@article {pmid38601152,
year = {2024},
author = {Soto-Dávila, M and Langlois Fiorotto, L and Heath, JW and Lumsden, JS and Reid, G and Dixon, B},
title = {The effects of Pediococcus acidilactici MA18/5M on growth performance, gut integrity, and immune response using in vitro and in vivo Pacific salmonid models.},
journal = {Frontiers in immunology},
volume = {15},
number = {},
pages = {1306458},
pmid = {38601152},
issn = {1664-3224},
mesh = {Animals ; *Pediococcus acidilactici ; *Probiotics/pharmacology ; Diet ; *Salmonidae ; Disease Resistance ; },
abstract = {Microbial management is central to aquaculture's efficiency. Pediococcus acidilactici MA18/5M has shown promising results promoting growth, modulation of the immune response, and disease resistance in many fishes. However, the mechanisms through which this strain confers health benefits in fish are poorly understood, particularly in Pacific salmonid models. Briefly, the aims of this study were to i) assess the protective effects of P. acidilactici MA18/5M by examining gut barrier function and the expression of tight junction (TJ) and immune genes in vitro and in vivo, and ii) to determine the protective effects of this strain against a common saltwater pathogen, Vibrio anguillarum J382. An in vitro model of the salmonid gut was employed utilizing the cell line RTgutGC. Barrier formation and integrity assessed by TEER measurements in RTgutGC, showed a significant decrease in resistance in cells exposed only to V. anguillarum J382 for 24 h, but pre-treatment with P. acidilactici MA18/5M for 48 h mitigated these effects. While P. acidilactici MA18/5M did not significantly upregulate tight junction and immune molecules, pre-treatment with this strain protected against pathogen-induced insults to the gut barrier. In particular, the expression of ocldn was significantly induced by V. anguillarum J382, suggesting that this molecule might play a role in the host response against this pathogen. To corroborate these observations in live fish, the effects of P. acidilactici MA18/5M was evaluated in Chinook salmon reared in real aquaculture conditions. Supplementation with P. acidilactici MA18/5M had no effect on Chinook salmon growth parameters after 10 weeks. Interestingly, histopathological results did not show alterations associated with P. acidilactici MA18/5M supplementation, indicating that this strain is safe to be used in the industry. Finally, the expression pattern of transcripts encoding TJ and immune genes in all the treatments suggest that variation in expression is more likely to be due to developmental processes rather than P. acidilactici MA18/5M supplementation. Overall, our results showed that P. acidilactici MA18/5M is a safe strain for use in fish production, however, to assess the effects on growth and immune response previously observed in other salmonid species, an assessment in adult fish is needed.},
}

Animals
*Pediococcus acidilactici
*Probiotics/pharmacology
Diet
*Salmonidae
Disease Resistance

@article {pmid38600604,
year = {2024},
author = {Hong, A and Umar, A and Chen, H and Yu, Z and Huang, J},
title = {Advances in the study of the interaction between schistosome infections and the host's intestinal microorganisms.},
journal = {Parasites & vectors},
volume = {17},
number = {1},
pages = {185},
pmid = {38600604},
issn = {1756-3305},
support = {2023JJ30651//Natural Science Foundation of Hunan Province/ ; 32300051//National Natural Science Foundation of China/ ; },
mesh = {Animals ; Humans ; Schistosoma/physiology ; *Schistosomiasis/pathology ; *Liver Diseases ; },
abstract = {Schistosomiasis, also called bilharziasis, is a neglected tropical disease induced by schistosomes that infects hundreds of millions of people worldwide. In the life cycle of schistosomiasis, eggs are regarded as the main pathogenic factor, causing granuloma formation in the tissues and organs of hosts, which can cause severe gastrointestinal and liver granulomatous immune responses and irreversible fibrosis. Increasing evidence suggests that the gut microbiome influences the progression of schistosomiasis and plays a central role in liver disease via the gut-liver axis. When used as pharmaceutical supplements or adjunctive therapy, probiotics have shown promising results in preventing, mitigating, and even treating schistosomiasis. This review elucidates the potential mechanisms of this three-way parasite-host-microbiome interaction by summarizing schistosome-mediated intestinal flora disorders, local immune changes, and host metabolic changes, and elaborates the important role of the gut microbiome in liver disease after schistosome infection through the gut-liver axis. Understanding the mechanisms behind this interaction may aid in the discovery of probiotics as novel therapeutic targets and sustainable control strategies for schistosomiasis.},
}

Animals
Humans
Schistosoma/physiology
*Schistosomiasis/pathology
*Liver Diseases

@article {pmid38594499,
year = {2024},
author = {Franceschetti, L and Lodetti, G and Blandino, A and Amadasi, A and Bugelli, V},
title = {Exploring the role of the human microbiome in forensic identification: opportunities and challenges.},
journal = {International journal of legal medicine},
volume = {},
number = {},
pages = {},
pmid = {38594499},
issn = {1437-1596},
abstract = {Forensic microbiology is rapidly emerging as a novel tool for human identification. The human microbiome, comprising diverse microbial communities including fungi, bacteria, protozoa, and viruses, is unique to each individual, offering a new dimension to forensic investigations. While traditional identification methods primarily rely on DNA profiling and fingerprint analysis, they face limitations when complete DNA or fingerprints profiles are unattainable or degraded. In this context, the microbial signatures of the human skin microbiome present a promising alternative due to their resilience to environmental stresses and individual-specific composition. This review explores the potential of microbiome analysis in forensic human identification, evaluating its applications, advantages, limitations, and future prospects. The uniqueness of an individual's microbial community, particularly the skin microbiota, can provide distinctive biological markers for identification purposes, while technological advancements like 16 S rRNA sequencing and metagenomic shotgun sequencing are enhancing the specificity of microbial identification, enabling detailed analysis of these complex ecological communities. Despite these promising findings, current research has not yet achieved a level of identification probability that could establish microbial analysis as a stand-alone evidence tool. Therefore, it is presently considered ancillary to traditional methods, contributing to a more comprehensive biological profile of individuals.},
}

@article {pmid38593705,
year = {2024},
author = {Jian, C and Sorensen, N and Lutter, R and Albers, R and de Vos, W and Salonen, A and Mercenier, A},
title = {The impact of daily supplementation with rhamnogalacturonan-I on the gut microbiota in healthy adults: A randomized controlled trial.},
journal = {Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie},
volume = {174},
number = {},
pages = {116561},
doi = {10.1016/j.biopha.2024.116561},
pmid = {38593705},
issn = {1950-6007},
abstract = {Pectin and its derivatives have been shown to modulate immune signaling as well as gut microbiota in preclinical studies, which may constitute the mechanisms by which supplementation of specific pectic polysaccharides confers protection against viral respiratory infections. In a double-blind, placebo-controlled rhinovirus (RV16) challenge study, healthy volunteers were randomized to consume placebo (0.0 g/day) (N = 46), low-dose (0.3 g/day) (N = 49) or high-dose (1.5 g/day) (N = 51) of carrot derived rhamnogalacturonan-I (cRG-I) for eight weeks and they were subsequently challenged with RV-16. Here, the effect of 8-week cRG-I supplementation on the gut microbiota was studied. While the overall gut microbiota composition in the population was generally unaltered by this very low dose of fibre, the relative abundance of Bifidobacterium spp. (mainly B. adolescentis and B. longum) was significantly increased by both doses of cRG-1. Moreover, daily supplementation of cRG-I led to a dose-dependent reduction in inter- and intra-individual microbiota heterogeneity, suggesting a stabilizing effect on the gut microbiota. The severity of respiratory symptoms did not directly correlate with the cRG-I-induced microbial changes, but several dominant groups of the Ruminococcaceae family and microbiota richness were positively associated with a reduced and hence desired post-infection response. Thus, the present results on the modulation of the gut microbiota composition support the previously demonstrated immunomodulatory and protective effect of cRG-I during a common cold infection.},
}

@article {pmid38593079,
year = {2024},
author = {Zhong, Q and Liao, B and Liu, J and Shen, W and Wang, J and Wei, L and Ma, Y and Dong, PT and Bor, B and McLean, JS and Chang, Y and Shi, W and Cen, L and Wu, M and Liu, J and Li, Y and He, X and Le, S},
title = {Episymbiotic Saccharibacteria TM7x modulates the susceptibility of its host bacteria to phage infection and promotes their coexistence.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {121},
number = {16},
pages = {e2319790121},
doi = {10.1073/pnas.2319790121},
pmid = {38593079},
issn = {1091-6490},
support = {R01DE023810//HHS | NIH | National Institute of Dental and Craniofacial Research (NIDCR)/ ; R01DE030943//HHS | NIH | National Institute of Dental and Craniofacial Research (NIDCR)/ ; 31870167//MOST | National Natural Science Foundation of China (NSFC)/ ; R01AI087946//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; R01AI132818//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; },
abstract = {Bacteriophages (phages) play critical roles in modulating microbial ecology. Within the human microbiome, the factors influencing the long-term coexistence of phages and bacteria remain poorly investigated. Saccharibacteria (formerly TM7) are ubiquitous members of the human oral microbiome. These ultrasmall bacteria form episymbiotic relationships with their host bacteria and impact their physiology. Here, we showed that during surface-associated growth, a human oral Saccharibacteria isolate (named TM7x) protects its host bacterium, a Schaalia odontolytica strain (named XH001) against lytic phage LC001 predation. RNA-Sequencing analysis identified in XH001 a gene cluster with predicted functions involved in the biogenesis of cell wall polysaccharides (CWP), whose expression is significantly down-regulated when forming a symbiosis with TM7x. Through genetic work, we experimentally demonstrated the impact of the expression of this CWP gene cluster on bacterial-phage interaction by affecting phage binding. In vitro coevolution experiments further showed that the heterogeneous populations of TM7x-associated and TM7x-free XH001, which display differential susceptibility to LC001 predation, promote bacteria and phage coexistence. Our study highlights the tripartite interaction between the bacterium, episymbiont, and phage. More importantly, we present a mechanism, i.e., episymbiont-mediated modulation of gene expression in host bacteria, which impacts their susceptibility to phage predation and contributes to the formation of "source-sink" dynamics between phage and bacteria in biofilm, promoting their long-term coexistence within the human microbiome.},
}

@article {pmid38590477,
year = {2024},
author = {Vijayan, S and Kandi, V and Palacholla, PS and Rajendran, R and Jarugu, C and Ca, J and Pravallika, M and Reddy, SC and Sucharitha, AS},
title = {Probiotics in Allergy and Immunological Diseases: A Comprehensive Review.},
journal = {Cureus},
volume = {16},
number = {3},
pages = {e55817},
pmid = {38590477},
issn = {2168-8184},
abstract = {Allergy and immunological disorders like autoimmune diseases are vastly prevalent worldwide. These conditions account for a substantial amount of personal and social burden. Such illnesses have lengthy, uncertain, and spotted courses with unpredictable exacerbations. A definite tendency for improving the overall quality of life of individuals suffering from such diseases is crucial to tackling these diseases, especially through diet or lifestyle modification. Further, interventions like microbiome-based therapeutics such as prebiotics or probiotics were explored. Changes in the microbial population were evident during the flare-up of autoimmune and allergic conditions. The realization that the human microbiome is a central player in immunological diseases is a hallmark of its potential usefulness in therapy for such illnesses. This review focuses on the intricate symphony in the orchestra of the human microbiome and the immune system. New therapeutic strategies involving probiotics appear to be the future of personalized medicine. Through this review, we explore the narrative of probiotics and reaffirm their use as therapeutic and preventive agents in immunological disorders.},
}

@article {pmid38590114,
year = {2024},
author = {Rezzani, R and Favero, G and Gianò, M and Pinto, D and Labanca, M and van Noorden, CJF and Rinaldi, F},
title = {Transient Receptor Potential Channels in the Healthy and Diseased Blood-Brain Barrier.},
journal = {The journal of histochemistry and cytochemistry : official journal of the Histochemistry Society},
volume = {},
number = {},
pages = {221554241246032},
doi = {10.1369/00221554241246032},
pmid = {38590114},
issn = {1551-5044},
abstract = {The large family of transient receptor potential (TRP) channels are integral membrane proteins that function as environmental sensors and act as ion channels after activation by mechanical (touch), physical (heat, pain), and chemical stimuli (pungent compounds such as capsaicin). Most TRP channels are localized in the plasma membrane of cells but some of them are localized in membranes of organelles and function as intracellular Ca[2+]-ion channels. TRP channels are involved in neurological disorders but their precise role(s) and relevance in these disorders are not clear. Endothelial cells of the blood-brain barrier (BBB) express TRP channels such as TRP vanilloid 1-4 and are involved in thermal detection by regulating BBB permeability. In neurological disorders, TRP channels in the BBB are responsible for edema formation in the brain. Therefore, drug design to modulate locally activity of TRP channels in the BBB is a hot topic. Today, the application of TRP channel antagonists against neurological disorders is still limited.},
}

@article {pmid38587593,
year = {2024},
author = {Chung, IY and Kim, J and Koh, A},
title = {The Microbiome Matters: Its Impact on Cancer Development and Therapeutic Responses.},
journal = {Journal of microbiology (Seoul, Korea)},
volume = {},
number = {},
pages = {},
pmid = {38587593},
issn = {1976-3794},
support = {KFRM 22A0301L1//Korean Fund for Regenerative Medicine (KFRM)/ ; 2023R1A2C1002876//National Research Foundation of Korea (NRF)/ ; 2021R1I1A1A01052756//National Research Foundation of Korea (NRF)/ ; 2021R1A6C101A390//the Basic Science Institute/ ; },
abstract = {In the evolving landscape of cancer research, the human microbiome emerges as a pivotal determinant reshaping our understanding of tumorigenesis and therapeutic responses. Advanced sequencing technologies have uncovered a vibrant microbial community not confined to the gut but thriving within tumor tissues. Comprising bacteria, viruses, and fungi, this diverse microbiota displays distinct signatures across various cancers, with most research primarily focusing on bacteria. The correlations between specific microbial taxa within different cancer types underscore their pivotal roles in driving tumorigenesis and influencing therapeutic responses, particularly in chemotherapy and immunotherapy. This review amalgamates recent discoveries, emphasizing the translocation of the oral microbiome to the gut as a potential marker for microbiome dysbiosis across diverse cancer types and delves into potential mechanisms contributing to cancer promotion. Furthermore, it highlights the adverse effects of the microbiome on cancer development while exploring its potential in fortifying strategies for cancer prevention and treatment.},
}

@article {pmid38586050,
year = {2024},
author = {Ho, PY and Huang, KC},
title = {Challenges in quantifying functional redundancy and selection in microbial communities.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.03.26.586891},
pmid = {38586050},
abstract = {Microbiomes can exhibit large variations in species abundances but high reproducibility in abundances of functional units, an observation often considered evidence for functional redundancy. Based on such reduction in functional variability, selection is hypothesized to act on functional units in these ecosystems. However, the link between functional redundancy and selection remains unclear. Here, we show that reduction in functional variability does not always imply selection on functional profiles. We propose empirical null models to account for the confounding effects of statistical averaging and bias toward environment-independent beneficial functions. We apply our models to existing data sets, and find that the abundances of metabolic groups within microbial communities from bromeliad foliage do not exhibit any evidence of the previously hypothesized functional selection. By contrast, communities of soil bacteria or human gut commensals grown in vitro are selected for metabolic capabilities. By separating the effects of averaging and functional bias on functional variability, we find that the appearance of functional selection in gut microbiome samples from the Human Microbiome Project is artifactual, and that there is no evidence of selection for any molecular function represented by KEGG orthology. These concepts articulate a basic framework for quantifying functional redundancy and selection, advancing our understanding of the mapping between microbiome taxonomy and function.},
}

@article {pmid38585738,
year = {2024},
author = {Hunter, C and Dia, K and Boykins, J and Perry, K and Banerjee, N and Cuffee, J and Armstrong, E and Morgan, G and Banerjee, HN and Banerjee, A and Bhattacharya, S},
title = {An investigation for phylogenetic characterization of human Pancreatic cancer microbiome by 16SrDNA Sequencing and Bioinformatics techniques.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-4140368/v1},
pmid = {38585738},
abstract = {Pancreatic cancer is a significant public health concern, with increasing incidence rates and limited treatment options. Recent studies have highlighted the role of the human microbiome, particularly the gut microbiota, in the development and progression of this disease. Microbial dysbiosis, characterized by alterations in the composition and function of the gut microbiota, has been implicated in pancreatic carcinogenesis through mechanisms involving chronic inflammation, immune dysregulation, and metabolic disturbances. Researchers have identified specific microbial signatures associated with pancreatic cancer, offering potential biomarkers for early detection and prognostication. By leveraging advanced sequencing and bioinformatics tools, scientists have delineated differences in the gut microbiota between pancreatic cancer patients and healthy individuals, providing insights into disease pathogenesis and potential diagnostic strategies. Moreover, the microbiome holds promise as a therapeutic target in pancreatic cancer treatment. Interventions aimed at modulating the microbiome, such as probiotics, prebiotics, and fecal microbiota transplantation, have demonstrated potential in enhancing the efficacy of existing cancer therapies, including chemotherapy and immunotherapy. These approaches can influence immune responses, alter tumor microenvironments, and sensitize tumors to treatment, offering new avenues for improving patient outcomes and overcoming therapeutic resistance. Overall, understanding the complex interplay between the microbiome and pancreatic cancer is crucial for advancing our knowledge of disease mechanisms and identifying innovative therapeutic strategies. Here we report phylogenetic analysis of the 16S microbial sequences of the pancreatic cancer mice microbiome and corresponding age matched healthy mice microbiome. We successfully identified differentially abundance of microbiota in the pancreatic cancer.},
}

@article {pmid38585650,
year = {2024},
author = {Kiljunen, S and Resch, G},
title = {Editorial: Standards in personalized phage therapy: from phage collection to phage production.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1376386},
doi = {10.3389/fcimb.2024.1376386},
pmid = {38585650},
issn = {2235-2988},
}

@article {pmid38581020,
year = {2024},
author = {Douillard, FP and Derman, Y and Jian, C and Korpela, K and Saxén, H and Salonen, A and de Vos, WM and Korkeala, H and Lindström, M},
title = {Case report: Aberrant fecal microbiota composition of an infant diagnosed with prolonged intestinal botulism.},
journal = {Gut pathogens},
volume = {16},
number = {1},
pages = {20},
pmid = {38581020},
issn = {1757-4749},
abstract = {BACKGROUND: Intestinal botulism is primarily reported in small babies as a condition known as infant botulism. The condition results from the ingestion of environmental or foodborne spores of botulinum neurotoxin (BoNT) producing Clostridia, usually Clostridium botulinum, and subsequent spore germination into active botulinum neurotoxinogenic cultures in the gut. It is generally considered that small babies are susceptible to C. botulinum colonization because of their immature gut microbiota. Yet, it is poorly understood which host factors contribute to the clinical outcome of intestinal botulism. We previously reported a case of infant botulism where the infant recovered clinically in six weeks but continued to secrete C. botulinum cells and/or BoNT in the feces for seven months.

CASE PRESENTATION: To further understand the microbial ecology behind this exceptionally long-lasting botulinum neurotoxinogenic colonization, we characterized the infant fecal microbiota using 16S rRNA gene amplicon sequencing over the course of disease and recovery. C. botulinum could be detected in the infant fecal samples at low levels through the acute phase of the disease and three months after recovery. Overall, we observed a temporal delay in the maturation of the infant fecal microbiota associated with a persistently high-level bifidobacterial population and a low level of Lachnospiraceae, Bacteroidaceae and Ruminococcaceae compared to healthy infants over time.

CONCLUSION: This study brings novel insights into the infant fecal composition associated with intestinal botulism and provides a basis for a more systematic analysis of the gut microbiota of infants diagnosed with botulism. A better understanding of the gut microbial ecology associated with infant botulism may support the development of prophylactic strategies against this life-threatening disease in small babies.},
}

@article {pmid38579936,
year = {2024},
author = {Rivet-Noor, CR and Merchak, AR and Render, C and Gay, NM and Beiter, RM and Brown, R and Keeler, A and Brett Moreau, G and Li, S and Olgun, DG and Steigmeyer, AD and Ofer, R and Mihn Huu Phan, T and Vemuri, K and Chen, L and Mahoney, KE and Shin, JB and Malaker, SA and Deppmann, C and Verzi, M and Gaultier, A},
title = {Stress-induced mucin 13 reductions drive intestinal microbiome shifts and despair behaviors.},
journal = {Brain, behavior, and immunity},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.bbi.2024.03.028},
pmid = {38579936},
issn = {1090-2139},
abstract = {Depression is a prevalent psychological condition with limited treatment options. While its etiology is multifactorial, both chronic stress and changes in microbiome composition are associated with disease pathology. Stress is known to induce microbiome dysbiosis, defined here as a change in microbial composition associated with a pathological condition. This state of dysbiosis is known to feedback on depressive symptoms. While studies have demonstrated that targeted restoration of the microbiome can alleviate depressive-like symptoms in mice, translating these findings to human patients has proven challenging due to the complexity of the human microbiome. As such, there is an urgent need to identify factors upstream of microbial dysbiosis. Here we investigate the role of mucin 13 as an upstream mediator of microbiome composition changes in the context of stress. Using a model of chronic stress, we show that the glycocalyx protein, mucin 13, is selectively reduced after psychological stress exposure. We further demonstrate that the reduction of Muc13 is mediated by the Hnf4 transcription factor family. Finally, we determine that deleting Muc13 is sufficient to drive microbiome shifts and despair behaviors. These findings shed light on the mechanisms behind stress-induced microbial changes and reveal a novel regulator of mucin 13 expression.},
}

@article {pmid38577723,
year = {2024},
author = {Kozajda, A and Miśkiewicz, E and Jeżak, K},
title = {Zoonotic bacteria in the vicinity of animal farms as a factor disturbing the human microbiome: a review.},
journal = {International journal of occupational medicine and environmental health},
volume = {},
number = {},
pages = {},
doi = {10.13075/ijomeh.1896.02003},
pmid = {38577723},
issn = {1896-494X},
abstract = {This review is aimed at summarizing the current state of knowledge about the relationship between environmental exposure to the bioaerosol emitted by intensive livestock farming and changes in the microbiome of people living in livestock farm vicinity. The PubMed, Scopus and Web of Science databases were searched by crossing keywords from the following 3 groups: a) "livestock," "animal farms," "animal breeding"; b) "microbiome," "resistome"; c) "livestock vicinity," "farm vicinity," "neighborhoods and health" in 2010-2022. Literature screening did not reveal any paper related to the full microbiome composition in the population studied. In the study, the authors included 7 papers (5 from the Netherlands, 1 from the USA, and 1 from China). The studies confirmed the carriage of Staphylococcus aureus, including methicillin-resistant S. aureus (MRSA), livestockassociated MRSA (LA-MRSA MC398) and multidrug-resistant S. aureus (MDRSA) in the nasal microbiome of adults and children living within 500-2000 m from a livestock farm. Clostridium difficile, including LA-ribotype RT078 carriage, was detected in the intestinal microbiome of adults living within 500-1000 m. Extended-spectrum β-lactamase (ESBL) producing Enterobacteriaceae were confirmed in the intestinal microbiome of adults living within 500-6200 m. Knowledge on the composition of the microflora of people living in livestock farm vicinity is insufficient to conclude about changes in the microbiome caused by the environmental emission of bioaerosol. The carriage prevalence of the LA-bacteria, including both strains with antimicrobial resistance and antimicrobial resistance genes, confirms the presence of zoonotic bacteria in the human microflora in populations without occupational contact with animals. It cannot be ruled out that zoonotic bacteria, as a component of the microbiome, have a negative impact on people's health. Int J Occup Med Environ Health. 2024;37(2).},
}

@article {pmid38246133,
year = {2024},
author = {Chulenbayeva, L and Ganzhula, Y and Kozhakhmetov, S and Jarmukhanov, Z and Nurgaziyev, M and Nurgozhina, A and Muhanbetzhanov, N and Sergazy, S and Zhetkenev, S and Borykbay, Z and Tkachev, V and Urazova, S and Vinogradova, E and Kushugulova, A},
title = {The Trajectory of Successful Aging: Insights from Metagenome and Cytokine Profiling.},
journal = {Gerontology},
volume = {70},
number = {4},
pages = {390-407},
doi = {10.1159/000536082},
pmid = {38246133},
issn = {1423-0003},
abstract = {INTRODUCTION: The longevity is influenced by genetic, environmental, and lifestyle factors. The specific changes that occur in the gut microbiome during the aging process, and their relationship to longevity and immune function, have not yet been fully understood. The ongoing research of other microbiome based on longevity cohort in Kazakhstan provides preliminary information on longevity-related aging, where cytokine expression is associated with specific microbial communities and microbial functions.

METHODS: Metagenomic shotgun sequencing study of 40 long-lived individuals aged 90 years and over was carried out, who were conditionally healthy and active, able to serve themselves, without a history of serious infection and cancer, who had not taken any antimicrobials, including probiotics. Blood serum was analyzed for clinical and laboratory characteristics. The cytokine and chemokine profile in serum and stool samples was assessed using multiplex analysis.

RESULTS: We found a significant increase in the expression of pro-inflammatory cytokines IL-1a, IL-6, 12p70, IP-10, IFNα2, IL-15, TNFa, as well as chemokines MIP-1a/CCL3 and MIP-1b/CCL4, chemokine motif ligands MCP-3/CCL7 and MDC/CCL22(1c). Nonagenerians and centenarians demonstrated a greater diversity of core microbiota genera and showed an elevated prevalence of the genera Bacteroides, Clostridium, Escherichia, and Alistipes. Conversely, there was a decrease in the abundance of the genera Ruminococcus, Fusicatenibacter, Dorea, as well as the species Fusicatenibacter saccharivorans. Furthermore, functional analysis revealed that the microbiome in long-lived group has a high capacity for lipid metabolism, amino acid degradation, and potential signs of chronic inflammatory status.

CONCLUSION: Long-lived individuals exhibit an immune system imbalance and observed changes in the composition of the gut microbiota at the genus level between to the two age-groups. Age-related changes in the gut microbiome, metabolic functions of the microbial community, and chronic inflammation all contribute to immunosenescence. In turn, the inflammatory state and microbial composition of the gut is related to nutritional status.},
}

@article {pmid38577200,
year = {2024},
author = {Salvadori, M and Rosso, G},
title = {Update on the gut microbiome in health and diseases.},
journal = {World journal of methodology},
volume = {14},
number = {1},
pages = {89196},
pmid = {38577200},
issn = {2222-0682},
abstract = {The Human Microbiome Project, Earth Microbiome Project, and next-generation sequencing have advanced novel genome association, host genetic linkages, and pathogen identification. The microbiome is the sum of the microbes, their genetic information, and their ecological niche. This study will describe how millions of bacteria in the gut affect the human body in health and disease. The gut microbiome changes in relation with age, with an increase in Bacteroidetes and Firmicutes. Host and environmental factors affecting the gut microbiome are diet, drugs, age, smoking, exercise, and host genetics. In addition, changes in the gut microbiome may affect the local gut immune system and systemic immune system. In this study, we discuss how the microbiome may affect the metabolism of healthy subjects or may affect the pathogenesis of metabolism-generating metabolic diseases. Due to the high number of publications on the argument, from a methodologically point of view, we decided to select the best papers published in referred journals in the last 3 years. Then we selected the previously published papers. The major goals of our study were to elucidate which microbiome and by which pathways are related to healthy and disease conditions.},
}

@article {pmid38575895,
year = {2024},
author = {Zhang, M and Zhao, Y and Umar, A and Zhang, H and Yang, L and Huang, J and Long, Y and Yu, Z},
title = {Comparative analysis of microbial composition and functional characteristics in dental plaque and saliva of oral cancer patients.},
journal = {BMC oral health},
volume = {24},
number = {1},
pages = {411},
pmid = {38575895},
issn = {1472-6831},
support = {32170071 and 82273466//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: The oral cavity is home to various ecological niches, each with its own unique microbial composition. Understanding the microbial communities and gene composition in different ecological niches within the oral cavity of oral cancer (OC) patients is crucial for determining how these microbial populations contribute to disease progression.

METHODS: In this study, saliva and dental plaque samples were collected from patients with OC. Metagenomic sequencing was employed to analyze the microbial community classification and functional composition of the different sample groups.

RESULTS: The results of the study revealed significant differences in both the function and classification of microbial communities between saliva and dental plaque samples. The diversity of microbial species in saliva was found to be higher compared to  that in plaque samples. Notably, Actinobacteria were enriched in the dental plaque of OC patients. Furthermore, the study identified several inter-group differential marker species, including Prevotella intermedia, Haemophilus parahaemolyticus, Actinomyces radius, Corynebacterium matruchitii, and Veillonella atypica. Additionally, 1,353 differential genes were annotated into 23 functional pathways. Interestingly, a significant correlation was observed between differentially labeled species and Herpes simplex virus 1 (HSV-1) infection, which may be related to the occurrence and development of cancer.

CONCLUSIONS: Significant differences in the microbial and genetic composition of saliva and dental plaque samples were observed in OC patients. Furthermore, pathogenic bacteria associated with oral diseases were predominantly enriched in saliva. The identification of inter-group differential biomarkers and pathways provide insights into the relationship between oral microbiota and the occurrence and development of OC.},
}

@article {pmid38575862,
year = {2024},
author = {Zhang, M and Zhou, Y and Yao, S and Zhao, Y and Batool, SS and Huang, J and Jiang, L and Yan, D and Yan, W and Yu, Z},
title = {Effect of stress urinary incontinence on vaginal microbial communities.},
journal = {BMC microbiology},
volume = {24},
number = {1},
pages = {112},
pmid = {38575862},
issn = {1471-2180},
support = {32000054 and 32170071//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: Postpartum women often experience stress urinary incontinence (SUI) and vaginal microbial dysbiosis, which seriously affect women's physical and mental health. Understanding the relationship between SUI and vaginal microbiota composition may help to prevent vaginal diseases, but research on the potential association between these conditions is limited.

RESULTS: This study employed 16S rRNA gene sequencing to explore the association between SUI and vaginal dysbiosis. In terms of the vaginal microbiota, both species richness and evenness were significantly higher in the SUI group. Additionally, the results of NMDS and species composition indicated that there were differences in the composition of the vaginal microbiota between the two groups. Specifically, compared to postpartum women without SUI (Non-SUI), the relative abundance of bacteria associated with bacterial dysbiosis, such as Streptococcus, Prevotella, Dialister, and Veillonella, showed an increase, while the relative abundance of Lactobacillus decreased in SUI patients. Furthermore, the vaginal microbial co-occurrence network of SUI patients displayed higher connectivity, complexity, and clustering.

CONCLUSION: The study highlights the role of Lactobacillus in maintaining vaginal microbial homeostasis. It found a correlation between SUI and vaginal microbiota, indicating an increased risk of vaginal dysbiosis. The findings could enhance our understanding of the relationship between SUI and vaginal dysbiosis in postpartum women, providing valuable insights for preventing bacterial vaginal diseases and improving women's health.},
}

@article {pmid38569469,
year = {2024},
author = {Caffrey, EB and Sonnenburg, JL and Devkota, S},
title = {Our extended microbiome: The human-relevant metabolites and biology of fermented foods.},
journal = {Cell metabolism},
volume = {36},
number = {4},
pages = {684-701},
doi = {10.1016/j.cmet.2024.03.007},
pmid = {38569469},
issn = {1932-7420},
mesh = {Humans ; *Fermented Foods ; *Microbiota ; *Gastrointestinal Microbiome ; Biology ; },
abstract = {One of the key modes of microbial metabolism occurring in the gut microbiome is fermentation. This energy-yielding process transforms common macromolecules like polysaccharides and amino acids into a wide variety of chemicals, many of which are relevant to microbe-microbe and microbe-host interactions. Analogous transformations occur during the production of fermented foods, resulting in an abundance of bioactive metabolites. In foods, the products of fermentation can influence food safety and preservation, nutrient availability, and palatability and, once consumed, may impact immune and metabolic status, disease expression, and severity. Human signaling pathways perceive and respond to many of the currently known fermented food metabolites, though expansive chemical novelty remains to be defined. Here we discuss several aspects of fermented food-associated microbes and metabolites, including a condensed history, current understanding of their interactions with hosts and host-resident microbes, connections with commercial probiotics, and opportunities for future research on human health and disease and food sustainability.},
}

Humans
*Fermented Foods
*Microbiota
*Gastrointestinal Microbiome
Biology

@article {pmid38567073,
year = {2024},
author = {Wojciechowska, D and Salamon, S and Wróblewska-Seniuk, K},
title = {It's time to shed some light on the importance of fungi in neonatal intensive care units: what do we know about the neonatal mycobiome?.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1355418},
pmid = {38567073},
issn = {1664-302X},
abstract = {The 21st century, thanks to the development of molecular methods, including DNA barcoding, using Sanger sequencing, and DNA metabarcoding, based on next-generation sequencing (NGS), is characterized by flourishing research on the human microbiome. Microbial dysbiosis is perceived as a new pathogenetic factor for neonatal diseases. Fungi are crucial, but neglected, components of the neonatal microbiome, which, despite their low abundance, significantly impact morbidity and mortality rates of premature infants hospitalized in Neonatal Intensive Care Units (NICUs). The neonatal mycobiome's composition and effect on health remain poorly studied research areas. Our knowledge about neonatal mycobiome, composed of limited genera, is mainly based on research on the bacterial microbiome. We presume it is influenced by clinical factors, including prematurity, antibiotic therapy, and type of delivery. Understanding these risk factors may be useful in prevention strategies against dysbiosis and invasive fungal infections. Despite the methodological challenges resulting from the biology of the fungal cell, this topic is an attractive area of research that may contribute to more effective treatment, especially of newborns from risk groups. In this mini review, we discuss the current state of knowledge, research gaps, study difficulties, and future research directions on the neonatal mycobiome, concerning potential future clinical applications.},
}

@article {pmid38565750,
year = {2024},
author = {Núñez Casal, A},
title = {Race and indigeneity in human microbiome science: microbiomisation and the historiality of otherness.},
journal = {History and philosophy of the life sciences},
volume = {46},
number = {2},
pages = {17},
pmid = {38565750},
issn = {1742-6316},
support = {RYC2022-036985-I//Ministerio de Ciencia e Innovación/ ; },
mesh = {Humans ; United States ; *Microbiota ; },
abstract = {This article reformulates Stephan Helmreich´s the ¨microbiomisation of race¨ as the historiality of otherness in the foundations of human microbiome science. Through the lens of my ethnographic fieldwork of a transnational community of microbiome scientists that conducted a landmark human microbiome research on indigenous microbes and its affiliated and first personalised microbiome initiative, the American Gut Project, I follow and trace the key actors, experimental systems and onto-epistemic claims in the emergence of human microbiome science a decade ago. In doing so, I show the links between the reinscription of race, comparative research on the microbial genetic variation of human populations and the remining of bioprospected data for personalised medicine. In these unpredictable research movements, the microbiome of non-Western peoples and territories is much more than a side project or a specific approach within the field: it constitutes the nucleus of its experimental system, opening towards subsequent and cumulative research processes and knowledge production in human microbiome science. The article demonstrates that while human microbiome science is articulated upon the microbial 'makeup' of non-wester(nised) communities, societies, and locales, its results and therapeutics are only applicable to medical conditions affecting rich nations (i.e., inflammatory, autoimmune, and metabolic diseases). My reformulation of ¨microbiomisation of race¨ as the condition of possibility of human microbiome science reveals that its individual dimension is sustained by microbial DNA data from human populations through bioprospecting practices and gains meaning through personalised medicine initiatives, informal online networks of pseudoscientific and commodified microbial-related evidence.},
}

Humans
United States
*Microbiota

@article {pmid38563656,
year = {2024},
author = {Zhu, J and Yin, J and Chen, J and Hu, M and Lu, W and Wang, H and Zhang, H and Chen, W},
title = {Integrative analysis with microbial modelling and machine learning uncovers potential alleviators for ulcerative colitis.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2336877},
doi = {10.1080/19490976.2024.2336877},
pmid = {38563656},
issn = {1949-0984},
mesh = {Animals ; Mice ; Humans ; *Colitis, Ulcerative ; *Gastrointestinal Microbiome ; *Inflammatory Bowel Diseases ; *Colitis ; Machine Learning ; },
abstract = {Ulcerative colitis (UC) is a challenging form of inflammatory bowel disease, and its etiology is intricately linked to disturbances in the gut microbiome. To identify the potential alleviators of UC, we employed an integrative analysis combining microbial community modeling with advanced machine learning techniques. Using metagenomics data sourced from the Integrated Human Microbiome Project, we constructed individualized microbiome community models for each participant. Our analysis highlighted a significant decline in both α and β-diversity of strain-level microbial populations in UC subjects compared to controls. Distinct differences were also observed in the predicted fecal metabolite profiles and strain-to-metabolite contributions between the two groups. Using tree-based machine learning models, we successfully identified specific microbial strains and their associated metabolites as potential alleviators of UC. Notably, our experimental validation using a dextran sulfate sodium-induced UC mouse model demonstrated that the administration of Parabacteroides merdae ATCC 43,184 and N-acetyl-D-mannosamine provided notable relief from colitis symptoms. In summary, our study underscores the potential of an integrative approach to identify novel therapeutic avenues for UC, paving the way for future targeted interventions.},
}

Animals
Mice
Humans
*Colitis, Ulcerative
*Gastrointestinal Microbiome
*Inflammatory Bowel Diseases
*Colitis
Machine Learning

@article {pmid38560624,
year = {2024},
author = {Wilson, NG and Hernandez-Leyva, A and Schwartz, DJ and Bacharier, LB and Kau, AL},
title = {The gut metagenome harbors metabolic and antibiotic resistance signatures of moderate-to-severe asthma.},
journal = {FEMS microbes},
volume = {5},
number = {},
pages = {xtae010},
pmid = {38560624},
issn = {2633-6685},
abstract = {Asthma is a common allergic airway disease that has been associated with the development of the human microbiome early in life. Both the composition and function of the infant gut microbiota have been linked to asthma risk, but functional alterations in the gut microbiota of older patients with established asthma remain an important knowledge gap. Here, we performed whole metagenomic shotgun sequencing of 95 stool samples from a cross-sectional cohort of 59 healthy and 36 subjects with moderate-to-severe asthma to characterize the metagenomes of gut microbiota in adults and children 6 years and older. Mapping of functional orthologs revealed that asthma contributes to 2.9% of the variation in metagenomic content even when accounting for other important clinical demographics. Differential abundance analysis showed an enrichment of long-chain fatty acid (LCFA) metabolism pathways, which have been previously implicated in airway smooth muscle and immune responses in asthma. We also observed increased richness of antibiotic resistance genes (ARGs) in people with asthma. Several differentially abundant ARGs in the asthma cohort encode resistance to macrolide antibiotics, which are often prescribed to patients with asthma. Lastly, we found that ARG and virulence factor (VF) richness in the microbiome were correlated in both cohorts. ARG and VF pairs co-occurred in both cohorts suggesting that virulence and antibiotic resistance traits are coselected and maintained in the fecal microbiota of people with asthma. Overall, our results show functional alterations via LCFA biosynthetic genes and increases in antibiotic resistance genes in the gut microbiota of subjects with moderate-to-severe asthma and could have implications for asthma management and treatment.},
}

@article {pmid38555606,
year = {2024},
author = {Tutelyan, VA and Nikityuk, DB},
title = {[Key challenges in the dietary intake structure and cutting edge technologies for optimizing nutrition to protect the health of the Russian рopulation].},
journal = {Voprosy pitaniia},
volume = {93},
number = {1},
pages = {6-21},
doi = {10.33029/0042-8833-2024-93-1-6-21},
pmid = {38555606},
issn = {0042-8833},
support = {FGMF-2022-0001//The research was carried out using subsidies for the implementation of a state task/ ; },
mesh = {Humans ; *Nutritional Status ; *Food ; Food Safety/methods ; Russia ; Eating ; },
abstract = {This article presents an analysis of some of the results of the work of the Federal Research Center for Nutrition and Biotechnology (Center) in recent years, highlighting the most important, promising areas of Nutrition Science and Food Hygiene that need further development. The priority area of Center functioning is scientific support for the implementation of the Doctrine of Food Security of the Russian Federation (Decree of the President of the Russian Federation dated January 21, 2020 No. 20), Decree of the President of the Russian Federation dated July 21, 2020 No. 474 «On the national development goals of the Russian Federation for the period until 2030 «in terms of ensuring an increase in life expectancy and improving the life quality of the population, the Strategy for Improving the Quality of Food Products in the Russian Federation until 2030 (Order of the Government of the Russian Federation dated June 29, 2016 No. 1364-r). The Center coordinates all research on medical nutrition problems in the Russian Federation within the framework of the work of the Problem Commission on Nutrition Hygiene of the Scientific Council of the Federal Service for Supervision of Consumer Rights Protection and Human Welfare, the Scientific Council of the Russian Academy of Sciences on Medical Nutrition Problems, the Scientific and Technical Committee of the Comprehensive Scientific Program «Priority Research in the Field of Nutrition of the Population», Profile Commission on Dietetics of the Expert Council in the Field of Health of the Ministry of Healthcare of Russian Federation, ensuring the implementation of their results with the participation of members of the Consortium "Healthcare, Nutrition, Demography". The most important area of the Center's work is scientific and expert support in the field of international and national technical regulation of the production and turnover of foods and raw materials, in particular, the work of the Russian national contact point of the Codex Alimentarius Commission (established by FAO and WHO), as well as the work of the Russian side in the Eurasian Economic Commission regarding the preparation of proposals for technical regulations of the Customs Union in the field of food safety, evaluation of draft technical regulations and amendments and additions to them.},
}

Humans
*Nutritional Status
*Food
Food Safety/methods
Russia
Eating

@article {pmid38555566,
year = {2024},
author = {Kuehnast, T and Kumpitsch, C and Mohammadzadeh, R and Weichhart, T and Moissl-Eichinger, C and Heine, H},
title = {Exploring the human archaeome: its relevance for health and disease, and its complex interplay with the human immune system.},
journal = {The FEBS journal},
volume = {},
number = {},
pages = {},
doi = {10.1111/febs.17123},
pmid = {38555566},
issn = {1742-4658},
support = {COE 7//Austrian Science Fund/ ; P 32697//Austrian Science Fund/ ; SFB F83//Austrian Science Fund/ ; },
abstract = {This Review aims to coalesce existing knowledge on the human archaeome, a less-studied yet critical non-bacterial component of the human microbiome, with a focus on its interaction with the immune system. Despite a largely bacteria-centric focus in microbiome research, archaea present unique challenges and opportunities for understanding human health. We examine the archaeal distribution across different human body sites, such as the lower gastrointestinal tract (LGT), upper aerodigestive tract (UAT), urogenital tract (UGT), and skin. Variability in archaeal composition exists between sites; methanogens dominate the LGT, while Nitrososphaeria are prevalent on the skin and UAT. Archaea have yet to be classified as pathogens but show associations with conditions such as refractory sinusitis and vaginosis. In the LGT, methanogenic archaea play critical metabolic roles by converting bacterial end-products into methane, correlating with various health conditions, including obesity and certain cancers. Finally, this work looks at the complex interactions between archaea and the human immune system at the molecular level. Recent research has illuminated the roles of specific archaeal molecules, such as RNA and glycerolipids, in stimulating immune responses via innate immune receptors like Toll-like receptor 8 (TLR8) and 'C-type lectin domain family 4 member E' (CLEC4E; also known as MINCLE). Additionally, metabolic by-products of archaea, specifically methane, have demonstrated immunomodulatory effects through anti-inflammatory and anti-oxidative pathways. Despite these advancements, the mechanistic underpinnings of how archaea influence immune activity remain a fertile area for further investigation.},
}

@article {pmid38553666,
year = {2024},
author = {Ma, ZS},
title = {Towards a unified medical microbiome ecology of the OMU for metagenomes and the OTU for microbes.},
journal = {BMC bioinformatics},
volume = {25},
number = {1},
pages = {137},
pmid = {38553666},
issn = {1471-2105},
mesh = {Animals ; Humans ; Metagenome ; *Microbiota/genetics ; *Gastrointestinal Microbiome ; Biodiversity ; Sequence Analysis, DNA ; Metagenomics/methods ; },
abstract = {BACKGROUND: Metagenomic sequencing technologies offered unprecedented opportunities and also challenges to microbiology and microbial ecology particularly. The technology has revolutionized the studies of microbes and enabled the high-profile human microbiome and earth microbiome projects. The terminology-change from microbes to microbiomes signals that our capability to count and classify microbes (microbiomes) has achieved the same or similar level as we can for the biomes (macrobiomes) of plants and animals (macrobes). While the traditional investigations of macrobiomes have usually been conducted through naturalists' (Linnaeus & Darwin) naked eyes, and aerial and satellite images (remote-sensing), the large-scale investigations of microbiomes have been made possible by DNA-sequencing-based metagenomic technologies. Two major types of metagenomic sequencing technologies-amplicon sequencing and whole-genome (shotgun sequencing)-respectively generate two contrastingly different categories of metagenomic reads (data)-OTU (operational taxonomic unit) tables representing microorganisms and OMU (operational metagenomic unit), a new term coined in this article to represent various cluster units of metagenomic genes.

RESULTS: The ecological science of microbiomes based on the OTU representing microbes has been unified with the classic ecology of macrobes (macrobiomes), but the unification based on OMU representing metagenomes has been rather limited. In a previous series of studies, we have demonstrated the applications of several classic ecological theories (diversity, composition, heterogeneity, and biogeography) to the studies of metagenomes. Here I push the envelope for the unification of OTU and OMU again by demonstrating the applications of metacommunity assembly and ecological networks to the metagenomes of human gut microbiomes. Specifically, the neutral theory of biodiversity (Sloan's near neutral model), Ning et al.stochasticity framework, core-periphery network, high-salience skeleton network, special trio-motif, and positive-to-negative ratio are applied to analyze the OMU tables from whole-genome sequencing technologies, and demonstrated with seven human gut metagenome datasets from the human microbiome project.

CONCLUSIONS: All of the ecological theories demonstrated previously and in this article, including diversity, composition, heterogeneity, stochasticity, and complex network analyses, are equally applicable to OMU metagenomic analyses, just as to OTU analyses. Consequently, I strongly advocate the unification of OTU/OMU (microbiomes) with classic ecology of plants and animals (macrobiomes) in the context of medical ecology.},
}

Animals
Humans
Metagenome
*Microbiota/genetics
*Gastrointestinal Microbiome
Biodiversity
Sequence Analysis, DNA
Metagenomics/methods

@article {pmid38550775,
year = {2024},
author = {Monteiro, JS and Kaushik, K and de Arruda, JAA and Georgakopoulou, E and Vieira, AT and Silva, TA and Devadiga, D and Anyanechi, CE and Shetty, S},
title = {Fungal footprints in oral cancer: unveiling the oral mycobiome.},
journal = {Frontiers in oral health},
volume = {5},
number = {},
pages = {1360340},
pmid = {38550775},
issn = {2673-4842},
abstract = {Oral squamous cell carcinoma (OSCC) is the most common type of head and neck cancer, with a high mortality rate. There is growing evidence supporting a link between oral cancer and the microbiome. The microbiome can impact various aspects of cancer, such as pathogenesis, diagnosis, treatment, and prognosis. While there is existing information on bacteria and its connection to oral cancer, the fungi residing in the oral cavity represent a significant component of the microbiome that remains in its early stages of exploration and understanding. Fungi comprise a minuscule part of the human microbiome called the mycobiome. Mycobiome is ubiquitous in the human body but a weakened immune system offers a leeway space for fungi to showcase its virulence. The role of mycobiome as a colonizer, facilitator, or driver of carcinogenesis is still ambiguous. Reactivating the mycobiome that undergoes collateral damage associated with cancer treatment can be watershed event in cancer research. The coordinated, virulent, non-virulent behavior of the fungi once they reach a critical density must be hacked, considering its diagnostic, prognostic and therapeutic implications in cancer. This review highlights the diversity of the mycobiome and its potential role in oral cancer.},
}

@article {pmid38550941,
year = {2023},
author = {Ellinghaus, D},
title = {COVID-19 host genetics and ABO blood group susceptibility.},
journal = {Cambridge prisms. Precision medicine},
volume = {1},
number = {},
pages = {e10},
pmid = {38550941},
issn = {2752-6143},
abstract = {Twenty-five susceptibility loci for SARS-CoV-2 infection and/or COVID-19 disease severity have been identified in the human genome by genome-wide association studies, and the most frequently replicated genetic findings for susceptibility are genetic variants at the ABO gene locus on chromosome 9q34.2, which is supported by the association between ABO blood group distribution and COVID-19. The ABO blood group effect appears to influence a variety of disease conditions and pathophysiological mechanisms associated with COVID-19. Transmission models for SARS-CoV-2 combined with observational public health and genome-wide data from patients and controls, as well as receptor binding experiments in cell lines and human samples, indicate that there may be a reduction or slowing of infection events by up to 60% in certain ABO blood group constellations of index and contact person in the early phase of a SARS-CoV-2 outbreak. The strength of the ABO blood group effect on reducing infection rates further depends on the distribution of the ABO blood groups in the respective population and the proportion of blood group O in that population. To understand in detail the effect of ABO blood groups on COVID-19, further studies are needed in relation to different demographic characteristics, but also in relation to recent data on reinfection with new viral variants and in the context of the human microbiome.},
}

@article {pmid38549112,
year = {2024},
author = {Edwin, NR and Fitzpatrick, AH and Brennan, F and Abram, F and O'Sullivan, O},
title = {An in-depth evaluation of metagenomic classifiers for soil microbiomes.},
journal = {Environmental microbiome},
volume = {19},
number = {1},
pages = {19},
pmid = {38549112},
issn = {2524-6372},
support = {SFI/16/RC/3835//VistaMilk/ ; Ref: 2020019//Teagasc Walsh Scholarship Programme/ ; },
abstract = {BACKGROUND: Recent endeavours in metagenomics, exemplified by projects such as the human microbiome project and TARA Oceans, have illuminated the complexities of microbial biomes. A robust bioinformatic pipeline and meticulous evaluation of their methodology have contributed to the success of these projects. The soil environment, however, with its unique challenges, requires a specialized methodological exploration to maximize microbial insights. A notable limitation in soil microbiome studies is the dearth of soil-specific reference databases available to classifiers that emulate the complexity of soil communities. There is also a lack of in-vitro mock communities derived from soil strains that can be assessed for taxonomic classification accuracy.

RESULTS: In this study, we generated a custom in-silico mock community containing microbial genomes commonly observed in the soil microbiome. Using this mock community, we simulated shotgun sequencing data to evaluate the performance of three leading metagenomic classifiers: Kraken2 (supplemented with Bracken, using a custom database derived from GTDB-TK genomes along with its own default database), Kaiju, and MetaPhlAn, utilizing their respective default databases for a robust analysis. Our results highlight the importance of optimizing taxonomic classification parameters, database selection, as well as analysing trimmed reads and contigs. Our study showed that classifiers tailored to the specific taxa present in our samples led to fewer errors compared to broader databases including microbial eukaryotes, protozoa, or human genomes, highlighting the effectiveness of targeted taxonomic classification. Notably, an optimal classifier performance was achieved when applying a relative abundance threshold of 0.001% or 0.005%. The Kraken2 supplemented with bracken, with a custom database demonstrated superior precision, sensitivity, F1 score, and overall sequence classification. Using a custom database, this classifier classified 99% of in-silico reads and 58% of real-world soil shotgun reads, with the latter identifying previously overlooked phyla using a custom database.

CONCLUSION: This study underscores the potential advantages of in-silico methodological optimization in metagenomic analyses, especially when deciphering the complexities of soil microbiomes. We demonstrate that the choice of classifier and database significantly impacts microbial taxonomic profiling. Our findings suggest that employing Kraken2 with Bracken, coupled with a custom database of GTDB-TK genomes and fungal genomes at a relative abundance threshold of 0.001% provides optimal accuracy in soil shotgun metagenome analysis.},
}

@article {pmid38543670,
year = {2024},
author = {Tosado-Rodríguez, E and Alvarado-Vélez, I and Romaguera, J and Godoy-Vitorino, F},
title = {Vaginal Microbiota and HPV in Latin America: A Narrative Review.},
journal = {Microorganisms},
volume = {12},
number = {3},
pages = {},
pmid = {38543670},
issn = {2076-2607},
support = {U54MD007600/MD/NIMHD NIH HHS/United States ; P20GM103475/GM/NIGMS NIH HHS/United States ; U54MD007587/GM/NIGMS NIH HHS/United States ; CA096297/CA/NCI NIH HHS/United States ; },
abstract = {With the expansion of human microbiome studies in the last 15 years, we have realized the immense implications of microbes in human health. The human holobiont is now accepted, given the commensal relationships with bacteria, fungi, parasites, viruses, and human cells. The cervicovaginal microbiota is a specific case within the human microbiome where diversity is lower to maintain a chemical barrier of protection against infections. This narrative review focuses on the vaginal microbiome. It summarizes key findings on how native bacteria protect women from disease or predispose them to damaging inflammatory processes with an emphasis on the role of HPV infections in Latin America, one of the world's regions with the highest cervical cancer prevalence.},
}

@article {pmid38543514,
year = {2024},
author = {Efremova, I and Maslennikov, R and Medvedev, O and Kudryavtseva, A and Avdeeva, A and Krasnov, G and Romanikhin, F and Diatroptov, M and Fedorova, M and Poluektova, E and Levshina, A and Ivashkin, V},
title = {Gut Microbiota and Biomarkers of Intestinal Barrier Damage in Cirrhosis.},
journal = {Microorganisms},
volume = {12},
number = {3},
pages = {},
doi = {10.3390/microorganisms12030463},
pmid = {38543514},
issn = {2076-2607},
abstract = {Gut dysbiosis and subclinical intestinal damage are common in cirrhosis. The aim of this study was to examine the association of intestinal damage biomarkers (diamine oxidase [DAO], claudin 3, and intestinal fatty acid binding protein [I-FABP; FABP2]) with the state of the gut microbiota in cirrhosis. The blood levels of DAO were inversely correlated with blood levels of claudin 3, lipopolysaccharide (LPS), presepsin, TNF-α, and the severity of cirrhosis according to Child-Pugh scores. The blood level of I-FABP was directly correlated with the blood level of claudin 3 but not with that of DAO. Patients with small intestinal bacterial overgrowth (SIBO) had lower DAO levels than patients without SIBO. There was no significant difference in claudin 3 levels and I-FABP detection rates between patients with and without SIBO. The DAO level was directly correlated with the abundance of Akkermansiaceae, Akkermansia, Allisonella, Clostridiaceae, Dialister, Lactobacillus, Muribaculaceae, Negativibacillus, Ruminococcus, Thiomicrospiraceae, Verrucomicrobiae, and Verrucomicrobiota; and it was inversely correlated with the abundance of Anaerostipes, Erysipelatoclostridium, and Vibrio. The I-FABP level was directly correlated with Anaerostipes, Bacteroidia, Bacteroidota, Bilophila, Megamonas, and Selenomonadaceae; and it was inversely correlated with the abundance of Brucella, Pseudomonadaceae, Pseudomonas, and Vibrionaceae. The claudin 3 level was directly correlated with Anaerostipes abundance and was inversely correlated with the abundance of Brucella, Coriobacteriia, Eggerthellaceae, and Lactobacillus.},
}

@article {pmid38542770,
year = {2024},
author = {Nikoloudaki, O and Pinto, D and Acin Albiac, M and Celano, G and Da Ros, A and De Angelis, M and Rinaldi, F and Gobbetti, M and Di Cagno, R},
title = {Exploring the Gut Microbiome and Metabolome in Individuals with Alopecia Areata Disease.},
journal = {Nutrients},
volume = {16},
number = {6},
pages = {},
pmid = {38542770},
issn = {2072-6643},
mesh = {Adult ; Humans ; *Gastrointestinal Microbiome/genetics ; *Alopecia Areata ; Metabolome ; Feces/chemistry ; Biomarkers/analysis ; RNA, Ribosomal, 16S/genetics ; },
abstract = {In recent years, heightened attention has been devoted to unravelling the intricate interplay between genetic and environmental factors shaping the gut microbiota and its significance for human health. This study delves into exploring the plausible connection between Alopecia Areata (AA), an autoimmune disease, and the dynamics of the gut microbiome. Examining a cohort of healthy adults and individuals with AA, both the gut microbiota composition and volatile organic compound (VOC) metabolites from faeces and urine were analysed. While overall microbiota composition showed no significant differences, intra-individual variability revealed distinctions related to age, gender, and pathology status, with AA individuals exhibiting reduced species richness and evenness. Differential abundance analysis identified microbial biomarkers for AA, notably Firmicutes, Lachnospirales, and Blautia, while Coprococcus stood out for healthy individuals. The Data Integration Analysis for Biomarker discovery using Latent Components (DIABLO) method further supported these findings including metabolite biomarkers, such as esters of branched chain fatty acids and branched chain amino acids as predictors for AA, suggesting potential links to oxidative stress. Despite certain limitations, the study highlights the complexity of the gut microbiome and its metabolites in the context of AA, while the biomarkers identified could be useful starting points for upcoming studies.},
}

Adult
Humans
*Gastrointestinal Microbiome/genetics
*Alopecia Areata
Metabolome
Feces/chemistry
Biomarkers/analysis
RNA, Ribosomal, 16S/genetics

@article {pmid38542455,
year = {2024},
author = {Mak, AL and Augustijn, QJJ and Heymann, CJF and Havik, S and Verdoes, X and Rios-Morales, M and Bosmans, LA and Verheij, J and Meijnikman, AS and de Jonge, PA and Herrema, H and de Vos, WM and Nieuwdorp, M and Grefhorst, A and Holleboom, AG},
title = {Anaerobutyricum soehngenii Reduces Hepatic Lipogenic Pathways and Increases Intestinal Gluconeogenic Gene Expression in Metabolic-Dysfunction-Associated Steatotic Liver Disease (MASLD) Mice.},
journal = {International journal of molecular sciences},
volume = {25},
number = {6},
pages = {},
doi = {10.3390/ijms25063481},
pmid = {38542455},
issn = {1422-0067},
abstract = {Metabolic-dysfunction-associated steatotic liver disease (MASLD) is a growing health problem for which no therapy exists to date. The modulation of the gut microbiome may have treatment potential for MASLD. Here, we investigated Anaerobutyricum soehngenii, a butyrate-producing anaerobic bacterium with beneficial effects in metabolic syndrome, in a diet-induced MASLD mouse model. Male C57BL/6J mice received a Western-type high-fat diet and water with 15% fructose (WDF) to induce MASLD and were gavaged with A. soehngenii (10[8] or 10[9] colony-forming units (CFU) 3 times per week) or a placebo for 6 weeks. The A. soehngenii gavage increased the cecal butyrate concentrations. Although there was no effect on histological MASLD scores, A. soehngenii improved the glycemic response to insulin. In the liver, the WDF-associated altered expression of three genes relevant to the MASLD pathophysiology was reversed upon treatment with A. soehngenii: Lipin-1 (Lpin1), insulin-like growth factor binding protein 1 (Igfbp1) and Interleukin 1 Receptor Type 1 (Il1r1). A. soehngenii administration also increased the intestinal expression of gluconeogenesis and fructolysis genes. Although these effects did not translate into significant histological improvements in MASLD, these results provide a basis for combined gut microbial approaches to induce histological improvements in MASLD.},
}

@article {pmid38542265,
year = {2024},
author = {Uzelac, M and Xin, R and Ongkeko, WM},
title = {Microbiome Dysbiosis Is Associated with Castration Resistance and Cancer Stemness in Metastatic Prostate Cancer.},
journal = {International journal of molecular sciences},
volume = {25},
number = {6},
pages = {},
doi = {10.3390/ijms25063291},
pmid = {38542265},
issn = {1422-0067},
support = {RG096651//UC San Diego Academic Senate/ ; },
abstract = {Prostate cancer is the second leading cause of death in males in America, with advanced prostate cancers exhibiting a 5-year survival rate of only 32%. Castration resistance often develops during the course of treatment, but its pathogenesis is poorly understood. This study explores the human microbiome for its implications in castration resistance and metastasis in prostate cancer. RNA sequencing data were downloaded for the bone and soft tissue biopsies of patients with metastatic castration-resistant prostate cancer. These included both metastatic and adjacent normal biopsies. These sequences were mapped to bacterial sequences, yielding species-level counts. A vast majority of species were found to be significantly underabundant in the CRPC samples. Of these, numerous were found to correlate with the expression of known markers of castration resistance, including AR, PI3K, and AKT. Castration resistance-associated signaling pathways were also enriched with these species, including PI3K-AKT signaling and endocrine resistance. For their implications in cancer aggression and metastasis, cancer stem cell markers were further explored for a relation to these species. EGFR and SLC3A2 were widely downregulated, with a greater abundance of most species. Our results suggest that the microbiome is heavily associated with castration resistance and stemness in prostate cancer. By considering the microbiome's importance in these factors, we may better understand the highly aggressive and highly invasive nature of castration-resistant prostate cancer, allowing for the needed improvements in the treatment of this disease.},
}

@article {pmid38530031,
year = {2024},
author = {Cao, B and Wang, X and Yin, W and Gao, Z and Xia, B},
title = {The human microbiota is a beneficial reservoir for SARS-CoV-2 mutations.},
journal = {mBio},
volume = {},
number = {},
pages = {e0318723},
doi = {10.1128/mbio.03187-23},
pmid = {38530031},
issn = {2150-7511},
abstract = {UNLABELLED: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) mutations are rapidly emerging. In particular, beneficial mutations in the spike (S) protein, which can either make a person more infectious or enable immunological escape, are providing a significant obstacle to the prevention and treatment of pandemics. However, how the virus acquires a high number of beneficial mutations in a short time remains a mystery. We demonstrate here that variations of concern may be mutated due in part to the influence of the human microbiome. We searched the National Center for Biotechnology Information database for homologous fragments (HFs) after finding a mutation and the six neighboring amino acids in a viral mutation fragment. Among the approximate 8,000 HFs obtained, 61 mutations in S and other outer membrane proteins were found in bacteria, accounting for 62% of all mutation sources, which is 12-fold higher than the natural variable proportion. A significant proportion of these bacterial species-roughly 70%-come from the human microbiota, are mainly found in the lung or gut, and share a composition pattern with COVID-19 patients. Importantly, SARS-CoV-2 RNA-dependent RNA polymerase replicates corresponding bacterial mRNAs harboring mutations, producing chimeric RNAs. SARS-CoV-2 may collectively pick up mutations from the human microbiota that change the original virus's binding sites or antigenic determinants. Our study clarifies the evolving mutational mechanisms of SARS-CoV-2.

IMPORTANCE: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) mutations are rapidly emerging, in particular advantageous mutations in the spike (S) protein, which either increase transmissibility or lead to immune escape and are posing a major challenge to pandemic prevention and treatment. However, how the virus acquires a high number of advantageous mutations in a short time remains a mystery. Here, we provide evidence that the human microbiota is a reservoir of advantageous mutations and aids mutational evolution and host adaptation of SARS-CoV-2. Our findings demonstrate a conceptual breakthrough on the mutational evolution mechanisms of SARS-CoV-2 for human adaptation. SARS-CoV-2 may grab advantageous mutations from the widely existing microorganisms in the host, which is undoubtedly an "efficient" manner. Our study might open a new perspective to understand the evolution of virus mutation, which has enormous implications for comprehending the trajectory of the COVID-19 pandemic.},
}

@article {pmid38528457,
year = {2024},
author = {Buetas, E and Jordán-López, M and López-Roldán, A and D'Auria, G and Martínez-Priego, L and De Marco, G and Carda-Diéguez, M and Mira, A},
title = {Full-length 16S rRNA gene sequencing by PacBio improves taxonomic resolution in human microbiome samples.},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {310},
pmid = {38528457},
issn = {1471-2164},
support = {PRE2019-088126//Spanish Ministry of Science and Innovation/ ; RTI2018- 102032-B-I00//The Spanish Ministry of Innovation and Science/ ; },
mesh = {Humans ; RNA, Ribosomal, 16S/genetics ; Genes, rRNA ; Phylogeny ; Sequence Analysis, DNA/methods ; *Microbiota/genetics ; High-Throughput Nucleotide Sequencing/methods ; },
abstract = {BACKGROUND: Sequencing variable regions of the 16S rRNA gene (≃300 bp) with Illumina technology is commonly used to study the composition of human microbiota. Unfortunately, short reads are unable to differentiate between highly similar species. Considering that species from the same genus can be associated with health or disease it is important to identify them at the lowest possible taxonomic rank. Third-generation sequencing platforms such as PacBio SMRT, increase read lengths allowing to sequence the whole gene with the maximum taxonomic resolution. Despite its potential, full length 16S rRNA gene sequencing is not widely used yet. The aim of the current study was to compare the sequencing output and taxonomic annotation performance of the two approaches (Illumina short read sequencing and PacBio long read sequencing of 16S rRNA gene) in different human microbiome samples. DNA from saliva, oral biofilms (subgingival plaque) and faeces of 9 volunteers was isolated. Regions V3-V4 and V1-V9 were amplified and sequenced by Illumina Miseq and by PacBio Sequel II sequencers, respectively.

RESULTS: With both platforms, a similar percentage of reads was assigned to the genus level (94.79% and 95.06% respectively) but with PacBio a higher proportion of reads were further assigned to the species level (55.23% vs 74.14%). Regarding overall bacterial composition, samples clustered by niche and not by sequencing platform. In addition, all genera with > 0.1% abundance were detected in both platforms for all types of samples. Although some genera such as Streptococcus tended to be observed at higher frequency in PacBio than in Illumina (20.14% vs 14.12% in saliva, 10.63% vs 6.59% in subgingival plaque biofilm samples) none of the differences were statistically significant when correcting for multiple testing.

CONCLUSIONS: The results presented in the current manuscript suggest that samples sequenced using Illumina and PacBio are mostly comparable. Considering that PacBio reads were assigned at the species level with higher accuracy than Illumina, our data support the use of PacBio technology for future microbiome studies, although a higher cost is currently required to obtain an equivalent number of reads per sample.},
}

Humans
RNA, Ribosomal, 16S/genetics
Genes, rRNA
Phylogeny
Sequence Analysis, DNA/methods
*Microbiota/genetics
High-Throughput Nucleotide Sequencing/methods

@article {pmid38528097,
year = {2024},
author = {Wang, B and Sun, F and Luan, Y},
title = {Comparison of the effectiveness of different normalization methods for metagenomic cross-study phenotype prediction under heterogeneity.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {7024},
pmid = {38528097},
issn = {2045-2322},
support = {2018YFA0703900//National Key Research and Development Program of China/ ; 2018YFA0703900//National Key Research and Development Program of China/ ; 11971264//National Science Foundation of China/ ; 11971264//National Science Foundation of China/ ; },
mesh = {Humans ; *Microbiota/genetics ; Metagenome ; Metagenomics ; Research Design ; Phenotype ; },
abstract = {The human microbiome, comprising microorganisms residing within and on the human body, plays a crucial role in various physiological processes and has been linked to numerous diseases. To analyze microbiome data, it is essential to account for inherent heterogeneity and variability across samples. Normalization methods have been proposed to mitigate these variations and enhance comparability. However, the performance of these methods in predicting binary phenotypes remains understudied. This study systematically evaluates different normalization methods in microbiome data analysis and their impact on disease prediction. Our findings highlight the strengths and limitations of scaling, compositional data analysis, transformation, and batch correction methods. Scaling methods like TMM show consistent performance, while compositional data analysis methods exhibit mixed results. Transformation methods, such as Blom and NPN, demonstrate promise in capturing complex associations. Batch correction methods, including BMC and Limma, consistently outperform other approaches. However, the influence of normalization methods is constrained by population effects, disease effects, and batch effects. These results provide insights for selecting appropriate normalization approaches in microbiome research, improving predictive models, and advancing personalized medicine. Future research should explore larger and more diverse datasets and develop tailored normalization strategies for microbiome data analysis.},
}

Humans
*Microbiota/genetics
Metagenome
Metagenomics
Research Design
Phenotype

@article {pmid38526734,
year = {2024},
author = {Wan, X and Skurnik, M},
title = {Multidisciplinary Methods for Screening Toxic Proteins from Phages and Their Potential Molecular Targets.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2793},
number = {},
pages = {237-256},
pmid = {38526734},
issn = {1940-6029},
abstract = {This chapter presents a comprehensive methodology for the identification, characterization, and functional analyses of potentially toxic hypothetical proteins of unknown function (toxHPUFs) in phages. The methods begin with in vivo toxicity verification of toxHPUFs in bacterial hosts, utilizing conventional drop tests and following growth curves. Computational methods for structural and functional predictions of toxHPUFs are outlined, incorporating the use of tools such as Phyre2, HHpred, and AlphaFold2. To ascertain potential targets, a comparative genomic approach is described using bioinformatics toolkits for sequence alignment and functional annotation. Moreover, steps are provided to predict protein-protein interactions and visualizing these using PyMOL. The culmination of these methods equips researchers with an effective pipeline to identify and analyze toxHPUFs and their potential targets, laying the groundwork for future experimental confirmations.},
}

@article {pmid38522483,
year = {2024},
author = {Bijla, M and Saini, SK and Pathak, A and Bharadwaj, KP and Sukhavasi, K and Patil, A and Saini, D and Yadav, R and Singh, S and Leeuwenburgh, C and Kumar, P},
title = {Microbiome interactions with different risk factors in development of myocardial infarction.},
journal = {Experimental gerontology},
volume = {},
number = {},
pages = {112409},
doi = {10.1016/j.exger.2024.112409},
pmid = {38522483},
issn = {1873-6815},
abstract = {Among all non-communicable diseases, Cardiovascular Diseases (CVDs) stand as the leading global cause of mortality. Within this spectrum, Myocardial Infarction (MI) strikingly accounts for over 15 % of all deaths. The intricate web of risk factors for MI, comprising family history, tobacco use, oral health, hypertension, nutritional pattern, and microbial infections, is firmly influenced by the human gut and oral microbiota, their diversity, richness, and dysbiosis, along with their respective metabolites. Host genetic factors, especially allelic variations in signaling and inflammatory markers, greatly affect the progression or severity of the disease. Despite the established significance of the human microbiome-nutrient-metabolite interplay in associations with CVDs, the unexplored terrain of the gut-heart-oral axis has risen as a critical knowledge gap. Moreover, the pivotal role of the microbiome and the complex interplay with host genetics, compounded by age-related changes, emerges as an area of vital importance in the development of MI. In addition, a distinctive disease susceptibility and severity influenced by gender-based or ancestral differences, adds a crucial insights to the association with increased mortality. Here, we aimed to provide an overview on interactions of microbiome (oral and gut) with major risk factors (tobacco use, alcohol consumption, diet, hypertension host genetics, gender, and aging) in the development of MI and therapeutic regulation.},
}

@article {pmid38513074,
year = {2024},
author = {Khawaja, T and Kajova, M and Levonen, I and Pietilä, JP and Välimaa, H and Paajanen, J and Pakkanen, SH and Patjas, A and Montonen, R and Miettinen, S and Virtanen, J and Smura, T and Sironen, T and Fagerlund, R and Ugurlu, H and Iheozor-Ejiofor, R and Saksela, K and Vahlberg, T and Ranki, A and Vierikko, A and Ihalainen, J and Vapalahti, O and Kantele, A},
title = {Double-blinded, randomised, placebo-controlled trial of convalescent plasma for COVID-19: analyses by neutralising antibodies homologous to donors' variants.},
journal = {Infectious diseases (London, England)},
volume = {},
number = {},
pages = {1-11},
doi = {10.1080/23744235.2024.2329957},
pmid = {38513074},
issn = {2374-4243},
abstract = {INTRODUCTION: Convalescent plasma (CP) emerged as potential treatment for COVID-19 early in the pandemic. While efficacy in hospitalised patients has been lacklustre, CP may be beneficial at the first stages of disease. Despite multiple new variants emerging, no trials have involved analyses on variant-specific antibody titres of CP.

METHODS: We recruited hospitalised COVID-19 patients within 10 days of symptom onset and, employing a double-blinded approach, randomised them to receive 200 ml convalescent plasma with high (HCP) or low (LCP) neutralising antibody (NAb) titre against the ancestral strain (Wuhan-like variant) or placebo in 1:1:1 ratio. Primary endpoints comprised intubation, corticosteroids for symptom aggravation, and safety assessed as serious adverse events. For a preplanned ad hoc analysis, the patients were regrouped by infused CP's NAb titers to variants infecting the recipients i.e. by titres of homologous HCP (hHCP) or LCP (hLCP).

RESULTS: Of the 57 patients, 18 received HCP, 19 LCP and 20 placebo, all groups smaller than planned. No significant differences were found for primary endpoints. In ad hoc analysis, hHCPrecipients needed significantly less respiratory support, and appeared to be given corticosteroids less frequently (1/14; 7.1%) than those receiving hLCP (9/23; 39.1%) or placebo (8/20; 40%), (p = 0.077).

DISCUSSION: Our double-blinded, placebo-controlled CP therapy trial remained underpowered and does not allow any firm conclusions for early-stage hospitalised COVID-19 patients. Interestingly, however, regrouping by homologous - recipients' variant-specific - CP titres suggested benefits for hHCP. We encourage similar re-analysis of ongoing/previous larger CP studies.

TRIAL REGISTRATION: ClinTrials.gov identifier: NCT0473040.},
}

@article {pmid38510311,
year = {2023},
author = {Gellman, RH and Olm, MR and Terrapon, N and Enam, F and Higginbottom, SK and Sonnenburg, JL and Sonnenburg, ED},
title = {Hadza Prevotella require diet-derived microbiota-accessible carbohydrates to persist in mice.},
journal = {Cell reports},
volume = {42},
number = {11},
pages = {},
pmid = {38510311},
issn = {2211-1247},
support = {DP1 AT009892/AT/NCCIH NIH HHS/United States ; R01 DK085025/DK/NIDDK NIH HHS/United States ; },
mesh = {Animals ; Mice ; *Microbiota ; Diet ; *Gastrointestinal Microbiome ; Carbohydrates ; Bacteroides ; Prevotella ; },
abstract = {Industrialization has transformed the gut microbiota, reducing the prevalence of Prevotella relative to Bacteroides. Here, we isolate Bacteroides and Prevotella strains from the microbiota of Hadza hunter-gatherers in Tanzania, a population with high levels of Prevotella. We demonstrate that plant-derived microbiota-accessible carbohydrates (MACs) are required for persistence of Prevotella copri but not Bacteroides thetaiotaomicron in vivo. Differences in carbohydrate metabolism gene content, expression, and in vitro growth reveal that Hadza Prevotella strains specialize in degrading plant carbohydrates, while Hadza Bacteroides isolates use both plant and host-derived carbohydrates, a difference mirrored in Bacteroides from non-Hadza populations. When competing directly, P. copri requires plant-derived MACs to maintain colonization in the presence of B. thetaiotaomicron, as a no-MAC diet eliminates P. copri colonization. Prevotella's reliance on plant-derived MACs and Bacteroides' ability to use host mucus carbohydrates could explain the reduced prevalence of Prevotella in populations consuming a low-MAC, industrialized diet.},
}

Animals
Mice
*Microbiota
Diet
*Gastrointestinal Microbiome
Carbohydrates
Bacteroides
Prevotella

@article {pmid38506889,
year = {2024},
author = {Koskenvuo, L and Lunkka, P and Varpe, P and Hyöty, M and Satokari, R and Haapamäki, C and Lepistö, A and Sallinen, V},
title = {Morbidity After Mechanical Bowel Preparation and Oral Antibiotics Prior to Rectal Resection: The MOBILE2 Randomized Clinical Trial.},
journal = {JAMA surgery},
volume = {},
number = {},
pages = {},
pmid = {38506889},
issn = {2168-6262},
abstract = {IMPORTANCE: Surgical site infections (SSIs)-especially anastomotic dehiscence-are major contributors to morbidity and mortality after rectal resection. The role of mechanical and oral antibiotics bowel preparation (MOABP) in preventing complications of rectal resection is currently disputed.

OBJECTIVE: To assess whether MOABP reduces overall complications and SSIs after elective rectal resection compared with mechanical bowel preparation (MBP) plus placebo.

This multicenter, double-blind, placebo-controlled randomized clinical trial was conducted at 3 university hospitals in Finland between March 18, 2020, and October 10, 2022. Patients aged 18 years and older undergoing elective resection with primary anastomosis of a rectal tumor 15 cm or less from the anal verge on magnetic resonance imaging were eligible for inclusion. Outcomes were analyzed using a modified intention-to-treat principle, which included all patients who were randomly allocated to and underwent elective rectal resection with an anastomosis.

INTERVENTIONS: Patients were stratified according to tumor distance from the anal verge and neoadjuvant treatment given and randomized in a 1:1 ratio to receive MOABP with an oral regimen of neomycin and metronidazole (n = 277) or MBP plus matching placebo tablets (n = 288). All study medications were taken the day before surgery, and all patients received intravenous antibiotics approximately 30 minutes before surgery.

MAIN OUTCOMES AND MEASURES: The primary outcome was overall cumulative postoperative complications measured using the Comprehensive Complication Index. Key secondary outcomes were SSI and anastomotic dehiscence within 30 days after surgery.

RESULTS: In all, 565 patients were included in the analysis, with 288 in the MBP plus placebo group (median [IQR] age, 69 [62-74] years; 190 males [66.0%]) and 277 in the MOABP group (median [IQR] age, 70 [62-75] years; 158 males [57.0%]). Patients in the MOABP group experienced fewer overall postoperative complications (median [IQR] Comprehensive Complication Index, 0 [0-8.66] vs 8.66 [0-20.92]; Wilcoxon effect size, 0.146; P < .001), fewer SSIs (23 patients [8.3%] vs 48 patients [16.7%]; odds ratio, 0.45 [95% CI, 0.27-0.77]), and fewer anastomotic dehiscences (16 patients [5.8%] vs 39 patients [13.5%]; odds ratio, 0.39 [95% CI, 0.21-0.72]) compared with patients in the MBP plus placebo group.

CONCLUSIONS AND RELEVANCE: Findings of this randomized clinical trial indicate that MOABP reduced overall postoperative complications as well as rates of SSIs and anastomotic dehiscences in patients undergoing elective rectal resection compared with MBP plus placebo. Based on these findings, MOABP should be considered as standard treatment in patients undergoing elective rectal resection.

TRIAL REGISTRATION: ClinicalTrials.gov Identifier: NCT04281667.},
}

@article {pmid38504586,
year = {2024},
author = {Brogna, C and Montano, L and Zanolin, ME and Bisaccia, DR and Ciammetti, G and Viduto, V and Fabrowski, M and Baig, AM and Gerlach, J and Gennaro, I and Bignardi, E and Brogna, B and Frongillo, A and Cristoni, S and Piscopo, M},
title = {A retrospective cohort study on early antibiotic use in vaccinated and unvaccinated COVID-19 patients.},
journal = {Journal of medical virology},
volume = {96},
number = {3},
pages = {e29507},
doi = {10.1002/jmv.29507},
pmid = {38504586},
issn = {1096-9071},
mesh = {Humans ; *Anti-Bacterial Agents/therapeutic use ; *COVID-19/prevention & control ; Rifaximin ; SARS-CoV-2 ; Post-Acute COVID-19 Syndrome ; COVID-19 Vaccines ; Retrospective Studies ; Anti-Inflammatory Agents, Non-Steroidal ; Adrenal Cortex Hormones ; },
abstract = {The bacteriophage behavior of SARS-CoV-2 during the acute and post-COVID-19 phases appears to be an important factor in the development of the disease. The early use of antibiotics seems to be crucial to inhibit disease progression-to prevent viral replication in the gut microbiome, and control toxicological production from the human microbiome. To study the impact of specific antibiotics on recovery from COVID-19 and long COVID (LC) taking into account: vaccination status, comorbidities, SARS-CoV-2 wave, time of initiation of antibiotic therapy and concomitant use of corticosteroids and nonsteroidal anti-inflammatory drugs (NSAIDs). A total of 211 COVID-19 patients were included in the study: of which 59 were vaccinated with mRNA vaccines against SARS-CoV-2 while 152 were unvaccinated. Patients were enrolled in three waves: from September 2020 to October 2022, corresponding to the emergence of the pre-Delta, Delta, and Omicron variants of the SARS-CoV-2 virus. The three criteria for enrolling patients were: oropharyngeal swab positivity or fecal findings; moderate symptoms with antibiotic intake; and measurement of blood oxygen saturation during the period of illness. The use of antibiotic combinations, such as amoxicillin with clavulanic acid (875 + 125 mg tablets, every 12 h) plus rifaximin (400 mg tablets every 12 h), as first choice, as suggested from the previous data, or azithromycin (500 mg tablets every 24 h), plus rifaximin as above, allows healthcare professionals to focus on the gut microbiome and its implications in COVID-19 disease during patient care. The primary outcome measured in this study was the estimated average treatment effect, which quantified the difference in mean recovery between patients receiving antibiotics and those not receiving antibiotics at 3 and 9 days after the start of treatment. In the analysis, both vaccinated and unvaccinated groups had a median illness duration of 7 days (interquartile range [IQR] 6-9 days for each; recovery crude hazard ratio [HR] = 0.94, p = 0.700). The median illness duration for the pre-Delta and Delta waves was 8 days (IQR 7-10 days), while it was shorter, 6.5 days, for Omicron (IQR 6-8 days; recovery crude HR = 1.71, p < 0.001). These results were confirmed by multivariate analysis. Patients with comorbidities had a significantly longer disease duration: median 8 days (IQR 7-10 days) compared to 7 days (IQR 6-8 days) for those without comorbidities (crude HR = 0.75, p = 0.038), but this result was not confirmed in multivariate analysis as statistical significance was lost. Early initiation of antibiotic therapy resulted in a significantly shorter recovery time (crude HR = 4.74, p < 0.001). Concomitant use of NSAIDs did not reduce disease duration and in multivariate analysis prolonged the disease (p = 0.041). A subgroup of 42 patients receiving corticosteroids for a median of 3 days (IQR 3-6 days) had a longer recovery time (median 9 days, IQR 8-10 days) compared to others (median 7 days, IQR 6-8 days; crude HR = 0.542, p < 0.001), as confirmed also by the adjusted HR. In this study, a statistically significant reduction in recovery time was observed among patients who received early antibiotic treatment. Early initiation of antibiotics played a crucial role in maintaining higher levels of blood oxygen saturation. In addition, it is worth noting that a significant number of patients who received antibiotics in the first 3 days and for a duration of 7 days, during the acute phase did not develop LC.},
}

Humans
*Anti-Bacterial Agents/therapeutic use
*COVID-19/prevention & control
Rifaximin
SARS-CoV-2
Post-Acute COVID-19 Syndrome
COVID-19 Vaccines
Retrospective Studies
Anti-Inflammatory Agents, Non-Steroidal
Adrenal Cortex Hormones

@article {pmid38497260,
year = {2024},
author = {Singh, A and Luallen, RJ},
title = {Understanding the factors regulating host-microbiome interactions using Caenorhabditis elegans.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {379},
number = {1901},
pages = {20230059},
pmid = {38497260},
issn = {1471-2970},
support = {R35 GM146836/GM/NIGMS NIH HHS/United States ; },
mesh = {Animals ; Humans ; Caenorhabditis elegans/genetics ; *Microbiota ; *Gastrointestinal Microbiome ; },
abstract = {The Human Microbiome Project was a research programme that successfully identified associations between microbial species and healthy or diseased individuals. However, a major challenge identified was the absence of model systems for studying host-microbiome interactions, which would increase our capacity to uncover molecular interactions, understand organ-specificity and discover new microbiome-altering health interventions. Caenorhabditis elegans has been a pioneering model organism for over 70 years but was largely studied in the absence of a microbiome. Recently, ecological sampling of wild nematodes has uncovered a large amount of natural genetic diversity as well as a slew of associated microbiota. The field has now explored the interactions of C. elegans with its associated gut microbiome, a defined and non-random microbial community, highlighting its suitability for dissecting host-microbiome interactions. This core microbiome is being used to study the impact of host genetics, age and stressors on microbiome composition. Furthermore, single microbiome species are being used to dissect molecular interactions between microbes and the animal gut. Being amenable to health altering genetic and non-genetic interventions, C. elegans has emerged as a promising system to generate and test new hypotheses regarding host-microbiome interactions, with the potential to uncover novel paradigms relevant to other systems. This article is part of the theme issue 'Sculpting the microbiome: how host factors determine and respond to microbial colonization'.},
}

Animals
Humans
Caenorhabditis elegans/genetics
*Microbiota
*Gastrointestinal Microbiome

@article {pmid38491556,
year = {2024},
author = {Elradi, M and Ahmed, AI and Saleh, AM and Abdel-Raouf, KMA and Berika, L and Daoud, Y and Amleh, A},
title = {Derivation of a novel antimicrobial peptide from the Red Sea Brine Pools modified to enhance its anticancer activity against U2OS cells.},
journal = {BMC biotechnology},
volume = {24},
number = {1},
pages = {14},
pmid = {38491556},
issn = {1472-6750},
mesh = {Animals ; Mice ; Humans ; Caspase 3/genetics/metabolism/pharmacology ; Survivin/genetics/metabolism/pharmacology ; Escherichia coli/metabolism ; Antimicrobial Peptides ; Cell Line, Tumor ; Indian Ocean ; Ki-67 Antigen/metabolism ; Staphylococcus aureus ; Apoptosis ; Peptides/pharmacology/metabolism ; *Antineoplastic Agents/pharmacology/chemistry ; *Anti-Infective Agents/pharmacology ; Annexins/pharmacology ; *Salts ; },
abstract = {Cancer associated drug resistance is a major cause for cancer aggravation, particularly as conventional therapies have presented limited efficiency, low specificity, resulting in long term deleterious side effects. Peptide based drugs have emerged as potential alternative cancer treatment tools due to their selectivity, ease of design and synthesis, safety profile, and low cost of manufacturing. In this study, we utilized the Red Sea metagenomics database, generated during AUC/KAUST Red Sea microbiome project, to derive a viable anticancer peptide (ACP). We generated a set of peptide hits from our library that shared similar composition to ACPs. A peptide with a homeodomain was selected, modified to improve its anticancer properties, verified to maintain high anticancer properties, and processed for further in-silico prediction of structure and function. The peptide's anticancer properties were then assessed in vitro on osteosarcoma U2OS cells, through cytotoxicity assay (MTT assay), scratch-wound healing assay, apoptosis/necrosis detection assay (Annexin/PI assay), RNA expression analysis of Caspase 3, KI67 and Survivin, and protein expression of PARP1. L929 mouse fibroblasts were also assessed for cytotoxicity treatment. In addition, the antimicrobial activity of the peptide was also examined on E coli and S. aureus, as sample representative species of the human bacterial microbiome, by examining viability, disk diffusion, morphological assessment, and hemolytic analysis. We observed a dose dependent cytotoxic response from peptide treatment of U2OS, with a higher tolerance in L929s. Wound closure was debilitated in cells exposed to the peptide, while annexin fluorescent imaging suggested peptide treatment caused apoptosis as a major mode of cell death. Caspase 3 gene expression was not altered, while KI67 and Survivin were both downregulated in peptide treated cells. Additionally, PARP-1 protein analysis showed a decrease in expression with peptide exposure. The peptide exhibited minimal antimicrobial activity on critical human microbiome species E. coli and S. aureus, with a low inhibition rate, maintenance of structural morphology and minimal hemolytic impact. These findings suggest our novel peptide displayed preliminary ACP properties against U2OS cells, through limited specificity, while triggering apoptosis as a primary mode of cell death and while having minimal impact on the microbiological species E. coli and S. aureus.},
}

Animals
Mice
Humans
Caspase 3/genetics/metabolism/pharmacology
Survivin/genetics/metabolism/pharmacology
Escherichia coli/metabolism
Antimicrobial Peptides
Cell Line, Tumor
Indian Ocean
Ki-67 Antigen/metabolism
Staphylococcus aureus
Apoptosis
Peptides/pharmacology/metabolism
*Antineoplastic Agents/pharmacology/chemistry
*Anti-Infective Agents/pharmacology
Annexins/pharmacology
*Salts

@article {pmid38489954,
year = {2024},
author = {Huang, Y and Zhang, R and Hong, X and Liu, S and Zhang, S and Guo, M and Shi, L and Li, Z and Liu, Y},
title = {Correlation between sarcopenia index and cognitive function in older adult women: A cross-sectional study using NHANES data.},
journal = {Journal of clinical neuroscience : official journal of the Neurosurgical Society of Australasia},
volume = {122},
number = {},
pages = {73-79},
doi = {10.1016/j.jocn.2024.02.026},
pmid = {38489954},
issn = {1532-2653},
abstract = {OBJECTIVES: The Sarcopenia Index (SI) has the potential as a biomarker for sarcopenia, which is characterized by muscle loss. There is a clear association between sarcopenia and cognitive impairment. However, the relationship between SI and cognitive impairment is yet to be fully understood.

METHODS: We employed data extracted from the U.S. National Health and Nutrition Examination Survey (NHANES) spanning the years 1999 to 2002. Our study encompassed individuals aged 65 to 80 who possessed accessible information regarding both SI and cognitive evaluations with a GFR ≥ 90. Cognitive function was assessed using the digit symbol substitution test (DSST). SI was calculated by serum creatinine (mg/dL)/cystatin C (mg/L)*100. Employing multivariate modeling, we estimated the connection between SI and cognitive performance. Furthermore, to enhance the reliability of our data analysis, we categorized SI using tertiles and subsequently calculated the P-value for trend.

RESULTS: After adjustment for potential confounders, we found SI was significantly and positively correlated with cognitive function scores both in older female in the American population [β = 0.160, 95 % confidence interval (CI) 0.050 to 0.271, P = 0.00461]. Similarly, when the total cognitive function score was treated as a categorical variable according to tertiles, higher SI was related to better total cognitive function scores in females [odds ratio (OR) = 3.968, 95 % CI 1.863 to 6.073, P = 0.00025] following adjustment for confounders.

CONCLUSIONS: Higher SI was correlated with a lower prevalence of cognitive impairment among older adult women with normal kidney function.},
}

@article {pmid38484733,
year = {2024},
author = {Zheng, J and Zhang, XM and Tang, W and Li, Y and Wang, P and Jin, J and Luo, Z and Fang, S and Yang, S and Wei, Z and Song, K and Huang, Z and Wang, Z and Zhu, Z and Shi, N and Xiao, D and Yuan, L and Shen, H and Huang, L and Li, B},
title = {An insular cortical circuit required for itch sensation and aversion.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2024.02.060},
pmid = {38484733},
issn = {1879-0445},
abstract = {Itch encompasses both sensory and emotional dimensions, with the two dimensions reciprocally exacerbating each other. However, whether a shared neural circuit mechanism governs both dimensions remains elusive. Here, we report that the anterior insular cortex (AIC) is activated by both histamine-dependent and -independent itch stimuli. The activation of AIC elicits aversive emotion and exacerbates pruritogen-induced itch sensation and aversion. Mechanistically, AIC excitatory neurons project to the GABAergic neurons in the dorsal bed nucleus of the stria terminalis (dBNST). Manipulating the activity of the AIC → dBNST pathway affects both itch sensation and itch-induced aversion. Our study discovers the shared neural circuit (AIC → dBNST pathway) underlying the itch sensation and aversion, highlights the critical role of the AIC as a central hub for the itch processing, and provides a framework to understand the neural mechanisms underlying the sensation and emotion interaction.},
}

@article {pmid38484036,
year = {2024},
author = {Guillen, MN and Li, C and Rosener, B and Mitchell, A},
title = {Antibacterial activity of nonantibiotics is orthogonal to standard antibiotics.},
journal = {Science (New York, N.Y.)},
volume = {},
number = {},
pages = {eadk7368},
doi = {10.1126/science.adk7368},
pmid = {38484036},
issn = {1095-9203},
abstract = {Numerous nonantibiotic drugs have potent antibacterial activity and can adversely impact the human microbiome. The mechanistic underpinning of this toxicity remains largely unknown. We investigated the antibacterial activity of 200 drugs using genetic screens with thousands of barcoded Escherichia coli knockouts. We analyzed 2 million gene-drug interactions underlying drug-specific toxicity. Network-based analysis of drug-drug similarities revealed that antibiotics clustered into modules consistent with the mode of action of their established classes, while nonantibiotics remained unconnected. Half of the nonantibiotics clustered into separate modules, potentially revealing shared and unexploited targets for novel antimicrobials. Analysis of efflux systems revealed they widely impact antibiotics and nonantibiotics alike, suggesting that the impact of nonantibiotics on antibiotic cross-resistance should be investigated closely in vivo.},
}

@article {pmid38479397,
year = {2024},
author = {Zhou, X and Shen, X and Johnson, JS and Spakowicz, DJ and Agnello, M and Zhou, W and Avina, M and Honkala, A and Chleilat, F and Chen, SJ and Cha, K and Leopold, S and Zhu, C and Chen, L and Lyu, L and Hornburg, D and Wu, S and Zhang, X and Jiang, C and Jiang, L and Jiang, L and Jian, R and Brooks, AW and Wang, M and Contrepois, K and Gao, P and Rose, SMS and Tran, TDB and Nguyen, H and Celli, A and Hong, BY and Bautista, EJ and Dorsett, Y and Kavathas, PB and Zhou, Y and Sodergren, E and Weinstock, GM and Snyder, MP},
title = {Longitudinal profiling of the microbiome at four body sites reveals core stability and individualized dynamics during health and disease.},
journal = {Cell host & microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2024.02.012},
pmid = {38479397},
issn = {1934-6069},
abstract = {To understand the dynamic interplay between the human microbiome and host during health and disease, we analyzed the microbial composition, temporal dynamics, and associations with host multi-omics, immune, and clinical markers of microbiomes from four body sites in 86 participants over 6 years. We found that microbiome stability and individuality are body-site specific and heavily influenced by the host. The stool and oral microbiome are more stable than the skin and nasal microbiomes, possibly due to their interaction with the host and environment. We identify individual-specific and commonly shared bacterial taxa, with individualized taxa showing greater stability. Interestingly, microbiome dynamics correlate across body sites, suggesting systemic dynamics influenced by host-microbial-environment interactions. Notably, insulin-resistant individuals show altered microbial stability and associations among microbiome, molecular markers, and clinical features, suggesting their disrupted interaction in metabolic disease. Our study offers comprehensive views of multi-site microbial dynamics and their relationship with host health and disease.},
}

@article {pmid38477427,
year = {2024},
author = {Zhang, J and Qi, H and Li, M and Wang, Z and Jia, X and Sun, T and Du, S and Su, C and Zhi, M and Du, W and Ouyang, Y and Wang, P and Huang, F and Jiang, H and Li, L and Bai, J and Wei, Y and Zhang, X and Wang, H and Zhang, B and Feng, Q},
title = {Diet Mediate the Impact of Host Habitat on Gut Microbiome and Influence Clinical Indexes by Modulating Gut Microbes and Serum Metabolites.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e2310068},
doi = {10.1002/advs.202310068},
pmid = {38477427},
issn = {2198-3844},
support = {R01-DK104371/DK/NIDDK NIH HHS/United States ; P30-DK056350/DK/NIDDK NIH HHS/United States ; },
abstract = {The impact of external factors on the human gut microbiota and how gut microbes contribute to human health is an intriguing question. Here, the gut microbiome of 3,224 individuals (496 with serum metabolome) with 109 variables is studied. Multiple analyses reveal that geographic factors explain the greatest variance of the gut microbiome and the similarity of individuals' gut microbiome is negatively correlated with their geographic distance. Main food components are the most important factors that mediate the impact of host habitats on the gut microbiome. Diet and gut microbes collaboratively contribute to the variation of serum metabolites, and correlate to the increase or decrease of certain clinical indexes. Specifically, systolic blood pressure is lowered by vegetable oil through increasing the abundance of Blautia and reducing the serum level of 1-palmitoyl-2-palmitoleoyl-GPC (16:0/16:1), but it is reduced by fruit intake through increasing the serum level of Blautia improved threonate. Besides, aging-related clinical indexes are also closely correlated with the variation of gut microbes and serum metabolites. In this study, the linkages of geographic locations, diet, the gut microbiome, serum metabolites, and physiological indexes in a Chinese population are characterized. It is proved again that gut microbes and their metabolites are important media for external factors to affect human health.},
}

@article {pmid38474213,
year = {2024},
author = {Hong, BY and Driscoll, M and Gratalo, D and Jarvie, T and Weinstock, GM},
title = {Improved DNA Extraction and Amplification Strategy for 16S rRNA Gene Amplicon-Based Microbiome Studies.},
journal = {International journal of molecular sciences},
volume = {25},
number = {5},
pages = {},
pmid = {38474213},
issn = {1422-0067},
mesh = {Humans ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/methods ; Genes, rRNA ; Reproducibility of Results ; DNA, Bacterial/genetics ; *Microbiota/genetics ; Bacteria/genetics ; High-Throughput Nucleotide Sequencing/methods ; },
abstract = {Next-generation sequencing technology has driven the rapid advancement of human microbiome studies by enabling community-level sequence profiling of microbiomes. Although all microbiome sequencing methods depend on recovering the DNA from a sample as a first critical step, lysis methods can be a major determinant of microbiome profile bias. Gentle enzyme-based DNA preparation methods preserve DNA quality but can bias the results by failing to open difficult-to-lyse bacteria. Mechanical methods like bead beating can also bias DNA recovery because the mechanical energy required to break tougher cell walls may shear the DNA of the more easily lysed microbes, and shearing can vary depending on the time and intensity of beating, influencing reproducibility. We introduce a non-mechanical, non-enzymatic, novel rapid microbial DNA extraction procedure suitable for 16S rRNA gene-based microbiome profiling applications that eliminates bead beating. The simultaneous application of alkaline, heat, and detergent ('Rapid' protocol) to milligram quantity samples provided consistent representation across the population of difficult and easily lysed bacteria equal to or better than existing protocols, producing sufficient high-quality DNA for full-length 16S rRNA gene PCR. The novel 'Rapid' method was evaluated using mock bacterial communities containing both difficult and easily lysed bacteria. Human fecal sample testing compared the novel Rapid method with a standard Human Microbiome Project (HMP) protocol for samples from lung cancer patients and controls. DNA recovered from both methods was analyzed using 16S rRNA gene sequencing of the V1V3 and V4 regions on the Illumina platform and the V1V9 region on the PacBio platform. Our findings indicate that the 'Rapid' protocol consistently yielded higher levels of Firmicutes species, which reflected the profile of the bacterial community structure more accurately, which was confirmed by mock community evaluation. The novel 'Rapid' DNA lysis protocol reduces population bias common to bead beating and enzymatic lysis methods, presenting opportunities for improved microbial community profiling, combined with the reduction in sample input to 10 milligrams or less, and it enables rapid transfer and simultaneous lysis of 96 samples in a standard plate format. This results in a 20-fold reduction in sample handling time and an overall 2-fold time advantage when compared to widely used commercial methods. We conclude that the novel 'Rapid' DNA extraction protocol offers a reliable alternative for preparing fecal specimens for 16S rRNA gene amplicon sequencing.},
}

Humans
RNA, Ribosomal, 16S/genetics
Sequence Analysis, DNA/methods
Genes, rRNA
Reproducibility of Results
DNA, Bacterial/genetics
*Microbiota/genetics
Bacteria/genetics
High-Throughput Nucleotide Sequencing/methods

@article {pmid38472421,
year = {2024},
author = {Cai, J and Lin, K and Luo, T and Weng, J and Liu, H and Yuan, Z and Wan, Z and Han, J and Lin, J and Liu, X and Wang, X and Huang, M and Luo, Y and Yu, H},
title = {Neoadjuvant chemotherapy is noninferior to chemoradiotherapy for early-onset locally advanced rectal cancer in the FOWARC trial.},
journal = {British journal of cancer},
volume = {},
number = {},
pages = {},
pmid = {38472421},
issn = {1532-1827},
support = {No. 81972245, YL; No. 82173067, YL; No. 81902877, HY; No. 82272965, HY//National Natural Science Foundation of China (National Science Foundation of China)/ ; No. 2022A1515012656, HY; No.2021A1515010134, MH;No.2020A1515010036, XL//Natural Science Foundation of Guangdong Province (Guangdong Natural Science Foundation)/ ; },
abstract = {BACKGROUND: The early-onset rectal cancer with rapidly increasing incidence is considered to have distinct clinicopathological and molecular profiles with high-risk features. This leads to challenges in developing specific treatment strategies for early-onset rectal cancer patients and questions of whether early-onset locally advanced rectal cancer (LARC) needs aggressive neoadjuvant treatment.

METHODS: In this post hoc analysis of FOWARC trial, we investigated the role of preoperative radiation in early-onset LARC by comparing the clinicopathological profiles and short-term and long-term outcomes between the early-onset and late-onset LARCs.

RESULTS: We revealed an inter-tumor heterogeneity of clinical profiles and treatment outcomes between the early-onset and late-onset LARCs. The high-risk features were more prevalent in early-onset LARC. The neoadjuvant radiation brought less benefits of tumor response and more risk of complications in early-onset group (pCR: OR = 3.75, 95% CI = 1.37-10.27; complications: HR = 11.35, 95% CI = 1.46-88.31) compared with late-onset group (pCR: OR = 5.33, 95% CI = 1.83-15.58; complications: HR = 5.80, 95% CI = 2.32-14.49). Furthermore, the addition of radiation to neoadjuvant chemotherapy didn't improve long-term OS (HR = 1.37, 95% CI = 0.49-3.87) and DFS (HR = 1.05, 95% CI = 0.58-1.90) for early-onset patients.

CONCLUSION: Preoperative radiation plus chemotherapy may not be superior to the chemotherapy alone in the early-onset LARC. Our findings provide insight into the treatment of early-onset LARC by interrogating the aggressive treatment and alternative regimens.},
}

@article {pmid38471667,
year = {2024},
author = {Ghelfenstein-Ferreira, T and Serris, A and Salmona, M and Lanternier, F and Alanio, A},
title = {Revealing the hidden interplay: the unexplored relationship between fungi and viruses beyond HIV, SARS-CoV-2 and influenza.},
journal = {Medical mycology},
volume = {},
number = {},
pages = {},
doi = {10.1093/mmy/myae021},
pmid = {38471667},
issn = {1460-2709},
abstract = {The complex interaction between viruses and fungi has profound implications, especially given the significant impact of these microorganisms on human health. While well-known examples such as HIV, influenza and SARS-CoV-2 are recognized as risk factors for invasive fungal diseases (IFD), the relationship between viruses and fungi remains largely underexplored outside of these cases. Fungi and viruses can engage in symbiotic or synergistic interactions. Remarkably, some viruses, known as mycoviruses, can directly infect fungi, may influencing their phenotype and potentially their virulence. In addition, viruses and fungi can coexist within the human microbiome, a complex ecosystem of microorganisms. Under certain conditions, viral infection might predispose the host to an invasive fungal infection, as observed with Influenza-associated pulmonary aspergillosis or COVID-19 associated pulmonary aspergillosis. We aim in this review to highlight potential connections between fungi and viruses (CMV and other herpesviruses, HTLV-1 and respiratory viruses), excluding SARS-CoV-2 and influenza.},
}

@article {pmid38467837,
year = {2024},
author = {Bhosle, A and Bae, S and Zhang, Y and Chun, E and Avila-Pacheco, J and Geistlinger, L and Pishchany, G and Glickman, JN and Michaud, M and Waldron, L and Clish, CB and Xavier, RJ and Vlamakis, H and Franzosa, EA and Garrett, WS and Huttenhower, C},
title = {Integrated annotation prioritizes metabolites with bioactivity in inflammatory bowel disease.},
journal = {Molecular systems biology},
volume = {},
number = {},
pages = {},
pmid = {38467837},
issn = {1744-4292},
support = {R24DK110499//HHS | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)/ ; },
abstract = {Microbial biochemistry is central to the pathophysiology of inflammatory bowel diseases (IBD). Improved knowledge of microbial metabolites and their immunomodulatory roles is thus necessary for diagnosis and management. Here, we systematically analyzed the chemical, ecological, and epidemiological properties of ~82k metabolic features in 546 Integrative Human Microbiome Project (iHMP/HMP2) metabolomes, using a newly developed methodology for bioactive compound prioritization from microbial communities. This suggested >1000 metabolic features as potentially bioactive in IBD and associated ~43% of prevalent, unannotated features with at least one well-characterized metabolite, thereby providing initial information for further characterization of a significant portion of the fecal metabolome. Prioritized features included known IBD-linked chemical families such as bile acids and short-chain fatty acids, and less-explored bilirubin, polyamine, and vitamin derivatives, and other microbial products. One of these, nicotinamide riboside, reduced colitis scores in DSS-treated mice. The method, MACARRoN, is generalizable with the potential to improve microbial community characterization and provide therapeutic candidates.},
}

@article {pmid38466102,
year = {2024},
author = {Cheng, G and Westerholm, M and Schnürer, A},
title = {Complete genome sequence of Citroniella saccharovorans DSM 29873, isolated from human fecal sample.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0001524},
doi = {10.1128/mra.00015-24},
pmid = {38466102},
issn = {2576-098X},
abstract = {A complete genome was recovered from Citroniella saccharovorans, strain DSM 29873, using Oxford Nanopore Technologies. The genome assembly contains 1,413,868 bp with 30.23% G+C content. The species belongs to the family Peptoniphilaceae and, as of yet, is the only cultivated representative of the genus Citroniella.},
}

@article {pmid38465728,
year = {2024},
author = {Michán-Doña, A and Vázquez-Borrego, MC and Michán, C},
title = {Are there any completely sterile organs or tissues in the human body? Is there any sacred place?.},
journal = {Microbial biotechnology},
volume = {17},
number = {3},
pages = {e14442},
pmid = {38465728},
issn = {1751-7915},
support = {PRYES223170ARJO//Fundación Científica Asociación Española Contra el Cáncer/ ; PI22/01213//Instituto de Salud Carlos III/ ; },
mesh = {Humans ; *Human Body ; Sequence Analysis, DNA ; *Infertility ; DNA, Ribosomal/genetics ; RNA/genetics ; RNA, Ribosomal, 16S/genetics ; },
abstract = {The human microbiome comprises an ample set of organisms that inhabit and interact within the human body, contributing both positively and negatively to our health. In recent years, several research groups have described the presence of microorganisms in organs or tissues traditionally considered as 'sterile' under healthy and pathological conditions. In this sense, microorganisms have been detected in several types of cancer, including those in 'sterile' organs. But how can the presence of microorganisms be detected? In most studies, 16S and internal transcribed spacer (ITS) ribosomal DNA (rDNA) sequencing has led to the identification of prokaryotes and fungi. However, a major limitation of this technique is that it cannot distinguish between living and dead organisms. RNA-based methods have been proposed to overcome this limitation, as the shorter half-life of the RNA would identify only the transcriptionally active microorganisms, although perhaps not all the viable ones. In this sense, metaproteomic techniques or the search for molecular metabolic signatures could be interesting alternatives for the identification of living microorganisms. In summary, new technological advances are challenging the notion of 'sterile' organs in our body. However, to date, evidence for a structured living microbiome in most of these organs is scarce or non-existent. The implementation of new technological approaches will be necessary to fully understand the importance of the microbiome in these organs, which could pave the way for the development of a wide range of new therapeutic strategies.},
}

Humans
*Human Body
Sequence Analysis, DNA
*Infertility
DNA, Ribosomal/genetics
RNA/genetics
RNA, Ribosomal, 16S/genetics

@article {pmid38464031,
year = {2024},
author = {Zolfo, M and Silverj, A and Blanco-Miguez, A and Manghi, P and Rota-Stabelli, O and Heidrich, V and Jensen, J and Maharjan, S and Franzosa, E and Menni, C and Visconti, A and Pinto, F and Ciciani, M and Huttenhower, C and Cereseto, A and Asnicar, F and Kitano, H and Yamada, T and Segata, N},
title = {Discovering and exploring the hidden diversity of human gut viruses using highly enriched virome samples.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.02.19.580813},
pmid = {38464031},
abstract = {Viruses are an abundant and crucial component of the human microbiome, but accurately discovering them via metagenomics is still challenging. Currently, the available viral reference genomes poorly represent the diversity in microbiome samples, and expanding such a set of viral references is difficult. As a result, many viruses are still undetectable through metagenomics even when considering the power of de novo metagenomic assembly and binning, as viruses lack universal markers. Here, we describe a novel approach to catalog new viral members of the human gut microbiome and show how the resulting resource improves metagenomic analyses. We retrieved >3,000 viral-like particles (VLP) enriched metagenomic samples (viromes), evaluated the efficiency of the enrichment in each sample to leverage the viromes of highest purity, and applied multiple analysis steps involving assembly and comparison with hundreds of thousands of metagenome-assembled genomes to discover new viral genomes. We reported over 162,000 viral sequences passing quality control from thousands of gut metagenomes and viromes. The great majority of the retrieved viral sequences (~94.4%) were of unknown origin, most had a CRISPR spacer matching host bacteria, and four of them could be detected in >50% of a set of 18,756 gut metagenomes we surveyed. We included the obtained collection of sequences in a new MetaPhlAn 4.1 release, which can quantify reads within a metagenome matching the known and newly uncovered viral diversity. Additionally, we released the viral database for further virome and metagenomic studies of the human microbiome.},
}

@article {pmid38460430,
year = {2024},
author = {Karisola, P and Nikkola, V and Joronen, H and Ylianttila, L and Grönroos, M and Partonen, T and Snellman, E and Alenius, H},
title = {Narrow-band UVB radiation triggers diverse changes in the gene expression and induces the accumulation of M1 macrophages in human skin.},
journal = {Journal of photochemistry and photobiology. B, Biology},
volume = {253},
number = {},
pages = {112887},
doi = {10.1016/j.jphotobiol.2024.112887},
pmid = {38460430},
issn = {1873-2682},
abstract = {BACKGROUND: The underlying molecular mechanisms that determine the biological effects of UVB radiation exposure on human skin are still only partially comprehended.

OBJECTIVES: Our goal is to examine the human skin transcriptome and related molecular mechanisms following a single exposure to UVB in the morning versus evening.

METHODS: We exposed 20 volunteer females to four-fold standard erythema doses (SED4) of narrow-band UVB (309-313 nm) in the morning or evening and studied skin transcriptome 24 h after the exposure. We performed enrichment analyses of gene pathways, predicted changes in skin cell composition using cellular deconvolution, and correlated cell proportions with gene expression.

RESULTS: In the skin transcriptome, UVB exposure yielded 1384 differentially expressed genes (DEGs) in the morning and 1295 DEGs in the evening, of which the most statistically significant DEGs enhanced proteasome and spliceosome pathways. Unexposed control samples showed difference by 321 DEGs in the morning vs evening, which was related to differences in genes associated with the circadian rhythm. After the UVB exposure, the fraction of proinflammatory M1 macrophages was significantly increased at both timepoints, and this increase was positively correlated with pathways on Myc targets and mTORC1 signaling. In the evening, the skin clinical erythema was more severe and had stronger positive correlation with the number of M1 macrophages than in the morning after UVB exposure. The fractions of myeloid and plasmacytoid dendritic cells and CD8 T cells were significantly decreased in the morning but not in the evening.

CONCLUSIONS: NB-UVB-exposure causes changes in skin transcriptome, inhibiting cell division, and promoting proteasome activity and repair responses, both in the morning and in the evening. Inflammatory M1 macrophages may drive the UV-induced skin responses by exacerbating inflammation and erythema. These findings highlight how the same UVB exposure influences skin responses differently in morning versus evening and presents a possible explanation to the differences in gene expression in the skin after UVB irradiation at these two timepoints.},
}

@article {pmid38455087,
year = {2024},
author = {Reid, G},
title = {A value chain to improve human, animal and insect health in developing countries.},
journal = {Microbiome research reports},
volume = {3},
number = {1},
pages = {10},
pmid = {38455087},
issn = {2771-5965},
}

@article {pmid38452522,
year = {2024},
author = {Jones, JM and Reinke, SN and Mousavi-Derazmahalleh, M and Garssen, J and Jenmalm, MC and Srinivasjois, R and Silva, D and Keelan, J and Prescott, SL and Palmer, DJ and Christophersen, CT},
title = {Maternal prebiotic supplementation during pregnancy and lactation modifies the microbiome and short chain fatty acid profile of both mother and infant.},
journal = {Clinical nutrition (Edinburgh, Scotland)},
volume = {43},
number = {4},
pages = {969-980},
doi = {10.1016/j.clnu.2024.02.030},
pmid = {38452522},
issn = {1532-1983},
abstract = {BACKGROUND & AIMS: Improving maternal gut health in pregnancy and lactation is a potential strategy to improve immune and metabolic health in offspring and curtail the rising rates of inflammatory diseases linked to alterations in gut microbiota. Here, we investigate the effects of a maternal prebiotic supplement (galacto-oligosaccharides and fructo-oligosaccharides), ingested daily from <21 weeks' gestation to six months' post-partum, in a double-blinded, randomised placebo-controlled trial.

METHODS: Stool samples were collected at multiple timepoints from 74 mother-infant pairs as part of a larger, double-blinded, randomised controlled allergy intervention trial. The participants were randomised to one of two groups; with one group receiving 14.2 g per day of prebiotic powder (galacto-oligosaccharides GOS and fructo-oligosaccharides FOS in ratio 9:1), and the other receiving a placebo powder consisting of 8.7 g per day of maltodextrin. The faecal microbiota of both mother and infants were assessed based on the analysis of bacterial 16S rRNA gene (V4 region) sequences, and short chain fatty acid (SCFA) concentrations in stool.

RESULTS: Significant differences in the maternal microbiota profiles between baseline and either 28-weeks' or 36-weeks' gestation were found in the prebiotic supplemented women. Infant microbial beta-diversity also significantly differed between prebiotic and placebo groups at 12-months of age. Supplementation was associated with increased abundance of commensal Bifidobacteria in the maternal microbiota, and a reduction in the abundance of Negativicutes in both maternal and infant microbiota. There were also changes in SCFA concentrations with maternal prebiotics supplementation, including significant differences in acetic acid concentration between intervention and control groups from 20 to 28-weeks' gestation.

CONCLUSION: Maternal prebiotic supplementation of 14.2 g per day GOS/FOS was found to favourably modify both the maternal and the developing infant gut microbiome. These results build on our understanding of the importance of maternal diet during pregnancy, and indicate that it is possible to intervene and modify the development of the infant microbiome by dietary modulation of the maternal gut microbiome.},
}

@article {pmid38452399,
year = {2024},
author = {Lucchetti, M and Oluwasegun, AK and Grandmougin, L and Jäger, C and Perez-Escriva, P and Letellier, E and Mosig, AS and Wilmes, P},
title = {An Organ-on-chip Platform for Simulating Drug Metabolism along the Gut-liver Axis.},
journal = {Advanced healthcare materials},
volume = {},
number = {},
pages = {e2303943},
doi = {10.1002/adhm.202303943},
pmid = {38452399},
issn = {2192-2659},
abstract = {The human microbiome significantly influences drug metabolism through the gut-liver axis, leading to modified drug responses and potential toxicity. Due to the complex nature of the human gut environment, our understanding of microbiome-driven impacts on these processes is limited. To address this, we introduce a multiorgan-on-a-chip (MOoC) platform that combines the human microbial-crosstalk (HuMiX) gut-on-chip (GoC) and the Dynamic42 liver-on-chip (LoC), mimicking the bidirectional interconnection between the gut and liver known as the gut-liver axis. This platform supports the viability and functionality of intestinal and liver cells. In a proof-of-concept study, we replicated the metabolism of irinotecan, a widely used colorectal cancer drug, within our MOoC. Utilizing liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS), we tracked irinotecan metabolites, confirming the platform's ability to represent drug metabolism along the gut-liver axis. Furthermore, using our gut-liver platform, we show that the colorectal cancer-associated gut bacterium, Escherichia coli, modifies irinotecan metabolism through the transformation of its inactive metabolite SN-38G into its toxic metabolite SN-38. This platform serves as a robust tool for investigating the intricate interplay between gut microbes and pharmaceuticals, offering a representative alternative to animal models and providing novel drug development strategies. This article is protected by copyright. All rights reserved.},
}

@article {pmid38450162,
year = {2024},
author = {Bragazzi, NL and Woldegerima, WA and Siri, A},
title = {Economic microbiology: exploring microbes as agents in economic systems.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1305148},
pmid = {38450162},
issn = {1664-302X},
abstract = {Microbial communities exhibit striking parallels with economic markets, resembling intricate ecosystems where microorganisms engage in resource exchange akin to human market transactions. This dynamic network of resource swapping mirrors economic trade in human markets, with microbes specializing in metabolic functions much like businesses specializing in goods and services. Cooperation and competition are central dynamics in microbial communities, with alliances forming for mutual benefit and species vying for dominance, similar to businesses seeking market share. The human microbiome, comprising trillions of microorganisms within and on our bodies, is not only a marker of socioeconomic status but also a critical factor contributing to persistent health inequalities. Social and economic factors shape the composition of the gut microbiota, impacting healthcare access and quality of life. Moreover, these microbes exert indirect influence over human decisions by affecting neurotransmitter production, influencing mood, behavior, and choices related to diet and emotions. Human activities significantly impact microbial communities, from dietary choices and antibiotic use to environmental changes, disrupting these ecosystems. Beyond their natural roles, humans harness microbial communities for various applications, manipulating their interactions and resource exchanges to achieve specific goals in fields like medicine, agriculture, and environmental science. In conclusion, the concept of microbial communities as biological markets offers valuable insights into their intricate functioning and adaptability. It underscores the profound interplay between microbial ecosystems and human health and behavior, with far-reaching implications for multiple disciplines. To paraphrase Alfred Marshall, "the Mecca of the economist lies in economic microbiology."},
}

@article {pmid38441984,
year = {2024},
author = {Greenzaid, JD and Chan, LJ and Chandani, BM and Kiritsis, NR and Feldman, SR},
title = {Microbiome modulators for atopic eczema: a systematic review of experimental and investigational therapeutics.},
journal = {Expert opinion on investigational drugs},
volume = {},
number = {},
pages = {1-16},
doi = {10.1080/13543784.2024.2326625},
pmid = {38441984},
issn = {1744-7658},
abstract = {INTRODUCTION: Atopic dermatitis (AD) is a common inflammatory cutaneous disease that arises due to dysregulation of the Th2 immune response, impaired skin barrier integrity, and dysbiosis of the skin and gut microbiota. An abundance of Staphylococcus aureus biofilms in AD lesions increases the Th2 immune response, and gut bacteria release breakdown products such as Short Chain Fatty Acids that regulate the systemic immune response.

AREAS COVERED: We aim to evaluate therapies that modulate the microbiome in humans and discuss the clinical implications of these treatments. We performed a review of the literature in which 2,673 records were screened, and describe the findings of 108 studies that were included after full-text review. All included studies discussed the effects of therapies on the human microbiome and AD severity. Oral probiotics, topical probiotics, biologics, and investigational therapies were included in our analysis.

EXPERT OPINION: Oral probiotics demonstrate mixed efficacy at relieving AD symptoms. Topical probiotics reduce S. aureus abundance in AD lesional skin, yet for moderate-severe disease, these therapies may not reduce AD severity scores to the standard of biologics. Dupilumab and tralokinumab target key inflammatory pathways in AD and modulate the skin microbiome, further improving disease severity.},
}

@article {pmid38441977,
year = {2024},
author = {Chen, H and Huang, S and Zhao, Y and Sun, R and Wang, J and Yao, S and Huang, J and Yu, Z},
title = {Metagenomic analysis of the intestinal microbiome reveals the potential mechanism involved in Bacillus amyloliquefaciens in treating schistosomiasis japonica in mice.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0373523},
doi = {10.1128/spectrum.03735-23},
pmid = {38441977},
issn = {2165-0497},
abstract = {UNLABELLED: Schistosomiasis japonica is one of the neglected tropical diseases characterized by chronic hepatic, intestinal granulomatous inflammation and fibrosis, as well as dysbiosis of intestinal microbiome. Previously, the probiotic Bacillus amyloliquefaciens has been shown to alleviate the pathological injuries in mice infected with Schistosoma japonicum by improving the disturbance of the intestinal microbiota. However, the underlying mechanisms involved in this process remain unclear. In this study, metagenomics sequencing and functional analysis were employed to investigate the differential changes in taxonomic composition and functional genes of the intestinal microbiome in S. japonicum-infected mice treated with B. amyloliquefaciens. The results revealed that intervention with B. amyloliquefaciens altered the taxonomic composition of the intestinal microbiota at the species level in infected mice and significantly increased the abundance of beneficial bacteria. Moreover, the abundance of predicted genes in the intestinal microbiome was also significantly changed, and the abundance of xfp/xpk and genes translated to urease was significantly restored. Further analysis showed that Limosilactobacillus reuteri was positively correlated with several KEGG Orthology (KO) genes and metabolic reactions, which might play important roles in alleviating the pathological symptoms caused by S. japonicum infection, indicating that it has the potential to function as another effective therapeutic agent for schistosomiasis. These data suggested that treatment of murine schistosomiasis japonica by B. amyloliquefaciens might be induced by alterations in the taxonomic composition and functional gene of the intestinal microbiome in mice. We hope this study will provide adjuvant strategies and methods for the early prevention and treatment of schistosomiasis japonica.

IMPORTANCE: Targeted interventions of probiotics on gut microbiome were used to explore the mechanism of alleviating schistosomiasis japonica. Through metagenomic analysis, there were significant changes in the composition of gut microbiota in mice infected with Schistosoma japonicum and significant increase in the abundance of beneficial bacteria after the intervention of Bacillus amyloliquefaciens. At the same time, the abundance of functional genes was found to change significantly. The abundance of genes related to urease metabolism and xfp/xpk related to D-erythrose 4-phosphate production was significantly restored, highlighting the importance of Limosilactobacillus reuteri in the recovery and abundance of predicted genes of the gut microbiome. These results indicated potential regulatory mechanism between the gene function of gut microbiome and host immune response. Our research lays the foundation for elucidating the regulatory mechanism of probiotic intervention in alleviating schistosomiasis japonica, and provides potential adjuvant treatment strategies for early prevention and treatment of schistosomiasis japonica.},
}

@article {pmid38440794,
year = {2024},
author = {Favero, G and Gianò, M and Franco, C and Pinto, D and van Noorden, CJF and Rinaldi, F and Rezzani, R},
title = {Relation Between Reactive Oxygen Species Production and Transient Receptor Potential Vanilloid1 Expression in Human Skin During Aging.},
journal = {The journal of histochemistry and cytochemistry : official journal of the Histochemistry Society},
volume = {},
number = {},
pages = {221554241236537},
doi = {10.1369/00221554241236537},
pmid = {38440794},
issn = {1551-5044},
abstract = {Skin sensitivity and impaired epidermal barrier function are associated with aging and are at least partly due to increased production of reactive oxygen species (ROS). Transient receptor potential vanilloid1 (TRPV1) is expressed in keratinocytes, fibroblasts, mast cells, and endothelial cells in skin. We investigated in skin biopsies of adult and elderly donors whether TRPV1 expression is involved in the skin aging process. We found that aging skin showed a strongly reduced epidermal thickness, strongly increased oxidative stress, protease expression, and mast cell degranulation and strongly increased TRPV1 expression both in epidermis and dermis. Based on our findings, the aging-related changes observed in the epidermis of the skin level are associated with increased ROS production, and hypothesized alterations in TRPV1 expression are mechanistically linked to this process.},
}

@article {pmid38436256,
year = {2024},
author = {Ling, J and Hryckowian, AJ},
title = {Re-framing the importance of Group B Streptococcus as a gut-resident pathobiont.},
journal = {Infection and immunity},
volume = {},
number = {},
pages = {e0047823},
doi = {10.1128/iai.00478-23},
pmid = {38436256},
issn = {1098-5522},
abstract = {Streptococcus agalactiae (Group B Streptococcus, GBS) is a Gram-positive bacterial species that causes disease in humans across the lifespan. While antibiotics are used to mitigate GBS infections, it is evident that antibiotics disrupt human microbiomes (which can predispose people to other diseases later in life), and antibiotic resistance in GBS is on the rise. Taken together, these unintended negative impacts of antibiotics highlight the need for precision approaches for minimizing GBS disease. One possible approach involves selectively depleting GBS in its commensal niches before it can cause disease at other body sites or be transmitted to at-risk individuals. One understudied commensal niche of GBS is the adult gastrointestinal (GI) tract, which may predispose colonization at other body sites in individuals at risk for GBS disease. However, a better understanding of the host-, microbiome-, and GBS-determined variables that dictate GBS GI carriage is needed before precise GI decolonization approaches can be developed. In this review, we synthesize current knowledge of the diverse body sites occupied by GBS as a pathogen and as a commensal. We summarize key molecular factors GBS utilizes to colonize different host-associated niches to inform future efforts to study GBS in the GI tract. We also discuss other GI commensals that are pathogenic in other body sites to emphasize the broader utility of precise de-colonization approaches for mitigating infections by GBS and other bacterial pathogens. Finally, we highlight how GBS treatments could be improved with a more holistic understanding of GBS enabled by continued GI-focused study.},
}

@article {pmid38432422,
year = {2024},
author = {Murali, SK and Mansell, TJ},
title = {Next generation probiotics: Engineering live biotherapeutics.},
journal = {Biotechnology advances},
volume = {},
number = {},
pages = {108336},
doi = {10.1016/j.biotechadv.2024.108336},
pmid = {38432422},
issn = {1873-1899},
abstract = {The population dynamics of the human microbiome have been associated with inflammatory bowel disease, cancer, obesity, autoimmune diseases, and many other human disease states. An emerging paradigm in treatment is the administration of live engineered organisms, so- called next-generation probiotics. However, the efficacy of these microbial therapies can be limited by the organism's overall performance in the harsh and nutrient-limited environment of the gut. In this review, we summarize the current state of the art use of bacterial and yeast strains as probiotics, highlight the recent development of genetic tools for engineering new therapeutic functions in these organisms, and report on the latest therapeutic applications of engineered probiotics, including recent clinical trials. We also discuss the supplementation of prebiotics as a method of manipulating the microbiome and improving the overall performance of engineered live biotherapeutics.},
}

@article {pmid38430912,
year = {2024},
author = {Fang, S and Luo, Z and Wei, Z and Qin, Y and Zheng, J and Zhang, H and Jin, J and Li, J and Miao, C and Yang, S and Li, Y and Liang, Z and Yu, XD and Zhang, XM and Xiong, W and Zhu, H and Gan, WB and Huang, L and Li, B},
title = {Sexually dimorphic control of affective state processing and empathic behaviors.},
journal = {Neuron},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.neuron.2024.02.001},
pmid = {38430912},
issn = {1097-4199},
abstract = {Recognizing the affective states of social counterparts and responding appropriately fosters successful social interactions. However, little is known about how the affective states are expressed and perceived and how they influence social decisions. Here, we show that male and female mice emit distinct olfactory cues after experiencing distress. These cues activate distinct neural circuits in the piriform cortex (PiC) and evoke sexually dimorphic empathic behaviors in observers. Specifically, the PiC → PrL pathway is activated in female observers, inducing a social preference for the distressed counterpart. Conversely, the PiC → MeA pathway is activated in male observers, evoking excessive self-grooming behaviors. These pathways originate from non-overlapping PiC neuron populations with distinct gene expression signatures regulated by transcription factors and sex hormones. Our study unveils how internal states of social counterparts are processed through sexually dimorphic mechanisms at the molecular, cellular, and circuit levels and offers insights into the neural mechanisms underpinning sex differences in higher brain functions.},
}

@article {pmid38429112,
year = {2024},
author = {Pust, MM and Rocha Castellanos, DM and Rzasa, K and Dame, A and Pishchany, G and Assawasirisin, C and Liss, A and Fernandez-Del Castillo, C and Xavier, RJ},
title = {Absence of a pancreatic microbiome in intraductal papillary mucinous neoplasm.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2023-331012},
pmid = {38429112},
issn = {1468-3288},
abstract = {OBJECTIVE: This study aims to validate the existence of a microbiome within intraductal papillary mucinous neoplasm (IPMN) that can be differentiated from the taxonomically diverse DNA background of next-generation sequencing procedures.

DESIGN: We generated 16S rRNA amplicon sequencing data to analyse 338 cyst fluid samples from 190 patients and 19 negative controls, the latter collected directly from sterile syringes in the operating room. A subset of samples (n=20) and blanks (n=5) were spiked with known concentrations of bacterial cells alien to the human microbiome to infer absolute abundances of microbial traces. All cyst fluid samples were obtained intraoperatively and included IPMNs with various degrees of dysplasia as well as other cystic neoplasms. Follow-up culturing experiments were conducted to assess bacterial growth for microbiologically significant signals.

RESULTS: Microbiome signatures of cyst fluid samples were inseparable from those of negative controls, with no difference in taxonomic diversity, and microbial community composition. In a patient subgroup that had recently undergone invasive procedures, a bacterial signal was evident. This outlier signal was not characterised by higher taxonomic diversity but by an increased dominance index of a gut-associated microbe, leading to lower taxonomic evenness compared with the background signal.

CONCLUSION: The 'microbiome' of IPMNs and other pancreatic cystic neoplasms does not deviate from the background signature of negative controls, supporting the concept of a sterile environment. Outlier signals may appear in a small fraction of patients following recent invasive endoscopic procedures. No associations between microbial patterns and clinical or cyst parameters were apparent.},
}

@article {pmid38426063,
year = {2024},
author = {Argentini, C and Lugli, GA and Tarracchini, C and Fontana, F and Mancabelli, L and Viappiani, A and Anzalone, R and Angelini, L and Alessandri, G and Longhi, G and Bianchi, MG and Taurino, G and Bussolati, O and Milani, C and van Sinderen, D and Turroni, F and Ventura, M},
title = {Genomic and ecological approaches to identify the Bifidobacterium breve prototype of the healthy human gut microbiota.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1349391},
pmid = {38426063},
issn = {1664-302X},
abstract = {Members of the genus Bifidobacterium are among the first microorganisms colonizing the human gut. Among these species, strains of Bifidobacterium breve are known to be commonly transmitted from mother to her newborn, while this species has also been linked with activities supporting human wellbeing. In the current study, an in silico approach, guided by ecology- and phylogenome-based analyses, was employed to identify a representative strain of B. breve to be exploited as a novel health-promoting candidate. The selected strain, i.e., B. breve PRL2012, was found to well represent the genetic content and functional genomic features of the B. breve taxon. We evaluated the ability of PRL2012 to survive in the gastrointestinal tract and to interact with other human gut commensal microbes. When co-cultivated with various human gut commensals, B. breve PRL2012 revealed an enhancement of its metabolic activity coupled with the activation of cellular defense mechanisms to apparently improve its survivability in a simulated ecosystem resembling the human microbiome.},
}

@article {pmid38424056,
year = {2024},
author = {Istvan, P and Birkeland, E and Avershina, E and Kværner, AS and Bemanian, V and Pardini, B and Tarallo, S and de Vos, WM and Rognes, T and Berstad, P and Rounge, TB},
title = {Exploring the gut DNA virome in fecal immunochemical test stool samples reveals associations with lifestyle in a large population-based study.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {1791},
pmid = {38424056},
issn = {2041-1723},
support = {198048//Kreftforeningen (Norwegian Cancer Society)/ ; 190179//Kreftforeningen (Norwegian Cancer Society)/ ; 2022067//Ministry of Health and Care Services | Helse Sør-Øst RHF (Southern and Eastern Norway Regional Health Authority)/ ; },
abstract = {Stool samples for fecal immunochemical tests (FIT) are collected in large numbers worldwide as part of colorectal cancer screening programs. Employing FIT samples from 1034 CRCbiome participants, recruited from a Norwegian colorectal cancer screening study, we identify, annotate and characterize more than 18000 DNA viruses, using shotgun metagenome sequencing. Only six percent of them are assigned to a known taxonomic family, with Microviridae being the most prevalent viral family. Linking individual profiles to comprehensive lifestyle and demographic data shows 17/25 of the variables to be associated with the gut virome. Physical activity, smoking, and dietary fiber consumption exhibit strong and consistent associations with both diversity and relative abundance of individual viruses, as well as with enrichment for auxiliary metabolic genes. We demonstrate the suitability of FIT samples for virome analysis, opening an opportunity for large-scale studies of this enigmatic part of the gut microbiome. The diverse viral populations and their connections to the individual lifestyle uncovered herein paves the way for further exploration of the role of the gut virome in health and disease.},
}

@article {pmid38422909,
year = {2024},
author = {Cena, JA and Belmok, A and Kyaw, CM and Dame-Teixeira, N},
title = {The Archaea domain: Exploring historical and contemporary perspectives with in silico primer coverage analysis for future research in Dentistry.},
journal = {Archives of oral biology},
volume = {161},
number = {},
pages = {105936},
doi = {10.1016/j.archoralbio.2024.105936},
pmid = {38422909},
issn = {1879-1506},
abstract = {OBJECTIVE: The complete picture of how the human microbiome interacts with its host is still largely unknown, particularly concerning microorganisms beyond bacteria. Although existing in very low abundance and not directly linked to causing diseases, archaea have been detected in various sites of the human body, including the gastrointestinal tract, oral cavity, skin, eyes, respiratory and urinary systems. But what exactly are these microorganisms? In the early 1990 s, archaea were classified as a distinct domain of life, sharing a more recent common ancestor with eukaryotes than with bacteria. While archaea's presence and potential significance in Dentistry remain under-recognized, there are concerns that they may contribute to oral dysbiosis. However, detecting archaea in oral samples presents challenges, including difficulties in culturing, the selection of DNA extraction methods, primer design, bioinformatic analysis, and databases.

DESIGN: This is a comprehensive review on the oral archaeome, presenting an in-depth in silico analysis of various primers commonly used for detecting archaea in human body sites.

RESULTS: Among several primer pairs used for detecting archaea in human samples across the literature, only one specifically designed for detecting methanogenic archaea in stool samples, exhibited exceptional coverage levels for the domain and various archaea phyla.

CONCLUSIONS: Our in silico analysis underscores the need for designing new primers targeting not only methanogenic archaea but also nanoarchaeal and thaumarchaeota groups to gain a comprehensive understanding of the archaeal oral community. By doing so, researchers can pave the way for further advancements in the field of oral archaeome research.},
}

@article {pmid38419554,
year = {2024},
author = {Korpela, K and Hurley, S and Ford, SA and Franklin, R and Byrne, S and Lunjani, N and Forde, B and Neogi, U and Venter, C and Walter, J and Hourihane, J and O'Mahony, L and , },
title = {Association between gut microbiota development and allergy in infants born during pandemic-related social distancing restrictions.},
journal = {Allergy},
volume = {},
number = {},
pages = {},
doi = {10.1111/all.16069},
pmid = {38419554},
issn = {1398-9995},
support = {/SFI_/Science Foundation Ireland/Ireland ; },
abstract = {BACKGROUND: Several hypotheses link reduced microbial exposure to increased prevalence of allergies. Here we capitalize on the opportunity to study a cohort of infants (CORAL), raised during COVID-19 associated social distancing measures, to identify the environmental exposures and dietary factors that contribute to early life microbiota development and to examine their associations with allergic outcomes.

METHODS: Fecal samples were sequenced from infants at 6 (n = 351) and repeated at 12 (n = 343) months, using 16S sequencing. Published 16S data from pre-pandemic cohorts were included for microbiota comparisons. Online questionnaires collected epidemiological information on home environment, healthcare utilization, infant health, allergic diseases, and diet. Skin prick testing (SPT) was performed at 12 (n = 343) and 24 (n = 320) months of age, accompanied by atopic dermatitis and food allergy assessments.

RESULTS: The relative abundance of bifidobacteria was higher, while environmentally transmitted bacteria such as Clostridia was lower in CORAL infants compared to previous cohorts. The abundance of multiple Clostridia taxa correlated with a microbial exposure index. Plant based foods during weaning positively impacted microbiota development. Bifidobacteria levels at 6 months of age, and relative abundance of butyrate producers at 12 months of age, were negatively associated with AD and SPT positivity. The prevalence of allergen sensitization, food allergy, and AD did not increase over pre-pandemic levels.

CONCLUSIONS: Environmental exposures and dietary components significantly impact microbiota community assembly. Our results also suggest that vertically transmitted bacteria and appropriate dietary supports may be more important than exposure to environmental microbes alone for protection against allergic diseases in infancy.},
}

@article {pmid38416678,
year = {2024},
author = {Schwartzman, JA and Lebreton, F and Salamzade, R and Shea, T and Martin, MJ and Schaufler, K and Urhan, A and Abeel, T and Camargo, ILBC and Sgardioli, BF and Prichula, J and Guedes Frazzon, AP and Giribet, G and Van Tyne, D and Treinish, G and Innis, CJ and Wagenaar, JA and Whipple, RM and Manson, AL and Earl, AM and Gilmore, MS},
title = {Global diversity of enterococci and description of 18 previously unknown species.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {121},
number = {10},
pages = {e2310852121},
doi = {10.1073/pnas.2310852121},
pmid = {38416678},
issn = {1091-6490},
support = {AI083214//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; U19AI110818//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; F32GM121005//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; Sabbatical Grant//Research to Prevent Blindness (RPB)/ ; },
abstract = {Enterococci are gut microbes of most land animals. Likely appearing first in the guts of arthropods as they moved onto land, they diversified over hundreds of millions of years adapting to evolving hosts and host diets. Over 60 enterococcal species are now known. Two species, Enterococcus faecalis and Enterococcus faecium, are common constituents of the human microbiome. They are also now leading causes of multidrug-resistant hospital-associated infection. The basis for host association of enterococcal species is unknown. To begin identifying traits that drive host association, we collected 886 enterococcal strains from widely diverse hosts, ecologies, and geographies. This identified 18 previously undescribed species expanding genus diversity by >25%. These species harbor diverse genes including toxins and systems for detoxification and resource acquisition. Enterococcus faecalis and E. faecium were isolated from diverse hosts highlighting their generalist properties. Most other species showed a more restricted distribution indicative of specialized host association. The expanded species diversity permitted the Enterococcus genus phylogeny to be viewed with unprecedented resolution, allowing features to be identified that distinguish its four deeply rooted clades, and the entry of genes associated with range expansion such as B-vitamin biosynthesis and flagellar motility to be mapped to the phylogeny. This work provides an unprecedentedly broad and deep view of the genus Enterococcus, including insights into its evolution, potential new threats to human health, and where substantial additional enterococcal diversity is likely to be found.},
}

@article {pmid38409417,
year = {2024},
author = {Raslan, MA and Raslan, SA and Shehata, EM and Mahmoud, AS and Viana, MVC and Aburjaile, F and Barh, D and Sabri, NA and Azevedo, V},
title = {Mass Spectrometry Applications to Study Human Microbiome.},
journal = {Advances in experimental medicine and biology},
volume = {1443},
number = {},
pages = {87-101},
pmid = {38409417},
issn = {0065-2598},
mesh = {Humans ; *Microbiota ; Mass Spectrometry/methods ; *Gastrointestinal Microbiome ; Metabolomics/methods ; High-Throughput Nucleotide Sequencing ; },
abstract = {Microbiotas are an adaptable component of ecosystems, including human ecology. Microorganisms influence the chemistry of their specialized niche, such as the human gut, as well as the chemistry of distant surroundings, such as other areas of the body. Metabolomics based on mass spectrometry (MS) is one of the primary methods for detecting and identifying small compounds generated by the human microbiota, as well as understanding the functional significance of these microbial metabolites. This book chapter gives basic knowledge on the kinds of untargeted mass spectrometry as well as the data types that may be generated in the context of microbiome study. While data analysis remains a barrier, the emphasis is on data analysis methodologies and integrative analysis, particularly the integration of microbiome sequencing data. Mass spectrometry (MS)-based techniques have resurrected culture methods for studying the human gut microbiota, filling in the gaps left by high-throughput sequencing methods in terms of culturing minor populations.},
}

Humans
*Microbiota
Mass Spectrometry/methods
*Gastrointestinal Microbiome
Metabolomics/methods
High-Throughput Nucleotide Sequencing

@article {pmid38402077,
year = {2024},
author = {Burton, JP and Kofoed, RH and Rust, R},
title = {Science around the world.},
journal = {Trends in molecular medicine},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.molmed.2024.01.008},
pmid = {38402077},
issn = {1471-499X},
}

@article {pmid38401105,
year = {2024},
author = {Vijayanna, ST and Mane, S and Bhalerao, S and Jaideep, SS},
title = {Ayurvedic Therapies to Target the Microbiome: Evidence and Possibilities.},
journal = {Alternative therapies in health and medicine},
volume = {},
number = {},
pages = {},
pmid = {38401105},
issn = {1078-6791},
abstract = {CONTEXT: The microbiome is a constantly evolving entity, being influenced by diet, lifestyle, age, genetics, medication, and environment; keeping the microbiome in good health is a step toward better health for the body. Ayurveda emphasizes a healthy internal milieu that synchronizes with the circadian and seasonal rhythms, in addition to reacting to other stressors.

OBJECTIVE: The current review intended to provide an overview of Ayurvedic principles related to health and disease and their management and to briefly discuss the current understanding of the human microbiome and explore Ayurvedic herbs and therapies that have been studied for their effects on the microbiome.

DESIGN: The team included researchers in India and Canada. A Pubmed search was performed using the keywords Ayurveda therapies, Ayurvedic therapies, Gut microbiome, Panchakarma, Therapeutic purgation, Therapeutic emesis, medicated enema.

RESULTS: Research connecting Ayurvedic interventions and the gut microbiome is yet in a nascent stage. Several Ayurvedic herbs have been researched for their potential in altering the gut microbiome. Among the Ayurvedic therapies, virechana (therapeutic purgation) and basti (medicated enema) have been studied for their gut microbiome altering effects. However, the limited number of such studies prevents from drawing categorical conclusions currently, about the effects of Ayurvedic Panchakarma therapy on the human microbiome.

CONCLUSIONS: Studying where and how the Ayurvedic herbs and therapies can exert their influence on the human microbiome provides a challenging yet novel opportunity and can help address multiple health and disease conditions.},
}

@article {pmid38400752,
year = {2024},
author = {He, Z and Xie, H and Xu, H and Wu, J and Zeng, W and He, Q and Jobin, C and Jin, S and Lan, P},
title = {Chemotherapy-induced microbiota exacerbates the toxicity of chemotherapy through the suppression of interleukin-10 from macrophages.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2319511},
pmid = {38400752},
issn = {1949-0984},
mesh = {Humans ; Mice ; Animals ; Oxaliplatin/toxicity ; Interleukin-10/genetics ; *Gastrointestinal Microbiome/genetics ; *Microbiota ; Macrophages ; *Probiotics/pharmacology/therapeutic use ; *Antineoplastic Agents/adverse effects ; },
abstract = {The gut microbiota has been shown to influence the efficacy and toxicity of chemotherapy, thereby affecting treatment outcomes. Understanding the mechanism by which microbiota affects chemotherapeutic toxicity would have a profound impact on cancer management. In this study, we report that fecal microbiota transplantation from oxaliplatin-exposed mice promotes toxicity in recipient mice. Splenic RNA sequencing and macrophage depletion experiment showed that the microbiota-induced toxicity of oxaliplatin in mice was dependent on macrophages. Furthermore, oxaliplatin-mediated toxicity was exacerbated in Il10[-/-] mice, but not attenuated in Rag1[-/-] mice. Adoptive transfer of macrophage into Il10[-/-] mice confirmed the role of macrophage-derived IL-10 in the improvement of oxaliplatin-induced toxicity. Depletion of fecal Lactobacillus and Bifidobacterium was associated with the exacerbation of oxaliplatin-mediated toxicity, whereas supplementation with these probiotics alleviated chemotherapy-induced toxicity. Importantly, IL-10 administration and probiotics supplementation did not attenuate the antitumor efficacy of chemotherapy. Clinically, patients with colorectal cancer exposed to oxaliplatin exhibited downregulation of peripheral CD45[+]IL-10[+] cells. Collectively, our findings indicate that microbiota-mediated IL-10 production influences tolerance to chemotherapy, and thus represents a potential clinical target.},
}

Humans
Mice
Animals
Oxaliplatin/toxicity
Interleukin-10/genetics
*Gastrointestinal Microbiome/genetics
*Microbiota
Macrophages
*Probiotics/pharmacology/therapeutic use
*Antineoplastic Agents/adverse effects

@article {pmid38398875,
year = {2024},
author = {Simões, R and Ribeiro, AC and Dias, R and Freitas, V and Soares, S and Pérez-Gregorio, R},
title = {Unveiling the Immunomodulatory Potential of Phenolic Compounds in Food Allergies.},
journal = {Nutrients},
volume = {16},
number = {4},
pages = {},
doi = {10.3390/nu16040551},
pmid = {38398875},
issn = {2072-6643},
abstract = {Food allergies are becoming ever more prevalent around the world. This pathology is characterized by the breakdown of oral tolerance to ingested food allergens, resulting in allergic reactions in subsequent exposures. Due to the possible severity of the symptoms associated with this pathology, new approaches to prevent it and reduce associated symptoms are of utmost importance. In this framework, dietary phenolic compounds appear as a tool with a not fully explored potential. Some phenolic compounds have been pointed to with the ability to modulate food allergies and possibly reduce their symptoms. These compounds can modulate food allergies through many different mechanisms, such as altering the bioaccessibility and bioavailability of potentially immunogenic peptides, by modulating the human immune system and by modulating the composition of the human microbiome that resides in the oral cavity and the gastrointestinal tract. This review deepens the state-of-the-art of the modulation of these mechanisms by phenolic compounds. While this review shows clear evidence that dietary supplementation with foods rich in phenolic compounds might constitute a new approach to the management of food allergies, it also highlights the need for further research to delve into the mechanisms of action of these compounds and decipher systematic structure/activity relationships.},
}

@article {pmid38397866,
year = {2024},
author = {Longo, S and Del Chierico, F and Scanu, M and Toto, F and Legramante, JM and Rizza, S and Putignani, L and Federici, M},
title = {An Investigation of Metabolic Risk Factors and Gut Microbiota in Unexplained Syncope.},
journal = {Biomedicines},
volume = {12},
number = {2},
pages = {},
doi = {10.3390/biomedicines12020264},
pmid = {38397866},
issn = {2227-9059},
support = {2017FM74HK//Ministry of University and Research (MUR) Progetti di Ricerca di Interesse Nazionale (PRIN)/ ; 875534//SOPHIA Innovative Medicines Initiative 2 Joint Undertaking (JU) under grant agreement/ ; ARS01_00876//PON BIO-D/ ; PE00000019//MUR-PNRR M4C2I1.3 PE6 project/ ; DM1062//RTDa contract/ ; },
abstract = {BACKGROUND: The pathogenesis of many syncopal episodes remains unexplained. Intestinal dysbiosis could be involved in the pathophysiological mechanisms of syncope due to its connection with the central nervous system via the microbiota-gut-brain axis. This pilot study aimed to explore the specific cardiometabolic risk factors and gut microbiota in unexplained syncope (US), compared to other types of syncope, to assess their similarity or verify their different origins.

METHODS: We studied 86 participants with syncope, who were divided into four groups: an orthostatic syncope group (OH, n = 24), a neuromediated syncope group (NMS, n = 26), a cardiological syncope group (CS, n = 9), and an unexplained syncope group (US, n = 27). We evaluated the anthropometric, clinical, and metabolic characteristics of the four groups; the α- and β-diversity; and the differences in the abundance of the microbial taxa.

RESULTS: The US group had a lower incidence of systolic hypertension at the first visit and a lower frequency of patients with nocturnal hypertension than the CS group. Compared to the OH and NMS groups, the US group had a higher incidence of carotid plaques and greater carotid intima-media thickness, respectively. The microbiota differed significantly between the US and CS groups, but not between the US group and the OH or NMS group.

CONCLUSIONS: We observed significant differences in the gut microbiota between CS and US. Future studies are necessary to evaluate the involvement of the gut microbiota in the complex pathogenesis of syncope and whether its analysis could support the interpretation of the pathophysiological mechasnisms underlying some episodes classifiable as US.},
}

@article {pmid38396668,
year = {2024},
author = {Efremova, I and Maslennikov, R and Poluektova, E and Medvedev, O and Kudryavtseva, A and Krasnov, G and Fedorova, M and Romanikhin, F and Bakhitov, V and Aliev, S and Sedova, N and Kuropatkina, T and Ivanova, A and Zharkova, M and Pervushova, E and Ivashkin, V},
title = {Gut Microbiota and Biomarkers of Endothelial Dysfunction in Cirrhosis.},
journal = {International journal of molecular sciences},
volume = {25},
number = {4},
pages = {},
doi = {10.3390/ijms25041988},
pmid = {38396668},
issn = {1422-0067},
support = {National Research Grant Russia 2019//Biocodex (France)/ ; },
abstract = {Our aim was to study the association of endothelial dysfunction biomarkers with cirrhosis manifestations, bacterial translocation, and gut microbiota taxa. The fecal microbiome was assessed using 16S rRNA gene sequencing. Plasma levels of nitrite, big endothelin-1, asymmetric dimethylarginine (ADMA), presepsin, and claudin were measured as biomarkers of endothelial dysfunction, bacterial translocation, and intestinal barrier dysfunction. An echocardiography with simultaneous determination of blood pressure and heart rate was performed to evaluate hemodynamic parameters. Presepsin, claudin 3, nitrite, and ADMA levels were higher in cirrhosis patients than in controls. Elevated nitrite levels were associated with high levels of presepsin and claudin 3, the development of hemodynamic circulation, hypoalbuminemia, grade 2-3 ascites, overt hepatic encephalopathy, high mean pulmonary artery pressure, increased abundance of Proteobacteria and Erysipelatoclostridium, and decreased abundance of Oscillospiraceae, Subdoligranulum, Rikenellaceae, Acidaminococcaceae, Christensenellaceae, and Anaerovoracaceae. Elevated ADMA levels were associated with higher Child-Pugh scores, lower serum sodium levels, hypoalbuminemia, grade 2-3 ascites, milder esophageal varices, overt hepatic encephalopathy, lower mean pulmonary artery pressure, and low abundance of Erysipelotrichia and Erysipelatoclostridiaceae. High big endothelin-1 levels were associated with high levels of presepsin and sodium, low levels of fibrinogen and cholesterol, hypocoagulation, increased Bilophila and Coprobacillus abundances, and decreased Alloprevotella abundance.},
}

@article {pmid38394022,
year = {2024},
author = {Mayes, C and Morar, N},
title = {Environmental Injustices within Us: The Case of the Human Microbiome and the Need for More Creative Bioethics.},
journal = {The American journal of bioethics : AJOB},
volume = {24},
number = {3},
pages = {67-70},
doi = {10.1080/15265161.2024.2303135},
pmid = {38394022},
issn = {1536-0075},
}

@article {pmid38392903,
year = {2024},
author = {Babar, S and Liu, E and Kaur, S and Hussain, J and Danaher, PJ and Anstead, GM},
title = {Pseudopropionibacterium propionicum as a Cause of Empyema; A Diagnosis with Next-Generation Sequencing.},
journal = {Pathogens (Basel, Switzerland)},
volume = {13},
number = {2},
pages = {},
doi = {10.3390/pathogens13020165},
pmid = {38392903},
issn = {2076-0817},
support = {n/a//MicroGenDX/ ; },
abstract = {Pseudopropionibacterium propionicum (P.p.) is an anaerobic, Gram-positive, branching beaded rod that is a component of the human microbiome. An infection of the thoracic cavity with P.p. can mimic tuberculosis (TB), nocardiosis, and malignancy. We present a case of a 77-year-old male who presented with dyspnea and a productive cough who was initially misdiagnosed with TB based on positive acid-fast staining of a pleural biopsy specimen and an elevated adenosine deaminase level of the pleural fluid. He was then diagnosed with nocardiosis based on the Gram stain of his pleural fluid that showed a Gram-positive beaded and branching rod. The pleural fluid specimen was culture-negative, but the diagnosis of thoracic P.p. infection was determined with next-generation sequencing (NGS). The patient was initially treated with imipenem and minocycline, then ceftriaxone and minocycline, and later changed to minocycline only. This report shows the utility of NGS in making a microbiological diagnosis when other techniques either failed to provide a result (culture) or gave misleading information (histopathologic exam, pleural fluid adenosine deaminase determination, and organism morphology on Gram stain).},
}

@article {pmid38392650,
year = {2024},
author = {Kamel, M and Aleya, S and Alsubih, M and Aleya, L},
title = {Microbiome Dynamics: A Paradigm Shift in Combatting Infectious Diseases.},
journal = {Journal of personalized medicine},
volume = {14},
number = {2},
pages = {},
pmid = {38392650},
issn = {2075-4426},
support = {RGP2/343/44//Deanship of Scientific Research at King Khalid University/ ; },
abstract = {Infectious diseases have long posed a significant threat to global health and require constant innovation in treatment approaches. However, recent groundbreaking research has shed light on a previously overlooked player in the pathogenesis of disease-the human microbiome. This review article addresses the intricate relationship between the microbiome and infectious diseases and unravels its role as a crucial mediator of host-pathogen interactions. We explore the remarkable potential of harnessing this dynamic ecosystem to develop innovative treatment strategies that could revolutionize the management of infectious diseases. By exploring the latest advances and emerging trends, this review aims to provide a new perspective on combating infectious diseases by targeting the microbiome.},
}

@article {pmid38391403,
year = {2024},
author = {Nguyen, M and Ahn, P and Dawi, J and Gargaloyan, A and Kiriaki, A and Shou, T and Wu, K and Yazdan, K and Venketaraman, V},
title = {The Interplay between Mycobacterium tuberculosis and Human Microbiome.},
journal = {Clinics and practice},
volume = {14},
number = {1},
pages = {198-213},
doi = {10.3390/clinpract14010017},
pmid = {38391403},
issn = {2039-7275},
abstract = {Tuberculosis (TB), a respiratory disease caused by Mycobacterium tuberculosis (Mtb), is a significant cause of mortality worldwide. The lung, a breeding ground for Mtb, was once thought to be a sterile environment, but has now been found to host its own profile of microbes. These microbes are critical in the development of the host immune system and can produce metabolites that aid in host defense against various pathogens. Mtb infection as well as antibiotics can shift the microbial profile, causing dysbiosis and dampening the host immune response. Additionally, increasing cases of drug resistant TB have impacted the success rates of the traditional therapies of isoniazid, rifampin, pyrazinamide, and ethambutol. Recent years have produced tremendous research into the human microbiome and its role in contributing to or attenuating disease processes. Potential treatments aimed at altering the gut-lung bacterial axis may offer promising results against drug resistant TB and help mitigate the effects of TB.},
}

@article {pmid38390467,
year = {2024},
author = {Acosta-Pagán, K and Bolaños-Rosero, B and Pérez, C and Ortíz, AP and Godoy-Vitorino, F},
title = {Ecological competition in the oral mycobiome of Hispanic adults living in Puerto Rico associates with periodontitis.},
journal = {Journal of oral microbiology},
volume = {16},
number = {1},
pages = {2316485},
doi = {10.1080/20002297.2024.2316485},
pmid = {38390467},
issn = {2000-2297},
abstract = {Background: Fungi are a major component of the human microbiome that only recently received attention. The imbalance of indigenous fungal communities and environmental fungi present in the oral cavity may have a role in oral dysbiosis, which could exacerbate oral inflammatory diseases. Methods: We performed a cross-sectional study and recruited 88 participants aged 21 to 49 from sexually transmitted infection clinics in Puerto Rico. A full-mouth periodontal examination following the NHANES protocol defined periodontal severity (CDC/AAP). ITS2 (fungal) genes were amplified and sequenced for mycobiota characterization of yeast and environmental fungi. Environmental outdoor spore levels were measured daily by the American Academy of Allergy Asthma and Immunology San Juan station and defined by quartiles as spore scores. Results: Our data indicate polymicrobial colonization of yeast and environmental fungi in the oral cavity. Dominant taxa associated with periodontal disease included Saccharomyces cerevisiae, Rigidoporus vinctus, and Aspergillus penicilloides, while Candida albicans were found to be ubiquitous. Fungal aerosols were found to impact the oral cavity biofilm, likely due to competition and neutralization by inhaled outdoor and indoor fungal spores. Conclusion: To our knowledge, this is the first report showcasing the ecological competition of measured outdoor environmental fungi with the human oral mycobiota.},
}

@article {pmid38390219,
year = {2023},
author = {Mortazavi, SMJ and Said-Salman, I and Mortazavi, AR and El Khatib, S and Sihver, L},
title = {How the adaptation of the human microbiome to harsh space environment can determine the chances of success for a space mission to Mars and beyond.},
journal = {Frontiers in microbiology},
volume = {14},
number = {},
pages = {1237564},
doi = {10.3389/fmicb.2023.1237564},
pmid = {38390219},
issn = {1664-302X},
abstract = {The ability of human cells to adapt to space radiation is essential for the well-being of astronauts during long-distance space expeditions, such as voyages to Mars or other deep space destinations. However, the adaptation of the microbiomes should not be overlooked. Microorganisms inside an astronaut's body, or inside the space station or other spacecraft, will also be exposed to radiation, which may induce resistance to antibiotics, UV, heat, desiccation, and other life-threatening factors. Therefore, it is essential to consider the potential effects of radiation not only on humans but also on their microbiomes to develop effective risk reduction strategies for space missions. Studying the human microbiome in space missions can have several potential benefits, including but not limited to a better understanding of the major effects space travel has on human health, developing new technologies for monitoring health and developing new radiation therapies and treatments. While radioadaptive response in astronauts' cells can lead to resistance against high levels of space radiation, radioadaptive response in their microbiome can lead to resistance against UV, heat, desiccation, antibiotics, and radiation. As astronauts and their microbiomes compete to adapt to the space environment. The microorganisms may emerge as the winners, leading to life-threatening situations due to lethal infections. Therefore, understanding the magnitude of the adaptation of microorganisms before launching a space mission is crucial to be able to develop effective strategies to mitigate the risks associated with radiation exposure. Ensuring the safety and well-being of astronauts during long-duration space missions and minimizing the risks linked with radiation exposure can be achieved by adopting this approach.},
}

@article {pmid38388538,
year = {2024},
author = {Cao, Z and Fan, D and Sun, Y and Huang, Z and Li, Y and Su, R and Zhang, F and Li, Q and Yang, H and Zhang, F and Miao, Y and Lan, P and Wu, X and Zuo, T},
title = {The gut ileal mucosal virome is disturbed in patients with Crohn's disease and exacerbates intestinal inflammation in mice.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {1638},
pmid = {38388538},
issn = {2041-1723},
support = {82172323//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32100134//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82060107//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Gut bacteriome dysbiosis is known to be implicated in the pathogenesis of inflammatory bowel disease (IBD). Crohn's disease (CD) is an IBD subtype with extensive mucosal inflammation, yet the mucosal virome, an empirical modulator of the bacteriome and mucosal immunity, remains largely unclear regarding its composition and role. Here, we exploited trans-cohort CD patients and healthy individuals to compositionally and functionally investigate the small bowel (terminal ileum) virome and bacteriome. The CD ileal virome was characterised by an under-representation of both lytic and temperate bacteriophages (especially those targeting bacterial pathogens), particularly in patients with flare-up. Meanwhile, the virome-bacteriome ecology in CD ileal mucosa was featured by a lack of Bifidobacterium- and Lachnospiraceae-led mutualistic interactions between bacteria and bacteriophages; surprisingly it was more pronounced in CD remission than flare-up, underlining the refractory and recurrent nature of mucosal inflammation in CD. Lastly, we substantiated that ileal virions from CD patients causally exacerbated intestinal inflammation in IBD mouse models, by reshaping a gut virome-bacteriome ecology preceding intestinal inflammation (microbial trigger) and augmenting microbial sensing/defence pathways in the intestine cells (host response). Altogether, our results highlight the significance of mucosal virome in CD pathogenesis and importance of mucosal virome restoration in CD therapeutics.},
}

@article {pmid38384263,
year = {2024},
author = {Li, L and Li, M and Chen, Y and Yu, Z and Cheng, P and Yu, Z and Cheng, W and Zhang, W and Wang, Z and Gao, X and Sun, H and Wang, X},
title = {Function and therapeutic prospects of next-generation probiotic Akkermansia muciniphila in infectious diseases.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1354447},
pmid = {38384263},
issn = {1664-302X},
abstract = {Akkermansia muciniphila is a gram-negative bacterium that colonizes the human gut, making up 3-5% of the human microbiome. A. muciniphila is a promising next-generation probiotic with clinical application prospects. Emerging studies have reported various beneficial effects of A. muciniphila including anti-cancer, delaying aging, reducing inflammation, improving immune function, regulating nervous system function, whereas knowledge on its roles and mechanism in infectious disease is currently unclear. In this review, we summarized the basic characteristics, genome and phenotype diversity, the influence of A. muciniphila and its derived components on infectious diseases, such as sepsis, virus infection, enteric infection, periodontitis and foodborne pathogen induced infections. We also provided updates on mechanisms how A. muciniphila protects intestinal barrier integrity and modulate host immune response. In summary, we believe that A. muciniphila is a promising therapeutic probiotic that may be applied for the treatment of a variety of infectious diseases.},
}

@article {pmid38383422,
year = {2024},
author = {Gaire, TN and Scott, HM and Noyes, NR and Ericsson, AC and Tokach, MD and William, H and Menegat, MB and Vinasco, J and Nagaraja, TG and Volkova, VV},
title = {Temporal dynamics of the fecal microbiome in female pigs from early life through estrus, parturition, and weaning of the first litter of piglets.},
journal = {Animal microbiome},
volume = {6},
number = {1},
pages = {7},
pmid = {38383422},
issn = {2524-4671},
abstract = {BACKGROUND: Age-associated changes in the gastrointestinal microbiome of young pigs have been robustly described; however, the temporal dynamics of the fecal microbiome of the female pig from early life to first parity are not well understood. Our objective was to describe microbiome and antimicrobial resistance dynamics of the fecal microbiome of breeding sows from early life through estrus, parturition and weaning of the first litter of piglets (i.e., from 3 to 53 weeks of age).

RESULTS: Our analysis revealed that fecal bacterial populations in developing gilts undergo changes consistent with major maturation milestones. As the pigs progressed towards first estrus, the fecal bacteriome shifted from Rikenellaceae RC9 gut group- and UCG-002-dominated enterotypes to Treponema- and Clostridium sensu stricto 1-dominated enterotypes. After first estrus, the fecal bacteriome stabilized, with minimal changes in enterotype transition and associated microbial diversity from estrus to parturition and subsequent weaning of first litter piglets. Unlike bacterial communities, fecal fungal communities exhibited low diversity with high inter- and intra-pig variability and an increased relative abundance of certain taxa at parturition, including Candida spp. Counts of resistant fecal bacteria also fluctuated over time, and were highest in early life and subsequently abated as the pigs progressed to adulthood.

CONCLUSIONS: This study provides insights into how the fecal microbial community and antimicrobial resistance in female pigs change from three weeks of age throughout their first breeding lifetime. The fecal bacteriome enterotypes and diversity are found to be age-driven and established by the time of first estrus, with minimal changes observed during subsequent physiological stages, such as parturition and lactation, when compared to the earlier age-related shifts. The use of pigs as a model for humans is well-established, however, further studies are needed to understand how our results compare to the human microbiome dynamics. Our findings suggest that the fecal microbiome exhibited consistent changes across individual pigs and became more diverse with age, which is a beneficial characteristic for an animal model system.},
}

@article {pmid38376378,
year = {2024},
author = {Kitamura, N and Kajihara, T and Volpiano, CG and Naung, M and Méric, G and Hirabayashi, A and Yano, H and Yamamoto, M and Yoshida, F and Kobayashi, T and Yamanashi, S and Kawamura, T and Matsunaga, N and Okochi, J and Sugai, M and Yahara, K},
title = {Exploring the effects of antimicrobial treatment on the gut and oral microbiomes and resistomes from elderly long-term care facility residents via shotgun DNA sequencing.},
journal = {Microbial genomics},
volume = {10},
number = {2},
pages = {},
doi = {10.1099/mgen.0.001180},
pmid = {38376378},
issn = {2057-5858},
mesh = {Aged ; Humans ; Angiotensin Receptor Antagonists ; Cross-Sectional Studies ; Long-Term Care ; Angiotensin-Converting Enzyme Inhibitors ; DNA ; Sequence Analysis, DNA ; *Microbiota ; *Anti-Infective Agents ; },
abstract = {Monitoring antibiotic-resistant bacteria (ARB) and understanding the effects of antimicrobial drugs on the human microbiome and resistome are crucial for public health. However, no study has investigated the association between antimicrobial treatment and the microbiome-resistome relationship in long-term care facilities, where residents act as reservoirs of ARB but are not included in the national surveillance for ARB. We conducted shotgun metagenome sequencing of oral and stool samples from long-term care facility residents and explored the effects of antimicrobial treatment on the human microbiome and resistome using two types of comparisons: cross-sectional comparisons based on antimicrobial treatment history in the past 6 months and within-subject comparisons between stool samples before, during and 2-4 weeks after treatment using a single antimicrobial drug. Cross-sectional analysis revealed two characteristics in the group with a history of antimicrobial treatment: the archaeon Methanobrevibacter was the only taxon that significantly increased in abundance, and the total abundance of antimicrobial resistance genes (ARGs) was also significantly higher. Within-subject comparisons showed that taxonomic diversity did not decrease during treatment, suggesting that the effect of the prescription of a single antimicrobial drug in usual clinical treatment on the gut microbiota is likely to be smaller than previously thought, even among very elderly people. Additional analysis of the detection limit of ARGs revealed that they could not be detected when contig coverage was <2.0. This study is the first to report the effects of usual antimicrobial treatments on the microbiome and resistome of long-term care facility residents.},
}

Aged
Humans
Angiotensin Receptor Antagonists
Cross-Sectional Studies
Long-Term Care
Angiotensin-Converting Enzyme Inhibitors
DNA
Sequence Analysis, DNA
*Microbiota
*Anti-Infective Agents

@article {pmid38374338,
year = {2024},
author = {Buiatte, V and Fonseca, A and Alonso Madureira, P and Nakashima Vaz, AC and Tizioto, PC and Centola Vidal, AM and Ganda, E and de Azevedo Ruiz, VL},
title = {A comparative study of the bacterial diversity and composition of nursery piglets' oral fluid, feces, and housing environment.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {4119},
pmid = {38374338},
issn = {2045-2322},
support = {2017/22184-7//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 001//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; PEN04752//Hatch/ ; },
mesh = {Swine ; Animals ; Humans ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; Housing ; Bacteria/genetics ; Feces/microbiology ; Firmicutes/genetics ; },
abstract = {The oral cavity is the portal of entry for many microorganisms that affect swine, and the swine oral fluid has been used as a specimen for the diagnosis of several infectious diseases. The oral microbiota has been shown to play important roles in humans, such as protection against non-indigenous bacteria. In swine, studies that have investigated the microbial composition of the oral cavity of pigs are scarce. This study aimed to characterize the oral fluid microbiota of weaned pigs from five commercial farms in Brazil and compare it to their respective fecal and environmental microbiotas. Bacterial compositions were determined by 16S rRNA gene sequencing and analyzed in R Studio. Oral fluid samples were significantly less diverse (alpha diversity) than pen floor and fecal samples (P < 0.01). Alpha diversity changed among farms in oral fluid and pen floor samples, but no differences were observed in fecal samples. Permutational ANOVA revealed that beta diversity was significantly different among sample types (P = 0.001) and farms (P = 0.001), with separation of sample types (feces, pen floor, and oral fluid) on the principal coordinates analysis. Most counts obtained from oral fluid samples were classified as Firmicutes (80.4%) and Proteobacteria (7.7%). The genera Streptococcus, members of the Pasteurellaceae family, and Veillonella were differentially abundant in oral fluid samples when compared to fecal samples, in which Streptococcus was identified as a core genus that was strongly correlated (SparCC) with other taxa. Firmicutes and Bacteroidota were the most relatively abundant phyla identified in fecal and pen floor samples, and Prevotella_9 was the most classified genus. No differentially abundant taxa were identified when comparing fecal samples and pen floor samples. We concluded that under the conditions of our study, the oral fluid microbiota of weaned piglets is different (beta diversity) and less diverse (alpha diversity) than the fecal and environmental microbiotas. Several differentially abundant taxa were identified in the oral fluid samples, and some have been described as important colonizers of the oral cavity in human microbiome studies. Further understanding of the relationship between the oral fluid microbiota and swine is necessary and would create opportunities for the development of innovative solutions that target the microbiota to improve swine health and production.},
}

Swine
Animals
Humans
*Gastrointestinal Microbiome
RNA, Ribosomal, 16S/genetics
Housing
Bacteria/genetics
Feces/microbiology
Firmicutes/genetics

@article {pmid38371926,
year = {2024},
author = {Yang, MQ and Wang, ZJ and Zhai, CB and Chen, LQ},
title = {Research progress on the application of 16S rRNA gene sequencing and machine learning in forensic microbiome individual identification.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1360457},
pmid = {38371926},
issn = {1664-302X},
abstract = {Forensic microbiome research is a field with a wide range of applications and a number of protocols have been developed for its use in this area of research. As individuals host radically different microbiota, the human microbiome is expected to become a new biomarker for forensic identification. To achieve an effective use of this procedure an understanding of factors which can alter the human microbiome and determinations of stable and changing elements will be critical in selecting appropriate targets for investigation. The 16S rRNA gene, which is notable for its conservation and specificity, represents a potentially ideal marker for forensic microbiome identification. Gene sequencing involving 16S rRNA is currently the method of choice for use in investigating microbiomes. While the sequencing involved with microbiome determinations can generate large multi-dimensional datasets that can be difficult to analyze and interpret, machine learning methods can be useful in surmounting this analytical challenge. In this review, we describe the research methods and related sequencing technologies currently available for application of 16S rRNA gene sequencing and machine learning in the field of forensic identification. In addition, we assess the potential value of 16S rRNA and machine learning in forensic microbiome science.},
}

@article {pmid38371919,
year = {2024},
author = {Wang, Q and Fan, X and Wu, S and Su, X},
title = {PM-CNN: microbiome status recognition and disease detection model based on phylogeny and multi-path neural network.},
journal = {Bioinformatics advances},
volume = {4},
number = {1},
pages = {vbae013},
pmid = {38371919},
issn = {2635-0041},
abstract = {MOTIVATION: The human microbiome, found throughout various body parts, plays a crucial role in health dynamics and disease development. Recent research has highlighted microbiome disparities between patients with different diseases and healthy individuals, suggesting the microbiome's potential in recognizing health states. Traditionally, microbiome-based status classification relies on pre-trained machine learning (ML) models. However, most ML methods overlook microbial relationships, limiting model performance.

RESULTS: To address this gap, we propose PM-CNN (Phylogenetic Multi-path Convolutional Neural Network), a novel phylogeny-based neural network model for multi-status classification and disease detection using microbiome data. PM-CNN organizes microbes based on their phylogenetic relationships and extracts features using a multi-path convolutional neural network. An ensemble learning method then fuses these features to make accurate classification decisions. We applied PM-CNN to human microbiome data for status and disease detection, demonstrating its significant superiority over existing ML models. These results provide a robust foundation for microbiome-based state recognition and disease prediction in future research and applications.

PM-CNN software is available at https://github.com/qdu-bioinfo/PM_CNN.},
}

@article {pmid38369542,
year = {2024},
author = {Zou, S and Yang, C and Zhang, J and Zhong, D and Meng, M and Zhang, L and Chen, H and Fang, L},
title = {Multi-omic profiling reveals associations between the gut microbiome, host genome and transcriptome in patients with colorectal cancer.},
journal = {Journal of translational medicine},
volume = {22},
number = {1},
pages = {175},
pmid = {38369542},
issn = {1479-5876},
support = {82373512//National Natural Science Foundation of China/ ; 82222056//National Natural Science Foundation of China/ ; 82302910//National Natural Science Foundation of China/ ; 2022A1515012316//Natural Science Foundation of Guangdong Province/ ; 2021B1212010004//Natural Science Foundation of Guangdong Province/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Transcriptome/genetics ; *Colorectal Neoplasms/diagnosis ; Multiomics ; *Microbiota ; },
abstract = {BACKGROUND: Colorectal cancer (CRC) is the leading cancer worldwide. Microbial agents have been considered to contribute to the pathogenesis of different disease. But the underlying relevance between CRC and microbiota remain unclear.

METHODS: We dissected the fecal microbiome structure and genomic and transcriptomic profiles of matched tumor and normal mucosa tissues from 41 CRC patients. Of which, the relationship between CRC-associated bacterial taxa and their significantly correlated somatic mutated gene was investigated by exome sequencing technology. Differentially expressed functional genes in CRC were clustered according to their correlation with differentially abundant species, following by annotation with DAVID. The composition of immune and stromal cell types was identified by XCELL.

RESULTS: We identified a set of 22 microbial gut species associated with CRC and estimate the relative abundance of KEGG ontology categories. Next, the interactions between CRC-related gut microbes and clinical phenotypes were evaluated. 4 significantly mutated gene: TP53, APC, KRAS, SMAD4 were pointed out and the associations with cancer related microbes were identified. Among them, Fusobacterium nucleatum positively corelated with different host metabolic pathways. Finally, we revealed that Fusobacterium nucleatum modified the tumor immune environment by TNFSF9 gene expression.

CONCLUSION: Collectively, our multi-omics data could help identify novel biomarkers to inform clinical decision-making in the detection and diagnosis of CRC.},
}

Humans
*Gastrointestinal Microbiome/genetics
Transcriptome/genetics
*Colorectal Neoplasms/diagnosis
Multiomics
*Microbiota

@article {pmid38361239,
year = {2024},
author = {Mohamed, ME and Saqr, A and Staley, C and Onyeaghala, G and Teigen, L and Dorr, CR and Remmel, RP and Guan, W and Oetting, WS and Matas, AJ and Israni, AK and Jacobson, PA},
title = {Pharmacomicrobiomics: Immunosuppressive Drugs and Microbiome Interactions in Transplantation.},
journal = {Transplantation},
volume = {},
number = {},
pages = {},
pmid = {38361239},
issn = {1534-6080},
abstract = {The human microbiome is associated with human health and disease. Exogenous compounds, including pharmaceutical products, are also known to be affected by the microbiome, and this discovery has led to the field of pharmacomicobiomics. The microbiome can also alter drug pharmacokinetics and pharmacodynamics, possibly resulting in side effects, toxicities, and unanticipated disease response. Microbiome-mediated effects are referred to as drug-microbiome interactions (DMI). Rapid advances in the field of pharmacomicrobiomics have been driven by the availability of efficient bacterial genome sequencing methods and new computational and bioinformatics tools. The success of fecal microbiota transplantation for recurrent Clostridioides difficile has fueled enthusiasm and research in the field. This review focuses on the pharmacomicrobiome in transplantation. Alterations in the microbiome in transplant recipients are well documented, largely because of prophylactic antibiotic use, and the potential for DMI is high. There is evidence that the gut microbiome may alter the pharmacokinetic disposition of tacrolimus and result in microbiome-specific tacrolimus metabolites. The gut microbiome also impacts the enterohepatic recirculation of mycophenolate, resulting in substantial changes in pharmacokinetic disposition and systemic exposure. The mechanisms of these DMI and the specific bacteria or communities of bacteria are under investigation. There are little or no human DMI data for cyclosporine A, corticosteroids, and sirolimus. The available evidence in transplantation is limited and driven by small studies of heterogeneous designs. Larger clinical studies are needed, but the potential for future clinical application of the pharmacomicrobiome in avoiding poor outcomes is high.},
}

@article {pmid38352704,
year = {2024},
author = {Kadyan, S and Park, G and Hochuli, N and Miller, K and Wang, B and Nagpal, R},
title = {Resistant starches from dietary pulses improve neurocognitive health via gut-microbiome-brain axis in aged mice.},
journal = {Frontiers in nutrition},
volume = {11},
number = {},
pages = {1322201},
pmid = {38352704},
issn = {2296-861X},
abstract = {INTRODUCTION: Cognitive decline is a common consequence of aging. Dietary patterns that lack fibers and are high in saturated fats worsen cognitive impairment by triggering pro-inflammatory pathways and metabolic dysfunctions. Emerging evidence highlights the neurocognitive benefits of fiber-rich diets and the crucial role of gut-microbiome-brain signaling. However, the mechanisms of this diet-microbiome-brain regulation remain largely unclear.

METHODS: Accordingly, we herein investigated the unexplored neuroprotective mechanisms of dietary pulses-derived resistant starch (RS) in improving aging-associated neurocognitive function in an aged (60-weeks old) murine model carrying a human microbiome.

RESULTS AND DISCUSSION: Following 20-weeks dietary regimen which included a western-style diet without (control; CTL) or with 5% w/w fortification with RS from pinto beans (PTB), black-eyed-peas (BEP), lentils (LEN), chickpeas (CKP), or inulin fiber (INU), we find that RS, particularly from LEN, ameliorate the cognitive impairments induced by western diet. Mechanistically, RS-mediated improvements in neurocognitive assessments are attributed to positive remodeling of the gut microbiome-metabolome arrays, which include increased short-chain fatty acids and reduced branched-chain amino acids levels. This microbiome-metabolite-brain signaling cascade represses neuroinflammation, cellular senescence, and serum leptin/insulin levels, while enhancing lipid metabolism through improved hepatic function. Altogether, the data demonstrate the prebiotic effects of RS in improving neurocognitive function via modulating the gut-brain axis.},
}

@article {pmid38352363,
year = {2024},
author = {Zhou, X and Shen, X and Johnson, JS and Spakowicz, DJ and Agnello, M and Zhou, W and Avina, M and Honkala, A and Chleilat, F and Chen, SJ and Cha, K and Leopold, S and Zhu, C and Chen, L and Lyu, L and Hornburg, D and Wu, S and Zhang, X and Jiang, C and Jiang, L and Jiang, L and Jian, R and Brooks, AW and Wang, M and Contrepois, K and Gao, P and Schüssler-Fiorenza Rose, SM and Binh Tran, TD and Nguyen, H and Celli, A and Hong, BY and Bautista, EJ and Dorsett, Y and Kavathas, P and Zhou, Y and Sodergren, E and Weinstock, GM and Snyder, MP},
title = {Longitudinal profiling of the microbiome at four body sites reveals core stability and individualized dynamics during health and disease.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.02.01.577565},
pmid = {38352363},
abstract = {UNLABELLED: To understand dynamic interplay between the human microbiome and host during health and disease, we analyzed the microbial composition, temporal dynamics, and associations with host multi-omics, immune and clinical markers of microbiomes from four body sites in 86 participants over six years. We found that microbiome stability and individuality are body-site-specific and heavily influenced by the host. The stool and oral microbiome were more stable than the skin and nasal microbiomes, possibly due to their interaction with the host and environment. Also, we identified individual-specific and commonly shared bacterial taxa, with individualized taxa showing greater stability. Interestingly, microbiome dynamics correlated across body sites, suggesting systemic coordination influenced by host-microbial-environment interactions. Notably, insulin-resistant individuals showed altered microbial stability and associations between microbiome, molecular markers, and clinical features, suggesting their disrupted interaction in metabolic disease. Our study offers comprehensive views of multi-site microbial dynamics and their relationship with host health and disease.

STUDY HIGHLIGHTS: The stability of the human microbiome varies among individuals and body sites.Highly individualized microbial genera are more stable over time.At each of the four body sites, systematic interactions between the environment, the host and bacteria can be detected.Individuals with insulin resistance have lower microbiome stability, a more diversified skin microbiome, and significantly altered host-microbiome interactions.},
}

@article {pmid38347963,
year = {2023},
author = {Jokiranta, ST and Miettinen, S and Salonen, S and Kareinen, L and Uusitalo, R and Korhonen, EM and Virtanen, J and Kivistö, I and Aaltonen, K and Mosselhy, DA and Lääveri, T and Kantele, A and Arstila, TP and Jarva, H and Vapalahti, O and Heinonen, S and Kekäläinen, E},
title = {Stable Levels of Antibodies Against Unrelated Toxoid Vaccines After COVID-19: COVID-19 Infection Does Not Affect Toxoid Vaccine Antibody Levels.},
journal = {Pathogens & immunity},
volume = {8},
number = {2},
pages = {74-87},
pmid = {38347963},
issn = {2469-2964},
abstract = {BACKGROUND: Lymphopenia is common in COVID-19. This has raised concerns that COVID-19 could affect the immune system akin to measles infection, which causes immune amnesia and a reduction in protective antibodies.

METHODS: We recruited COVID-19 patients (n = 59) in Helsinki, Finland, and collected plasma samples on 2 to 3 occasions during and after infection. We measured IgG antibodies to diphtheria toxin, tetanus toxoid, and pertussis toxin, along with total IgG, SARS-CoV-2 spike protein IgG, and neutralizing antibodies. We also surveyed the participants for up to 17 months for long-term impaired olfaction as a proxy for prolonged post-acute COVID-19 symptoms.

RESULTS: No significant differences were found in the unrelated vaccine responses while the serological response against COVID-19 was appropriate. During the acute phase of the disease, the SARSCoV-2 IgG levels were lower in outpatients when compared to inpatients. SARS-CoV-2 serology kinetics matched expectations. In the acute phase, anti-tetanus and anti-diphtheria IgG levels were lower in patients with prolonged impaired olfaction during follow up than in those without.

CONCLUSIONS: We could not detect significant decline in overall humoral immunity during or after COVID-19 infection. In severe COVID-19, there appears to be a temporary decline in total IgG levels.},
}

@article {pmid37963399,
year = {2024},
author = {Jennings, SAV and Clavel, T},
title = {Synthetic Communities of Gut Microbes for Basic Research and Translational Approaches in Animal Health and Nutrition.},
journal = {Annual review of animal biosciences},
volume = {12},
number = {},
pages = {283-300},
doi = {10.1146/annurev-animal-021022-025552},
pmid = {37963399},
issn = {2165-8110},
abstract = {Microbes and animals have a symbiotic relationship that greatly influences nutrient uptake and animal health. This relationship can be studied using selections of microbes termed synthetic communities, or SynComs. SynComs are used in many different animal hosts, including agricultural animals, to investigate microbial interactions with nutrients and how these affect animal health. The most common host focuses for SynComs are currently mouse and human, from basic mechanistic research through to translational disease models and live biotherapeutic products (LBPs) as treatments. We discuss SynComs used in basic research models and findings that relate to human and animal health and nutrition. Translational use cases of SynComs are discussed, followed by LBPs, especially within the context of agriculture. SynComs still face challenges, such as standardization for reproducibility and contamination risks. However, the future of SynComs is hopeful, especially in the areas of genome-guided SynCom design and custom SynCom-based treatments.},
}