and its impact on the efficacy of conventional treatments like chemotherapy and radiotherapy. The review also explores the effects of treatment modalities on the microbiome and discusses the potential of microbiome alterations to predict and influence treatment toxicities such as mucositis and xerostomia. Further research is warranted to characterize the microbiome-HNSCC association, which holds promise for advancing early diagnosis, enhancing prognostic accuracy, and personalizing treatment strategies to improve patient outcomes. The exploration of the microbiome in clinical trials indicates a burgeoning subject of microbiome-focused therapies, heralding a new frontier in most cancer care.},
}

@article {pmid39304775,
year = {2024},
author = {Ray, K},
title = {A resource for the food microbiome and its links with the human microbiome.},
journal = {Nature reviews. Gastroenterology & hepatology},
volume = {},
number = {},
pages = {},
pmid = {39304775},
issn = {1759-5053},
}

@article {pmid39303118,
year = {2024},
author = {Doré, J and Sansonetti, PJ},
title = {[The human microbiome: 340 years of history, 140 years of interrogations, technological innovations and emergence of "microbial medicine"].},
journal = {Medecine sciences : M/S},
volume = {40},
number = {8-9},
pages = {654-660},
doi = {10.1051/medsci/2024101},
pmid = {39303118},
issn = {1958-5381},
mesh = {Humans ; *Microbiota/physiology ; History, 20th Century ; History, 21st Century ; History, 19th Century ; Symbiosis ; Inventions/history/trends ; History, 18th Century ; Gastrointestinal Microbiome/physiology ; },
abstract = {For 350 years, we have known that the human body hosts microbes, then called "animalcules". For over a century, following the demonstration of the role of some of these microbes in diseases, questions have arisen about the role of the largely predominant ones colonizing human skin and mucous surfaces, particularly the rich microbial ecosystem of the intestine, the gut microbiota. From the invention of germ-free life - axenism - which experimentally validated the human-microbe symbiosis, resulting from a long coevolution, to the development of anaerobic culture methods, then to the invention of molecular diagnosis, deep sequencing opening up metagenomic and omics approaches in general, a remarkable race has taken place between technological innovations and conceptual advances. This race, beyond the exhaustive description of the microbiota in its intra- and inter-human diversity, and the essential symbiotic functions of the microbiome, has paved the way for a new field of medicine: microbial medicine.},
}

Humans
*Microbiota/physiology
History, 20th Century
History, 21st Century
History, 19th Century
Symbiosis
Inventions/history/trends
History, 18th Century
Gastrointestinal Microbiome/physiology

@article {pmid39300165,
year = {2024},
author = {Bisht, V and Das, B and Hussain, A and Kumar, V and Navani, NK},
title = {Understanding of probiotic origin antimicrobial peptides: a sustainable approach ensuring food safety.},
journal = {NPJ science of food},
volume = {8},
number = {1},
pages = {67},
pmid = {39300165},
issn = {2396-8370},
abstract = {The practice of preserving and adding value to food dates back to over 10,000 BCE, when unintentional microbial-driven chemical reactions imparted flavor and extended the shelf life of fermented foods. The process evolved, and with the urbanization of society, significant shifts in dietary habits emerged, accompanied by sporadic food poisoning incidents. The repercussions of the COVID-19 pandemic have intensified the search for antibiotic alternatives owing to the rise in antibiotic-resistant pathogens, emphasizing the exploration of probiotic-origin antimicrobial peptides to alleviate human microbiome collateral damage. Often termed 'molecular knives', these peptides outstand as potent antimicrobials due to their compatibility with innate microflora, amenability to bioengineering, target specificity, versatility and rapidity in molecular level mode of action. This review centres on bacteriocins sourced from lactic acid bacteria found in ethnic fermented foods, accentuating their desirable attributes, technological applications as nanobiotics and potential future applications in the modern context of ensuring food safety.},
}

@article {pmid39298326,
year = {2024},
author = {Gordon, JI and Barratt, MJ and Hibberd, MC and Rahman, M and Ahmed, T},
title = {Establishing human microbial observatory programs in low- and middle-income countries.},
journal = {Annals of the New York Academy of Sciences},
volume = {},
number = {},
pages = {},
doi = {10.1111/nyas.15224},
pmid = {39298326},
issn = {1749-6632},
support = {//Fondazione Internazionale Premio Balzan/ ; //Bill and Melinda Gates Foundation/ ; /NH/NIH HHS/United States ; },
abstract = {Studies of the human microbiome are progressing rapidly but have largely focused on populations living in high-income countries. With increasing evidence that the microbiome contributes to the pathogenesis of diseases that affect infants, children, and adults in low- and middle-income countries (LMICs), and with profound and rapid ongoing changes occurring in our lifestyles and biosphere, understanding the origins of and developing microbiome-directed therapeutics for treating a number of global health challenges requires the development of programs for studying human microbial ecology in LMICs. Here, we discuss how the establishment of long-term human microbial observatory programs in selected LMICs could provide one timely approach.},
}

@article {pmid39295911,
year = {2023},
author = {Panwar, S and Kumari, S and Verma, J and Bakshi, S and Narendrakumar, L and Paul, D and Das, B},
title = {Toxin-linked mobile genetic elements in major enteric bacterial pathogens.},
journal = {Gut microbiome (Cambridge, England)},
volume = {4},
number = {},
pages = {e5},
pmid = {39295911},
issn = {2632-2897},
abstract = {One of the fascinating outcomes of human microbiome studies adopting multi-omics technology is its ability to decipher millions of microbial encoded functions in the most complex and crowded microbial ecosystem, including the human gastrointestinal (GI) tract without cultivating the microbes. It is well established that several functions that modulate the human metabolism, nutrient assimilation, immunity, infections, disease severity and therapeutic efficacy of drugs are mostly of microbial origins. In addition, these microbial functions are dynamic and can disseminate between microbial taxa residing in the same ecosystem or other microbial ecosystems through horizontal gene transfer. For clinicians and researchers alike, understanding the toxins, virulence factors and drug resistance traits encoded by the microbes associated with the human body is of utmost importance. Nevertheless, when such traits are genetically linked with mobile genetic elements (MGEs) that make them transmissible, it creates an additional burden to public health. This review mainly focuses on the functions of gut commensals and the dynamics and crosstalk between commensal and pathogenic bacteria in the gut. Also, the review summarises the plethora of MGEs linked with virulence genes present in the genomes of various enteric bacterial pathogens, which are transmissible among other pathogens and commensals.},
}

@article {pmid39296724,
year = {2020},
author = {Hill, C},
title = {You have the microbiome you deserve.},
journal = {Gut microbiome (Cambridge, England)},
volume = {1},
number = {},
pages = {e3},
pmid = {39296724},
issn = {2632-2897},
abstract = {The human microbiome is one of the most exciting areas of microbiology. From a starting point of tens of papers annually a couple of decades ago, there are now thousands of papers published every year on the microbiome. Huge strides have been made in terms of defining the individual members of complex human microbiomes from different body sites. The individuality and diversity of the human microbiome almost surpasses our ability to comprehend it. Advances in metagenomics and computational sciences have increased the complexity of the field, while at the same time we have moved from regarding the human microbiome as a benign passenger to a situation where it has been linked to almost every chronic disease, including obesity, cancer and infectious disease. The microbiome tantalizes us with the promise of novel therapeutic molecules and modalities for a range of intractable diseases. And yet, very few microbiome-based therapies have made it to the clinic or the pharmacy and we still cannot really define a healthy microbiome. We are entering the most exciting phase of microbiome research, as we develop effective, evidence-based interventions to preserve and restore human health. But we need rigour and numeracy if we are to realize this vision.},
}

@article {pmid39295904,
year = {2023},
author = {Ruxton, CHS and Kajita, C and Rocca, P and Pot, B},
title = {Microbiota and probiotics: chances and challenges - a symposium report.},
journal = {Gut microbiome (Cambridge, England)},
volume = {4},
number = {},
pages = {e6},
pmid = {39295904},
issn = {2632-2897},
abstract = {The 10th International Yakult Symposium was held in Milan, Italy, on 13-14 October 2022. Two keynote lectures covered the crewed journey to space and its implications for the human microbiome, and how current regulatory systems can be adapted and updated to ensure the safety of microorganisms used as probiotics or food processing ingredients. The remaining lectures were split into sections entitled "Chances" and "Challenges." The "Chances" section explored opportunities for the science of probiotics and fermented foods to contribute to diverse areas of health such as irritable bowel syndrome, major depression, Parkinson's disease, immune dysfunction, infant colic, intensive care, respiratory infections, and promoting healthy longevity. The "Challenges" section included selecting appropriate clinical trial participants and methodologies to minimise heterogeneity in responses, how to view probiotics in the context of One Health, adapting regulatory frameworks, and understanding how substances of bacterial origin can cross the blood-brain barrier. The symposium provided evidence from cutting-edge research that gut eubiosis is vital for human health and, like space, the microbiota deserves further exploration of its vast potential.},
}

@article {pmid39292000,
year = {2024},
author = {Kilgore, PB and Sha, J and Hendrix, EK and Neil, BH and Lawrence, WS and Peel, JE and Hittle, L and Woolston, J and Sulakvelidze, A and Schwartz, JA and Chopra, AK},
title = {A bacteriophage cocktail targeting Yersinia pestis provides strong post-exposure protection in a rat pneumonic plague model.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0094224},
doi = {10.1128/spectrum.00942-24},
pmid = {39292000},
issn = {2165-0497},
abstract = {Yersinia pestis, one of the deadliest bacterial pathogens ever known, is responsible for three plague pandemics and several epidemics, with over 200 million deaths during recorded history. Due to high genomic plasticity, Y. pestis is amenable to genetic mutations as well as genetic engineering that can lead to the emergence or intentional development of pan-drug-resistant strains. Indeed, antibiotic-resistant strains (e.g., strains carrying multidrug-resistant or MDR plasmids) have been isolated in various countries and endemic areas. Thus, there is an urgent need to develop novel, safe, and effective treatment approaches for managing Y. pestis infections. This includes infections by antigenically distinct strains for which vaccines (none FDA approved yet) may not be effective and those that cannot be managed by currently available antibiotics. Lytic bacteriophages provide one such alternative approach. In this study, we examined post-exposure efficacy of a bacteriophage cocktail, YPP-401, to combat pneumonic plague caused by Y. pestis CO92. YPP-401 is a four-phage preparation effective against a panel of at least 68 genetically diverse Y. pestis strains. Using a pneumonic plague aerosol challenge model in gender-balanced Brown Norway rats, YPP-401 demonstrated ~88% protection when delivered 18 h post-exposure for each of two administration routes (i.e., intraperitoneal and intranasal) in a dose-dependent manner. Our studies provide proof-of-concept that YPP-401 could be an innovative, safe, and effective approach for managing Y. pestis infections, including those caused by naturally occurring or intentionally developed multidrug-resistant strains.IMPORTANCECurrently, there are no FDA-approved plague vaccines. Since antibiotic-resistant strains of Y. pestis have emerged or are being intentionally developed to be used as a biothreat agent, new treatment modalities are direly needed. Phage therapy provides a viable option against potentially antibiotic-resistant strains. Additionally, phages are nontoxic and have been approved by the FDA for use in the food industry. Our study provides the first evidence of the protective effect of a cocktail of four phages against pneumonic plague, the most severe form of disease. When treatment was initiated 18 h post infection by either the intranasal or intraperitoneal route in Brown Norway rats, up to 87.5% protection was observed. The phage cocktail had a minimal impact on a representative human microbiome panel, unlike antibiotics. This study provides strong proof-of-concept data for the further development of phage-based therapy to treat plague.},
}

@article {pmid39283061,
year = {2024},
author = {McBurney, MI and Cho, CE},
title = {Understanding the role of the human gut microbiome in overweight and obesity.},
journal = {Annals of the New York Academy of Sciences},
volume = {},
number = {},
pages = {},
doi = {10.1111/nyas.15215},
pmid = {39283061},
issn = {1749-6632},
abstract = {The gut microbiome may be related to the prevalence of overweight and obesity, but high interindividual variability of the human microbiome complicates our understanding. Obesity often occurs concomitantly with micronutrient deficiencies that impair energy metabolism. Microbiota composition is affected by diet. Host-microbiota interactions are bidirectional. We propose three pathways whereby these interactions may modulate the gut microbiome and obesity: (1) ingested compounds or derivatives affecting small intestinal transit, endogenous secretions, digestion, absorption, microbiome balance, and gut barrier function directly affect host metabolism; (2) substrate availability affecting colonic microbial composition and contact with the gut barrier; and (3) microbial end products affecting host metabolism. The quantity/concentration, duration, and/or frequency (circadian rhythm) of changes in these pathways can alter the gut microbiome, disrupt the gut barrier, alter host immunity, and increase the risk of and progression to overweight and obesity. Host-specific characteristics (e.g., genetic variations) may further affect individual sensitivity and/or resilience to diet- and microbiome-associated perturbations in the colonic environment. In this narrative review, the effects of selected interventions, including fecal microbiota transplantation, dietary calorie restriction, dietary fibers and prebiotics, probiotics and synbiotics, vitamins, minerals, and fatty acids, on the gut microbiome, body weight, and/or adiposity are summarized to help identify mechanisms of action and research opportunities.},
}

@article {pmid39273475,
year = {2024},
author = {Larson, J and Sather, B and Wang, L and Westrum, J and Tokmina-Lukaszewska, M and Pauley, J and Copié, V and McDermott, TR and Bothner, B},
title = {Metalloproteomics Reveals Multi-Level Stress Response in Escherichia coli When Exposed to Arsenite.},
journal = {International journal of molecular sciences},
volume = {25},
number = {17},
pages = {},
pmid = {39273475},
issn = {1422-0067},
support = {P42ES031007//University of North Carolina's Superfund Program/ ; DE-SC0020246//U.S. Department of Energy/ ; S10 OD028650/OD/NIH HHS/United States ; MCB 1714556//National Science Foundation/ ; P42 ES031007/ES/NIEHS NIH HHS/United States ; R24 GM137786/GM/NIGMS NIH HHS/United States ; R24GM137786/GM/NIGMS NIH HHS/United States ; P20 GM103474/GM/NIGMS NIH HHS/United States ; },
mesh = {*Arsenites/toxicity ; *Escherichia coli/genetics/metabolism/drug effects ; *Escherichia coli Proteins/genetics/metabolism ; *Proteomics/methods ; *Stress, Physiological ; *Gene Expression Regulation, Bacterial/drug effects ; *Operon/genetics ; Metalloproteins/metabolism/genetics ; Humans ; },
abstract = {The arsRBC operon encodes a three-protein arsenic resistance system. ArsR regulates the transcription of the operon, while ArsB and ArsC are involved in exporting trivalent arsenic and reducing pentavalent arsenic, respectively. Previous research into Agrobacterium tumefaciens 5A has demonstrated that ArsR has regulatory control over a wide range of metal-related proteins and metabolic pathways. We hypothesized that ArsR has broad regulatory control in other Gram-negative bacteria and set out to test this. Here, we use differential proteomics to investigate changes caused by the presence of the arsR gene in human microbiome-relevant Escherichia coli during arsenite (As[III]) exposure. We show that ArsR has broad-ranging impacts such as the expression of TCA cycle enzymes during As[III] stress. Additionally, we found that the Isc [Fe-S] cluster and molybdenum cofactor assembly proteins are upregulated regardless of the presence of ArsR under these same conditions. An important finding from this differential proteomics analysis was the identification of response mechanisms that were strain-, ArsR-, and arsenic-specific, providing new clarity to this complex regulon. Given the widespread occurrence of the arsRBC operon, these findings should have broad applicability across microbial genera, including sensitive environments such as the human gastrointestinal tract.},
}

*Arsenites/toxicity
*Escherichia coli/genetics/metabolism/drug effects
*Escherichia coli Proteins/genetics/metabolism
*Proteomics/methods
*Stress, Physiological
*Gene Expression Regulation, Bacterial/drug effects
*Operon/genetics
Metalloproteins/metabolism/genetics
Humans

@article {pmid39271424,
year = {2024},
author = {Bokulich, NA and Robeson, MS},
title = {Bioinformatics challenges for profiling the microbiome in cancer: pitfalls and opportunities.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2024.08.011},
pmid = {39271424},
issn = {1878-4380},
abstract = {Increasing evidence suggests that the human microbiome plays an important role in cancer risk and treatment. Untargeted 'omics' techniques have accelerated research into microbiome-cancer interactions, supporting the discovery of novel associations and mechanisms. However, these techniques require careful selection and use to avoid biases and other pitfalls. In this essay, we discuss selected challenges involved in the analysis of microbiome data in the context of cancer, including the application of machine learning (ML). We focus on DNA sequencing-based (e.g., metagenomics) methods, but many of the pitfalls and opportunities generalize to other omics technologies as well. We advocate for extended training opportunities, community standards, and best practices for sharing data and code to advance transparency and reproducibility in cancer microbiome research.},
}

@article {pmid39256307,
year = {2024},
author = {Rastegar, S and Skurnik, M and Niaz, H and Tadjrobehkar, O and Samareh, A and Hosseini-Nave, H and Sabouri, S},
title = {Isolation, characterization, and potential application of Acinetobacter baumannii phages against extensively drug-resistant strains.},
journal = {Virus genes},
volume = {},
number = {},
pages = {},
pmid = {39256307},
issn = {1572-994X},
support = {KMU.AC.IR.400000652//Hossein Hosseini-Nave1/ ; },
abstract = {One of the significant issues in treating bacterial infections is the increasing prevalence of extensively drug-resistant (XDR) strains of Acinetobacter baumannii. In the face of limited or no viable treatment options for extensively drug-resistant (XDR) bacteria, there is a renewed interest in utilizing bacteriophages as a treatment option. Three Acinetobacter phages (vB_AbaS_Ftm, vB_AbaS_Eva, and vB_AbaS_Gln) were identified from hospital sewage and analyzed for their morphology, host ranges, and their genome sequences were determined and annotated. These phages and vB_AbaS_SA1 were combined to form a phage cocktail. The antibacterial effects of this cocktail and its combinations with selected antimicrobial agents were evaluated against the XDR A. baumannii strains. The phages exhibited siphovirus morphology. Out of a total of 30 XDR A. baumannii isolates, 33% were sensitive to vB_AbaS_Ftm, 30% to vB_AbaS_Gln, and 16.66% to vB_AbaS_Eva. When these phages were combined with antibiotics, they demonstrated a synergistic effect. The genome sizes of vB_AbaS_Ftm, vB_AbaS_Eva, and vB_AbaS_Gln were 48487, 50174, and 50043 base pairs (bp), respectively, and showed high similarity. Phage cocktail, when combined with antibiotics, showed synergistic effects on extensively drug-resistant (XDR) strains of A. baumannii. However, the need for further study to fully understand the mechanisms of action and potential limitations of using these phages is highlighted.},
}

@article {pmid39295776,
year = {2022},
author = {Puhlmann, ML and Jokela, R and van Dongen, KCW and Bui, TPN and van Hangelbroek, RWJ and Smidt, H and de Vos, WM and Feskens, EJM},
title = {Dried chicory root improves bowel function, benefits intestinal microbial trophic chains and increases faecal and circulating short chain fatty acids in subjects at risk for type 2 diabetes.},
journal = {Gut microbiome (Cambridge, England)},
volume = {3},
number = {},
pages = {e4},
pmid = {39295776},
issn = {2632-2897},
abstract = {We investigated the impact of dried chicory root in a randomised, placebo-controlled trial with 55 subjects at risk for type 2 diabetes on bowel function, gut microbiota and its products, and glucose homeostasis. The treatment increased stool softness (+1.1 ± 0.3 units; p = 0.034) and frequency (+0.6 ± 0.2 defecations/day; p < 0.001), strongly modulated gut microbiota composition (7 % variation; p = 0.001), and dramatically increased relative levels (3-4-fold) of Anaerostipes and Bifidobacterium spp., in a dose-dependent, reversible manner. A synthetic community, including selected members of these genera and a Bacteroides strain, generated a butyrogenic trophic chain from the product. Faecal acetate, propionate and butyrate increased by 25.8 % (+13.0 ± 6.3 mmol/kg; p = 0.023) as did their fasting circulating levels by 15.7 % (+7.7 ± 3.9 μM; p = 0.057). In the treatment group the glycaemic coefficient of variation decreased from 21.3 ± 0.94 to 18.3 ± 0.84 % (p = 0.004), whereas fasting glucose and HOMA-ir decreased in subjects with low baseline Blautia levels (-0.3 ± 0.1 mmol/L fasting glucose; p = 0.0187; -0.14 ± 0.1 HOMA-ir; p = 0.045). Dried chicory root intake rapidly and reversibly affects bowel function, benefits butyrogenic trophic chains, and promotes glycaemic control.},
}

@article {pmid39256189,
year = {2024},
author = {Yılmaz, SS and Kuşkucu, MA and Çakan, H and Aygün, G},
title = {Effective use of skin microbiome signatures for fingerprint identification.},
journal = {Skin research and technology : official journal of International Society for Bioengineering and the Skin (ISBS) [and] International Society for Digital Imaging of Skin (ISDIS) [and] International Society for Skin Imaging (ISSI)},
volume = {30},
number = {9},
pages = {e70052},
pmid = {39256189},
issn = {1600-0846},
support = {28100//Research Fund of Istanbul University-Cerrahpaşa/ ; },
mesh = {Humans ; *Microbiota/genetics ; *Skin/microbiology ; Adult ; Male ; Female ; Staphylococcus epidermidis/isolation & purification/genetics ; Ribotyping/methods ; Dermatoglyphics ; RNA, Ribosomal, 16S/genetics ; Young Adult ; Minisatellite Repeats ; },
abstract = {BACKGROUND: Recent advances have increased the importance of the human microbiome, including the skin microbiome. Despite the hand microbiome research, the factors affecting the composition of the hand microbiome and their personal characteristics are incompletely known.

OBJECTIVES: Despite changing environmental factors and personal variation, we aimed to indicate the interpersonal distinction between skin microbiota using simple and rapid molecular methods.

METHODS: Over a non-consecutive 10-day period, samples were taken from 10 adult individuals, and ribotyping analysis of the 16S and 23S genes of S. epidermidis was performed on each skin sample. Additionally, EcoRI and HindIII enzyme reactions and variable number tandem repeat (VNTR) reactions of S. epidermidis obtained from DNA samples were performed. The skin microbiomes of individuals were evaluated along with the microbiome profiles left on the surfaces they touched.

RESULTS: In the environmental samples taken, it has been observed that people preserve their core skin microbiota characters and carry them to their environment. It was determined that the highest similarity rate was 77.14%, and the lowest similarity rate was 31.74%.

CONCLUSION: Our study showed that the core skin microbiota retains its characteristics and leaves traces in environments. The fact that the personal microbiome remains unchanged despite environmental differences and has characteristic features has shown that it can be used in forensic sciences to distinguish individuals from each other. These results with simple and rapid methods further increased the importance and significance of the study. The findings indicate that personal skin microbiota can provide a significant contribution to criminal investigations by increasing accuracy and reliability, especially in forensic analyses.},
}

Humans
*Microbiota/genetics
*Skin/microbiology
Adult
Male
Female
Staphylococcus epidermidis/isolation & purification/genetics
Ribotyping/methods
Dermatoglyphics
RNA, Ribosomal, 16S/genetics
Young Adult
Minisatellite Repeats

@article {pmid39255394,
year = {2024},
author = {Ginsberg, SD and Blaser, MJ},
title = {Alzheimer's Disease Has Its Origins in Early Life via a Perturbed Microbiome.},
journal = {The Journal of infectious diseases},
volume = {230},
number = {Supplement_2},
pages = {S141-S149},
pmid = {39255394},
issn = {1537-6613},
support = {//Emch Foundation/ ; //Infectious Diseases Society of America/ ; U01 AI122285/NH/NIH HHS/United States ; R01 AG072599/AG/NIA NIH HHS/United States ; //C & D Fund/ ; },
mesh = {*Alzheimer Disease/microbiology ; Humans ; *Gastrointestinal Microbiome/physiology ; Animals ; Brain/microbiology/pathology ; Anti-Bacterial Agents/therapeutic use ; Microbiota ; },
abstract = {Alzheimer's disease (AD) is a neurodegenerative disorder with limited therapeutic options. Accordingly, new approaches for prevention and treatment are needed. One focus is the human microbiome, the consortium of microorganisms that live in and on us, which contributes to human immune, metabolic, and cognitive development and that may have mechanistic roles in neurodegeneration. AD and Alzheimer's disease-related dementias (ADRD) are recognized as spectrum disorders with complex pathobiology. AD/ADRD onset begins before overt clinical signs, but initiation triggers remain undefined. We posit that disruption of the normal gut microbiome in early life leads to a pathological cascade within septohippocampal and cortical brain circuits. We propose investigation to understand how early-life microbiota changes may lead to hallmark AD pathology in established AD/ADRD models. Specifically, we hypothesize that antibiotic exposure in early life leads to exacerbated AD-like disease endophenotypes that may be amenable to specific microbiological interventions. We propose suitable models for testing these hypotheses.},
}

*Alzheimer Disease/microbiology
Humans
*Gastrointestinal Microbiome/physiology
Animals
Brain/microbiology/pathology
Anti-Bacterial Agents/therapeutic use
Microbiota

@article {pmid39254049,
year = {2024},
author = {Harris, RM and Pace, F and Kuntz, TM and Morgan, XC and Hyland, P and Summers, K and McDermott, E and Blumen, K and Watnick, PI},
title = {Testosterone treatment impacts the intestinal microbiome of transgender individuals.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0055724},
doi = {10.1128/msphere.00557-24},
pmid = {39254049},
issn = {2379-5042},
abstract = {Medical modulation of sex hormone levels is a cornerstone of treatment for many conditions that impact well-being, including cancer, fertility/infertility, gender dysphoria, and chronic metabolic diseases such as diabetes and obesity. The microbial residents of the intestine, known as the microbiota, interact with sex hormones in the intestine, and there is correlative evidence that this interaction is bidirectional. Based on these published findings, we hypothesized that transgender individuals receiving exogenous testosterone as part of their gender-affirming medical treatment might undergo changes in their intestinal microbiome. To test this, we collected 26 stool samples from nine individuals before and up to 8 months after initiation of treatment with exogenous testosterone and subjected these samples to metagenomic analysis. While no species were significantly associated with the duration of testosterone therapy, pathways that generate glutamate increased in abundance, while those that consume glutamate decreased. Glutamate is a precursor of arginine, and testosterone is known to increase levels of arginine and its metabolites in the plasma. We hypothesize that testosterone increases the uptake of glutamate by enterocytes, thus decreasing access of the microbiota to this amino acid. While this pilot study establishes the impact of testosterone therapy on the intestinal microbiome, a more comprehensive study is necessary to establish the impact of testosterone-driven metagenomic shifts on the stool metatranscriptome, the stool metabolome, and the plasma metabolome.IMPORTANCEThe human intestine is inhabited by a large community of microbes known as the microbiome. Members of the microbiome consume the diet along with their human host. Thus, the metabolomes of the host and microbe are intricately linked. Testosterone alters the plasma metabolome. In particular, plasma levels of arginine and its metabolites and testosterone are positively correlated. To investigate the impact of exogenous testosterone on the microbiome, we analyzed the stool metagenomes of transgender individuals before and after the initiation of testosterone treatment. In this pilot project, we found a modest impact on the microbiome community structure but an increase in the abundance of metabolic pathways that generate glutamate and spare glutamate consumption. We propose that the host uses glutamate to generate arginine, decreasing the amount available for the microbiome.},
}

@article {pmid39251326,
year = {2024},
author = {Zhou, Q and Lei, L and Cheng, J and Chen, J and Du, Y and Zhang, X and Li, Q and Li, C and Deng, H and Wong, CC and Zhuang, B and Li, G and Bai, X},
title = {Microbiota-induced S100A11-RAGE axis underlies immune evasion in right-sided colon adenomas and is a therapeutic target to boost anti-PD1 efficacy.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2024-332193},
pmid = {39251326},
issn = {1468-3288},
abstract = {BACKGROUND: Tumourigenesis in right-sided and left-sided colons demonstrated distinct features.

OBJECTIVE: We aimed to characterise the differences between the left-sided and right-sided adenomas (ADs) representing the early stage of colonic tumourigenesis.

DESIGN: Single-cell and spatial transcriptomic datasets were analysed to reveal alterations between right-sided and left-sided colon ADs. Cells, animal experiments and clinical specimens were used to verify the results.

RESULTS: Single-cell analysis revealed that in right-sided ADs, there was a significant reduction of goblet cells, and these goblet cells were dysfunctional with attenuated mucin biosynthesis and defective antigen presentation. An impairment of the mucus barrier led to biofilm formation in crypts and subsequent bacteria invasion into right-sided ADs. The regions spatially surrounding the crypts with biofilm occupation underwent an inflammatory response by lipopolysaccharide (LPS) and an apoptosis process, as revealed by spatial transcriptomics. A distinct S100A11[+] epithelial cell population in the right-sided ADs was identified, and its expression level was induced by bacterial LPS and peptidoglycan. S100A11 expression facilitated tumour growth in syngeneic immunocompetent mice with increased myeloid-derived suppressor cells (MDSC) but reduced cytotoxic CD8+ T cells. Targeting S100A11 with well-tolerated antagonists of its receptor for advanced glycation end product (RAGE) (Azeliragon) significantly impaired tumour growth and MDSC infiltration, thereby boosting the efficacy of anti-programmed cell death protein 1 therapy in colon cancer.

CONCLUSION: Our findings unravelled that dysfunctional goblet cells and consequential bacterial translocation activated the S100A11-RAGE axis in right-sided colon ADs, which recruits MDSCs to promote immune evasion. Targeting this axis by Azeliragon improves the efficacy of immunotherapy in colon cancer.},
}

@article {pmid39244168,
year = {2024},
author = {Govender, P and Ghai, M},
title = {Population-specific differences in the human microbiome: Factors defining the diversity.},
journal = {Gene},
volume = {},
number = {},
pages = {148923},
doi = {10.1016/j.gene.2024.148923},
pmid = {39244168},
issn = {1879-0038},
abstract = {Differences in microbial communities at different body habitats define the microbiome composition of the human body. The gut, oral, skin vaginal fluid and tissue microbiome, are pivotal for human development and immune response and cross talk between these microbiomes is evident. Population studies reveal that various factors, such as host genetics, diet, lifestyle, aging, and geographical location are strongly associated with population-specific microbiome differences. The present review discusses the factors that shape microbiome diversity in humans, and microbiome differences in African, Asian and Caucasian populations. Gut microbiome studies show that microbial species Bacteroides is commonly found in individuals living in Western countries (Caucasian populations), while Prevotella is prevalent in non-Western countries (African and Asian populations). This association is mainly due to the high carbohydrate, high fat diet in western countries in contrast to high fibre, low fat diets in African/ Asian regions. Majority of the microbiome studies focus on the bacteriome component; however, interesting findings reveal that increased bacteriophage richness, which makes up the virome component, correlates with decreased bacterial diversity, and causes microbiome dysbiosis. An increase of Caudovirales (bacteriophages) is associated with a decrease in enteric bacteria in inflammatory bowel diseases. Future microbiome studies should evaluate the interrelation between bacteriome and virome to fully understand their significance in the pathogenesis and progression of human diseases. With ethnic health disparities becoming increasingly apparent, studies need to emphasize on the association of population-specific microbiome differences and human diseases, to develop microbiome-based therapeutics. Additionally, targeted phage therapy is emerging as an attractive alternative to antibiotics for bacterial infections. With rapid rise in microbiome research, focus should be on standardizing protocols, advanced bioinformatics tools, and reducing sequencing platform related biases. Ultimately, integration of multi-omics data (genomics, transcriptomics, proteomics and metabolomics) will lead to precision models for personalized microbiome therapeutics advancement.},
}

@article {pmid39243797,
year = {2024},
author = {Rodriguez, J and Hassani, Z and Alves Costa Silva, C and Betsou, F and Carraturo, F and Fasano, A and Israelsen, M and Iyappan, A and Krag, A and Metwaly, A and Schierwagen, R and Trebicka, J and Zwart, H and Doré, J and Cordaillat-Simmons, M and Druart, C and , },
title = {State of the art and the future of microbiome-based biomarkers: a multidisciplinary Delphi consensus.},
journal = {The Lancet. Microbe},
volume = {},
number = {},
pages = {100948},
doi = {10.1016/j.lanmic.2024.07.011},
pmid = {39243797},
issn = {2666-5247},
abstract = {Although microbiome signatures have been identified in various contexts (ie, pathogenesis of non-communicable diseases and treatment response), qualified microbiome-based biomarkers are currently not in use in clinical practice. The Human Microbiome Action consortium initiated a Delphi survey to establish a consensus on the needs, challenges, and limitations in developing qualified microbiome-based biomarkers. The questionnaire was developed by a scientific committee via literature review and expert interviews. To ensure broad applicability of the results, 307 experts were invited to participate; 114 of them responded to the first round of the survey, 93 of whom completed the second and final round as well. The survey highlighted the experts' confidence in the potential of microbiome-based biomarkers for several indications or pathologies. The paucity of validated analytical methods appears to be the principal factor hindering the qualification of these biomarkers. The survey also showed that clinical implementation of these biomarkers would only be possible if kitted and validated molecular assays with simple interpretation are developed. This initiative serves as a foundation for designing and implementing public-private collaborative projects to overcome the challenges and promote clinical application of microbiome-based biomarkers.},
}

@article {pmid39240756,
year = {2024},
author = {Torrillo, PA and Lieberman, TD},
title = {Reversions mask the contribution of adaptive evolution in microbiomes.},
journal = {eLife},
volume = {13},
number = {},
pages = {},
pmid = {39240756},
issn = {2050-084X},
support = {1DP2GM140922-01/NH/NIH HHS/United States ; Graduate Research Fellowship Program//National Science Foundation/ ; },
mesh = {*Mutation ; *Evolution, Molecular ; Selection, Genetic ; Genome, Bacterial ; Microbiota/genetics ; Gastrointestinal Microbiome/genetics ; Bacteroides/genetics ; Adaptation, Physiological/genetics ; Models, Genetic ; Bacteria/genetics/classification ; },
abstract = {When examining bacterial genomes for evidence of past selection, the results depend heavily on the mutational distance between chosen genomes. Even within a bacterial species, genomes separated by larger mutational distances exhibit stronger evidence of purifying selection as assessed by dN/dS, the normalized ratio of nonsynonymous to synonymous mutations. Here, we show that the classical interpretation of this scale dependence, weak purifying selection, leads to problematic mutation accumulation when applied to available gut microbiome data. We propose an alternative, adaptive reversion model with opposite implications for dynamical intuition and applications of dN/dS. Reversions that occur and sweep within-host populations are nearly guaranteed in microbiomes due to large population sizes, short generation times, and variable environments. Using analytical and simulation approaches, we show that adaptive reversion can explain the dN/dS decay given only dozens of locally fluctuating selective pressures, which is realistic in the context of Bacteroides genomes. The success of the adaptive reversion model argues for interpreting low values of dN/dS obtained from long timescales with caution as they may emerge even when adaptive sweeps are frequent. Our work thus inverts the interpretation of an old observation in bacterial evolution, illustrates the potential of mutational reversions to shape genomic landscapes over time, and highlights the importance of studying bacterial genomic evolution on short timescales.},
}

*Mutation
*Evolution, Molecular
Selection, Genetic
Genome, Bacterial
Microbiota/genetics
Gastrointestinal Microbiome/genetics
Bacteroides/genetics
Adaptation, Physiological/genetics
Models, Genetic
Bacteria/genetics/classification

@article {pmid39238383,
year = {2024},
author = {Sanyal, S and Nigam, K and Singh, S and Lohani, P and Dwivedi, M},
title = {Pathophysiological and Clinical Potential of Human Microbiome: Microbe-based Therapeutic Insights.},
journal = {Current pharmaceutical biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.2174/0113892010314433240823113111},
pmid = {39238383},
issn = {1873-4316},
abstract = {The human microbiota represents the community and diverse population of microbes within the human body, which comprises approximately 100 trillion micro-organisms. They exist in the human gastrointestinal tract and various other organs and are now considered virtual body organs. It is mainly represented by bacteria but also includes viruses, fungi, and protozoa. Although there is a heritable component to the gut microbiota, environmental factors related to diet, drugs, and anthropometry determine the composition of the microbiota. Besides the gastrointestinal tract, the human body also harbours microbial communities in the skin, oral and nasal cavities, and reproductive tract. The current review demonstrates the role of gut microbiota and its involvement in processing food, drugs, and immune responses. The discussion focuses on the implications of human microbiota in developing several diseases, such as gastrointestinal infections, metabolic disorders, malignancies, etc., through symbiotic relationships. The microbial population may vary depending on the pathophysiological condition of an individual and thus may be exploited as a therapeutic and clinical player. Further, we need a more thorough investigation to establish the correlation between microbes and pathophysiology in humans and propose them as potential therapeutic targets.},
}

@article {pmid39235252,
year = {2024},
author = {Sweet, P and Burroughs, M and Jang, S and Contreras, L},
title = {TolRad, a model for predicting radiation tolerance using Pfam annotations, identifies novel radiosensitive bacterial species from reference genomes and MAGs.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0383823},
doi = {10.1128/spectrum.03838-23},
pmid = {39235252},
issn = {2165-0497},
abstract = {UNLABELLED: The trait of ionizing radiation (IR) tolerance is variable between bacterium, with species succumbing to acute doses as low as 60 Gy and extremophiles able to survive doses exceeding 10,000 Gy. While survival screens have identified multiple highly radioresistant bacteria, such systemic searches have not been conducted for IR-sensitive bacteria. The taxonomy-level diversity of IR sensitivity is poorly understood, as are genetic elements that influence IR sensitivity. Using the protein domain (Pfam) frequencies from 61 bacterial species with experimentally determined D10 values (the dose at which only 10% of the population survives), we trained TolRad, a random forest binary classifier, to distinguish between radiosensitive (D10 < 200 Gy) and radiation-tolerant (D10 > 200 Gy) bacteria. On untrained species, TolRad had an accuracy of 0.900. We applied TolRad to 152 UniProt-hosted bacterial proteomes associated with the human microbiome, including 37 strains from the ATCC Human Microbiome Collection, and classified 34 species as radiosensitive. Whereas IR-sensitive species (D10 < 200 Gy) in the training data set had been confined to the phylum Proteobacterium, this initial TolRad screen identified radiosensitive bacteria in two additional phyla. We experimentally validated the predicted radiosensitivity of a Bacteroidota species from the human microbiome. To demonstrate that TolRad can be applied to metagenome-assembled genomes (MAGs), we tested the accuracy of TolRad on Egg-NOG assembled proteomes (0.965) and partial proteomes. Finally, three collections of MAGs were screened using TolRad, identifying further phyla with radiosensitive species and suggesting that environmental conditions influence the abundance of radiosensitive bacteria.

IMPORTANCE: Bacterial species have vast genetic diversity, allowing for life in extreme environments and the conduction of complex chemistry. The ability to harness the full potential of bacterial diversity is hampered by the lack of high-throughput experimental or bioinformatic methods for characterizing bacterial traits. Here, we present a computational model that uses de novo-generated genome annotations to classify a bacterium as tolerant of ionizing radiation (IR) or as radiosensitive. This model allows for rapid screening of bacterial communities for low-tolerance species that are of interest for both mechanistic studies into bacterial sensitivity to IR and biomarkers of IR exposure.},
}

@article {pmid39233526,
year = {2024},
author = {Kim, TH and Cho, BK and Lee, DH},
title = {Synthetic Biology-Driven Microbial Therapeutics for Disease Treatment.},
journal = {Journal of microbiology and biotechnology},
volume = {34},
number = {10},
pages = {1-12},
doi = {10.4014/jmb.2407.07004},
pmid = {39233526},
issn = {1738-8872},
abstract = {The human microbiome, consisting of microorganisms that coexist symbiotically with the body, impacts health from birth. Alterations in gut microbiota driven by factors such as diet and medication can contribute to diseases beyond the gut. Synthetic biology has paved the way for engineered microbial therapeutics, presenting promising treatments for a variety of conditions. Using genetically encoded biosensors and dynamic regulatory tools, engineered microbes can produce and deliver therapeutic agents, detect biomarkers, and manage diseases. This review organizes engineered microbial therapeutics by disease type, emphasizing innovative strategies and recent advancements. The scope of diseases includes gastrointestinal disorders, cancers, metabolic diseases, infections, and other ailments. Synthetic biology facilitates precise targeting and regulation, improving the efficacy and safety of these therapies. With promising results in animal models, engineered microbial therapeutics provide a novel alternative to traditional treatments, heralding a transformative era in diagnostics and treatment for numerous diseases.},
}

@article {pmid39232070,
year = {2024},
author = {Jang, H and Koh, H},
title = {A unified web cloud computing platform MiMedSurv for microbiome causal mediation analysis with survival responses.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {20650},
pmid = {39232070},
issn = {2045-2322},
support = {2021R1C1C1013861//National Research Foundation of Korea/ ; },
mesh = {Humans ; *Microbiota ; *Cloud Computing ; *Internet ; Software ; Survival Analysis ; },
abstract = {In human microbiome studies, mediation analysis has recently been spotlighted as a practical and powerful analytic tool to survey the causal roles of the microbiome as a mediator to explain the observed relationships between a medical treatment/environmental exposure and a human disease. We also note that, in a clinical research, investigators often trace disease progression sequentially in time; as such, time-to-event (e.g., time-to-disease, time-to-cure) responses, known as survival responses, are prevalent as a surrogate variable for human health or disease. In this paper, we introduce a web cloud computing platform, named as microbiome mediation analysis with survival responses (MiMedSurv), for comprehensive microbiome mediation analysis with survival responses on user-friendly web environments. MiMedSurv is an extension of our prior web cloud computing platform, named as microbiome mediation analysis (MiMed), for survival responses. The two main features that are well-distinguished are as follows. First, MiMedSurv conducts some baseline exploratory non-mediational survival analysis, not involving microbiome, to survey the disparity in survival response between medical treatments/environmental exposures. Then, MiMedSurv identifies the mediating roles of the microbiome in various aspects: (i) as a microbial ecosystem using ecological indices (e.g., alpha and beta diversity indices) and (ii) as individual microbial taxa in various hierarchies (e.g., phyla, classes, orders, families, genera, species). To illustrate its use, we survey the mediating roles of the gut microbiome between antibiotic treatment and time-to-type 1 diabetes. MiMedSurv is freely available on our web server (http://mimedsurv.micloud.kr).},
}

Humans
*Microbiota
*Cloud Computing
*Internet
Software
Survival Analysis

@article {pmid39230701,
year = {2024},
author = {Hera, MR and Liu, S and Wei, W and Rodriguez, JS and Ma, C and Koslicki, D},
title = {Metagenomic functional profiling: to sketch or not to sketch?.},
journal = {Bioinformatics (Oxford, England)},
volume = {40},
number = {Supplement_2},
pages = {ii165-ii173},
pmid = {39230701},
issn = {1367-4811},
support = {R01 GM146462/GM/NIGMS NIH HHS/United States ; R01GM146462/GF/NIH HHS/United States ; },
mesh = {*Metagenomics/methods ; *Software ; *Algorithms ; *Metagenome/genetics ; Humans ; Microbiota/genetics ; Databases, Genetic ; },
abstract = {MOTIVATION: Functional profiling of metagenomic samples is essential to decipher the functional capabilities of microbial communities. Traditional and more widely used functional profilers in the context of metagenomics rely on aligning reads against a known reference database. However, aligning sequencing reads against a large and fast-growing database is computationally expensive. In general, k-mer-based sketching techniques have been successfully used in metagenomics to address this bottleneck, notably in taxonomic profiling. In this work, we describe leveraging FracMinHash (implemented in sourmash, a publicly available software), a k-mer-sketching algorithm, to obtain functional profiles of metagenome samples.

RESULTS: We show how pieces of the sourmash software (and the resulting FracMinHash sketches) can be put together in a pipeline to functionally profile a metagenomic sample. We named our pipeline fmh-funprofiler. We report that the functional profiles obtained using this pipeline demonstrate comparable completeness and better purity compared to the profiles obtained using other alignment-based methods when applied to simulated metagenomic data. We also report that fmh-funprofiler is 39-99× faster in wall-clock time, and consumes up to 40-55× less memory. Coupled with the KEGG database, this method not only replicates fundamental biological insights but also highlights novel signals from the Human Microbiome Project datasets.

This fast and lightweight metagenomic functional profiler is freely available and can be accessed here: https://github.com/KoslickiLab/fmh-funprofiler. All scripts of the analyses we present in this manuscript can be found on GitHub.},
}

*Metagenomics/methods
*Software
*Algorithms
*Metagenome/genetics
Humans
Microbiota/genetics
Databases, Genetic

@article {pmid39230353,
year = {2024},
author = {Bland, CM and Love, BL and Jones, BM},
title = {Human microbiome: Impact of newly approved treatments on C. difficile infection.},
journal = {American journal of health-system pharmacy : AJHP : official journal of the American Society of Health-System Pharmacists},
volume = {},
number = {},
pages = {},
doi = {10.1093/ajhp/zxae249},
pmid = {39230353},
issn = {1535-2900},
abstract = {DISCLAIMER: In an effort to expedite the publication of articles, AJHP is posting manuscripts online as soon as possible after acceptance. Accepted manuscripts have been peer-reviewed and copyedited, but are posted online before technical formatting and author proofing. These manuscripts are not the final version of record and will be replaced with the final article (formatted per AJHP style and proofed by the authors) at a later time.

PURPOSE: The primary purposes of this review are to provide a brief overview of the microbiome, discuss the most relevant outcome data and key characteristics of each live microbiome agent, and pose questions for consideration going forward as these agents are integrated into clinical practice.

SUMMARY: The management of Clostridiodes difficile infection (CDI) remains a difficult clinical conundrum, with recurrent CDI occurring in 15% to 35% of patients and causing significant morbidity and decreased quality of life. For patients with frequent CDI recurrences, fecal microbiota transplantation (FMT) has been demonstrated to have significant benefit but also significant risks, and FMT is not approved by the US Food and Drug Administration (FDA) for that indication. FDA has established a new therapeutic class for agents known as live biotherapeutic products (LBPs) that offer significant advantages over FMT, including standardized screening, testing, and manufacturing as well as known quantities of organisms contained within. Two new live microbiome products within this class were recently approved by FDA for prevention of CDI recurrences in adult patients following treatment for recurrent CDI with standard antimicrobial therapy. Both agents had demonstrated efficacy in registry trials in preventing CDI recurrence but differ significantly in a number of characteristics, such as route of administration. Cost as well as logistics are current obstacles to use of these therapies.

CONCLUSION: Live microbiome therapy is a promising solution for patients with recurrent CDI. Future studies should provide further evidence within yet-to-be-evaluated populations not included in registry studies. This along with real-world evidence will inform future use and clinical guideline placement.},
}

@article {pmid39230261,
year = {2024},
author = {Tu, V and Ren, Y and Tanes, C and Mukhopadhyay, S and Daniel, SG and Li, H and Bittinger, K},
title = {A quantitative approach to measure and predict microbiome response to antibiotics.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0048824},
doi = {10.1128/msphere.00488-24},
pmid = {39230261},
issn = {2379-5042},
abstract = {UNLABELLED: Although antibiotics induce sizable perturbations in the human microbiome, we lack a systematic and quantitative method to measure and predict the microbiome's response to specific antibiotics. Here, we introduce such a method, which takes the form of a microbiome response index (MiRIx) for each antibiotic. Antibiotic-specific MiRIx values quantify the overall susceptibility of the microbiota to an antibiotic, based on databases of bacterial phenotypes and published data on intrinsic antibiotic susceptibility. We applied our approach to five published microbiome studies that carried out antibiotic interventions with vancomycin, metronidazole, ciprofloxacin, amoxicillin, and doxycycline. We show how MiRIx can be used in conjunction with existing microbiome analytical approaches to gain a deeper understanding of the microbiome response to antibiotics. Finally, we generate antibiotic response predictions for the oral, skin, and gut microbiome in healthy humans. Our approach is implemented as open-source software and is readily applied to microbiome data sets generated by 16S rRNA marker gene sequencing or shotgun metagenomics.

IMPORTANCE: Antibiotics are potent influencers of the human microbiome and can be a source for enduring dysbiosis and antibiotic resistance in healthcare. Existing microbiome data analysis methods can quantify perturbations of bacterial communities but cannot evaluate whether the differences are aligned with the expected activity of a specific antibiotic. Here, we present a novel method to quantify and predict antibiotic-specific microbiome changes, implemented in a ready-to-use software package. This has the potential to be a critical tool to broaden our understanding of the relationship between the microbiome and antibiotics.},
}

@article {pmid39229171,
year = {2024},
author = {Lebrun-Corbin, M and Cheung, BH and Hullahalli, K and Dailey, K and Bailey, K and Waldor, MK and Wunderink, RG and Bachta, KER and Hauser, AR},
title = {Pseudomonas aeruginosa population dynamics in a vancomycin-induced murine model of gastrointestinal carriage.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.08.19.608679},
pmid = {39229171},
issn = {2692-8205},
abstract = {UNLABELLED: Pseudomonas aeruginosa is a common nosocomial pathogen and a major cause of morbidity and mortality in hospitalized patients. Multiple reports highlight that P. aeruginosa gastrointestinal colonization may precede systemic infections by this pathogen. Gaining a deeper insight into the dynamics of P. aeruginosa gastrointestinal carriage is an essential step in managing gastrointestinal colonization and could contribute to preventing bacterial transmission and progression to systemic infection. Here, we present a clinically relevant mouse model relying on parenteral vancomycin pretreatment and a single orogastric gavage of a controlled dose of P. aeruginosa. Robust carriage was observed with multiple clinical isolates, and carriage persisted for up to 60 days. Histological and microbiological examination of mice indicated that this model indeed represented carriage and not infection. We then used a barcoded P. aeruginosa library along with the sequence tag-based analysis of microbial populations (STAMPR) analytic pipeline to quantify bacterial population dynamics and bottlenecks during the establishment of the gastrointestinal carriage. Analysis indicated that most of the P. aeruginosa population was rapidly eliminated in the stomach, but the few bacteria that moved to the small intestine and the caecum expanded significantly. Hence, the stomach constitutes a significant barrier against gastrointestinal carriage of P. aeruginosa, which may have clinical implications for hospitalized patients.

IMPORTANCE: While P. aeruginosa is rarely part of the normal human microbiome, carriage of the bacterium is quite frequent in hospitalized patients and residents of long-term care facilities. P. aeruginosa carriage is a precursor to infection. Options for treating infections caused by difficult-to-treat P. aeruginosa strains are dwindling, underscoring the urgency to better understand and impede pre-infection stages, such as colonization. Here, we use vancomycin-treated mice to model antibiotic-treated patients who become colonized with P. aeruginosa in their gastrointestinal tracts. We identify the stomach as a major barrier to the establishment of gastrointestinal carriage. These findings suggest that efforts to prevent gastrointestinal colonization should focus not only on judicious use of antibiotics but also on investigation into how the stomach eliminates orally ingested P. aeruginosa .},
}

@article {pmid39227641,
year = {2024},
author = {Donnelly, SC and Varela-Mattatall, GE and Hassan, S and Sun, Q and Gelman, N and Thiessen, JD and Thompson, RT and Prato, FS and Burton, JP and Goldhawk, DE},
title = {Bacterial association with metals enables in vivo monitoring of urogenital microbiota using magnetic resonance imaging.},
journal = {Communications biology},
volume = {7},
number = {1},
pages = {1079},
pmid = {39227641},
issn = {2399-3642},
support = {ALLRP576699-22//Gouvernement du Canada | Natural Sciences and Engineering Research Council of Canada (Conseil de Recherches en Sciences Naturelles et en Génie du Canada)/ ; },
mesh = {Humans ; *Magnetic Resonance Imaging/methods ; *Microbiota ; Female ; Bacteria/metabolism/isolation & purification ; Metals/metabolism ; Urogenital System/microbiology ; Manganese/metabolism/analysis ; },
abstract = {Bacteria constitute a significant part of the biomass of the human microbiota, but their interactions are complex and difficult to replicate outside the host. Exploiting the superior resolution of magnetic resonance imaging (MRI) to examine signal parameters of selected human isolates may allow tracking of their dispersion throughout the body. Here we investigate longitudinal and transverse MRI relaxation rates and found significant differences between several bacterial strains. Common commensal strains of lactobacilli display notably high MRI relaxation rates, partially explained by elevated cellular manganese content, while other species contain more iron than manganese. Lactobacillus crispatus show particularly high values, 4-fold greater than any other species; up to 60-fold greater signal than relevant tissue background; and a linear relationship between relaxation rate and fraction of live cells. Different bacterial strains have detectable, repeatable MRI relaxation rates that in the future may enable monitoring of their persistence in the human body for enhanced molecular imaging.},
}

Humans
*Magnetic Resonance Imaging/methods
*Microbiota
Female
Bacteria/metabolism/isolation & purification
Metals/metabolism
Urogenital System/microbiology
Manganese/metabolism/analysis

@article {pmid39226354,
year = {2024},
author = {Chimileski, S and Borisy, GG and Dewhirst, FE and Mark Welch, JL},
title = {Tip extension and simultaneous multiple fission in a filamentous bacterium.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {121},
number = {37},
pages = {e2408654121},
doi = {10.1073/pnas.2408654121},
pmid = {39226354},
issn = {1091-6490},
support = {2245229//NSF | ENG | Division of Emerging Frontiers and Multidisciplinary Activities (EFMA)/ ; DE022586//HHS | NIH | National Institute of Dental and Craniofacial Research (NIDCR)/ ; 2245229//NSF | ENG | Division of Emerging Frontiers and Multidisciplinary Activities (EFMA)/ ; },
mesh = {*Peptidoglycan/metabolism ; Corynebacterium/metabolism/growth & development ; Biofilms/growth & development ; Cell Division ; Humans ; Dental Plaque/microbiology ; },
abstract = {Organisms display an immense variety of shapes, sizes, and reproductive strategies. At microscopic scales, bacterial cell morphology and growth dynamics are adaptive traits that influence the spatial organization of microbial communities. In one such community-the human dental plaque biofilm-a network of filamentous Corynebacterium matruchotii cells forms the core of bacterial consortia known as hedgehogs, but the processes that generate these structures are unclear. Here, using live-cell time-lapse microscopy and fluorescent D-amino acids to track peptidoglycan biosynthesis, we report an extraordinary example of simultaneous multiple division within the domain Bacteria. We show that C. matruchotii cells elongate at one pole through tip extension, similar to the growth strategy of soil-dwelling Streptomyces bacteria. Filaments elongate rapidly, at rates more than five times greater than other closely related bacterial species. Following elongation, many septa form simultaneously, and each cell divides into 3 to 14 daughter cells, depending on the length of the mother filament. The daughter cells then nucleate outgrowth of new thinner vegetative filaments, generating the classic "whip handle" morphology of this taxon. Our results expand the known diversity of bacterial cell cycles and help explain how this filamentous bacterium can compete for space, access nutrients, and form important interspecies interactions within dental plaque.},
}

*Peptidoglycan/metabolism
Corynebacterium/metabolism/growth & development
Biofilms/growth & development
Cell Division
Humans
Dental Plaque/microbiology

@article {pmid39221598,
year = {2024},
author = {Divakara, N and Dempsey, Z and Saraswati, C and Garssen, J and Silva, D and Keelan, JA and Christophersen, CT and Cooper, MN and Prescott, SL and Palmer, DJ and Verhasselt, V and Macchiaverni, P},
title = {Effect of maternal prebiotic supplementation on human milk immunological composition: Insights from the SYMBA study.},
journal = {Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology},
volume = {35},
number = {9},
pages = {e14226},
doi = {10.1111/pai.14226},
pmid = {39221598},
issn = {1399-3038},
support = {RA/1/3027/386//WA Child Research Fund (WACRF)/ ; //Family Larsson-Rosenquist Foundation/ ; //National Health and Medical Research Council/ ; //Telethon Kids Institute Ascend Fellowship/ ; //Telethon-Perth Children's Hospital Research Fund/ ; //Paul Ramsay Foundation/ ; //Commonwealth Government of Australia/ ; //NHMRC Medical Research Future Fund (MRFF)/ ; },
mesh = {Humans ; *Milk, Human/immunology/chemistry ; *Prebiotics/administration & dosage ; Female ; Double-Blind Method ; *Dietary Supplements ; Pregnancy ; Infant ; Adult ; Male ; Lactation/immunology ; Oligosaccharides/administration & dosage ; Infant, Newborn ; Breast Feeding ; Cytokines/metabolism ; },
abstract = {BACKGROUND: Immunomodulatory proteins in human milk (HM) can shape infant immune development. However, strategies to modulate their levels are currently unknown. This study investigated whether maternal prebiotic supplementation alters the levels of immunomodulatory proteins in HM.

METHODS: The study was nested within the SYMBA double-blind randomized controlled trial (ACTRN12615001075572), which investigated the effects of maternal prebiotic (short-chain galacto-oligosaccharides/long-chain fructo-oligosaccharides) supplementation from <21 weeks gestation during pregnancy until 6 months postnatal during lactation on child allergic disease risk. Mother-child dyads receiving prebiotics (n = 46) or placebo (n = 54) were included in this study. We measured the levels of 24 immunomodulatory proteins in HM collected at 2, 4, and 6 months.

RESULTS: Cluster analysis showed that the overall immunomodulatory protein composition of milk samples from both groups was similar. At 2 months, HM of prebiotic-supplemented women had decreased levels of TGF-β1 and TSLP (95% CI: -17.4 [-29.68, -2.28] and -57.32 [-94.22, -4.7] respectively) and increased levels of sCD14 (95% CI: 1.81 [0.17, 3.71]), when compared to the placebo group. At 4 months, IgG1 was lower in the prebiotic group (95% CI: -1.55 [-3.55, -0.12]) compared to placebo group.

CONCLUSION: This exploratory study shows that prebiotic consumption by lactating mothers selectively alters specific immunomodulatory proteins in HM. This finding is crucial for understanding how prebiotic dietary recommendations for pregnant and lactating women can modify the immune properties of HM and potentially influence infant health outcomes through immune support from breastfeeding.},
}

Humans
*Milk, Human/immunology/chemistry
*Prebiotics/administration & dosage
Female
Double-Blind Method
*Dietary Supplements
Pregnancy
Infant
Adult
Male
Lactation/immunology
Oligosaccharides/administration & dosage
Infant, Newborn
Breast Feeding
Cytokines/metabolism

@article {pmid39218882,
year = {2024},
author = {Zhuang, Z and Lin, J and Wan, Z and Weng, J and Yuan, Z and Xie, Y and Liu, Z and Xie, P and Mao, S and Wang, Z and Wang, X and Huang, M and Luo, Y and Yu, H},
title = {Radiogenomic profiling of global DNA methylation associated with molecular phenotypes and immune features in glioma.},
journal = {BMC medicine},
volume = {22},
number = {1},
pages = {352},
pmid = {39218882},
issn = {1741-7015},
mesh = {Humans ; *Glioma/genetics/immunology ; *DNA Methylation/genetics ; Female ; *Magnetic Resonance Imaging ; Male ; *Brain Neoplasms/genetics/diagnostic imaging/immunology/pathology ; Middle Aged ; Adult ; Machine Learning ; Phenotype ; Aged ; Biomarkers, Tumor/genetics ; },
abstract = {BACKGROUND: The radiogenomic analysis has provided valuable imaging biomarkers with biological insights for gliomas. The radiogenomic markers for molecular profile such as DNA methylation remain to be uncovered to assist the molecular diagnosis and tumor treatment.

METHODS: We apply the machine learning approaches to identify the magnetic resonance imaging (MRI) features that are associated with molecular profiles in 146 patients with gliomas, and the fitting models for each molecular feature (MoRad) are developed and validated. To provide radiological annotations for the molecular profiles, we devise two novel approaches called radiomic oncology (RO) and radiomic set enrichment analysis (RSEA).

RESULTS: The generated MoRad models perform well for profiling each molecular feature with radiomic features, including mutational, methylation, transcriptional, and protein profiles. Among them, the MoRad models have a remarkable performance in quantitatively mapping global DNA methylation. With RO and RSEA approaches, we find that global DNA methylation could be reflected by the heterogeneity in volumetric and textural features of enhanced regions in T2-weighted MRI. Finally, we demonstrate the associations of global DNA methylation with clinicopathological, molecular, and immunological features, including histological grade, mutations of IDH and ATRX, MGMT methylation, multiple methylation-high subtypes, tumor-infiltrating lymphocytes, and long-term survival outcomes.

CONCLUSIONS: Global DNA methylation is highly associated with radiological profiles in glioma. Radiogenomic global methylation is an imaging-based quantitative molecular biomarker that is associated with specific consensus molecular subtypes and immune features.},
}

Humans
*Glioma/genetics/immunology
*DNA Methylation/genetics
Female
*Magnetic Resonance Imaging
Male
*Brain Neoplasms/genetics/diagnostic imaging/immunology/pathology
Middle Aged
Adult
Machine Learning
Phenotype
Aged
Biomarkers, Tumor/genetics

@article {pmid39217206,
year = {2024},
author = {Duller, S and Vrbancic, S and Szydłowski, Ł and Mahnert, A and Blohs, M and Predl, M and Kumpitsch, C and Zrim, V and Högenauer, C and Kosciolek, T and Schmitz, RA and Eberhard, A and Dragovan, M and Schmidberger, L and Zurabischvili, T and Weinberger, V and Moser, AM and Kolb, D and Pernitsch, D and Mohammadzadeh, R and Kühnast, T and Rattei, T and Moissl-Eichinger, C},
title = {Targeted isolation of Methanobrevibacter strains from fecal samples expands the cultivated human archaeome.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {7593},
pmid = {39217206},
issn = {2041-1723},
support = {P 30796//Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung)/ ; SFB F-83//Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung)/ ; COE 7//Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung)/ ; },
mesh = {*Methanobrevibacter/genetics/isolation & purification/metabolism ; Humans ; *Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; *Genome, Archaeal ; Methane/metabolism ; Phylogeny ; Adult ; Male ; Female ; Gastrointestinal Tract/microbiology ; },
abstract = {Archaea are vital components of the human microbiome, yet their study within the gastrointestinal tract (GIT) is limited by the scarcity of cultured representatives. Our study presents a method for the targeted enrichment and isolation of methanogenic archaea from human fecal samples. The procedure combines methane breath testing, in silico metabolic modeling, media optimization, FACS, dilution series, and genomic sequencing through Nanopore technology. Additional analyzes include the co-cultured bacteriome, comparative genomics of archaeal genomes, functional comparisons, and structure-based protein function prediction of unknown differential traits. Successful establishment of stable archaeal cultures from 14 out of 16 fecal samples yielded nine previously uncultivated strains, eight of which are absent from a recent archaeome genome catalog. Comparative genomic and functional assessments of Methanobrevibacter smithii and Candidatus Methanobrevibacter intestini strains from individual donors revealed features potentially associated with gastrointestinal diseases. Our work broadens available archaeal representatives for GIT studies, and offers insights into Candidatus Methanobrevibacter intestini genomes' adaptability in critical microbiome contexts.},
}

*Methanobrevibacter/genetics/isolation & purification/metabolism
Humans
*Feces/microbiology
*Gastrointestinal Microbiome/genetics
*Genome, Archaeal
Methane/metabolism
Phylogeny
Adult
Male
Female
Gastrointestinal Tract/microbiology

@article {pmid39214080,
year = {2024},
author = {Carlino, N and Blanco-Míguez, A and Punčochář, M and Mengoni, C and Pinto, F and Tatti, A and Manghi, P and Armanini, F and Avagliano, M and Barcenilla, C and Breselge, S and Cabrera-Rubio, R and Calvete-Torre, I and Coakley, M and Cobo-Díaz, JF and De Filippis, F and Dey, H and Leech, J and Klaassens, ES and Knobloch, S and O'Neil, D and Quijada, NM and Sabater, C and Skírnisdóttir, S and Valentino, V and Walsh, L and , and Alvarez-Ordóñez, A and Asnicar, F and Fackelmann, G and Heidrich, V and Margolles, A and Marteinsson, VT and Rota Stabelli, O and Wagner, M and Ercolini, D and Cotter, PD and Segata, N and Pasolli, E},
title = {Unexplored microbial diversity from 2,500 food metagenomes and links with the human microbiome.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2024.07.039},
pmid = {39214080},
issn = {1097-4172},
abstract = {Complex microbiomes are part of the food we eat and influence our own microbiome, but their diversity remains largely unexplored. Here, we generated the open access curatedFoodMetagenomicData (cFMD) resource by integrating 1,950 newly sequenced and 583 public food metagenomes. We produced 10,899 metagenome-assembled genomes spanning 1,036 prokaryotic and 108 eukaryotic species-level genome bins (SGBs), including 320 previously undescribed taxa. Food SGBs displayed significant microbial diversity within and between food categories. Extension to >20,000 human metagenomes revealed that food SGBs accounted on average for 3% of the adult gut microbiome. Strain-level analysis highlighted potential instances of food-to-gut transmission and intestinal colonization (e.g., Lacticaseibacillus paracasei) as well as SGBs with divergent genomic structures in food and humans (e.g., Streptococcus gallolyticus and Limosilactobabillus mucosae). The cFMD expands our knowledge on food microbiomes, their role in shaping the human microbiome, and supports future uses of metagenomics for food quality, safety, and authentication.},
}

@article {pmid39211550,
year = {2024},
author = {Chung, RS and Wong, S and Lin, D and Kokot, NC and Sinha, UK and Han, AY},
title = {Mechanisms of crosstalk between the oropharyngeal microbiome and human papillomavirus in oropharyngeal carcinogenesis: a mini review.},
journal = {Frontiers in oncology},
volume = {14},
number = {},
pages = {1425545},
pmid = {39211550},
issn = {2234-943X},
abstract = {Head and neck squamous cell carcinoma (HNSCC) is the sixth most common cancer globally. Notably, human papillomavirus (HPV)-positive oropharyngeal squamous cell carcinoma (OPSCC) is on the rise, accounting for 70% of all OPSCC cases. Persistent high-risk HPV infection is linked to various cancers, but HPV infection alone is not sufficient to cause cancer. Advances in next-generation sequencing have improved our understanding of changes in the human microbiome of cancerous environments. Yet, there remains a dearth of knowledge on the impact of HPV-microbiome crosstalk in HPV-positive OPSCC. In this review, we examine what is known about the oropharyngeal microbiome and the compositional shifts in this microbiome in HPV-positive OPSCC. We also review potential mechanisms of crosstalk between HPV and specific microorganisms. Additional research is needed to understand these interactions and their roles on cancer development and progression.},
}

@article {pmid39207108,
year = {2024},
author = {Crouch, AL and Monsey, L and Rambeau, M and Ramos, C and Yracheta, JM and Anderson, MZ},
title = {Metagenomic discovery of microbial eukaryotes in stool microbiomes.},
journal = {mBio},
volume = {},
number = {},
pages = {e0206324},
doi = {10.1128/mbio.02063-24},
pmid = {39207108},
issn = {2150-7511},
abstract = {Host-associated microbiota form complex microbial communities that are increasingly associated with host behavior and disease. While these microbes include bacterial, archaeal, viral, and eukaryotic constituents, most studies have focused on bacteria due to their dominance in the human host and available tools for investigation. Accumulating evidence suggests microbial eukaryotes in the microbiome play pivotal roles in host health, but our understandings of these interactions are limited to a few readily identifiable taxa because of technical limitations in unbiased eukaryote exploration. Here, we combined cell sorting, optimized eukaryotic cell lysis, and shotgun sequencing to accelerate metagenomic discovery and analysis of host-associated microbial eukaryotes. Using synthetic communities with a 1% microbial eukaryote representation, the eukaryote-optimized cell lysis and DNA recovery method alone yielded a 38-fold increase in eukaryotic DNA. Automated sorting of eukaryotic cells from stool samples of healthy adults increased the number of microbial eukaryote reads in metagenomic pools by up to 28-fold compared to commercial kits. Read frequencies for identified fungi increased by 10,000× on average compared to the Human Microbiome Project and allowed for the identification of novel taxa, de novo assembly of contigs from previously unknown microbial eukaryotes, and gene prediction from recovered genomic segments. These advances pave the way for the unbiased inclusion of microbial eukaryotes in deciphering determinants of health and disease in the host-associated microbiome.IMPORTANCEMicrobial eukaryotes are common constituents of the human gut where they can contribute to local ecology and host health, but they are often overlooked in microbiome studies. The lack of attention is due to current technical limitations that are heavily biased or poorly recovered DNA from microbial eukaryotes. We developed a method to increase the representation of these eukaryotes in metagenomic sequencing of microbiome samples that allows to improve their detection compared to prior methods and allows for the identification of new species. Application of the technique to gut microbiome samples improved detection of fungi, protists, and helminths. New eukaryotic taxa and their encoded genes could be identified by sequencing a small number of samples. This approach can improve the inclusion of eukaryotes into microbiome research.},
}

@article {pmid39206540,
year = {2024},
author = {Walker, M and Federico, E and Espinoza, JL and Dupont, CL},
title = {Unveiling Molecular Diversity in Cerebral Thrombi via Spatial Transcriptomics.},
journal = {Stroke},
volume = {},
number = {},
pages = {},
doi = {10.1161/STROKEAHA.124.047907},
pmid = {39206540},
issn = {1524-4628},
}

@article {pmid39206530,
year = {2024},
author = {Gupta, CL and Jaganathasamy, N and Madkaikar, M},
title = {Microbiome in sickle cell disease: Pathophysiology and therapeutic insights.},
journal = {British journal of haematology},
volume = {},
number = {},
pages = {},
doi = {10.1111/bjh.19736},
pmid = {39206530},
issn = {1365-2141},
abstract = {Sickle cell disease (SCD) is a complex genetic blood disorder characterized by abnormal haemoglobin, resulting in sickle-shaped red blood cells. While extensive research has concentrated on the genetic and physiological aspects of SCD, recent studies suggest a potential role of the human microbiome in SCD pathophysiology, adding new dimensions to its understanding. This review synthesizes current knowledge on the microbiome's involvement in SCD, focusing on alterations in the gut microbiome composition and diversity compared to healthy individuals, and their implications for disease pathogenesis. We explore how microbiome changes may contribute to vaso-occlusive crises and other complications, along with the possible associations of specific microbial taxa or markers with disease crises and clinical outcomes. Additionally, we discuss the potential of microbiome-targeted interventions, including probiotics, dietary modifications, and faecal microbiota transplantation, in managing SCD complications and improving patient outcomes. Understanding the intricate relationship between the microbiome and SCD could lead to innovative therapeutic strategies and personalized interventions for better managing the disease. This review underscores the importance of further microbiome research and its integration into holistic SCD care.},
}

@article {pmid39203520,
year = {2024},
author = {Maslennikov, R and Benuni, N and Levshina, A and Adzhieva, F and Demina, T and Kucher, A and Pervushova, E and Yuryeva, E and Poluektova, E and Zolnikova, O and Kozlov, E and Sigidaev, A and Ivashkin, V},
title = {Effect of Saccharomyces boulardii on Liver Diseases: A Systematic Review.},
journal = {Microorganisms},
volume = {12},
number = {8},
pages = {},
doi = {10.3390/microorganisms12081678},
pmid = {39203520},
issn = {2076-2607},
abstract = {We aimed to systematize the results of published studies on the use of Saccharomyces boulardii (SB) for the treatment of various liver disorders (CRD42022378050). Searches were conducted using PubMed and Scopus on 1 August 2022. The PubMed search was updated on 15 June 2024. The review included sixteen studies: ten experimental animal studies (EASs) and six randomized controlled trials (RCTs). The CNCM I-745 strain was used in 68.8% of the included studies. SB reduced the severity of many manifestations of cirrhosis, and lowered the Child-Pugh scores in RCT. SB reduced the serum concentrations of TNF-α, IL-1β, IL-6, and IL-4 in animals with metabolic dysfunction-associated steatotic liver disease (MASLD); lowered the serum TNF-α and IL-6 levels in experimental cirrhosis in rats; and reduced the CRP levels in decompensated cirrhosis. The EAS of MASLD revealed that SB reduced liver steatosis and inflammation and lowered the liver expression of genes of TNF-α, IL-1β, interferon-γ, and IL-10. In studies on experimental cirrhosis and MASLD, SB reduced the liver expression of genes of TGF-β, α-SMA, and collagen as well as liver fibrosis. SB reduced the abundance of Escherichia (Proteobacteria), increased the abundance of Bacteroidetes in the gut microbiota, prevented an increase in intestinal barrier permeability, and reduced bacterial translocation and endotoxemia.},
}

@article {pmid39203484,
year = {2024},
author = {Węgrzyn, K and Jasińska, A and Janeczek, K and Feleszko, W},
title = {The Role of Postbiotics in Asthma Treatment.},
journal = {Microorganisms},
volume = {12},
number = {8},
pages = {},
doi = {10.3390/microorganisms12081642},
pmid = {39203484},
issn = {2076-2607},
abstract = {In recent years, there has been abundant research concerning human microbiome and its impact on the host's health. Studies have shown that not only the commensal bacteria itself, but also postbiotics, understood as inanimate microorganisms, possibly with the presence of their components, may themselves have an effect on various elements of human physiology. In this review, we take a closer look at the specific ways in which postbiotics can alter immune response in allergic asthma, which is one of the most prevalent allergic diseases in today's world and a serious subject of concern. Through altering patients' immune response, not only to allergens but also to pathogens, postbiotics could have a significant role in lowering the number of asthma exacerbations. We suggest that more profound research should be undertaken in order to launch postbiotics into clinical standards of asthma treatment, given the greatly promising findings in terms of their immunomodulating potential.},
}

@article {pmid39201629,
year = {2024},
author = {Kim, JH and Seo, H and Kim, S and Rahim, MA and Jo, S and Barman, I and Tajdozian, H and Sarafraz, F and Song, HY and Song, YS},
title = {Different Prostatic Tissue Microbiomes between High- and Low-Grade Prostate Cancer Pathogenesis.},
journal = {International journal of molecular sciences},
volume = {25},
number = {16},
pages = {},
doi = {10.3390/ijms25168943},
pmid = {39201629},
issn = {1422-0067},
support = {RS-2024-00333544//National Research Foundation of Korea/ ; RS-2023-00219563//National Research Foundation of Korea/ ; Soonchunhyang University Research Fund//Soonchunhyang University/ ; },
mesh = {Male ; Humans ; *Prostatic Neoplasms/microbiology/pathology ; *Microbiota ; *Neoplasm Grading ; Bacteria/classification/genetics ; Prostate/microbiology/pathology ; Middle Aged ; Aged ; High-Throughput Nucleotide Sequencing ; Cell Proliferation ; Cell Line, Tumor ; },
abstract = {Numerous human pathologies, such as neoplasia, are related to particular bacteria and changes in microbiome constituents. To investigate the association between an imbalance of bacteria and prostate carcinoma, the microbiome and gene functionality from tissues of patients with high-grade prostate tumor (HGT) and low-grade prostate tumor (LGT) were compared utilizing next-generation sequencing (NGS) technology. The results showed abnormalities in the bacterial profiles between the HGT and LGT specimens, indicating alterations in the make-up of bacterial populations and gene functionalities. The HGT specimens showed higher frequencies of Cutibacterium, Pelomonas, and Corynebacterium genera than the LGT specimens. Cell proliferation and cytokine assays also showed a significant proliferation of prostate cancer cells and elevated cytokine levels in the cells treated with Cutibacterium, respectively, supporting earlier findings. In summary, the HGT and LGT specimens showed differences in bacterial populations, suggesting that different bacterial populations might characterize high-grade and low-grade prostate malignancies.},
}

Male
Humans
*Prostatic Neoplasms/microbiology/pathology
*Microbiota
*Neoplasm Grading
Bacteria/classification/genetics
Prostate/microbiology/pathology
Middle Aged
Aged
High-Throughput Nucleotide Sequencing
Cell Proliferation
Cell Line, Tumor

@article {pmid39191760,
year = {2024},
author = {Hartikainen, AK and Jalanka, J and Lahtinen, P and Ponsero, AJ and Mertsalmi, T and Finnegan, L and Crispie, F and Cotter, PD and Arkkila, P and Satokari, R},
title = {Fecal microbiota transplantation influences microbiota without connection to symptom relief in irritable bowel syndrome patients.},
journal = {NPJ biofilms and microbiomes},
volume = {10},
number = {1},
pages = {73},
pmid = {39191760},
issn = {2055-5008},
support = {316338//Academy of Finland (Suomen Akatemia)/ ; 323156//Academy of Finland (Suomen Akatemia)/ ; },
mesh = {*Irritable Bowel Syndrome/therapy/microbiology ; Humans ; *Fecal Microbiota Transplantation/methods ; *RNA, Ribosomal, 16S/genetics ; Female ; Male ; Adult ; Treatment Outcome ; *Gastrointestinal Microbiome ; Middle Aged ; Feces/microbiology ; Metagenomics/methods ; Bacteria/classification/genetics/isolation & purification ; },
abstract = {Imbalanced microbiota may contribute to the pathophysiology of irritable bowel syndrome (IBS), thus fecal microbiota transplantation (FMT) has been suggested as a potential treatment. Previous studies on the relationship between clinical improvement and microbiota after FMT have been inconclusive. In this study, we used 16S rRNA gene amplicon and shotgun metagenomics data from a randomized, placebo controlled FMT trial on 49 IBS patients to analyze changes after FMT in microbiota composition and its functional potential, and to identify connections between microbiota and patients' clinical outcome. As a result, we found that the successful modulation of microbiota composition and functional profiles by FMT from a healthy donor was not associated with the resolution of symptoms in IBS patients. Notably, a donor derived strain of Prevotella copri dominated the microbiota in those patients in the FMT group who had a low relative abundance of P. copri pre-FMT. The results highlight the multifactorial nature of IBS and the role of recipient's microbiota in the colonization of donor's strains.},
}

*Irritable Bowel Syndrome/therapy/microbiology
Humans
*Fecal Microbiota Transplantation/methods
*RNA, Ribosomal, 16S/genetics
Female
Male
Adult
Treatment Outcome
*Gastrointestinal Microbiome
Middle Aged
Feces/microbiology
Metagenomics/methods
Bacteria/classification/genetics/isolation & purification

@article {pmid39188957,
year = {2024},
author = {Xiang, B and Hu, J and Zhang, M and Zhi, M},
title = {The involvement of oral bacteria in inflammatory bowel disease.},
journal = {Gastroenterology report},
volume = {12},
number = {},
pages = {goae076},
pmid = {39188957},
issn = {2052-0034},
abstract = {Microorganisms play an important role in the pathogenesis of inflammatory bowel disease (IBD). The oral cavity, the second-largest microbial niche, is connected to the gastro-intestinal tract. Ectopic gut colonization by oral microbes is a signature of IBD. Current studies suggest that patients with IBD often report more oral manifestations and these oral issues are closely linked with disease activity. Murine studies have indicated that several oral microbes exacerbate intestinal inflammation. Moreover, intestinal inflammation can promote oral microbial dysbiosis and the migration of oral microbes to the gastro-intestinal tract. The reciprocal consequences of oral microbial dysbiosis and IBD, specifically through metabolic alterations, have not yet been elucidated. In this review, we summarize the relationship between oral bacteria and IBD from multiple perspectives, including clinical manifestations, microbial dysbiosis, and metabolic alterations, and find that oral pathogens increase anti-inflammatory metabolites and decrease inflammation-related metabolites.},
}

@article {pmid39172744,
year = {2024},
author = {Cabrera, LE and Jokiranta, ST and Mäki, S and Miettinen, S and Kant, R and Kareinen, L and Sironen, T and Pietilä, JP and Kantele, A and Kekäläinen, E and Lindgren, H and Mattila, P and Kipar, A and Vapalahti, O and Strandin, T},
title = {The assembly of neutrophil inflammasomes during COVID-19 is mediated by type I interferons.},
journal = {PLoS pathogens},
volume = {20},
number = {8},
pages = {e1012368},
pmid = {39172744},
issn = {1553-7374},
mesh = {*COVID-19/immunology ; Humans ; *Neutrophils/immunology/metabolism ; *Interferon Type I/metabolism/immunology ; *Inflammasomes/immunology/metabolism ; Animals ; *SARS-CoV-2/immunology ; Mice ; Male ; Female ; Middle Aged ; Immunity, Innate ; Adult ; Mice, Inbred C57BL ; },
abstract = {The severity of COVID-19 is linked to excessive inflammation. Neutrophils represent a critical arm of the innate immune response and are major mediators of inflammation, but their role in COVID-19 pathophysiology remains poorly understood. We conducted transcriptomic profiling of neutrophils obtained from patients with mild and severe COVID-19, as well as from SARS-CoV-2 infected mice, in comparison to non-infected healthy controls. In addition, we investigated the inflammasome formation potential in neutrophils from patients and mice upon SARS-CoV-2 infection. Transcriptomic analysis of polymorphonuclear cells (PMNs), consisting mainly of mature neutrophils, revealed a striking type I interferon (IFN-I) gene signature in severe COVID-19 patients, contrasting with mild COVID-19 and healthy controls. Notably, low-density granulocytes (LDGs) from severe COVID-19 patients exhibited an immature neutrophil phenotype and lacked this IFN-I signature. Moreover, PMNs from severe COVID-19 patients showed heightened nigericin-induced caspase1 activation, but reduced responsiveness to exogenous inflammasome priming. Furthermore, IFN-I emerged as a priming stimulus for neutrophil inflammasomes. These findings suggest a potential role for neutrophil inflammasomes in driving inflammation during severe COVID-19. Altogether, these findings open promising avenues for targeted therapeutic interventions to mitigate the pathological processes associated with the disease.},
}

*COVID-19/immunology
Humans
*Neutrophils/immunology/metabolism
*Interferon Type I/metabolism/immunology
*Inflammasomes/immunology/metabolism
Animals
*SARS-CoV-2/immunology
Mice
Male
Female
Middle Aged
Immunity, Innate
Adult
Mice, Inbred C57BL

@article {pmid39167930,
year = {2024},
author = {Mohamed, KA and Kruf, S and Büll, C},
title = {Putting a cap on the glycome: Dissecting human sialyltransferase functions.},
journal = {Carbohydrate research},
volume = {544},
number = {},
pages = {109242},
doi = {10.1016/j.carres.2024.109242},
pmid = {39167930},
issn = {1873-426X},
abstract = {Human glycans are capped with sialic acids and these nine-carbon sugars mediate many of the biological functions and interactions of glycans. Structurally diverse sialic acid caps mark human cells as self and they form the ligands for the Siglec immune receptors and other glycan-binding proteins. Sialic acids enable host interactions with the human microbiome and many human pathogens utilize sialic acids to infect host cells. Alterations in sialic acid-carrying glycans, sialoglycans, can be found in every major human disease including inflammatory conditions and cancer. Twenty sialyltransferase family members in the Golgi apparatus of human cells transfer sialic acids to distinct glycans and glycoconjugates. Sialyltransferases catalyze specific reactions to form unique sialoglycans or they have shared functions where multiple family members generate the same sialoglycan product. Moreover, some sialyltransferases compete for the same glycan substrate, but create different sialic acid caps. The redundant and competing functions make it difficult to understand the individual roles of the human sialyltransferases in biology and to reveal the specific contributions to pathobiological processes. Recent insights hint towards the existence of biosynthetic rules formed by the individual functions of sialyltransferases, their interactions, and cues from the local Golgi environment that coordinate sialoglycan biosynthesis. In this review, we discuss the current structural and functional understanding of the human sialyltransferase family and we review recent technological advances that enable the dissection of individual sialyltransferase activities.},
}

@article {pmid39166876,
year = {2024},
author = {de Palma, TH and Powers, C and McPartland, MJ and Mark Welch, J and Ramsey, M},
title = {Essential genes for Haemophilus parainfluenzae survival and biofilm growth.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0067424},
doi = {10.1128/msystems.00674-24},
pmid = {39166876},
issn = {2379-5077},
abstract = {Haemophilus parainfluenzae (Hp) is a Gram-negative, highly prevalent, and abundant commensal in the human oral cavity, and an infrequent extraoral opportunistic pathogen. Hp occupies multiple niches in the oral cavity, including the supragingival plaque biofilm. Little is known about how Hp interacts with its neighbors in healthy biofilms nor its mechanisms of pathogenesis as an opportunistic pathogen. To address this, we identified the essential genome and conditionally essential genes in in vitro biofilms aerobically and anaerobically. Using transposon insertion sequencing (TnSeq) with a highly saturated mariner transposon library in two strains, the ATCC33392 type-strain (Hp 392) and oral isolate EL1 (Hp EL1), we show that the essential genomes of Hp 392 and Hp EL1 are composed of 395 (20%) and 384 (19%) genes, respectively. The core essential genome, consisting of 341 (17%) essential genes conserved between both strains, was composed of genes associated with genetic information processing, carbohydrate, protein, and energy metabolism. We also identified conditionally essential genes for aerobic and anaerobic biofilm growth, which were associated with carbohydrate and energy metabolism in both strains. RNAseq analysis determined that most genes upregulated during anaerobic growth are not essential for Hp 392 anaerobic survival. The completion of this library and analysis under these conditions gives us a foundational insight into the basic biology of H. parainfluenzae in differing oxygen conditions, similar to its in vivo habitat. This library presents a valuable tool for investigation into conditionally essential genes for an organism that lives in close contact with many microbial species in the human oral habitat.IMPORTANCEHaemophilus parainfluenzae is a highly abundant human commensal microbe, present in most healthy individuals where it colonizes the mouth. H. parainfluenzae correlates with good oral health and may play a role in preservation of healthy host status. Also, H. parainfluenzae can cause opportunistic infections outside of the oral cavity. To date, little is known about how H. parainfluenzae colonizes the human host, despite being such a frequent and abundant part of our human microbiome. Here, we demonstrate the creation and use of a powerful tool, a TnSeq library, used to identify genes necessary for both the outright growth of this organism and also genes conditionally essential for growth in varying oxygen status which it can encounter in the human host. This tool and these data serve as a foundation for further study of this relatively unknown organism that may play a role in preserving human health.},
}

@article {pmid39163860,
year = {2024},
author = {Torres, MDT and Brooks, EF and Cesaro, A and Sberro, H and Gill, MO and Nicolaou, C and Bhatt, AS and de la Fuente-Nunez, C},
title = {Mining human microbiomes reveals an untapped source of peptide antibiotics.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2024.07.027},
pmid = {39163860},
issn = {1097-4172},
abstract = {Drug-resistant bacteria are outpacing traditional antibiotic discovery efforts. Here, we computationally screened 444,054 previously reported putative small protein families from 1,773 human metagenomes for antimicrobial properties, identifying 323 candidates encoded in small open reading frames (smORFs). To test our computational predictions, 78 peptides were synthesized and screened for antimicrobial activity in vitro, with 70.5% displaying antimicrobial activity. As these compounds were different compared with previously reported antimicrobial peptides, we termed them smORF-encoded peptides (SEPs). SEPs killed bacteria by targeting their membrane, synergizing with each other, and modulating gut commensals, indicating a potential role in reconfiguring microbiome communities in addition to counteracting pathogens. The lead candidates were anti-infective in both murine skin abscess and deep thigh infection models. Notably, prevotellin-2 from Prevotella copri presented activity comparable to the commonly used antibiotic polymyxin B. Our report supports the existence of hundreds of antimicrobials in the human microbiome amenable to clinical translation.},
}

@article {pmid39160377,
year = {2024},
author = {Li, Q and Liu, D and Liang, M and Zhu, Y and Yousaf, M and Wu, Y},
title = {Mechanism of probiotics in the intervention of colorectal cancer: a review.},
journal = {World journal of microbiology & biotechnology},
volume = {40},
number = {10},
pages = {306},
pmid = {39160377},
issn = {1573-0972},
mesh = {*Probiotics/therapeutic use ; Humans ; *Colorectal Neoplasms/microbiology/prevention & control/therapy ; *Gastrointestinal Microbiome ; Apoptosis ; Animals ; Bacteria/metabolism ; },
abstract = {The human microbiome interacts with the host mainly in the intestinal lumen, where putrefactive bacteria are suggested to promote colorectal cancer (CRC). In contrast, probiotics and their isolated components and secreted substances, display anti-tumor properties due to their ability to modulate gut microbiota composition, promote apoptosis, enhance immunity, resist oxidation and alter metabolism. Probiotics help to form a solid intestinal barrier against damaging agents via altering the gut microbiota and preventing harmful microbes from colonization. Probiotic strains that specifically target essential proteins involved in the process of apoptosis can overcome CRC resistance to apoptosis. They can increase the production of anti-inflammatory cytokines, essential in preventing carcinogenesis, and eliminate cancer cells by activating T cell-mediated immune responses. There is a clear indication that probiotics optimize the antioxidant system, decrease radical generation, and detect and degrade potential carcinogens. In this review, the pathogenic mechanisms of pathogens in CRC and the recent insights into the mechanism of probiotics in CRC prevention and therapy are discussed to provide a reference for the actual application of probiotics in CRC.},
}

*Probiotics/therapeutic use
Humans
*Colorectal Neoplasms/microbiology/prevention & control/therapy
*Gastrointestinal Microbiome
Apoptosis
Animals
Bacteria/metabolism

@article {pmid39152482,
year = {2024},
author = {Luo, W and Zhao, M and Dwidar, M and Gao, Y and Xiang, L and Wu, X and Medema, MH and Xu, S and Li, X and Schäfer, H and Chen, M and Feng, R and Zhu, Y},
title = {Microbial assimilatory sulfate reduction-mediated H2S: an overlooked role in Crohn's disease development.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {152},
pmid = {39152482},
issn = {2049-2618},
support = {82370551//National Natural Science Foundation of China/ ; 82270579//National Natural Science Foundation of China/ ; 82100577//National Natural Science Foundation of China/ ; 2024GXNSFFA010009//Natural Science Foundation of Guangxi Zhuang Autonomous Region/ ; },
mesh = {*Crohn Disease/microbiology ; Humans ; *Gastrointestinal Microbiome ; *Hydrogen Sulfide/metabolism ; Animals ; Mice ; *Sulfates/metabolism ; Escherichia coli/genetics/metabolism ; Feces/microbiology ; Dysbiosis/microbiology ; Colon/microbiology ; Metagenomics ; Oxidation-Reduction ; Disease Models, Animal ; Female ; },
abstract = {BACKGROUND: H2S imbalances in the intestinal tract trigger Crohn's disease (CD), a chronic inflammatory gastrointestinal disorder characterized by microbiota dysbiosis and barrier dysfunction. However, a comprehensive understanding of H2S generation in the gut, and the contributions of both microbiota and host to systemic H2S levels in CD, remain to be elucidated. This investigation aimed to enhance comprehension regarding the sulfidogenic potential of both the human host and the gut microbiota.

RESULTS: Our analysis of a treatment-naive CD cohorts' fecal metagenomic and biopsy metatranscriptomic data revealed reduced expression of host endogenous H2S generation genes alongside increased abundance of microbial exogenous H2S production genes in correlation with CD. While prior studies focused on microbial H2S production via dissimilatory sulfite reductases, our metagenomic analysis suggests the assimilatory sulfate reduction (ASR) pathway is a more significant contributor in the human gut, given its high prevalence and abundance. Subsequently, we validated our hypothesis experimentally by generating ASR-deficient E. coli mutants ∆cysJ and ∆cysM through the deletion of sulfite reductase and L-cysteine synthase genes. This alteration significantly affected bacterial sulfidogenic capacity, colon epithelial cell viability, and colonic mucin sulfation, ultimately leading to colitis in murine model. Further study revealed that gut microbiota degrade sulfopolysaccharides and assimilate sulfate to produce H2S via the ASR pathway, highlighting the role of sulfopolysaccharides in colitis and cautioning against their use as food additives.

CONCLUSIONS: Our study significantly advances understanding of microbial sulfur metabolism in the human gut, elucidating the complex interplay between diet, gut microbiota, and host sulfur metabolism. We highlight the microbial ASR pathway as an overlooked endogenous H2S producer and a potential therapeutic target for managing CD. Video Abstract.},
}

*Crohn Disease/microbiology
Humans
*Gastrointestinal Microbiome
*Hydrogen Sulfide/metabolism
Animals
Mice
*Sulfates/metabolism
Escherichia coli/genetics/metabolism
Feces/microbiology
Dysbiosis/microbiology
Colon/microbiology
Metagenomics
Oxidation-Reduction
Disease Models, Animal
Female

@article {pmid39148051,
year = {2024},
author = {Zhu, H and Hao, H and Yu, L},
title = {Identification of microbe-disease signed associations via multi-scale variational graph autoencoder based on signed message propagation.},
journal = {BMC biology},
volume = {22},
number = {1},
pages = {172},
pmid = {39148051},
issn = {1741-7007},
support = {62072353//National Natural Science Foundation of China/ ; 62272065//National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Microbiota ; Computational Biology/methods ; Algorithms ; Disease ; },
abstract = {BACKGROUND: Plenty of clinical and biomedical research has unequivocally highlighted the tremendous significance of the human microbiome in relation to human health. Identifying microbes associated with diseases is crucial for early disease diagnosis and advancing precision medicine.

RESULTS: Considering that the information about changes in microbial quantities under fine-grained disease states helps to enhance a comprehensive understanding of the overall data distribution, this study introduces MSignVGAE, a framework for predicting microbe-disease sign associations using signed message propagation. MSignVGAE employs a graph variational autoencoder to model noisy signed association data and extends the multi-scale concept to enhance representation capabilities. A novel strategy for propagating signed message in signed networks addresses heterogeneity and consistency among nodes connected by signed edges. Additionally, we utilize the idea of denoising autoencoder to handle the noise in similarity feature information, which helps overcome biases in the fused similarity data. MSignVGAE represents microbe-disease associations as a heterogeneous graph using similarity information as node features. The multi-class classifier XGBoost is utilized to predict sign associations between diseases and microbes.

CONCLUSIONS: MSignVGAE achieves AUROC and AUPR values of 0.9742 and 0.9601, respectively. Case studies on three diseases demonstrate that MSignVGAE can effectively capture a comprehensive distribution of associations by leveraging signed information.},
}

Humans
*Microbiota
Computational Biology/methods
Algorithms
Disease

@article {pmid39146817,
year = {2024},
author = {Caukwell, J and Assenza, S and Hassan, KA and Neilan, BA and Clulow, AJ and Salvati Manni, L and Fong, WK},
title = {Lipidic drug delivery systems are responsive to the human microbiome.},
journal = {Journal of colloid and interface science},
volume = {677},
number = {Pt B},
pages = {293-302},
doi = {10.1016/j.jcis.2024.07.216},
pmid = {39146817},
issn = {1095-7103},
abstract = {In vitro and in vivo tests for therapeutic agents are typically conducted in sterile environments, but many target areas for drug delivery are home to thousands of microbial species. Here, we examine the behaviour of lipidic nanomaterials after exposure to representative strains of four bacterial species found in the gastrointestinal tract and skin. Small angle X-ray scattering measurements show that the nanostructure of monoolein cubic and inverse hexagonal phases are transformed, respectively, into inverse hexagonal and inverse micellar cubic phases upon exposure to a strain of live Staphylococcus aureus often present on skin and mucosa. Further investigation demonstrates that enzymatic hydrolysis and cell membrane lipid transfer are both likely responsible for this effect. The structural responses to S. aureus are rapid and significantly reduce the rate of drug release from monoolein-based nanomaterials. These findings are the first to demonstrate how a key species in the live human microbiome can trigger changes in the structure and drug release properties of lipidic nanomaterials. The effect appears to be strain specific, varies from patient to patient and body region to body region, and is anticipated to affect the bioapplication of monoglyceride-based formulations.},
}

@article {pmid39146797,
year = {2024},
author = {Castells-Nobau, A and Mayneris-Perxachs, J and Fernández-Real, JM},
title = {Unlocking the mind-gut connection: Impact of human microbiome on cognition.},
journal = {Cell host & microbe},
volume = {32},
number = {8},
pages = {1248-1263},
doi = {10.1016/j.chom.2024.07.019},
pmid = {39146797},
issn = {1934-6069},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Cognition/physiology ; *Brain-Gut Axis/physiology ; Brain/physiology/microbiology ; Bacteria ; Metabolic Diseases/microbiology ; },
abstract = {This perspective explores the current understanding of the gut microbiota's impact on cognitive function in apparently healthy humans and in individuals with metabolic disease. We discuss how alterations in gut microbiota can influence cognitive processes, focusing not only on bacterial composition but also on often overlooked components of the gut microbiota, such as bacteriophages and eukaryotes, as well as microbial functionality. We examine the mechanisms through which gut microbes might communicate with the central nervous system, highlighting the complexity of these interactions. We provide a comprehensive overview of the emerging field of microbiota-gut-brain interactions and its significance for cognitive health. Additionally, we summarize novel therapeutic strategies designed to promote cognitive resilience and reduce the risk of cognitive disorders, focusing on interventions that target the gut microbiota. An in-depth understanding of the microbiome-brain axis is imperative for developing innovative treatments aimed at improving cognitive health.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Cognition/physiology
*Brain-Gut Axis/physiology
Brain/physiology/microbiology
Bacteria
Metabolic Diseases/microbiology

@article {pmid39143108,
year = {2024},
author = {Grahnemo, L and Kambur, O and Lahti, L and Jousilahti, P and Niiranen, T and Knight, R and Salomaa, V and Havulinna, AS and Ohlsson, C},
title = {Associations between gut microbiota and incident fractures in the FINRISK cohort.},
journal = {NPJ biofilms and microbiomes},
volume = {10},
number = {1},
pages = {69},
pmid = {39143108},
issn = {2055-5008},
support = {2020-01392//Vetenskapsrådet (Swedish Research Council)/ ; LU2021-0096//IngaBritt och Arne Lundbergs Forskningsstiftelse (Ingabritt and Arne Lundberg Research Foundation)/ ; NNF 190C0055250 and 22OC0078421//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; KAW 2015.0317//Knut och Alice Wallenbergs Stiftelse (Knut and Alice Wallenberg Foundation)/ ; },
mesh = {*Gastrointestinal Microbiome ; Humans ; Male ; Female ; *Fractures, Bone/microbiology/epidemiology/etiology ; Middle Aged ; Finland/epidemiology ; Aged ; Bacteria/classification/genetics/isolation & purification ; Metagenome ; Cohort Studies ; Incidence ; Metagenomics/methods ; Proteobacteria/genetics/isolation & purification ; Risk Factors ; Adult ; },
abstract = {The gut microbiota (GM) can regulate bone mass, but its association with incident fractures is unknown. We used Cox regression models to determine whether the GM composition is associated with incident fractures in the large FINRISK 2002 cohort (n = 7043, 1092 incident fracture cases, median follow-up time 18 years) with information on GM composition and functionality from shotgun metagenome sequencing. Higher alpha diversity was associated with decreased fracture risk (hazard ratio [HR] 0.92 per standard deviation increase in Shannon index, 95% confidence interval 0.87-0.96). For beta diversity, the first principal component was associated with fracture risk (Aitchison distance, HR 0.90, 0.85-0.96). In predefined phyla analyses, we observed that the relative abundance of Proteobacteria was associated with increased fracture risk (HR 1.14, 1.07-1.20), while the relative abundance of Tenericutes was associated with decreased fracture risk (HR 0.90, 0.85-0.96). Explorative sub-analyses within the Proteobacteria phylum showed that higher relative abundance of Gammaproteobacteria was associated with increased fracture risk. Functionality analyses showed that pathways related to amino acid metabolism and lipopolysaccharide biosynthesis associated with fracture risk. The relative abundance of Proteobacteria correlated with pathways for amino acid metabolism, while the relative abundance of Tenericutes correlated with pathways for butyrate synthesis. In conclusion, the overall GM composition was associated with incident fractures. The relative abundance of Proteobacteria, especially Gammaproteobacteria, was associated with increased fracture risk, while the relative abundance of Tenericutes was associated with decreased fracture risk. Functionality analyses demonstrated that pathways known to regulate bone health may underlie these associations.},
}

*Gastrointestinal Microbiome
Humans
Male
Female
*Fractures, Bone/microbiology/epidemiology/etiology
Middle Aged
Finland/epidemiology
Aged
Bacteria/classification/genetics/isolation & purification
Metagenome
Cohort Studies
Incidence
Metagenomics/methods
Proteobacteria/genetics/isolation & purification
Risk Factors
Adult

@article {pmid39139405,
year = {2024},
author = {Attaye, I and Witjes, JJ and Koopen, AM and van der Vossen, EWJ and Zwirs, D and Wortelboer, K and Collard, D and Kemper, EM and Winkelmeijer, M and Holst, JJ and Hazen, SL and Kuipers, F and Stroes, ESG and Groen, AK and de Vos, WM and Nieuwdorp, M and Herrema, H},
title = {Oral Anaerobutyricum soehngenii augments glycemic control in type 2 diabetes.},
journal = {iScience},
volume = {27},
number = {8},
pages = {110455},
pmid = {39139405},
issn = {2589-0042},
abstract = {This randomized, double-blind, placebo-controlled trial investigated the impact of 14-day Anaerobutyricum soehngenii L2-7 supplementation on postprandial glucose levels in 25 White Dutch males with type 2 diabetes (T2D) on stable metformin therapy. The primary endpoint was the effect of A. soehngenii versus placebo on glucose excursions and variability as determined by continuous glucose monitoring. Secondary endpoints were changes in ambulatory 24-h blood pressure, incretins, circulating metabolites and excursions of plasma short-chain fatty acids (SCFAs) and bile acids upon a standardized meal. Results showed that A. soehngenii supplementation for 14 days significantly improved glycemic variability and mean arterial blood pressure, without notable changes in SCFAs, bile acids, incretin levels, or anthropometric parameters as compared to placebo-treated controls. Although well-tolerated and effective in improving glycemic control in the intervention group, further research in larger and more diverse populations is needed to generalize these findings.},
}

@article {pmid39137463,
year = {2024},
author = {Fang, Q and Qiu, T and Ye, T and Feng, Z and Tian, X and Cao, Y and Bai, J and Liu, Y},
title = {Prenatal ozone exposure and variations of the gut microbiome: Evidence from a Chinese mother-infant cohort.},
journal = {Ecotoxicology and environmental safety},
volume = {283},
number = {},
pages = {116861},
doi = {10.1016/j.ecoenv.2024.116861},
pmid = {39137463},
issn = {1090-2414},
abstract = {BACKGROUND: The gut microbiome is central to human health, but the potential impact of ozone (O3) exposure on its establishment in early life has not been thoroughly examined. Therefore, this study aimed to investigate the relationship between prenatal O3 exposure and the variations of the human gut microbiome during the first two years of life.

DESIGN: A cohort study design was used. Pregnant women in the third trimester were recruited from an obstetric clinic, and long-term follow-ups were conducted after delivery. The gut microbiome was analyzed using the 16 S rRNA V3-V4 gene regions. Functional pathway analyses of gut microbial communities in neonates were performed using Tax4fun. The average concentrations of ambient O3 and other air pollutants from pregnancy to delivery were calculated using the China High Air Pollutants (CHAP) dataset, based on the permanent residential addresses of participants. Multiple linear regression and mixed linear models were utilized to investigate the associations between prenatal O3 exposure and gut microbiome features.

RESULTS: Prenatal O3 exposure did not significantly affect the gut microbial alpha diversity of mothers and neonates. However, it was found to be positively associated with the gut microbial alpha diversity in 24-month-old infants. Prenatal O3 exposure explained 13.1 % of the variation in neonatal gut microbial composition. After controlling for potential covariates, prenatal O3 exposure was associated with neonatal-specific gut microbial taxa and functional pathways. Furthermore, the mixed linear models showed that prenatal O3 exposure was negatively associated with variations of Streptococcus (p-value = 0.001, q-value = 0.005), Enterococcus (p-value = 0.001, q-value = 0.005), Escherichia-Shigella (p-value = 0.010, q-value = 0.025), and Bifidobacterium (p-value = 0.003, q-value = 0.010).

CONCLUSIONS: This study is the first to examine the effects of prenatal O3 exposure on gut microbial homeostasis and variations. It demonstrates that prenatal O3 exposure is associated with variations in certain aspects of the gut microbiome. These findings provide novel insights into the dynamics and establishment of the human microbiome during the first two years of life.},
}

@article {pmid39136453,
year = {2024},
author = {Etlin, S and Rose, J and Bielski, L and Walter, C and Kleinman, AS and Mason, CE},
title = {The human microbiome in space: parallels between Earth-based dysbiosis, implications for long-duration spaceflight, and possible mitigation strategies.},
journal = {Clinical microbiology reviews},
volume = {},
number = {},
pages = {e0016322},
doi = {10.1128/cmr.00163-22},
pmid = {39136453},
issn = {1098-6618},
abstract = {SUMMARYThe human microbiota encompasses the diverse communities of microorganisms that reside in, on, and around various parts of the human body, such as the skin, nasal passages, and gastrointestinal tract. Although research is ongoing, it is well established that the microbiota exert a substantial influence on the body through the production and modification of metabolites and small molecules. Disruptions in the composition of the microbiota-dysbiosis-have also been linked to various negative health outcomes. As humans embark upon longer-duration space missions, it is important to understand how the conditions of space travel impact the microbiota and, consequently, astronaut health. This article will first characterize the main taxa of the human gut microbiota and their associated metabolites, before discussing potential dysbiosis and negative health consequences. It will also detail the microbial changes observed in astronauts during spaceflight, focusing on gut microbiota composition and pathogenic virulence and survival. Analysis will then turn to how astronaut health may be protected from adverse microbial changes via diet, exercise, and antibiotics before concluding with a discussion of the microbiota of spacecraft and microbial culturing methods in space. The implications of this review are critical, particularly with NASA's ongoing implementation of the Moon to Mars Architecture, which will include weeks or months of living in space and new habitats.},
}

@article {pmid39125810,
year = {2024},
author = {Rezzani, R and Favero, G and Cominelli, G and Pinto, D and Rinaldi, F},
title = {Skin Aging and the Upcoming Role of Ferroptosis in Geroscience.},
journal = {International journal of molecular sciences},
volume = {25},
number = {15},
pages = {},
pmid = {39125810},
issn = {1422-0067},
mesh = {*Ferroptosis ; Humans ; *Skin Aging ; Iron/metabolism ; Animals ; Skin/metabolism/pathology ; Aging/metabolism ; Geriatrics ; },
abstract = {The skin is considered the most important organ system in mammals, and as the population ages, it is important to consider skin aging and anti-aging therapeutic strategies. Exposure of the skin to various insults induces significant changes throughout our lives, differentiating the skin of a young adult from that of an older adult. These changes are caused by a combination of intrinsic and extrinsic aging. We report the interactions between skin aging and its metabolism, showing that the network is due to several factors. For example, iron is an important nutrient for humans, but its level increases with aging, inducing deleterious effects on cellular functions. Recently, it was discovered that ferroptosis, or iron-dependent cell death, is linked to aging and skin diseases. The pursuit of new molecular targets for ferroptosis has recently attracted attention. Prevention of ferroptosis is an effective therapeutic strategy for the treatment of diseases, especially in old age. However, the pathological and biological mechanisms underlying ferroptosis are still not fully understood, especially in skin diseases such as melanoma and autoimmune diseases. Only a few basic studies on regulated cell death exist, and the challenge is to turn the studies into clinical applications.},
}

*Ferroptosis
Humans
*Skin Aging
Iron/metabolism
Animals
Skin/metabolism/pathology
Aging/metabolism
Geriatrics

@article {pmid39122010,
year = {2024},
author = {Hashimoto, Y and Ishigami, K and Hassaninasab, A and Kishi, K and Kumano, T and Kobayashi, M},
title = {Curcumin degradation in a soil microorganism: Screening and characterization of a β-diketone hydrolase.},
journal = {The Journal of biological chemistry},
volume = {},
number = {},
pages = {107647},
doi = {10.1016/j.jbc.2024.107647},
pmid = {39122010},
issn = {1083-351X},
abstract = {Curcumin is a plant-derived secondary metabolite exhibiting antitumor, neuroprotective, anti-diabetic activities, and so on. We previously isolated Escherichia coli as an enterobacterium exhibiting curcumin-converting activity from human feces, and discovered an enzyme showing this activity (CurA) and named it NADPH-dependent curcumin/dihydrocurcumin reductase. From soil, here, we isolated a curcumin-degrading microorganism (No. 34) using the screening medium containing curcumin as the sole carbon source and identified as Rhodococcus sp. A curcumin-degrading enzyme designated as CurH was purified from this strain and characterized, and compared with CurA. CurH catalyzed hydrolytic cleavage of a carbon-carbon bond in the β-diketone moiety of curcumin and its analogs, yielding two products bearing a methyl ketone terminus and a carboxylic acid terminus, respectively. These findings demonstrated that a curcumin degradation reaction catalyzed by CurH in the soil environment was completely different from the one catalyzed by CurA in the human microbiome. Of all the curcumin analogs tested, suitable substrates for the enzyme were curcuminoids (i.e., curcumin and bisdemethoxycurcumin) and tetrahydrocurcuminoids. Thus, we named this enzyme curcuminoid hydrolase. The deduced amino acid sequence of curH exhibited similarity to those of members of acetyl-CoA C-acetyltransferase family. Considering results of oxygen isotope analyses and a series of site-directed mutagenesis experiments on our enzyme, we propose a possible catalytic mechanism of CurH, which is unique and distinct from those of enzymes degrading β-diketone moieties such as β-diketone hydrolases known so far.},
}

@article {pmid39119866,
year = {2024},
author = {Schweitzer, M and Wlasak, M and Wassermann, B and Marcher, F and Poglitsch, C and Pirker, J and Berg, G},
title = {'Tiny Biome Tales': A gamified review about the influence of lifestyle choices on the human microbiome.},
journal = {Microbial biotechnology},
volume = {17},
number = {8},
pages = {e14544},
pmid = {39119866},
issn = {1751-7915},
support = {//Federal Ministry of Education, Science and Research, Austria/ ; },
mesh = {Humans ; *Microbiota ; *Video Games ; *Life Style ; Female ; Pregnancy ; Adult ; },
abstract = {In the last two decades, new discoveries from microbiome research have changed our understanding of human health. It became evident that daily habits and lifestyle choices shape the human microbiome and ultimately determine health or disease. Therefore, we developed 'Tiny Biome Tales' (https://microbiome.gamelabgraz.at/), a science pedagogy video game designed like a scientific review based exclusively on peer-reviewed articles, to teach about the influence of lifestyle choices on the human microbiome during pregnancy, early and adult life, and related health consequences. Despite the scientific character, it can be played by a broad audience. Here, we also present a scientific assessment and showed that playing the game significantly contributed to knowledge gain. The innovative style of the 'gamified review' represents an ideal platform to disseminate future findings from microbiome research by updating existing and adding new scenes to the game.},
}

Humans
*Microbiota
*Video Games
*Life Style
Female
Pregnancy
Adult

@article {pmid39114281,
year = {2024},
author = {Manske, S},
title = {The Microbiome: A Foundation for Integrative Medicine.},
journal = {Integrative medicine (Encinitas, Calif.)},
volume = {23},
number = {3},
pages = {28-31},
pmid = {39114281},
issn = {1546-993X},
abstract = {CONTEXT: No organ system better integrates interconnectivity across specialties and disciplines than the microbiome. Scientific focus is shifting from microbes as harbingers of disease toward microbes as symbiotic, balanced, commensal ecologies.

OBJECTIVE: The study intended to discuss and examine the human microbiome, including its development in early life; its impact on various physiological processes that occur throughout the body; and its relationship to dysbiosis; and to investigate microbial mechanisms with clinical applicability across medical specialties.

SETTING: The study took place at Biocidin Botanicals in Watsonville CA, USA.

RESULTS: Accumulating research upholds the human microbiome as both a predictive biomarker for disease risk and a viable treatment option for modulating the course of illness. Prebiotic and probiotic interventions continue to demonstrate clinical utility, particularly for gastrointestinal, dermatological, inflammatory, metabolic, and mental-health disorders.

CONCLUSIONS: Just as germ theory revolutionized infection control in the twentieth century, microbiome systems science stands to transform the conceptualization of health as the balanced coexistence of human and microbial cells in the twenty-first century.},
}

@article {pmid39113194,
year = {2024},
author = {Tae, IH and Lee, J and Kang, Y and Lee, JM and Park, K and Yang, H and Kim, HW and Ko, JH and Park, DS and Kim, DS and Son, MY and Cho, HS},
title = {Induction of Cell Death by Bifidobacterium infantis DS1685 in Colorectal and Breast Cancers via SMAD4/TGF-Beta Activation.},
journal = {Journal of microbiology and biotechnology},
volume = {34},
number = {8},
pages = {1-7},
doi = {10.4014/jmb.2404.04055},
pmid = {39113194},
issn = {1738-8872},
abstract = {Therapeutic advancements in treatments for cancer, a leading cause of mortality worldwide, have lagged behind the increasing incidence of this disease. There is a growing interest in multifaceted approaches for cancer treatment, such as chemotherapy, targeted therapy, and immunotherapy, but due to their low efficacy and severe side effects, there is a need for the development of new cancer therapies. Recently, the human microbiome, which is comprised of various microorganisms, has emerged as an important research field due to its potential impact on cancer treatment. Among these microorganisms, Bifidobacterium infantis has been shown to significantly improve the efficacy of various anticancer drugs. However, research on the role of B. infantis in cancer treatment remains insufficient. Thus, in this study, we explored the anticancer effect of treatment with B. infantis DS1685 supernatant (BI sup) in colorectal and breast cancer cell lines. Treatment with BI sup induced SMAD4 expression to suppress cell growth in colon and breast cancer cells. Furthermore, a decrease in tumor cohesion was observed through the disruption of the regulation of EMT-related genes by BI sup in 3D spheroid models. Based on these findings, we anticipate that BI sup could play an adjunctive role in cancer therapy, and future cotreatment of BI sup with various anticancer drugs may lead to synergistic effects in cancer treatment.},
}

@article {pmid39113097,
year = {2024},
author = {Gray, SM and Moss, AD and Herzog, JW and Kashiwagi, S and Liu, B and Young, JB and Sun, S and Bhatt, AP and Fodor, AA and Balfour Sartor, R},
title = {Mouse adaptation of human inflammatory bowel diseases microbiota enhances colonization efficiency and alters microbiome aggressiveness depending on the recipient colonic inflammatory environment.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {147},
pmid = {39113097},
issn = {2049-2618},
support = {T32DK007737//NIH/NIDDK/ ; T32DK007737//NIH/NIDDK/ ; NSF Cooperative Agreement No. EEC-2133504//The Engineering Research Centers Program of the National Science Foundation/ ; },
mesh = {Animals ; Humans ; Mice ; *Fecal Microbiota Transplantation ; *Gastrointestinal Microbiome ; *Inflammatory Bowel Diseases/microbiology ; *Disease Models, Animal ; *Dysbiosis/microbiology ; *Interleukin-10/genetics ; Colitis/microbiology ; Feces/microbiology ; Colon/microbiology ; Mice, Knockout ; Mice, Inbred C57BL ; Female ; Bacteria/classification/genetics/isolation & purification ; Inflammation ; Male ; },
abstract = {BACKGROUND: Understanding the cause vs consequence relationship of gut inflammation and microbial dysbiosis in inflammatory bowel diseases (IBD) requires a reproducible mouse model of human-microbiota-driven experimental colitis.

RESULTS: Our study demonstrated that human fecal microbiota transplant (FMT) transfer efficiency is an underappreciated source of experimental variability in human microbiota-associated (HMA) mice. Pooled human IBD patient fecal microbiota engrafted germ-free (GF) mice with low amplicon sequence variant (ASV)-level transfer efficiency, resulting in high recipient-to-recipient variation of microbiota composition and colitis severity in HMA Il-10[-/-] mice. In contrast, mouse-to-mouse transfer of mouse-adapted human IBD patient microbiota transferred with high efficiency and low compositional variability resulting in highly consistent and reproducible colitis phenotypes in recipient Il-10[-/-] mice. Engraftment of human-to-mouse FMT stochastically varied with individual transplantation events more than mouse-adapted FMT. Human-to-mouse FMT caused a population bottleneck with reassembly of microbiota composition that was host inflammatory environment specific. Mouse-adaptation in the inflamed Il-10[-/-] host reassembled a more aggressive microbiota that induced more severe colitis in serial transplant to Il-10[-/-] mice than the distinct microbiota reassembled in non-inflamed WT hosts.

CONCLUSIONS: Our findings support a model of IBD pathogenesis in which host inflammation promotes aggressive resident bacteria, which further drives a feed-forward process of dysbiosis exacerbated by gut inflammation. This model implies that effective management of IBD requires treating both the dysregulated host immune response and aggressive inflammation-driven microbiota. We propose that our mouse-adapted human microbiota model is an optimized, reproducible, and rigorous system to study human microbiome-driven disease phenotypes, which may be generalized to mouse models of other human microbiota-modulated diseases, including metabolic syndrome/obesity, diabetes, autoimmune diseases, and cancer. Video Abstract.},
}

Animals
Humans
Mice
*Fecal Microbiota Transplantation
*Gastrointestinal Microbiome
*Inflammatory Bowel Diseases/microbiology
*Disease Models, Animal
*Dysbiosis/microbiology
*Interleukin-10/genetics
Colitis/microbiology
Feces/microbiology
Colon/microbiology
Mice, Knockout
Mice, Inbred C57BL
Female
Bacteria/classification/genetics/isolation & purification
Inflammation
Male

@article {pmid39110597,
year = {2024},
author = {Fu, Y and Yu, S and Li, J and Lao, Z and Yang, X and Lin, Z},
title = {DeepMineLys: Deep mining of phage lysins from human microbiome.},
journal = {Cell reports},
volume = {43},
number = {8},
pages = {114583},
doi = {10.1016/j.celrep.2024.114583},
pmid = {39110597},
issn = {2211-1247},
abstract = {Vast shotgun metagenomics data remain an underutilized resource for novel enzymes. Artificial intelligence (AI) has increasingly been applied to protein mining, but its conventional performance evaluation is interpolative in nature, and these trained models often struggle to extrapolate effectively when challenged with unknown data. In this study, we present a framework (DeepMineLys [deep mining of phage lysins from human microbiome]) based on the convolutional neural network (CNN) to identify phage lysins from three human microbiome datasets. When validated with an independent dataset, our method achieved an F1-score of 84.00%, surpassing existing methods by 20.84%. We expressed 16 lysin candidates from the top 100 sequences in E. coli, confirming 11 as active. The best one displayed an activity 6.2-fold that of lysozyme derived from hen egg white, establishing it as the most potent lysin from the human microbiome. Our study also underscores several important issues when applying AI to biology questions. This framework should be applicable for mining other proteins.},
}

@article {pmid39109977,
year = {2024},
author = {Xiao, Y and Louwies, T and Mars, RAT and Kashyap, PC},
title = {The Human Microbiome-A Physiologic Perspective.},
journal = {Comprehensive Physiology},
volume = {14},
number = {3},
pages = {5491-5519},
doi = {10.1002/cphy.c230013},
pmid = {39109977},
issn = {2040-4603},
mesh = {Humans ; *Microbiota/physiology ; Gastrointestinal Microbiome/physiology ; },
abstract = {The human microbiome consists of the microorganisms associated with the body, such as bacteria, fungi, archaea, protozoa, and viruses, along with their gene content and products. These microbes are abundant in the digestive, respiratory, renal/urinary, and reproductive systems. While microbes found in other organs/tissues are often associated with diseases, some reports suggest their presence even in healthy individuals. Lack of microbial colonization does not indicate a lack of microbial influence, as their metabolites can affect distant locations through circulation. In a healthy state, these microbes maintain a mutualistic relationship and help shape the host's physiological functions. Unlike the host's genetic content, microbial gene content and expression are dynamic and influenced by factors such as ethnicity, genetic background, sex, age, lifestyle/diet, and psychological/physical conditions. Therefore, defining a healthy microbiome becomes challenging as it is context dependent and can vary over time for an individual. Although differences in microbial composition have been observed in various diseases, these changes may reflect host alterations rather than causing the disease itself. As the field is evolving, there is increased emphasis on understanding when changes in the microbiome are an important component of pathogenesis rather than the consequence of a disease state. This article focuses on the microbial component in the digestive and respiratory tracts-the primary sites colonized by microorganisms-and the physiological functions of microbial metabolites in these systems. It also discusses their physiological functions in the central nervous and cardiovascular systems, which have no microorganism colonization under healthy conditions based on human studies. © 2024 American Physiological Society. Compr Physiol 14:5491-5519, 2024.},
}

Humans
*Microbiota/physiology
Gastrointestinal Microbiome/physiology

@article {pmid39102545,
year = {2024},
author = {Duncan, RP and Moustafa, DA and Lewin, GR and Diggle, FL and Bomberger, JM and Whiteley, M and Goldberg, JB},
title = {Improvement of a mouse infection model to capture Pseudomonas aeruginosa chronic physiology in cystic fibrosis.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {121},
number = {33},
pages = {e2406234121},
doi = {10.1073/pnas.2406234121},
pmid = {39102545},
issn = {1091-6490},
support = {WHITELE20A0//Cystic Fibrosis Fouondation/ ; },
mesh = {*Cystic Fibrosis/microbiology/complications ; *Pseudomonas aeruginosa/physiology/pathogenicity ; Animals ; *Pseudomonas Infections/microbiology ; Mice ; *Disease Models, Animal ; Humans ; Respiratory Tract Infections/microbiology ; Host-Pathogen Interactions ; Sputum/microbiology ; },
abstract = {Laboratory models are central to microbiology research, advancing the understanding of bacterial physiology by mimicking natural environments, from soil to the human microbiome. When studying host-bacteria interactions, animal models enable investigators to examine bacterial dynamics associated with a host, and in the case of human infections, animal models are necessary to translate basic research into clinical treatments. Efforts toward improving animal infection models are typically based on reproducing host genotypes/phenotypes and disease manifestations, leaving a gap in how well the physiology of microbes reflects their behavior in a human host. Understanding bacterial physiology is vital because it dictates host response and bacterial interactions with antimicrobials. Thus, our goal was to develop an animal model that accurately recapitulates bacterial physiology in human infection. The system we chose to model was a chronic Pseudomonas aeruginosa respiratory infection in cystic fibrosis (CF). To accomplish this goal, we leveraged a framework that we recently developed to evaluate model accuracy by calculating the percentage of bacterial genes that are expressed similarly in a model to how they are expressed in their infection environment. We combined two complementary models of P. aeruginosa infection-an in vitro synthetic CF sputum model (SCFM2) and a mouse acute pneumonia model. This combined model captured the chronic physiology of P. aeruginosa in CF better than the standard mouse infection model, showing the power of a data-driven approach to refining animal models. In addition, the results of this work challenge the assumption that a chronic infection model requires long-term colonization.},
}

*Cystic Fibrosis/microbiology/complications
*Pseudomonas aeruginosa/physiology/pathogenicity
Animals
*Pseudomonas Infections/microbiology
Mice
*Disease Models, Animal
Humans
Respiratory Tract Infections/microbiology
Host-Pathogen Interactions
Sputum/microbiology

@article {pmid39101047,
year = {2024},
author = {Liu, J and Zhang, X and Lin, T and Chen, R and Zhong, Y and Chen, T and Wu, T and Liu, C and Huang, A and Nguyen, TT and Lee, EE and Jeste, DV and Tu, XM},
title = {A New Paradigm for High-dimensional Data: Distance-Based Semiparametric Feature Aggregation Framework via Between-Subject Attributes.},
journal = {Scandinavian journal of statistics, theory and applications},
volume = {51},
number = {2},
pages = {672-696},
pmid = {39101047},
issn = {0303-6898},
support = {K23 MH118435/MH/NIMH NIH HHS/United States ; K23 MH119375/MH/NIMH NIH HHS/United States ; R01 MH094151/MH/NIMH NIH HHS/United States ; },
abstract = {This article proposes a distance-based framework incentivized by the paradigm shift towards feature aggregation for high-dimensional data, which does not rely on the sparse-feature assumption or the permutation-based inference. Focusing on distance-based outcomes that preserve information without truncating any features, a class of semiparametric regression has been developed, which encapsulates multiple sources of high-dimensional variables using pairwise outcomes of between-subject attributes. Further, we propose a strategy to address the interlocking correlations among pairs via the U-statistics-based estimating equations (UGEE), which correspond to their unique efficient influence function (EIF). Hence, the resulting semiparametric estimators are robust to distributional misspecification while enjoying root-n consistency and asymptotic optimality to facilitate inference. In essence, the proposed approach not only circumvents information loss due to feature selection but also improves the model's interpretability and computational feasibility. Simulation studies and applications to the human microbiome and wearables data are provided, where the feature dimensions are tens of thousands.},
}

@article {pmid39100447,
year = {2024},
author = {Kakkar, A and Kandwal, G and Nayak, T and Jaiswal, LK and Srivastava, A and Gupta, A},
title = {Engineered bacteriophages: A panacea against pathogenic and drug resistant bacteria.},
journal = {Heliyon},
volume = {10},
number = {14},
pages = {e34333},
pmid = {39100447},
issn = {2405-8440},
abstract = {Antimicrobial resistance (AMR) is a major global concern; antibiotics and other regular treatment methods have failed to overcome the increasing number of infectious diseases. Bacteriophages (phages) are viruses that specifically target/kill bacterial hosts without affecting other human microbiome. Phage therapy provides optimism in the current global healthcare scenario with a long history of its applications in humans that has now reached various clinical trials. Phages in clinical trials have specific requirements of being exclusively lytic, free from toxic genes with an enhanced host range that adds an advantage to this requisite. This review explains in detail the various phage engineering methods and their potential applications in therapy. To make phages more efficient, engineering has been attempted using techniques like conventional homologous recombination, Bacteriophage Recombineering of Electroporated DNA (BRED), clustered regularly interspaced short palindromic repeats (CRISPR)-Cas, CRISPY-BRED/Bacteriophage Recombineering with Infectious Particles (BRIP), chemically accelerated viral evolution (CAVE), and phage genome rebooting. Phages are administered in cocktail form in combination with antibiotics, vaccines, and purified proteins, such as endolysins. Thus, phage therapy is proving to be a better alternative for treating life-threatening infections, with more specificity and fewer detrimental consequences.},
}