@article {pmid38628202,
year = {2024},
author = {Khalil, NA and ALFaris, NA and ALTamimi, JZ and Mohamed Ahmed, IA},
title = {Anti-inflammatory effects of bay laurel (Laurus nobilis L.) towards the gut microbiome in dextran sodium sulfate induced colitis animal models.},
journal = {Food science & nutrition},
volume = {12},
number = {4},
pages = {2650-2660},
pmid = {38628202},
issn = {2048-7177},
abstract = {Bay laurel (Laurus nobilis L.) contains active antioxidative phenolic components that are beneficial to human health. However, none was examined and reported utilizing health effects related to inflammatory bowel diseases (IBD) mainly ulcerative colitis (UC) in correlation to gut microbiota (GM). Thus, the current study aimed to investigate the impacts of bay leaves on UC albino rats targeting on the GM composition and their metabolites production (i.e., short-chain fatty acids; SCFAs) for improving the gut barrier functions. UC models were induced by supplementing 5% DSS into their drinking water. The models were then divided randomly for the diet with 1%, 2%, and 3% of bay leaves, as well as two control studies (positive and negative). Colon-to-body weight ratio was used as an indicator for the presence of edema tissue. From the collected fecal samples at 0, 24 h, and final day, the population changes of gut microbiota (Lactobacillus, Bifidobacteria, Clostridium, and sulfate-reducing bacteria) and SCFAs production were evaluated using fluorescence in situ hybridization (FISH) and gas-liquid chromatography (GC). The colon-to-body weight ratio of the rat models consuming 2% and 3% bay leaves was found to be significantly lower with better recovery of colonic function. Models consuming 3% bay leaves showed the best treatment effects on GM compositions; promoting the growth of Bifidobacteria and Lactobacillus in addition to producing high butyric acid levels. Meanwhile, the number of Clostridium and SRB was significantly reduced. Conclusively, consuming bay leaves brought significant colon health benefits other than stimulating appetite for a better taste.},
}

@article {pmid38628125,
year = {2024},
author = {Baiz, MD and Wood, AW and Toews, DPL},
title = {Association between the gut microbiome and carotenoid plumage phenotype in an avian hybrid zone.},
journal = {Proceedings. Biological sciences},
volume = {291},
number = {2021},
pages = {20240238},
pmid = {38628125},
issn = {1471-2954},
mesh = {Humans ; Animals ; *Gastrointestinal Microbiome ; Phenotype ; Vertebrates ; *Passeriformes ; Carotenoids ; },
abstract = {Vertebrates host complex microbiomes that impact their physiology. In many taxa, including colourful wood-warblers, gut microbiome similarity decreases with evolutionary distance. This may suggest that as host populations diverge, so do their microbiomes, because of either tight coevolutionary dynamics, or differential environmental influences, or both. Hybridization is common in wood-warblers, but the effects of evolutionary divergence on the microbiome during secondary contact are unclear. Here, we analyse gut microbiomes in two geographically disjunct hybrid zones between blue-winged warblers (Vermivora cyanoptera) and golden-winged warblers (Vermivora chrysoptera). We performed 16S faecal metabarcoding to identify species-specific bacteria and test the hypothesis that host admixture is associated with gut microbiome disruption. Species identity explained a small amount of variation between microbiomes in only one hybrid zone. Co-occurrence of species-specific bacteria was rare for admixed individuals, yet microbiome richness was similar among admixed and parental individuals. Unexpectedly, we found several bacteria that were more abundant among admixed individuals with a broader deposition of carotenoid-based plumage pigments. These bacteria are predicted to encode carotenoid biosynthesis genes, suggesting birds may take advantage of pigments produced by their gut microbiomes. Thus, host admixture may facilitate beneficial symbiotic interactions which contribute to plumage ornaments that function in sexual selection.},
}

Humans
Animals
*Gastrointestinal Microbiome
Phenotype
Vertebrates
*Passeriformes
Carotenoids

@article {pmid38628120,
year = {2024},
author = {Rohner, PT and Moczek, AP},
title = {Vertically inherited microbiota and environment modifying behaviours conceal genetic variation in dung beetle life history.},
journal = {Proceedings. Biological sciences},
volume = {291},
number = {2021},
pages = {20240122},
pmid = {38628120},
issn = {1471-2954},
mesh = {Animals ; *Coleoptera/genetics ; *Microbiota/genetics ; Larva/genetics ; Biological Evolution ; Genetic Variation ; },
abstract = {Diverse organisms actively manipulate their (sym)biotic and physical environment in ways that feed back on their own development. However, the degree to which these processes affect microevolution remains poorly understood. The gazelle dung beetle both physically modifies its ontogenetic environment and structures its biotic interactions through vertical symbiont transmission. By experimentally eliminating (i) physical environmental modifications and (ii) the vertical inheritance of microbes, we assess how environment modifying behaviour and microbiome transmission shape heritable variation and evolutionary potential. We found that depriving larvae of symbionts and environment modifying behaviours increased additive genetic variance and heritability for development time but not body size. This suggests that larvae's ability to manipulate their environment has the potential to modify heritable variation and to facilitate the accumulation of cryptic genetic variation. This cryptic variation may become released and selectable when organisms encounter environments that are less amenable to organismal manipulation or restructuring. Our findings also suggest that intact microbiomes, which are commonly thought to increase genetic variation of their hosts, may instead reduce and conceal heritable variation. More broadly, our findings highlight that the ability of organisms to actively manipulate their environment may affect the potential of populations to evolve when encountering novel, stressful conditions.},
}

Animals
*Coleoptera/genetics
*Microbiota/genetics
Larva/genetics
Biological Evolution
Genetic Variation

@article {pmid38627868,
year = {2024},
author = {Ho, M and Nguyen, HN and Van Hoang, M and Bui, TTT and Vu, BQ and Dinh, THT and Vo, HTM and Blaydon, DC and Eldirany, SA and Bunick, CG and Bui, CB},
title = {Altered skin microbiome, inflammation, and JAK/STAT signaling in Southeast Asian ichthyosis patients.},
journal = {Human genomics},
volume = {18},
number = {1},
pages = {38},
pmid = {38627868},
issn = {1479-7364},
support = {K08AR070290/AR/NIAMS NIH HHS/United States ; },
mesh = {Humans ; Case-Control Studies ; Leukocytes, Mononuclear ; Southeast Asian People ; Inflammation/genetics ; *Microbiota/genetics ; *Ichthyosis/genetics ; },
abstract = {BACKGROUND: Congenital ichthyosis (CI) is a collective group of rare hereditary skin disorders. Patients present with epidermal scaling, fissuring, chronic inflammation, and increased susceptibility to infections. Recently, there is increased interest in the skin microbiome; therefore, we hypothesized that CI patients likely exhibit an abnormal profile of epidermal microbes because of their various underlying skin barrier defects. Among recruited individuals of Southeast Asian ethnicity, we performed skin meta-genomics (i.e., whole-exome sequencing to capture the entire multi-kingdom profile, including fungi, protists, archaea, bacteria, and viruses), comparing 36 CI patients (representing seven subtypes) with that of 15 CI age-and gender-matched controls who had no family history of CI.

RESULTS: This case-control study revealed 20 novel and 31 recurrent pathogenic variants. Microbiome meta-analysis showed distinct microbial populations, decreases in commensal microbiota, and higher colonization by pathogenic species associated with CI; these were correlated with increased production of inflammatory cytokines and Th17- and JAK/STAT-signaling pathways in peripheral blood mononuclear cells. In the wounds of CI patients, we identified specific changes in microbiota and alterations in inflammatory pathways, which are likely responsible for impaired wound healing.

CONCLUSIONS: Together, this research enhances our understanding of the microbiological, immunological, and molecular properties of CI and should provide critical information for improving therapeutic management of CI patients.},
}

Humans
Case-Control Studies
Leukocytes, Mononuclear
Southeast Asian People
Inflammation/genetics
*Microbiota/genetics
*Ichthyosis/genetics

@article {pmid38627822,
year = {2024},
author = {Williams, J and Pettorelli, N and Hartmann, AC and Quinn, RA and Plaisance, L and O'Mahoney, M and Meyer, CP and Fabricius, KE and Knowlton, N and Ransome, E},
title = {Decline of a distinct coral reef holobiont community under ocean acidification.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {75},
pmid = {38627822},
issn = {2049-2618},
support = {NE/R012229/1//Natural Environment Research Council/ ; 2022717//National Science Foundation/ ; 1558868//National Science Foundation/ ; 1558868//National Science Foundation/ ; },
mesh = {Animals ; Coral Reefs ; Ecosystem ; Hydrogen-Ion Concentration ; Ocean Acidification ; Seawater ; *Anthozoa/physiology ; *Microbiota ; },
abstract = {BACKGROUND: Microbes play vital roles across coral reefs both in the environment and inside and upon macrobes (holobionts), where they support critical functions such as nutrition and immune system modulation. These roles highlight the potential ecosystem-level importance of microbes, yet most knowledge of microbial functions on reefs is derived from a small set of holobionts such as corals and sponges. Declining seawater pH - an important global coral reef stressor - can cause ecosystem-level change on coral reefs, providing an opportunity to study the role of microbes at this scale. We use an in situ experimental approach to test the hypothesis that under such ocean acidification (OA), known shifts among macrobe trophic and functional groups may drive a general ecosystem-level response extending across macrobes and microbes, leading to reduced distinctness between the benthic holobiont community microbiome and the environmental microbiome.

RESULTS: We test this hypothesis using genetic and chemical data from benthic coral reef community holobionts sampled across a pH gradient from CO2 seeps in Papua New Guinea. We find support for our hypothesis; under OA, the microbiome and metabolome of the benthic holobiont community become less compositionally distinct from the sediment microbiome and metabolome, suggesting that benthic macrobe communities are colonised by environmental microbes to a higher degree under OA conditions. We also find a simplification and homogenisation of the benthic photosynthetic community, and an increased abundance of fleshy macroalgae, consistent with previously observed reef microbialisation.

CONCLUSIONS: We demonstrate a novel structural shift in coral reefs involving macrobes and microbes: that the microbiome of the benthic holobiont community becomes less distinct from the sediment microbiome under OA. Our findings suggest that microbialisation and the disruption of macrobe trophic networks are interwoven general responses to environmental stress, pointing towards a universal, undesirable, and measurable form of ecosystem changed. Video Abstract.},
}

Animals
Coral Reefs
Ecosystem
Hydrogen-Ion Concentration
Ocean Acidification
Seawater
*Anthozoa/physiology
*Microbiota

@article {pmid38627726,
year = {2024},
author = {Su, C and Wan, S and Ding, J and Ni, G and Ding, H},
title = {Blood lipids mediate the effects of gut microbiome on endometriosis: a mendelian randomization study.},
journal = {Lipids in health and disease},
volume = {23},
number = {1},
pages = {110},
pmid = {38627726},
issn = {1476-511X},
support = {82201820//National Natural Science Foundation of China/ ; 82201820//National Natural Science Foundation of China/ ; 82201820//National Natural Science Foundation of China/ ; 82201820//National Natural Science Foundation of China/ ; },
mesh = {Female ; Humans ; *Gastrointestinal Microbiome/genetics ; *Endometriosis/genetics ; Bayes Theorem ; Genome-Wide Association Study ; Mendelian Randomization Analysis ; Lipids ; Triglycerides ; },
abstract = {BACKGROUND: There is evidence for an association between the gut microbiome and endometriosis. However, their causal relationship and the mediating role of lipid metabolism remain unclear.

METHODS: Using genome-wide association study (GWAS) data, we conducted a bidirectional Mendelian randomization (MR) analysis to investigate the causal relationships between gut microbiome and endometriosis. The inverse variance weighted (IVW) method was used as the primary model, with other MR models used for comparison. Sensitivity analysis based on different statistical assumptions was used to evaluate whether the results were robust. A two-step MR analysis was further conducted to explore the mediating effects of lipids, by integrating univariable MR and the multivariate MR method based on the Bayesian model averaging method (MR-BMA).

RESULTS: We identified four possible intestinal bacteria genera associated with the risk of endometriosis through the IVW method, including Eubacterium ruminantium group (odds ratio [OR] = 0.881, 95% CI: 0.795-0.976, P = 0.015), Anaerotruncus (OR = 1.252, 95% CI: 1.028-1.525, P = 0.025), Olsenella (OR = 1.110, 95% CI: 1.007-1.223, P = 0.036), and Oscillospira (OR = 1.215, 95% CI: 1.014-1.456, P = 0.035). The further two-step MR analysis identified that the effect of Olsenella on endometriosis was mediated by triglycerides (proportion mediated: 3.3%; 95% CI = 1.5-5.1%).

CONCLUSION: This MR study found evidence for specific gut microbiomes associated with the risk of endometriosis, which might partially be mediated by triglycerides.},
}

Female
Humans
*Gastrointestinal Microbiome/genetics
*Endometriosis/genetics
Bayes Theorem
Genome-Wide Association Study
Mendelian Randomization Analysis
Lipids
Triglycerides

@article {pmid38627687,
year = {2024},
author = {Zhang, K and Paul, K and Jacobs, JP and Cockburn, MG and Bronstein, JM and Del Rosario, I and Ritz, B},
title = {Ambient long-term exposure to organophosphorus pesticides and the human gut microbiome: an observational study.},
journal = {Environmental health : a global access science source},
volume = {23},
number = {1},
pages = {41},
pmid = {38627687},
issn = {1476-069X},
support = {K01AG07204401/AG/NIA NIH HHS/United States ; R01ES031106/ES/NIEHS NIH HHS/United States ; },
mesh = {Animals ; Humans ; Aged ; *Pesticides/adverse effects ; *Gastrointestinal Microbiome ; Organophosphorus Compounds ; *Parkinson Disease ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; Bacteria ; },
abstract = {BACKGROUND: Organophosphorus pesticides (OP) have been associated with various human health conditions. Animal experiments and in-vitro models suggested that OP may also affect the gut microbiota. We examined associations between ambient chronic exposure to OP and gut microbial changes in humans.

METHODS: We recruited 190 participants from a community-based epidemiologic study of Parkinson's disease living in a region known for heavy agricultural pesticide use in California. Of these, 61% of participants had Parkinson's disease and their mean age was 72 years. Microbiome and predicted metagenome data were generated by 16S rRNA gene sequencing of fecal samples. Ambient long-term OP exposures were assessed using pesticide application records combined with residential addresses in a geographic information system. We examined gut microbiome differences due to OP exposures, specifically differences in microbial diversity based on the Shannon index and Bray-Curtis dissimilarities, and differential taxa abundance and predicted Metacyc pathway expression relying on regression models and adjusting for potential confounders.

RESULTS: OP exposure was not associated with alpha or beta diversity of the gut microbiome. However, the predicted metagenome was sparser and less evenly expressed among those highly exposed to OP (p = 0.04). Additionally, we found that the abundance of two bacterial families, 22 genera, and the predicted expression of 34 Metacyc pathways were associated with long-term OP exposure. These pathways included perturbed processes related to cellular respiration, increased biosynthesis and degradation of compounds related to bacterial wall structure, increased biosynthesis of RNA/DNA precursors, and decreased synthesis of Vitamin B1 and B6.

CONCLUSION: In support of previous animal studies and in-vitro findings, our results suggest that ambient chronic OP pesticide exposure alters gut microbiome composition and its predicted metabolism in humans.},
}

Animals
Humans
Aged
*Pesticides/adverse effects
*Gastrointestinal Microbiome
Organophosphorus Compounds
*Parkinson Disease
RNA, Ribosomal, 16S/genetics
*Microbiota
Bacteria

@article {pmid38627617,
year = {2024},
author = {Chen, M and Feng, S and Lv, H and Wang, Z and Zeng, Y and Shao, C and Lin, W and Zhang, Z},
title = {OsCIPK2 mediated rice root microorganisms and metabolites to improve plant nitrogen uptake.},
journal = {BMC plant biology},
volume = {24},
number = {1},
pages = {285},
pmid = {38627617},
issn = {1471-2229},
support = {2021J01093//National Natural Science Foundation of Fujian/ ; },
mesh = {*Oryza ; Plant Roots/metabolism ; Nitrogen/metabolism ; *Nitrogen-Fixing Bacteria/metabolism ; Soil ; Rhizosphere ; Citric Acid ; Soil Microbiology ; },
abstract = {Crop roots are colonized by large numbers of microorganisms, collectively known as the root-microbiome, which modulate plant growth, development and contribute to elemental nutrient uptake. In conditions of nitrogen limitation, the over-expressed Calcineurin B-like interacting protein kinase 2 (OsCIPK2) gene with root-specific promoter (RC) has been shown to enhance growth and nitrogen uptake in rice. Analysis of root-associated bacteria through high-throughput sequencing revealed that OsCIPK2 has a significant impact on the diversity of the root microbial community under low nitrogen stress. The quantification of nifH gene expression demonstrated a significant enhancement in nitrogen-fixing capabilities in the roots of RC transgenetic rice. Synthetic microbial communities (SynCom) consisting of six nitrogen-fixing bacterial strains were observed to be enriched in the roots of RC, leading to a substantial improvement in rice growth and nitrogen uptake in nitrogen-deficient soils. Forty and twenty-three metabolites exhibiting differential abundance were identified in the roots and rhizosphere soils of RC transgenic rice compared to wild-type (WT) rice. These findings suggest that OSCIPK2 plays a role in restructuring the microbial community in the roots through the regulation of metabolite synthesis and secretion. Further experiments involving the exogenous addition of citric acid revealed that an optimal concentration of this compound facilitated the growth of nitrogen-fixing bacteria and substantially augmented their population in the soil, highlighting the importance of citric acid in promoting nitrogen fixation under conditions of low nitrogen availability. These findings suggest that OsCIPK2 plays a role in enhancing nitrogen uptake by rice plants from the soil by influencing the assembly of root microbial communities, thereby offering valuable insights for enhancing nitrogen utilization in rice cultivation.},
}

*Oryza
Plant Roots/metabolism
Nitrogen/metabolism
*Nitrogen-Fixing Bacteria/metabolism
Soil
Rhizosphere
Citric Acid
Soil Microbiology

@article {pmid38626906,
year = {2024},
author = {Bongers, KS and Massett, A and O'Dwyer, DN},
title = {The Oral-Lung Microbiome Axis in Connective Tissue Disease-Related Interstitial Lung Disease.},
journal = {Seminars in respiratory and critical care medicine},
volume = {},
number = {},
pages = {},
doi = {10.1055/s-0044-1785673},
pmid = {38626906},
issn = {1098-9048},
abstract = {Connective tissue disease-related interstitial lung disease (CTD-ILD) is a frequent and serious complication of CTD, leading to high morbidity and mortality. Unfortunately, its pathogenesis remains poorly understood; however, one intriguing contributing factor may be the microbiome of the mouth and lungs. The oral microbiome, which is a major source of the lung microbiome through recurrent microaspiration, is altered in ILD patients. Moreover, in recent years, several lines of evidence suggest that changes in the oral and lung microbiota modulate the pulmonary immune response and thus may play a role in the pathogenesis of ILDs, including CTD-ILD. Here, we review the existing data demonstrating oral and lung microbiota dysbiosis and possible contributions to the development of CTD-ILD in rheumatoid arthritis, Sjögren's syndrome, systemic sclerosis, and systemic lupus erythematosus. We identify several areas of opportunity for future investigations into the role of the oral and lung microbiota in CTD-ILD.},
}

@article {pmid38626862,
year = {2024},
author = {Peixoto, S and Morgado, RG and Prodana, M and Cardoso, DN and Malheiro, C and Neves, J and Santos, C and Khodaparast, Z and Pavlaki, MD and Rodrigues, S and Rodrigues, SM and Henriques, I and Loureiro, S},
title = {Responses of soil microbiome to copper-based materials (nano and bulk) for agricultural applications: An indoor-mesocosm experiment.},
journal = {NanoImpact},
volume = {},
number = {},
pages = {100506},
doi = {10.1016/j.impact.2024.100506},
pmid = {38626862},
issn = {2452-0748},
abstract = {The foreseen increasing application of copper-based nanomaterials (Cu-NMs), replacing or complementing existing Cu-agrochemicals, may negatively impact the soil microbiome. Thus, we studied the effects on soil microbiome function and composition of nano copper oxide (nCuO) or copper hydroxide NMs in a commercial (Kocide®3000) or a lab-synthetized formulation (nCu(OH)2) or bulk copper hydroxide (Cu(OH)2-B), at the commonly recommended Cu dose of 50 mg(Cu)kg[-1] soil. Microbial responses were studied over 28 days in a designed indoor mesocosm. On day-28, in comparison to non-treated soil (CT), all Cu-treatments led to a reduction in dehydrogenase (95% to 68%), arylsulfatase (41% to 27%), and urease (40% to 20%) activity. There was a 32% increase in the utilization of carbon substrates in the nCuO-treatment and an increased abundance of viable bacteria in the nCu(OH)2-treatment (75% of heterotrophic and 69% of P-solubilizing bacteria). The relative abundance of Acidobacteria [Kocide®3000, nCuO, and Cu(OH)2-B treatments] and Flavobacteriia [nCu(OH)2-treatment] was negatively affected by Cu exposure. The abundance of Cu-tolerant bacteria increased in soils treated with Kocide®3000 (Clostridia) and nCu(OH)2 (Gemmatimonadetes). All Cu-treated soils exhibited a reduced abundance of denitrification-related genes (0.05% of nosZ gene). The DTPA-extractable pool of ionic Cu(II) varied among treatments: Cu(OH)2-B > Kocide®3000 ~ nCuO>nCu(OH)2, which may explain changes on the soil microbiome composition, at the genera and OTU levels. Thus, our study revealed that Cu-materials (nano and bulk) influence the soil microbiome with implications on its ecological role. It highlights the importance of assessing the impact of Cu-materials under dynamic and complex exposure scenarios and emphasizes the need for specific regulatory frameworks for NMs.},
}

@article {pmid38626296,
year = {2024},
author = {Denburg, JA and O'Byrne, PM and Gauvreau, GM},
title = {Eosinophil Plasticity and Diversity: Proceedings of the 2023 International Eosinophil Society Symposium.},
journal = {Journal of leukocyte biology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jleuko/qiae089},
pmid = {38626296},
issn = {1938-3673},
abstract = {This issue highlights and details the programme and scientific presentations at the International Eosinophil Society's 12th biennial Symposium, which was held in Hamilton, Ontario, Canada in July 2023. The meeting included sessions on regulation of eosinophil development; cell death, stress, and autophagy in eosinophils; local immunity interactions of eosinophils with multiple cell types; eosinophils in host defense; eosinophils and mast cells in gastrointestinal disorders; reciprocal interactions between eosinophils and the microbiome in homeostasis and dysbiosis; and, eosinophils in tissue injury and repair, in tumor biology and cancer therapy. There was a mixture of special invited lectures and cutting-edge abstracts on specific aspects of eosinophil science, as well as enlivened pro-con debates on targeting eosinophils with biologics. A major thrust and overarching theme was that eosinophils exhibit remarkable plasticity and heterogeneity in executing their functions both in homeostasis and in pathobiology; there is a new "Eo-verse" to understand. We trust that this special volume of the Journal of Leukocyte Biology will be of interest across many disciplines and medical sub-specialties in biomedical sciences and demonstrate both the complexity and versatility of the eosinophil in biology and medicine.},
}

@article {pmid38625898,
year = {2024},
author = {Goforth, M and Cooper, MA and Oliver, AS and Pinzon, J and Skots, M and Obergh, V and Suslow, TV and Flores, GE and Huynh, S and Parker, CT and Mackelprang, R and Cooper, KK},
title = {Bacterial community shifts of commercial apples, oranges, and peaches at different harvest points across multiple growing seasons.},
journal = {PloS one},
volume = {19},
number = {4},
pages = {e0297453},
pmid = {38625898},
issn = {1932-6203},
mesh = {Humans ; *Prunus persica ; Seasons ; Bacteria ; *Citrus sinensis/microbiology ; Fruit/microbiology ; },
abstract = {Assessing the microbes present on tree fruit carpospheres as the fruit enters postharvest processing could have useful applications, as these microbes could have a major influence on spoilage, food safety, verification of packing process controls, or other aspects of processing. The goal of this study was to establish a baseline profile of bacterial communities associated with apple (pome fruit), peach (stone fruit), and Navel orange (citrus fruit) at harvest. We found that commercial peaches had the greatest bacterial richness followed by oranges then apples. Time of harvest significantly changed bacterial diversity in oranges and peaches, but not apples. Shifts in diversity varied by fruit type, where 70% of the variability in beta diversity on the apple carposphere was driven by the gain and loss of species (i.e., nestedness). The peach and orange carposphere bacterial community shifts were driven by nearly an even split between turnover (species replacement) and nestedness. We identified a small core microbiome for apples across and between growing seasons that included only Methylobacteriaceae and Sphingomonadaceae among the samples, while peaches had a larger core microbiome composed of five bacterial families: Bacillaceae, Geodermtophilaceae, Nocardioidaceae, Micrococcaeceae, and Trueperaceae. There was a relatively diverse core microbiome for oranges that shared all the families present on apples and peaches, except for Trueperaceae, but also included an additional nine bacterial families not shared including Oxalobacteraceae, Cytophagaceae, and Comamonadaceae. Overall, our findings illustrate the important temporal dynamics of bacterial communities found on major commercial tree fruit, but also the core bacterial families that constantly remain with both implications being important entering postharvest packing and processing.},
}

Humans
*Prunus persica
Seasons
Bacteria
*Citrus sinensis/microbiology
Fruit/microbiology

@article {pmid38625646,
year = {2024},
author = {Han, JH and Kim, HS},
title = {Skin Deep: The Potential of Microbiome Cosmetics.},
journal = {Journal of microbiology (Seoul, Korea)},
volume = {},
number = {},
pages = {},
pmid = {38625646},
issn = {1976-3794},
support = {2023R1A2C1007759//The National Research Foundation of Korea (NRF) grant funded by the Korea government (MSIT)/ ; HI23C086000//Korea Health Technology R&D Project through the Korea Health Industry Development Institute (KHIDI) funded by the Ministry of Health & Welfare, Republic of Korea/ ; },
abstract = {The interplay between the skin microbiome and its host is a complex facet of dermatological health and has become a critical focus in the development of microbiome cosmetics. The skin microbiome, comprising various microorganisms, is essential from birth, develops over the lifespan, and performs vital roles in protecting our body against pathogens, training the immune system, and facilitating the breakdown of organic matter. Dysbiosis, an imbalance of these microorganisms, has been implicated in a number of skin conditions such as acne, atopic dermatitis, and skin cancer. Recent scientific findings have spurred cosmetic companies to develop products that preserve and enhance the skin's microbial diversity balance. These products may incorporate elements like prebiotics, probiotics, and postbiotics, which are beneficial for the skin microbiome. Beyond topical products, there's increasing interest in ingestible beauty supplements (i.e. oral probiotics), highlighting the connection between the gut and skin. This review examines the influence of the microbiome on skin health and the emerging trends of microbiome skincare products.},
}

@article {pmid38625645,
year = {2024},
author = {Lee, C and Lee, S and Yoo, W},
title = {Metabolic Interaction Between Host and the Gut Microbiota During High-Fat Diet-Induced Colorectal Cancer.},
journal = {Journal of microbiology (Seoul, Korea)},
volume = {},
number = {},
pages = {},
pmid = {38625645},
issn = {1976-3794},
abstract = {Colorectal cancer (CRC) is the second-highest cause of cancer-associated mortality among both men and women worldwide. One of the risk factors for CRC is obesity, which is correlated with a high-fat diet prevalent in Western dietary habits. The association between an obesogenic high-fat diet and CRC has been established for several decades; however, the mechanisms by which a high-fat diet increases the risk of CRC remain unclear. Recent studies indicate that gut microbiota strongly influence the pathogenesis of both high-fat diet-induced obesity and CRC. The gut microbiota is composed of hundreds of bacterial species, some of which are implicated in CRC. In particular, the expansion of facultative anaerobic Enterobacteriaceae, which is considered a microbial signature of intestinal microbiota functional imbalance (dysbiosis), is associated with both high-fat diet-induced obesity and CRC. Here, we review the interaction between the gut microbiome and its metabolic byproducts in the context of colorectal cancer (CRC) during high-fat diet-induced obesity. In addition, we will cover how a high-fat diet can drive the expansion of genotoxin-producing Escherichia coli by altering intestinal epithelial cell metabolism during gut inflammation conditions.},
}

@article {pmid38625524,
year = {2024},
author = {Ing, NH and Steiner, JM},
title = {The Use of Diets in the Diagnosis and Treatment of Common Gastrointestinal Diseases in Dogs and Cats.},
journal = {Advances in experimental medicine and biology},
volume = {1446},
number = {},
pages = {39-53},
pmid = {38625524},
issn = {0065-2598},
mesh = {Cats ; Dogs ; Humans ; Animals ; *Cat Diseases/diagnosis/therapy ; Acute Disease ; *Pancreatitis ; *Dog Diseases/diagnosis/therapy ; Diet ; *Gastrointestinal Diseases/diagnosis/therapy/veterinary ; Diarrhea/diagnosis/therapy/veterinary ; *Inflammatory Bowel Diseases ; },
abstract = {The nutritional health of dogs and cats is important to pet owners around the world. Nutrition is inextricably linked to the health of the gastrointestinal system and vice versa. Gastrointestinal signs, such as vomiting, diarrhea, anorexia, or weight loss, are one of the most common reasons that dog and cat owners make non-routine appointments with veterinarians. Those patients are evaluated systematically to identify and/or rule out the causes of the symptoms. Some causes of chronic diarrhea are within the gastrointestinal tract while others are secondary to pathogenic factors outside the digestive system. Some useful biomarkers of chronic intestinal disease (enteropathy) exist in serum and feces. After determination that the clinical signs are due to primary gastrointestinal disease and that there is no parasitism, specific diets are used for at least two weeks. There are several types of diets for pets with chronic enteropathies. There are limited ingredient diets and hydrolyzed protein diets with reduced levels of allergens. There are also highly digestible and fiber-enhanced diets. Some diets contain probiotics and/or prebiotics. If symptoms do not improve and the patient is stable, a diet from a different class may be tried. For chronic enteropathies, the prognosis is generally good for symptom resolution or at least improvement. However, if interventions with novel diets do not ameliorate the symptoms of chronic enteropathy, then antibiotic, anti-inflammatory, or immunosuppressant therapy or further, more invasive diagnostics such as taking an intestinal biopsy, may be indicated. Pancreatitis is a common gastrointestinal disease in dogs and cats and patients may present with mild to severe disease. Many patients with mild to moderate disease can be successfully treated with early supportive care, including feeding a low-fat diet. A novel pharmaceutical, fuzapladib (Panoquell-CA1) looks very promising for treating more severe forms of acute pancreatitis in dogs. Maintenance on a low-fat diet may prevent pancreatitis in at-risk dogs. Future advances in medicine will allow pet owners and veterinarians to use dietary management to maximize the health of their dogs and cats.},
}

Cats
Dogs
Humans
Animals
*Cat Diseases/diagnosis/therapy
Acute Disease
*Pancreatitis
*Dog Diseases/diagnosis/therapy
Diet
*Gastrointestinal Diseases/diagnosis/therapy/veterinary
Diarrhea/diagnosis/therapy/veterinary
*Inflammatory Bowel Diseases

@article {pmid38625085,
year = {2024},
author = {Gottwald, J and Balke, J and Stellmacher, J and van Vorst, K and Ghazisaeed, F and Fulde, M and Alexiev, U},
title = {Cy3-based nanoviscosity determination of mucus: Effect of mucus collection methods and antibiotics treatment.},
journal = {Macromolecular bioscience},
volume = {},
number = {},
pages = {e2300437},
doi = {10.1002/mabi.202300437},
pmid = {38625085},
issn = {1616-5195},
abstract = {The integrity of the protective mucus layer as a primary defense against pathogen invasion and microbial leakage into the intestinal epithelium can be compromised by the effects of antibiotics on the commensal microbiome. Changes in mucus integrity directly affect the solvent viscosity in the immediate vicinity of the mucin network, i.e., the nanoviscosity, which in turn affects both biochemical reactions and selective transport. To assess mucus nanoviscosity, a reliable readout via the viscosity-dependent fluorescence lifetime of the molecular rotor dye Cy3 is established and nanoviscosities from porcine and murine ex vivo mucus are determined. To account for different mucin concentrations due to the removal of digestive residues during mucus collection, the power law dependence of mucin concentration on viscosity is used. The impact of antibiotics combinations (meropenem/vancomycin, gentamycin/ampicillin) on ex vivo intestinal mucus nanoviscosity is presented. The significant increase in viscosity of murine intestinal mucus after treatment suggests an effect of antibiotics on the microbiota that affects mucus integrity. The presented method will be a useful tool to assess how drugs, directly or indirectly, affect mucus integrity. Additionally, the method can be utilized to analyze the role of mucus nanoviscosity in health and disease, as well as in drug development. This article is protected by copyright. All rights reserved.},
}

@article {pmid38624222,
year = {2024},
author = {Ali, R and Chaluvadi, SR and Wang, X and Hazzouri, KM and Sudalaimuthuasari, N and Rafi, M and Al-Nuaimi, M and Sasi, S and Antepenko, E and Bennetzen, JL and Amiri, KMA},
title = {Microbiome properties in the root nodules of Prosopis cineraria, a leguminous desert tree.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0361723},
doi = {10.1128/spectrum.03617-23},
pmid = {38624222},
issn = {2165-0497},
abstract = {We conducted a comprehensive analysis of the total microbiome and transcriptionally active microbiome communities in the roots and root nodules of Prosopis cineraria, an important leguminous tree in arid regions of many Asian countries. Mature P. cineraria trees growing in the desert did not exhibit any detected root nodules. However, we observed root nodules on the roots of P. cineraria growing on a desert farm and on young plants growing in a growth chamber, when inoculated with rhizosphere soil, including with rhizosphere soil from near desert tree roots that had no nodules. Compared to nearby soil, non-nodulated roots were enriched with Actinobacteria (e.g., Actinophytocola sp.), whereas root nodules sampled from the desert farm and growth chamber had abundant Alphaproteobacteria (e.g., Ensifer sp.). These nodules yielded many microbes in addition to such nitrogen-fixing bacteria as Ensifer and Sinorhizobium species. Significant differences exist in the composition and abundance of microbial isolates between the nodule surface and the nodule endosphere. Shotgun metagenome analysis of nodule endospheres revealed that the root nodules comprised over 90% bacterial DNA, whereas metatranscriptome analysis showed that the plant produces vastly more transcripts than the microbes in these nodules. Control inoculations demonstrated that four out of six Rhizobium, Agrobacterium, or Ensifer isolates purified from P. cineraria nodules produced nodules in the roots of P. cineraria seedlings under greenhouse conditions. The best nodulation was achieved when seedlings were inoculated with a mixture of those bacterial strains. Though root nodulation could be achieved under water stress conditions, nodule number and nodule biomass increased with copious water availability. .IMPORTANCEMicrobial communities were investigated in roots and root nodules of Prosopis cineraria, a leguminous tree species in arid Asian regions that is responsible for exceptionally important contributions to soil fertility in these dramatically dry locations. Soil removed from regions near nodule-free roots on these mature plants contained an abundance of bacteria with the genetic ability to generate nodules and fix nitrogen but did not normally nodulate in their native rhizosphere environment, suggesting a very different co-evolved relationship than that observed for herbaceous legumes. The relative over-expression of the low-gene-density plant DNA compared to the bacterial DNA in the nodules was also unexpected, indicating a very powerful induction of host genetic contributions within the nodule. Finally, the water dependence of nodulation in inoculated seedlings suggested a possible link between early seedling growth (before a deep root system can be developed) and the early development of nitrogen-fixing capability.},
}

@article {pmid38624107,
year = {2024},
author = {Zhang, YJ and Connearney, S and Hester, L and Du, M and Catacora, A and Akkara, A and Wen, A and Bry, L and Alm, EJ and Rosen, R},
title = {Longitudinal microbiome changes in children exposed to proton pump inhibitors.},
journal = {Clinical and translational gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.14309/ctg.0000000000000703},
pmid = {38624107},
issn = {2155-384X},
support = {R01 DK097112/DK/NIDDK NIH HHS/United States ; },
abstract = {INTRODUCTION: Proton pump inhibitor (PPI) use has been associated with an increased risk of gastrointestinal and upper respiratory infections in children. There are limited longitudinal data on the effect of PPI in children. The goal of this prospective observational study was to compare the stool and oropharyngeal microbiome of children before and after starting PPIs.

METHODS: We prospectively recruited participants from a gastroenterology clinic. Consented pariticpants provided stool samples and oropharyngeal swabs at baseline and after eight weeks of PPI therapy. Microbiome changes were measured by analyzing 16S sequencing from both body sites at both timepoints.

RESULTS: Thirty-four participants completed the study and provided samples both at baseline and after eight weeks on PPI therapy. Of those, 24 participants had sufficient sequencing from both stool and oropharyngeal samples at both time points. There were no differences between the pre- vs post-PPI samples using beta-diversity metrics in either the oropharynx or stool. There were, however, significant changes in specific taxa. There was an enrichment of Streptococcus in the stool in after PPI-use and a reduction in the relative abundance of Bifidobacterium, Peptostreptococcus and Turicibacter (p-values < 0.01). Furthermore, there was an increase in the relative abundance of oropharyngeal bacteria in the stool after PPI therapy. This enrichment of oropharyngeal bacteria in the stool was most prominent in younger participants.

DISCUSSION: Further investigation is needed to determine the clinical and microbial factors that predispose or protect against microbiome changes due to PPI-use, and why young children are more susceptible to this PPI effect.},
}

@article {pmid38623900,
year = {2024},
author = {Zhang, Y and Lo, KL and Liman, AN and Feng, XP and Ye, W},
title = {Tongue-Coating Microbial and Metabolic Characteristics in Halitosis.},
journal = {Journal of dental research},
volume = {},
number = {},
pages = {220345241230067},
doi = {10.1177/00220345241230067},
pmid = {38623900},
issn = {1544-0591},
abstract = {Halitosis is a common oral condition, which leads to social embarrassment and affects quality of life. Cumulative evidence has suggested the association of tongue-coating microbiome with the development of intraoral halitosis. The dynamic variations of tongue-coating microbiota and metabolites in halitosis have not been fully elucidated. Therefore, the present study aimed to determine the tongue-coating microbial and metabolic characteristics in halitosis subjects without other oral diseases using metagenomics and metabolomics analysis. The participants underwent oral examination, halitosis assessment, and tongue-coating sample collection for the microbiome and metabolome analysis. It was found that the microbiota richness and diversity were significantly elevated in the halitosis group. Furthermore, species from Actinomyces, Prevotella, Veillonella, and Solobacterium were significantly more abundant in the halitosis group. However, the Rothia and Streptococcus species exhibited opposite tendencies. Eleven Kyoto Encyclopedia of Genes and Genomes pathways were significantly enriched in the halitosis tongue coatings, including cysteine and methionine metabolism. Functional genes related to sulfur, indole, skatole, and cadaverine metabolic processes (such as serA, metH, metK and dsrAB) were identified to be more abundant in the halitosis samples. The metabolome analysis revealed that indole-3-acetic, ornithine, and L-tryptophan were significantly elevated in the halitosis samples. Furthermore, it was observed that the values of volatile sulfur compounds and indole-3-acetic abundances were positively correlated. The multiomics analysis identified the metagenomic and metabolomic characteristics to differentiate halitosis from healthy individuals using the least absolute shrinkage and selection operator logistic regression and random forest classifier. A total of 19 species and 39 metabolites were identified as features in halitosis patients, which included indole-3-acetic acid, Bacillus altitudinis, Candidatus Saccharibacteria, and Actinomyces species. In conclusion, an evident shift in microbiome and metabolome characteristics was observed in the halitosis tongue coating, which may have a potential etiological significance and provide novel insights into the mechanism for halitosis.},
}

@article {pmid38623757,
year = {2024},
author = {Wang, W and Liu, Y and Yao, Z and Chen, D and Tang, Y and Cui, J and Zhang, J and Liu, H and Hao, Z},
title = {A microfluidic-based gut-on-a-chip model containing the gut microbiota of patients with depression reveals physiological characteristics similar to depression.},
journal = {Lab on a chip},
volume = {},
number = {},
pages = {},
doi = {10.1039/d3lc01052j},
pmid = {38623757},
issn = {1473-0189},
abstract = {The diverse commensal microbiome of the human intestine has been considered to play a central role in depression. However, no host-microbiota co-culture system has been developed for depression, which hinders the controlled study of the interaction between depression and gut microbiota. We designed and manufactured a microfluidic-based gut-on-a-chip model containing the gut microbiota of patients with depression (depression-on-gut-chip, DoGC), which enables the extended co-culture of viable aerobic human intestinal epithelial cells and anaerobic gut microbiota, and allows the direct study of interactions between human gut microbiota and depression. We introduced representative gut microbiota from individuals with depression into our constructed DoGC model, successfully recapitulating the gut microbiota structure of depressed patients. This further led to the manifestation of physiological characteristics resembling depression, such as reduced gut barrier function, chronic low-grade inflammatory responses and decreased neurotransmitter 5-HT levels. Metabolome analysis of substances in the DoGC revealed a significant increase in lipopolysaccharides and tyrosine, while hyodeoxycholic acid, L-proline and L-threonine were significantly reduced, indicating the occurrence of depression. The proposed DoGC can serve as an effective platform for studying the gut microbiota of patients with depression, providing important cues for their roles in the pathology of this condition and acting as a powerful tool for personalized medicine.},
}

@article {pmid38623754,
year = {2024},
author = {Eckhoff, AM and Fletcher, AA and Kelly, MS and Dohlman, A and McIntyre, CA and Shen, X and Iyer, MK and Nussbaum, DP and Allen, PJ},
title = {Comprehensive Assessment of the Intrinsic Pancreatic Microbiome.},
journal = {Annals of surgery},
volume = {},
number = {},
pages = {},
doi = {10.1097/SLA.0000000000006299},
pmid = {38623754},
issn = {1528-1140},
abstract = {OBJECTIVE: We sought to comprehensively profile tissue and cyst fluid in patients with benign, precancerous, and cancerous conditions of the pancreas to characterize the intrinsic pancreatic microbiome.

SUMMARY BACKGROUND DATA: Small studies in pancreatic ductal adenocarcinoma (PDAC) and intraductal papillary mucinous neoplasm (IPMN) have suggested that intra-pancreatic microbial dysbiosis may drive malignant transformation.

METHODS: Pancreatic samples were collected at the time of resection from 109 patients. Samples included tumor tissue (control, n=20; IPMN, n=20; PDAC, n=19) and pancreatic cyst fluid (IPMN, n=30; SCA, n=10; MCN, n=10). Assessment of bacterial DNA by quantitative PCR and 16S ribosomal RNA gene sequencing was performed. Downstream analyses determined the relative abundances of individual taxa between groups and compared intergroup diversity. Whole-genome sequencing data from 140 patients with PDAC in the National Cancer Institute's Clinical Proteomic Tumor Analysis Consortium (CPTAC) were analyzed to validate findings.

RESULTS: Sequencing of pancreatic tissue yielded few microbial reads regardless of diagnosis, and analysis of pancreatic tissue showed no difference in the abundance and composition of bacterial taxa between normal pancreas, IPMN, or PDAC groups. Low-grade dysplasia (LGD) and high-grade dysplasia (HGD) IPMN were characterized by low bacterial abundances with no difference in tissue composition and a slight increase in Pseudomonas and Sediminibacterium in HGD cyst fluid. Decontamination analysis using the CPTAC database confirmed a low-biomass, low-diversity intrinsic pancreatic microbiome that did not differ by pathology.

CONCLUSIONS: Our analysis of the pancreatic microbiome demonstrated very low intrinsic biomass that is relatively conserved across diverse neoplastic conditions and thus unlikely to drive malignant transformation.},
}

@article {pmid38623584,
year = {2024},
author = {Qu, B and Zhang, XE and Feng, H and Yan, B and Bai, Y and Liu, S and He, Y},
title = {Microbial perspective on the skin-gut axis and atopic dermatitis.},
journal = {Open life sciences},
volume = {19},
number = {1},
pages = {20220782},
doi = {10.1515/biol-2022-0782},
pmid = {38623584},
issn = {2391-5412},
abstract = {Atopic dermatitis (AD) is a relapsing inflammatory skin condition that has become a global health issue with complex etiology and mounting prevalence. The association of AD with skin and gut microbiota has been revealed by virtue of the continuous development of sequencing technology and genomics analysis. Also, the gut-brain-skin axis and its mutual crosstalk mechanisms have been gradually verified. Accordingly, the microbiota-skin-gut axis also plays an important role in allergic skin inflammation. Herein, we reviewed the relationship between the microbiota-skin-gut axis and AD, explored the underlying signaling molecules and potential pathways, and focused on the potential mechanisms of probiotics, antimicrobial peptides (AMPs), coagulase-negative staphylococci transplantation, fecal microbiota transplantation, AMPs, and addition of essential fatty acids in alleviating AD, with the aim to provide a new perspective for targeting microbiota in the treatment of allergic skin inflammation.},
}

@article {pmid38623505,
year = {2024},
author = {Subhash, AJ and Bamigbade, GB and Tarique, M and Al-Ramadi, B and Abu-Jdayil, B and Kamal-Eldin, A and Nyström, L and Ayyash, M},
title = {Bioactive properties and gut microbiota modulation by date seed polysaccharides extracted using ultrasound-assisted deep eutectic solvent.},
journal = {Food chemistry: X},
volume = {22},
number = {},
pages = {101354},
pmid = {38623505},
issn = {2590-1575},
abstract = {Polysaccharides are abundant macromolecules. The study extracted date seed polysaccharides (UPS) using ultrasound-assisted deep eutectic solvent extraction to valorize date seeds. UPS were subjected to comprehensive characterization and evaluation of their bioactivity, prebiotic properties, and their potential to modulate the gut microbiome. Characterization revealed UPS's heteropolysaccharide composition with galactose, mannose, fructose, glucose, and galacturonic acid respectively in 66.1, 13.3, 9.9, 5.4, and 5.1%. UPS showed a concentration-dependent increase of radical scavenging and antioxidant activities, evidenced by FRAP, TAC, and RP assays. They also displayed antimicrobial efficacy against E. coli O157:H7, S. typhimurium, S. aureus, and L. monocytogenes. Rheological analysis showed UPS's elastic-dominant nature with thixotropic tendencies. UPS inhibited α-glycosidase, α-amylase, and ACE up to 86%, and reduced Caco-2 and MCF-7 cell viability by 70% and 46%, respectively. UPS favored beneficial gut microbiota growth, releasing significant SCFAs during fecal fermentation.},
}

@article {pmid38623309,
year = {2024},
author = {Kwon, Y and Cho, KH and Ma, S and Ko, H and Hong, GH and Lee, SY and Park, KY and Chung, JA and Jeong, SJ},
title = {Supplementation of Heat-Treated Lactiplantibacillus plantarum nF1 Changes the Production of Short-Chain Fatty Acids in Healthy Infants.},
journal = {Journal of nutrition and metabolism},
volume = {2024},
number = {},
pages = {5558566},
pmid = {38623309},
issn = {2090-0724},
abstract = {BACKGROUND: Imbalance of the gut microbiome and decrease in the number of short-chain fatty acid (SCFA)-producing bacteria often affect human health by altering intestinal and immune homeostasis. The use of probiotics has been shown to be an attractive method to modulate gut microbiota to prevent or treat intestinal dysbiosis. Likewise, this study aimed to determine whether the oral consumption of heat-treated Lactiplantibacillus plantarum nF1 (HLp-nF1) induces changes in the gut environment in healthy infants by measuring changes in fecal SCFAs.

METHODS: The study enrolled 43 infants aged under 2 months, with 30 infants in the HLp-nF1 group receiving HLp-nF1 orally (2.5 × 10[10] cells/g/pack, daily dose of two packs) for 8 weeks. The fecal samples were collected and the questionnaires were administered at weeks 0 and 8.

RESULTS: The concentrations of the total SCFAs, acetate, propionate, and butyrate significantly increased following HLp-nF1 supplementation (P < 0.0001, P < 0.0001, P < 0.0001, and P=0.028, respectively).

CONCLUSIONS: Supplementation of HLp-nF1 has a positive effect on SCFA production and could be a potentially useful and straightforward method to manipulate SCFA formation.},
}

@article {pmid38622950,
year = {2024},
author = {Zhang, E and Wong, SY and Czechowski, P and Terauds, A and Ray, AE and Benaud, N and Chelliah, DS and Wilkins, D and Montgomery, K and Ferrari, BC},
title = {Effects of increasing soil moisture on Antarctic desert microbial ecosystems.},
journal = {Conservation biology : the journal of the Society for Conservation Biology},
volume = {},
number = {},
pages = {e14268},
doi = {10.1111/cobi.14268},
pmid = {38622950},
issn = {1523-1739},
support = {AAS-4296//Australian Antarctic Division/ ; AAS-4406//Australian Antarctic Division/ ; HSF20/114//Herman Slade Foundation/ ; DP220103430//Australian Research Council/ ; FT170100341//Australian Research Council/ ; },
abstract = {Overgeneralization and a lack of baseline data for microorganisms in high-latitude environments have restricted the understanding of the microbial response to climate change, which is needed to establish Antarctic conservation frameworks. To bridge this gap, we examined over 17,000 sequence variants of bacteria and microeukarya across the hyperarid Vestfold Hills and Windmill Islands regions of eastern Antarctica. Using an extended gradient forest model, we quantified multispecies response to variations along 79 edaphic gradients to explore the effects of change and wind-driven dispersal on community dynamics under projected warming trends. We also analyzed a second set of soil community data from the Windmill Islands to test our predictions of major environmental tipping points. Soil moisture was the most robust predictor for shaping the regional soil microbiome; the highest rates of compositional turnover occurred at 10-12% soil moisture threshold for photoautotrophs, such as Cyanobacteria, Chlorophyta, and Ochrophyta. Dust profiles revealed a high dispersal propensity for Chlamydomonas, a microalga, and higher biomass was detected at trafficked research stations. This could signal the potential for algal blooms and increased nonendemic species dispersal as human activities increase in the region. Predicted increases in moisture availability on the Windmill Islands were accompanied by high photoautotroph abundances. Abundances of rare oligotrophic taxa, such as Eremiobacterota and Candidatus Dormibacterota, which play a crucial role in atmospheric chemosynthesis, declined over time. That photosynthetic taxa increased as soil moisture increased under a warming scenario suggests the potential for competition between primary production strategies and thus a more biotically driven ecosystem should the climate become milder. Better understanding of environmental triggers will aid conservation efforts, and it is crucial that long-term monitoring of our study sites be established for the protection of Antarctic desert ecosystems. Furthermore, the successful implementation of an improved gradient forest model presents an exciting opportunity to broaden its use on microbial systems globally.},
}

@article {pmid38622728,
year = {2024},
author = {Zhang, S and Li, B and Zeng, L and Yang, K and Jiang, J and Lu, F and Li, L and Li, W},
title = {Exploring the immune-inflammatory mechanism of Maxing Shigan Decoction in treating influenza virus A-induced pneumonia based on an integrated strategy of single-cell transcriptomics and systems biology.},
journal = {European journal of medical research},
volume = {29},
number = {1},
pages = {234},
pmid = {38622728},
issn = {2047-783X},
support = {81774126//National Natural Science Foundation of China/ ; 81973670//National Natural Science Foundation of China/ ; CX2015B325//the postgraduate scientific research innovation project of Hunan Province of China/ ; 2016JJ2095//Natural Science Foundation of Hunan Province of China/ ; 2017JJ3232//Natural Science Foundation of Hunan Province of China/ ; },
mesh = {Mice ; Animals ; Humans ; *Drugs, Chinese Herbal/pharmacology/therapeutic use ; *Alphainfluenzavirus ; *Influenza, Human/drug therapy/genetics ; *Pneumonia/drug therapy/genetics ; Inflammation ; *Orthomyxoviridae ; *Influenza A virus ; Systems Biology ; Gene Expression Profiling ; },
abstract = {BACKGROUND: Influenza is an acute respiratory infection caused by influenza virus. Maxing Shigan Decoction (MXSGD) is a commonly used traditional Chinese medicine prescription for the prevention and treatment of influenza. However, its mechanism remains unclear.

METHOD: The mice model of influenza A virus pneumonia was established by nasal inoculation. After 3 days of intervention, the lung index was calculated, and the pathological changes of lung tissue were detected by HE staining. Firstly, transcriptomics technology was used to analyze the differential genes and important pathways in mouse lung tissue regulated by MXSGD. Then, real-time fluorescent quantitative PCR (RT-PCR) was used to verify the changes in mRNA expression in lung tissues. Finally, intestinal microbiome and intestinal metabolomics were performed to explore the effect of MXSGD on gut microbiota.

RESULTS: The lung inflammatory cell infiltration in the MXSGD group was significantly reduced (p < 0.05). The results of bioinformatics analysis for transcriptomics results show that these genes are mainly involved in inflammatory factors and inflammation-related signal pathways mediated inflammation biological modules, etc. Intestinal microbiome showed that the intestinal flora Actinobacteriota level and Desulfobacterota level increased in MXSGD group, while Planctomycetota in MXSGD group decreased. Metabolites were mainly involved in primary bile acid biosynthesis, thiamine metabolism, etc. This suggests that MXSGD has a microbial-gut-lung axis regulation effect on mice with influenza A virus pneumonia.

CONCLUSION: MXSGD may play an anti-inflammatory and immunoregulatory role by regulating intestinal microbiome and intestinal metabolic small molecules, and ultimately play a role in the treatment of influenza A virus pneumonia.},
}

Mice
Animals
Humans
*Drugs, Chinese Herbal/pharmacology/therapeutic use
*Alphainfluenzavirus
*Influenza, Human/drug therapy/genetics
*Pneumonia/drug therapy/genetics
Inflammation
*Orthomyxoviridae
*Influenza A virus
Systems Biology
Gene Expression Profiling

@article {pmid38622632,
year = {2024},
author = {Whitfield-Cargile, CM and Chung, HC and Coleman, MC and Cohen, ND and Chamoun-Emanuelli, AM and Ivanov, I and Goldsby, JS and Davidson, LA and Gaynanova, I and Ni, Y and Chapkin, RS},
title = {Integrated analysis of gut metabolome, microbiome, and exfoliome data in an equine model of intestinal injury.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {74},
pmid = {38622632},
issn = {2049-2618},
support = {P30-ES029067/NH/NIH HHS/United States ; R35-CA197707/NH/NIH HHS/United States ; },
mesh = {Animals ; Horses/genetics ; *Microbiota ; Intestinal Mucosa/metabolism ; Metabolome ; Feces/microbiology ; Anti-Inflammatory Agents, Non-Steroidal/metabolism ; Inflammation/metabolism ; Phenylbutazone/metabolism ; RNA, Ribosomal, 16S/genetics/metabolism ; },
abstract = {BACKGROUND: The equine gastrointestinal (GI) microbiome has been described in the context of various diseases. The observed changes, however, have not been linked to host function and therefore it remains unclear how specific changes in the microbiome alter cellular and molecular pathways within the GI tract. Further, non-invasive techniques to examine the host gene expression profile of the GI mucosa have been described in horses but not evaluated in response to interventions. Therefore, the objectives of our study were to (1) profile gene expression and metabolomic changes in an equine model of non-steroidal anti-inflammatory drug (NSAID)-induced intestinal inflammation and (2) apply computational data integration methods to examine host-microbiota interactions.

METHODS: Twenty horses were randomly assigned to 1 of 2 groups (n = 10): control (placebo paste) or NSAID (phenylbutazone 4.4 mg/kg orally once daily for 9 days). Fecal samples were collected on days 0 and 10 and analyzed with respect to microbiota (16S rDNA gene sequencing), metabolomic (untargeted metabolites), and host exfoliated cell transcriptomic (exfoliome) changes. Data were analyzed and integrated using a variety of computational techniques, and underlying regulatory mechanisms were inferred from features that were commonly identified by all computational approaches.

RESULTS: Phenylbutazone induced alterations in the microbiota, metabolome, and host transcriptome. Data integration identified correlation of specific bacterial genera with expression of several genes and metabolites that were linked to oxidative stress. Concomitant microbiota and metabolite changes resulted in the initiation of endoplasmic reticulum stress and unfolded protein response within the intestinal mucosa.

CONCLUSIONS: Results of integrative analysis identified an important role for oxidative stress, and subsequent cell signaling responses, in a large animal model of GI inflammation. The computational approaches for combining non-invasive platforms for unbiased assessment of host GI responses (e.g., exfoliomics) with metabolomic and microbiota changes have broad application for the field of gastroenterology. Video Abstract.},
}

Animals
Horses/genetics
*Microbiota
Intestinal Mucosa/metabolism
Metabolome
Feces/microbiology
Anti-Inflammatory Agents, Non-Steroidal/metabolism
Inflammation/metabolism
Phenylbutazone/metabolism
RNA, Ribosomal, 16S/genetics/metabolism

@article {pmid38622589,
year = {2024},
author = {Gao, J and Yang, Y and Xiang, X and Zheng, H and Yi, X and Wang, F and Liang, Z and Chen, D and Shi, W and Wang, L and Wu, D and Feng, S and Huang, Q and Li, X and Shu, W and Chen, R and Zhong, N and Wang, Z},
title = {Human genetic associations of the airway microbiome in chronic obstructive pulmonary disease.},
journal = {Respiratory research},
volume = {25},
number = {1},
pages = {165},
pmid = {38622589},
issn = {1465-993X},
mesh = {Humans ; *Pulmonary Disease, Chronic Obstructive/diagnosis/genetics/complications ; *Microbiota/genetics ; Sputum ; Transcriptome ; Human Genetics ; Adaptor Proteins, Signal Transducing/genetics ; },
abstract = {Little is known about the relationships between human genetics and the airway microbiome. Deeply sequenced airway metagenomics, by simultaneously characterizing the microbiome and host genetics, provide a unique opportunity to assess the microbiome-host genetic associations. Here we performed a co-profiling of microbiome and host genetics with the identification of over 5 million single nucleotide polymorphisms (SNPs) through deep metagenomic sequencing in sputum of 99 chronic obstructive pulmonary disease (COPD) and 36 healthy individuals. Host genetic variation was the most significant factor associated with the microbiome except for geography and disease status, with its top 5 principal components accounting for 12.11% of the microbiome variability. Within COPD individuals, 113 SNPs mapped to candidate genes reported as genetically associated with COPD exhibited associations with 29 microbial species and 48 functional modules (P < 1 × 10[-5]), where Streptococcus salivarius exhibits the strongest association to SNP rs6917641 in TBC1D32 (P = 9.54 × 10[-8]). Integration of concurrent host transcriptomic data identified correlations between the expression of host genes and their genetically-linked microbiome features, including NUDT1, MAD1L1 and Veillonella parvula, TTLL9 and Stenotrophomonas maltophilia, and LTA4H and Haemophilus influenzae. Mendelian randomization analyses revealed a potential causal link between PARK7 expression and microbial type III secretion system, and a genetically-mediated association between COPD and increased relative abundance of airway Streptococcus intermedius. These results suggest a previously underappreciated role of host genetics in shaping the airway microbiome and provide fresh hypotheses for genetic-based host-microbiome interactions in COPD.},
}

Humans
*Pulmonary Disease, Chronic Obstructive/diagnosis/genetics/complications
*Microbiota/genetics
Sputum
Transcriptome
Human Genetics
Adaptor Proteins, Signal Transducing/genetics

@article {pmid38622529,
year = {2024},
author = {Hou, B and Zhang, H and Zhou, L and Hu, B and Tang, W and Ye, B and Wang, C and Xu, Y and Zou, L and Hu, J},
title = {In silico analysis of intestinal microbial instability and symptomatic markers in mice during the acute phase of severe burns.},
journal = {BMC microbiology},
volume = {24},
number = {1},
pages = {124},
pmid = {38622529},
issn = {1471-2180},
support = {CSTB2023NSCQ-MSX0759//Chongqing Natural Science Foundation/ ; KJZD-K202300101//Scientific and Technological Research Program of Chongqing Municipal Education Commission/ ; 2024ZDXM011//Chongqing Medical Scientific Research Project/ ; },
mesh = {Humans ; Animals ; Mice ; Bacteria/genetics ; *Microbiota ; *Gastrointestinal Microbiome ; Firmicutes/genetics ; RNA, Ribosomal, 16S/genetics ; *Burns ; },
abstract = {BACKGROUND: Severe burns may alter the stability of the intestinal flora and affect the patient's recovery process. Understanding the characteristics of the gut microbiota in the acute phase of burns and their association with phenotype can help to accurately assess the progression of the disease and identify potential microbiota markers.

METHODS: We established mouse models of partial thickness deep III degree burns and collected faecal samples for 16 S rRNA amplification and high throughput sequencing at two time points in the acute phase for independent bioinformatic analysis.

RESULTS: We analysed the sequencing results using alpha diversity, beta diversity and machine learning methods. At both time points, 4 and 6 h after burning, the Firmicutes phylum content decreased and the content of the Bacteroidetes phylum content increased, showing a significant decrease in the Firmicutes/Bacteroidetes ratio compared to the control group. Nine bacterial genera changed significantly during the acute phase and occupied the top six positions in the Random Forest significance ranking. Clustering results also clearly showed that there was a clear boundary between the communities of burned and control mice. Functional analyses showed that during the acute phase of burn, gut bacteria increased lipoic acid metabolism, seleno-compound metabolism, TCA cycling, and carbon fixation, while decreasing galactose metabolism and triglyceride metabolism. Based on the abundance characteristics of the six significantly different bacterial genera, both the XGboost and Random Forest models were able to discriminate between the burn and control groups with 100% accuracy, while both the Random Forest and Support Vector Machine models were able to classify samples from the 4-hour and 6-hour burn groups with 86.7% accuracy.

CONCLUSIONS: Our study shows an increase in gut microbiota diversity in the acute phase of deep burn injury, rather than a decrease as is commonly believed. Severe burns result in a severe imbalance of the gut flora, with a decrease in probiotics and an increase in microorganisms that trigger inflammation and cognitive deficits, and multiple pathways of metabolism and substance synthesis are affected. Simple machine learning model testing suggests several bacterial genera as potential biomarkers of severe burn phenotypes.},
}

Humans
Animals
Mice
Bacteria/genetics
*Microbiota
*Gastrointestinal Microbiome
Firmicutes/genetics
RNA, Ribosomal, 16S/genetics
*Burns

@article {pmid38622344,
year = {2024},
author = {Sarrazin-Gendron, R and Ghasemloo Gheidari, P and Butyaev, A and Keding, T and Cai, E and Zheng, J and Mutalova, R and Mounthanyvong, J and Zhu, Y and Nazarova, E and Drogaris, C and Erhart, K and , and , and Brouillette, A and Richard, G and Pitchford, R and Caisse, S and Blanchette, M and McDonald, D and Knight, R and Szantner, A and Waldispühl, J},
title = {Improving microbial phylogeny with citizen science within a mass-market video game.},
journal = {Nature biotechnology},
volume = {},
number = {},
pages = {},
pmid = {38622344},
issn = {1546-1696},
abstract = {Citizen science video games are designed primarily for users already inclined to contribute to science, which severely limits their accessibility for an estimated community of 3 billion gamers worldwide. We created Borderlands Science (BLS), a citizen science activity that is seamlessly integrated within a popular commercial video game played by tens of millions of gamers. This integration is facilitated by a novel game-first design of citizen science games, in which the game design aspect has the highest priority, and a suitable task is then mapped to the game design. BLS crowdsources a multiple alignment task of 1 million 16S ribosomal RNA sequences obtained from human microbiome studies. Since its initial release on 7 April 2020, over 4 million players have solved more than 135 million science puzzles, a task unsolvable by a single individual. Leveraging these results, we show that our multiple sequence alignment simultaneously improves microbial phylogeny estimations and UniFrac effect sizes compared to state-of-the-art computational methods. This achievement demonstrates that hyper-gamified scientific tasks attract massive crowds of contributors and offers invaluable resources to the scientific community.},
}

@article {pmid38621967,
year = {2024},
author = {Wang, ZH and Liu, S and Yang, G and Lu, ZY and Zhu, RQ and Li, Y and Shen, Y and Kang, LP and Chen, ML},
title = {[Effects of organic fertilizer from traditional Chinese medicine residues on growth and soil microbial community of Salvia miltiorrhiza by metagenomic technique].},
journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica},
volume = {49},
number = {5},
pages = {1206-1216},
doi = {10.19540/j.cnki.cjcmm.20231213.101},
pmid = {38621967},
issn = {1001-5302},
mesh = {Soil/chemistry ; *Salvia miltiorrhiza/chemistry ; Fertilizers ; Medicine, Chinese Traditional ; Bacteria/genetics ; *Mycobiome ; Soil Microbiology ; },
abstract = {Soil microbiome is a key evaluation index of soil health. Previous studies have shown that organic fertilizer from traditional Chinese medicine(TCM)residues can improve the yield and quality of cultivated traditional Chinese medicinal materials. However, there are few reports on the effects of organic fertilizer from TCM residues on soil microbiome. Therefore, on the basis of evaluating the effects of organic fertilizer from TCM residues on the yield and quality of cultivated Salvia miltiorrhiza, the metagenomic sequencing technique was used to study the effects of organic fertilizer from TCM residues on rhizosphere microbiome community and function of cultivated S. miltiorrhiza. The results showed that:(1) the application of organic fertilizer from TCM residues promoted the growth of S. miltiorrhiza and the accumulation of active components, and the above-ground and underground dry weight and fresh weight of S. miltiorrhiza increased by 371.4%, 288.3%, 313.4%, and 151.9%. The increases of rosmarinic acid and salvianolic acid B were 887.0% and 183.0%.(2)The application of organic fertilizer from TCM residues significantly changed the rhizosphere bacterial and fungal community structures, and the microbial community composition was significantly different.(3)The relative abundance of soil-beneficial bacteria, such as Nitrosospira multiformis, Bacillus subtilis, Lysobacter enzymogenes, and Trichoderma was significantly increased by the application of organic fertilizer from TCM residues.(4)KEGG function prediction analysis showed that metabolism-related microorganisms were more easily enriched in the soil environment after organic fertilizer application. The abundance of functional genes related to nitrification and denitrification could also be increased after the application of organic fertilizer from TCM residues. The results of this study provide guidance for the future application of organic fertilizer from TCM residues in the cultivation of traditio-nal Chinese medicinal materials and enrich the content of green cultivation technology of traditional Chinese medicinal materials.},
}

Soil/chemistry
*Salvia miltiorrhiza/chemistry
Fertilizers
Medicine, Chinese Traditional
Bacteria/genetics
*Mycobiome
Soil Microbiology

@article {pmid38621924,
year = {2024},
author = {Liu, J and MacNaughtan, J and Kerbert, AJC and Portlock, T and Martínez Gonzalez, J and Jin, Y and Clasen, F and Habtesion, A and Ji, H and Jin, Q and Phillips, A and De Chiara, F and Ingavle, G and Jimenez, C and Zaccherini, G and Husi, K and Rodriguez Gandia, MA and Cordero, P and Soeda, J and McConaghy, L and Oben, J and Church, K and Li, JV and Wu, H and Jalan, A and Gines, P and Solà, E and Eaton, S and Morgan, C and Kowalski, M and Green, D and Gander, A and Edwards, LA and Cox, IJ and Cortez-Pinto, H and Avery, T and Wiest, R and Durand, F and Caraceni, P and Elosua, R and Vila, J and Pavesi, M and Arroyo, V and Davies, N and Mookerjee, RP and Vargas, V and Sandeman, S and Mehta, G and Shoaie, S and Marchesi, J and Albillos, A and Andreola, F and Jalan, R},
title = {Clinical, experimental and pathophysiological effects of Yaq-001: a non-absorbab le, gut-restricted adsorbent in models and patients with cirrhosis.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2023-330699},
pmid = {38621924},
issn = {1468-3288},
abstract = {OBJECTIVE: Targeting bacterial translocation in cirrhosis is limited to antibiotics with risk of antimicrobial resistance. This study explored the therapeutic potential of a non-absorbable, gut-restricted, engineered carbon bead adsorbent, Yaq-001 in models of cirrhosis and acute-on-chronic liver failure (ACLF) and, its safety and tolerability in a clinical trial in cirrhosis.

DESIGN: Performance of Yaq-001 was evaluated in vitro. Two-rat models of cirrhosis and ACLF, (4 weeks, bile duct ligation with or without lipopolysaccharide), receiving Yaq-001 for 2 weeks; and two-mouse models of cirrhosis (6-week and 12-week carbon tetrachloride (CCl4)) receiving Yaq-001 for 6 weeks were studied. Organ and immune function, gut permeability, transcriptomics, microbiome composition and metabolomics were analysed. The effect of faecal water on gut permeability from animal models was evaluated on intestinal organoids. A multicentre, double-blind, randomised, placebo-controlled clinical trial in 28 patients with cirrhosis, administered 4 gr/day Yaq-001 for 3 months was performed.

RESULTS: Yaq-001 exhibited rapid adsorption kinetics for endotoxin. In vivo, Yaq-001 reduced liver injury, progression of fibrosis, portal hypertension, renal dysfunction and mortality of ACLF animals significantly. Significant impact on severity of endotoxaemia, hyperammonaemia, liver cell death, systemic inflammation and organ transcriptomics with variable modulation of inflammation, cell death and senescence in the liver, kidneys, brain and colon was observed. Yaq-001 reduced gut permeability in the organoids and impacted positively on the microbiome composition and metabolism. Yaq-001 regulated as a device met its primary endpoint of safety and tolerability in the clinical trial.

CONCLUSIONS: This study provides strong preclinical rationale and safety in patients with cirrhosis to allow clinical translation.

TRIAL REGISTRATION NUMBER: NCT03202498.},
}

@article {pmid38621534,
year = {2024},
author = {Soromotin, AV and Lanza, GR and Sizov, OS and Lobotrosova, SA and Abakumov, EV and Zverev, AO and Yakimov, AS and Konstantinov, AO and Kurasova, AO and Prihod'ko, NV and Salavatulin, VM and Varentsov, MI and Alharbi, SA and Alotaibi, KD and Kuzyakov, Y},
title = {Cyclic and linear trajectories of ecosystem evolution in Siberian taiga sand dunes: A comprehensive analysis.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {172265},
doi = {10.1016/j.scitotenv.2024.172265},
pmid = {38621534},
issn = {1879-1026},
abstract = {Extensive unforested sandy areas on the margins of floodplains and riverbeds, formed by dunes, barchans, and accumulation berms, are a ubiquitous feature across northern Eurasia and Alaska. These dynamic landscapes, which bear witness to the complex Holocene and modern climatic fluctuations, provide a unique opportunity to study ecosystem evolution. Within this heterogeneous assemblage, active dunes, characterized by their sparse plant communities, contrast sharply with the surrounding taiga (boreal) forests, which characterize stabilized dunes. This juxtaposition makes these regions into natural laboratories for studying vegetation succession and soil evolution. Through a comprehensive analysis of climate, geomorphology, vegetation, soil properties, and microbiome composition, we elucidate the intricacies of cyclic and linear ecosystem evolution within a representative sandy area located along the lower Nadym River in Siberia, approximately 100 km south of the Arctic Circle. The shift in the Holocene wind regime and the slow development of vegetation under harsh climatic conditions promoted cyclical ecosystem dynamics that precluded the attainment of a steady state. This cyclical trajectory is exemplified by Arenosols, characterized by extremely sparse vegetation and undifferentiated horizons. Conversely, accelerated vegetation growth within wind-protected enclaves on marginally stabilized soils facilitated sand stabilization and subsequent pedogenesis towards Podzols. Based on soil acidification due to litter input (mainly needles, lichens, and mosses) and the succession of microbial communities, we investigated constraints on carbon and nutrient availability during the initial stages of pedogenesis. In summary, the comprehensive study of initial ecosystem development on sand dunes within taiga forests has facilitated the elucidation of both common phases and spatiotemporal dynamics of vegetation and soil succession. This analysis has further clarified the existence of both cyclic and linear trajectories within the successional process.},
}

@article {pmid38621454,
year = {2024},
author = {Kończak, B and Wiesner-Sękala, M and Ziembińska-Buczyńska, A},
title = {THE EUROPEAN TREES PHYLLOSPHERE CHARACTERISTICS AND ITS POTENTIAL IN AIR BIOREMEDIATION.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {123977},
doi = {10.1016/j.envpol.2024.123977},
pmid = {38621454},
issn = {1873-6424},
abstract = {The air pollution remediation is naturally carried out by plants. Their overground parts called phyllosphere are a type of a natural filter on which pollutants can be adsorb. Moreover, microbial communities living in phyllosphere perform a variety of biochemical processes removing also chemical pollutants. As their pollution is nowadays a burning issue especially for highly developed countries, the development of effective and ecological technologies for air treatment are of the utmost importance. The use of phyllosphere bacteria in the process of air bioremediation is a promising technology. This article reviews the role of phyllospheric bacteria in air bioremediation processes especially linked with the moderate climate plants. Research results published so far indicate that phyllosphere bacteria are able to metabolize the air pollutants but their potential is strictly determined by plant-phyllospheric bacteria interaction. The European tree species most commonly used for this purpose are also presented. The collected information filled the gap in the practical use of tree species in air bioremediation in the moderate climate zone.},
}

@article {pmid38621362,
year = {2024},
author = {Vital, ST and Clausen, U and Füssel, J and Neumann-Schaal, M and Lambertus, P and Gehler, M and Scheve, S and Wöhlbrand, L and Dittmar, T and Rabus, R},
title = {Global growth phase response of the gut bacterium Phocaeicola vulgatus (phylum Bacteroidota).},
journal = {Microbial physiology},
volume = {},
number = {},
pages = {},
doi = {10.1159/000538914},
pmid = {38621362},
issn = {2673-1673},
abstract = {Phocaeicola vulgatus belongs to the intestinal microbiome, where it fermentatively breaks down of food-derived biopolymers , thereby, contributing to the gut metabolome. Moreover, due to its product range, P. vulgatus is a potential nonstandard platform organism for sustainable production of basic organic chemicals. Complementing a recent physiologic-proteomic report deciphering the strain's versatile fermentation network [1], the present study focuses on the global growth phase-dependent response. P. vulgatus was anaerobically cultivated with glucose in process-controlled bioreactors. Close sampling was conducted to measure growth parameters (OD, CDW, ATP content, substrate/product profiles) to determine growth stoichiometry. A coarser sampling (½ODmax, ODmax, and ODstat) served the molecular analysis of the global growth phase-dependent response, applying proteomics (soluble and membrane fractions, nanoLC-ESI-MS/MS) and targeted/untargeted metabolome analyses. The determined growth performance of features 1.74 h doubling time, 0.06 gCDW/mmolGlc biomass yield, 0.36 (succinate) and 0.61 (acetate) mmolP/mmolGlc as predominant fermentation product yields, and 0.43 mmolATP/mmolC as theoretically calculated ATP yield. The fermentation pathway displayed growth phase-dependent dynamics: the levels of proteins and their accompanying metabolites constituting the upper part of glycolysis peaked at ½ODmax, whereas those of the lower part of glycolysis and of the fermentation routes in particular towards predominant acetate and succinate were highest at ODmax and ODstat. While identified proteins of monomer biosynthesis displayed rather unspecific profiles, most of the intracellular amino acids peaked at ODmax. By contrast, proteins and metabolites related to stress response and quorum sensing showed increased abundances at ODmax and ODstat. The composition of the exometabolome expanded from 2,317 molecular formulas at ½ODmax via 4,258 at ODmax to 4,501 at ODstat, with growth phase-specific subsets increasing in parallel. The present study provides insights into the distinct growth phase-dependent behavior of P. vulgatus during cultivation in bioreactors. This could serve as a valuable knowledge base for further developing P. vulgatus as a non-conventional platform organism for biotechnological applications. In addition, the findings shed new light on the potential growth phase-dependent imprints of P. vulgatus on the gut microbiome environment, e.g. by indicating interactions via quorum sensing and by unraveling the complex exometabolic background against which fermentation products and secondary metabolites are formed.},
}

@article {pmid38619794,
year = {2024},
author = {Van Holm, W and Zayed, N and Lauwens, K and Saghi, M and Axelsson, J and Aktan, MK and Braem, A and Simoens, K and Vanbrabant, L and Proost, P and Van Holm, B and Maes, P and Boon, N and Bernaerts, K and Teughels, W},
title = {Oral Biofilm Composition, Dissemination to Keratinocytes, and Inflammatory Attenuation Depend on Probiotic and Synbiotic Strain Specificity.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {38619794},
issn = {1867-1314},
support = {C24/17/086//KU Leuven/ ; C16/17/010//KU Leuven/ ; C16/17/010//KU Leuven/ ; C24/17/086//KU Leuven/ ; G091218N//Fonds Wetenschappelijk Onderzoek/ ; G091218N//Fonds Wetenschappelijk Onderzoek/ ; },
abstract = {Several inflammatory diseases are characterized by a disruption in the equilibrium between the host and its microbiome. Due to the increase in resistance, the use of antibiotics for the widespread, nonspecific killing of microorganisms is at risk. Pro-microbial approaches focused on stimulating or introducing beneficial species antagonistic toward pathobionts may be a viable alternative for restoring the host-microbiome equilibrium. Unfortunately, not all potential probiotic or synbiotic species and even subspecies (to strain level) are equally effective for the designated pathology, leading to conflicting accounts of their efficacy. To assess the extent of these species- and strain-specific effects, 13 probiotic candidates were evaluated for their probiotic and synbiotic potential with glycerol on in vitro oral biofilms, dissemination from biofilms to keratinocytes, and anti-inflammatory activity. Species- and strain-specific effects and efficacies were observed in how they functioned as probiotics or synbiotics by influencing oral pathobionts and commensals within biofilms and affected the dissemination of pathobionts to keratinocytes, ranging from ineffective strains to strains that reduced pathobionts by 3 + log. In addition, a minority of the candidates exhibited the ability to mitigate the inflammatory response of LPS-stimulated monocytes. For a comprehensive assessment of probiotic therapy for oral health, a judicious selection of fully characterized probiotic strains that are specifically tailored to the designated pathology is required. This approach aims to challenge the prevailing perception of probiotics, shifting the focus away from "form over function." Rather than using unproven, hypothetical probiotic strains from known genera or species, one should choose strains that are actually functional in resolving the desired pathology before labelling them probiotics.},
}

@article {pmid38619710,
year = {2024},
author = {Ai, X and Liu, Y and Shi, J and Xie, X and Li, L and Duan, R and Lv, Y and Xiong, K and Miao, Y and Zhang, Y},
title = {Structural characteristics of gut microbiota in longevity from Changshou town, Hubei, China.},
journal = {Applied microbiology and biotechnology},
volume = {108},
number = {1},
pages = {300},
pmid = {38619710},
issn = {1432-0614},
support = {WJ2023M173//Hubei Provincial Health Commission Project/ ; 2022BCE060//Hubei Province Key R&D Project/ ; 2022YFZD022//Jingmen Key Science and Technology Project/ ; 2022YFZD051//Jingmen Key Science and Technology Project/ ; },
mesh = {Middle Aged ; Humans ; Aged ; Female ; Male ; Adult ; Aged, 80 and over ; *Gastrointestinal Microbiome ; *Microbiota ; China ; Akkermansia ; Bacteroidetes ; Lactobacillus ; },
abstract = {The gut microbiota (GM) and its potential functions play a crucial role in maintaining host health and longevity. The aim of this study was to investigate the potential relationship between GM and longevity. We collected fecal samples from 92 healthy volunteers (middle-aged and elderly: 43-79 years old; longevity: ≥ 90 years old) from Changshou Town, Zhongxiang City, Hubei, China. In addition, we collected samples from 30 healthy middle-aged and elderly controls (aged 51-70 years) from Wuhan, Hubei. The 16S rDNA V3 + V4 region of the fecal samples was sequenced using high-throughput sequencing technology. Diversity analysis results showed that the elderly group with longevity and the elderly group with low body mass index (BMI) exhibited higher α diversity. However, no significant difference was observed in β diversity. The results of the microbiome composition indicate that Firmicutes, Proteobacteria, and Bacteroidota are the core phyla in all groups. Compared to younger elderly individuals, Akkermansia and Lactobacillus are significantly enriched in the long-lived elderly group, while Megamonas is significantly reduced. In addition, a high abundance of Akkermansia is a significant characteristic of elderly populations with low BMI values. Furthermore, the functional prediction results showed that the elderly longevity group had higher abilities in short-chain fatty acid metabolism, amino acid metabolism, and xenobiotic biodegradation. Taken together, our study provides characteristic information on GM in the long-lived elderly population in Changshou Town. This study can serve as a valuable addition to the current research on age-related GM. KEY POINTS: • The gut microbiota of elderly individuals with longevity and low BMI exhibit higher alpha diversity • Gut microbiota diversity did not differ significantly between genders in the elderly population • Several potentially beneficial bacteria (e.g., Akkermansia and Lactobacillus) are enriched in long-lived individuals.},
}

Middle Aged
Humans
Aged
Female
Male
Adult
Aged, 80 and over
*Gastrointestinal Microbiome
*Microbiota
China
Akkermansia
Bacteroidetes
Lactobacillus

@article {pmid38619680,
year = {2024},
author = {Al-Fakhrany, OM and Elekhnawy, E},
title = {Next-generation probiotics: the upcoming biotherapeutics.},
journal = {Molecular biology reports},
volume = {51},
number = {1},
pages = {505},
pmid = {38619680},
issn = {1573-4978},
mesh = {Humans ; *Gastrointestinal Microbiome ; Immunotherapy ; Oxygen ; *Probiotics/therapeutic use ; },
abstract = {Recent and continuing advances in gut microbiome research have pointed out the role of the gut microbiota as an unexplored source of potentially beneficial probiotic microbes. Along the lines of these advances, both public awareness and acceptance of probiotics are increasing. That's why; academic and industrial research is dedicated to identifying and investigating new microbial strains for the development of next-generation probiotics (NGPs). At this time, there is a growing interest in NGPs as biotherapeutics that alter the gut microbiome and affect various diseases development. In this work, we have focused on some emergent and promising NGPs, specifically Eubacterium hallii, Faecalibacterium prausnitzii, Roseburia spp., Akkermansia muciniphila, and Bacteroides fragilis, as their presence in the gut can have an impact on the development of various diseases. Emerging studies point out the beneficial roles of these NGPs and open up novel promising therapeutic options. Interestingly, these NGPs were found to enhance gastrointestinal immunity, enhance immunotherapy efficacy in cancer patients, retain the intestinal barrier integrity, generate valuable metabolites, especially short-chain fatty acids, and decrease complications of chemotherapy and radiotherapy. Although many of these NGPs are considered promising for the prevention and treatment of several chronic diseases, research on humans is still lacking. Therefore, approval of these microbes from regulatory agencies is rare. Besides, some issues limit their wide use in the market, such as suitable methods for the culture and storage of these oxygen-sensitive microbes. The present review goes over the main points related to NGPs and gives a viewpoint on the key issues that still hinder their wide application. Furthermore, we have focused on the advancement in NGPs and human healthiness investigations by clarifying the limitations of traditional probiotic microorganisms, discussing the characteristics of emerging NGPs and defining their role in the management of certain ailments. Future research should emphasize the isolation, mechanisms of action of these probiotics, safety, and clinical efficacy in humans.},
}

Humans
*Gastrointestinal Microbiome
Immunotherapy
Oxygen
*Probiotics/therapeutic use

@article {pmid38619307,
year = {2024},
author = {Toyoshima, H and Yamamoto, N and Komiya, S},
title = {Letter to the editor: Gut feelings: associations of emotions and emotion regulation with the gut microbiome in women.},
journal = {Psychological medicine},
volume = {},
number = {},
pages = {1-2},
doi = {10.1017/S0033291724000874},
pmid = {38619307},
issn = {1469-8978},
}

@article {pmid38619233,
year = {2024},
author = {Tomasiewicz, K and Woron, J and Kobayashi, A and Krasinski, Z and Rydzewska, G and Szymanski, FM},
title = {Post-COVID-19 syndrome in everyday clinical practice: interdisciplinary expert position statement endorsed by the Polish Society of Civilization Diseases.},
journal = {Polish archives of internal medicine},
volume = {},
number = {},
pages = {},
doi = {10.20452/pamw.16728},
pmid = {38619233},
issn = {1897-9483},
abstract = {Post-COVID-19 syndrome, also known as long-COVID-19 syndrome, is a complex set of symptoms that persist for weeks or months after recovery from the acute phase of COVID-19. These symptoms can affect various body systems, including the respiratory, nervous, cardiovascular, and digestive systems. The most common complaints are fatigue, shortness of breath, joint pain, taste and smell disorders, as well as problems with memory and concentration. The pathogenesis of the post-COVID-19 syndrome is complicated and not fully understood, but it is likely related to an overactive immune system, disturbances in the intestinal microbiome, and cell and tissue damage caused by the virus. Incorporating a multidisciplinary approach to treating and rehabilitating patients and further research into this syndrome's underlying mechanisms and therapy is crucial for understanding and effectively treating this complex and multi-faced condition.},
}

@article {pmid38618969,
year = {2024},
author = {Kersten, A and Lorenz, A and Nottmeier, C and Schmidt, M and Roesner, A and Richter, FC and Röhrborn, K and Witte, AV and Hahnel, S and Koehne, T and Blüher, M and Stumvoll, M and Rohde-Zimmermann, K and Schamarek, I},
title = {The Obese Taste Bud study: Objectives and study design.},
journal = {Diabetes, obesity & metabolism},
volume = {},
number = {},
pages = {},
doi = {10.1111/dom.15563},
pmid = {38618969},
issn = {1463-1326},
support = {Nachwuchsförderung//Medical Faculty, University of Leipzig: Junior research grant/ ; 2021_EKEA.30//Else Kröner-Fresenius-Foundation/ ; },
abstract = {AIMS: Taste modifies eating behaviour, impacting body weight and potentially obesity development. The Obese Taste Bud (OTB) Study is a prospective cohort study launched in 2020 at the University of Leipzig Obesity Centre in cooperation with the HI-MAG Institute. OTB will test the hypothesis that taste cell homeostasis and taste perception are linked to obesity. Here, we provide the study design, data collection process and baseline characteristics.

MATERIALS AND METHODS: Participants presenting overweight, obesity or normal weight undergo taste and smell tests, anthropometric, and taste bud density (TBD) assessment on Day 1. Information on physical and mental health, eating behaviour, physical activity, and dental hygiene are obtained, while biomaterial (saliva, tongue swap, blood) is collected in the fasted state. Further blood samples are taken during a glucose tolerance test. A stool sample is collected at home prior to Day 2, on which a taste bud biopsy follows dental examination. A subsample undergoes functional magnetic resonance imaging while exposed to eating-related cognitive tasks. Follow-up investigations after conventional weight loss interventions and bariatric surgery will be included.

RESULTS: Initial results show that glycated haemoglobin levels and age are negatively associated with TBD, while an unfavourable metabolic profile, current dieting, and vegan diet are related to taste perception. Olfactory function negatively correlates with age and high-density lipoprotein cholesterol.

CONCLUSION: Initial findings suggest that metabolic alterations are relevant for taste and smell function and TBD. By combining omics data from collected biomaterial with physiological, metabolic and psychological data related to taste perception and eating behaviour, the OTB study aims to strengthen our understanding of taste perception in obesity.},
}

@article {pmid38618507,
year = {2024},
author = {Hajivalizadeh, S and Akhondzadeh, S},
title = {The Role of Biotechnology in Latest Therapeutic Approaches for Diabetes Mellitus.},
journal = {Avicenna journal of medical biotechnology},
volume = {16},
number = {2},
pages = {66-67},
pmid = {38618507},
issn = {2008-2835},
}

@article {pmid38618010,
year = {2024},
author = {Kropp, DR and Rainville, JR and Glover, ME and Tsyglakova, M and Samanta, R and Hage, TR and Carlson, AE and Clinton, SM and Hodes, GE},
title = {Chronic variable stress leads to sex specific gut microbiome alterations in mice.},
journal = {Brain, behavior, & immunity - health},
volume = {37},
number = {},
pages = {100755},
pmid = {38618010},
issn = {2666-3546},
abstract = {Stress has been implicated in the incidence and severity of psychiatric and gastrointestinal disorders. The immune system is capable of modulating the activity and composition of the gut following stress and vice versa. In this study we sought to examine the sequential relationship between immune signaling and microbiome composition occurring in male and female mice over time using a variable stress paradigm. Tissue was collected prior to, during, and after the stress paradigm from the same mice. Cytokines from plasma and brain were quantified using a multiplexed cytokine assay. Fecal samples were collected at the same timepoints and 16S rRNA amplicon sequencing was performed to determine the relative abundance of microbiota residing in the guts of stressed and control mice. We found sex differences in the response of the gut microbiota to stress following 28 days of chronic variable stress but not 6 days of sub-chronic variable stress. Immune activation was quantified in the nucleus accumbens immediately following Sub-chronic variable when alterations of gut composition had not yet occurred. In both sexes, 28 days of stress induced significant changes in the proportion of Erysipelotrichaceae and Lactobacillaceae, but in opposite directions for male and female mice. Alterations to the gut microbiome in both sexes were associated with changes in cytokines related to eosinophilic immune activity. Our use of an animal stress model reveals the immune mechanisms that may underly changes in gut microbiome composition during and after stress. This study reveals potential drug targets and microbiota of interest for the intervention of stress related conditions.},
}

@article {pmid38617943,
year = {2024},
author = {Dai, S and Guo, X and Liu, S and Tu, L and Hu, X and Cui, J and Ruan, Q and Tan, X and Lu, H and Jiang, T and Xu, J},
title = {Application of intelligent tongue image analysis in Conjunction with microbiomes in the diagnosis of MAFLD.},
journal = {Heliyon},
volume = {10},
number = {7},
pages = {e29269},
pmid = {38617943},
issn = {2405-8440},
abstract = {BACKGROUND: Metabolic associated fatty liver disease (MAFLD) is a widespread liver disease that can lead to liver fibrosis and cirrhosis. Therefore, it is essential to develop early diagnosic and screening methods.

METHODS: We performed a cross-sectional observational study. In this study, based on data from 92 patients with MAFLD and 74 healthy individuals, we observed the characteristics of tongue images, tongue coating and intestinal flora. A generative adversarial network was used to extract tongue image features, and 16S rRNA sequencing was performed using the tongue coating and intestinal flora. We then applied tongue image analysis technology combined with microbiome technology to obtain an MAFLD early screening model with higher accuracy. In addition, we compared different modelling methods, including Extreme Gradient Boosting (XGBoost), random forest, neural networks(MLP), stochastic gradient descent(SGD), and support vector machine(SVM).

RESULTS: The results show that tongue-coating Streptococcus and Rothia, intestinal Blautia, and Streptococcus are potential biomarkers for MAFLD. The diagnostic model jointly incorporating tongue image features, basic information (gender, age, BMI), and tongue coating marker flora (Streptococcus, Rothia), can have an accuracy of 96.39%, higher than the accuracy value except for bacteria.

CONCLUSION: Combining computer-intelligent tongue diagnosis with microbiome technology enhances MAFLD diagnostic accuracy and provides a convenient early screening reference.},
}

@article {pmid38617841,
year = {2024},
author = {Gao, X and Jiang, J},
title = {Exploring the regulatory mechanism of intestinal flora based on PD-1 receptor/ligand targeted cancer immunotherapy.},
journal = {Frontiers in immunology},
volume = {15},
number = {},
pages = {1359029},
pmid = {38617841},
issn = {1664-3224},
mesh = {Humans ; *Gastrointestinal Microbiome ; Programmed Cell Death 1 Receptor ; B7-H1 Antigen ; Immune Checkpoint Inhibitors/therapeutic use ; Ligands ; Immunotherapy ; *Neoplasms/therapy ; },
abstract = {Serving as a pivotal immunotherapeutic approach against tumors, anti-PD-1/PD-L1 therapy amplifies the immune cells' capability to eliminate tumors by obstructing the interaction between PD-1 and PD-L1. Research indicates that immune checkpoint inhibitors are effective when a patient's gut harbors unique beneficial bacteria. As such, it has further been revealed that the gut microbiome influences tumor development and the efficacy of cancer treatments, with metabolites produced by the microbiome playing a regulatory role in the antitumor efficacy of Immune checkpoint inhibitors(ICBs). This article discusses the mechanism of anti-PD-1 immunotherapy and the role of intestinal flora in immune regulation. This review focuses on the modulation of intestinal flora in the context of PD-1 immunotherapy, which may offer a new avenue for combination therapy in tumor immunotherapy.},
}

Humans
*Gastrointestinal Microbiome
Programmed Cell Death 1 Receptor
B7-H1 Antigen
Immune Checkpoint Inhibitors/therapeutic use
Ligands
Immunotherapy
*Neoplasms/therapy

@article {pmid38617734,
year = {2024},
author = {Magro, DO and Sassaki, LY and Chebli, JMF},
title = {Interaction between diet and genetics in patients with inflammatory bowel disease.},
journal = {World journal of gastroenterology},
volume = {30},
number = {12},
pages = {1644-1650},
pmid = {38617734},
issn = {2219-2840},
mesh = {Humans ; *Inflammatory Bowel Diseases/genetics ; *Crohn Disease/genetics ; *MicroRNAs ; *Colitis, Ulcerative ; *Diet, Mediterranean ; },
abstract = {In this editorial, we comment on the article by Marangoni et al, published in the recent issue of the World Journal of Gastroenterology 2023; 29: 5618-5629, about "Diet as an epigenetic factor in inflammatory bowel disease". The authors emphasized the role of diet, especially the interaction with genetics, in promoting the inflammatory process in inflammatory bowel disease (IBD) patients, focusing on DNA methylation, histone modifications, and the influence of microRNAs. In this editorial, we explore the interaction between genetics, gut microbiota, and diet, in an only way. Furthermore, we provided dietary recommendations for patients with IBD. The Western diet, characterized by a low fiber content and deficiency the micronutrients, impacts short-chain fatty acids production and may be related to the pathogenesis of IBD. On the other hand, the consumption of the Mediterranean diet and dietary fibers are associated with reduced risk of IBD flares, particularly in Crohn's disease (CD) patients. According to the dietary guidance from the International Organization for the Study of Inflammatory Bowel Diseases (IOIBD), the regular consumption of fruits and vegetables while reducing the consumption of saturated, trans, dairy fat, additives, processed foods rich in maltodextrins, and artificial sweeteners containing sucralose or saccharine is recommended to CD patients. For patients with ulcerative colitis, the IOIBD recommends the increased intake of natural sources of omega-3 fatty acids and follows the same restrictive recommendations aimed at CD patients, with the possible inclusion of red meats. In conclusion, IBD is a complex and heterogeneous disease, and future studies are needed to elucidate the influence of epigenetics on diet and microbiota in IBD patients.},
}

Humans
*Inflammatory Bowel Diseases/genetics
*Crohn Disease/genetics
*MicroRNAs
*Colitis, Ulcerative
*Diet, Mediterranean

@article {pmid38617688,
year = {2024},
author = {Jayaprakash, J and B Gowda, SG and K Shukla, P and Gowda, D and Nath, LR and Chiba, H and Rao, R and Hui, SP},
title = {Sex-Specific Effect of Ethanol on Colon Content Lipidome in a Mice Model Using Nontargeted LC/MS.},
journal = {ACS omega},
volume = {9},
number = {14},
pages = {16044-16054},
pmid = {38617688},
issn = {2470-1343},
abstract = {Consumption of alcohol has widespread effects on the human body. The organs that are most significantly impacted are the liver and digestive system. When alcohol is consumed, it is absorbed in the intestines and processed by the liver. However, excessive alcohol use may affect gut epithelial integrity, microbiome composition, and lipid metabolism. Despite past studies investigating the effect of ethanol on hepatic lipid metabolism, the focus on colonic lipid metabolism has not been well explored. In this study, we investigated the sex-specific effect of ethanol on the colonic content lipidome in a mouse model using nontargeted liquid chromatography-mass spectrometry. Comprehensive lipidome analysis of colonic flush samples was performed using ethanol-fed (EF) and pair-fed (PF) mice of each sex. Partial least-squares discriminant analysis revealed that ethanol altered colonic lipid composition largely in male mice compared with female mice. A significant increase in free fatty acids, ceramides, and hexosylceramides and decreased phosphatidylglycerols (PG) was observed in the EF group compared to the PF group in male mice. Phosphatidylethanolamine (PE) levels were increased significantly in the EF group of both sexes compared to the PF group. The volcanic plot shows that PG (O-15:1/15:0) and PE (O-18:2/15:0) are common markers that are increased in both sexes of the EF group. In addition, decreased fatty acid esters of hydroxy fatty acids (FAHFA) were observed specifically in the EF group of female mice. Overall, a significant variation in the mice colonic content lipidome between the EF and PF groups was observed. Target pathways, such as sphingolipid metabolism in males, FAHFA in females, and PE metabolism in both sexes, were suggested. This study provides new insight into the sex-dependent lipid change associated with alcohol-induced gut-microbiota dysfunction and its potential health impacts.},
}

@article {pmid38617584,
year = {2024},
author = {Alqedari, H and Altabtbaei, K and Espinoza, JL and Bin-Hasan, S and Alghounaim, M and Alawady, A and Altabtabae, A and AlJamaan, S and Devarajan, S and AlShammari, T and Ben Eid, M and Matsuoka, M and Jang, H and Dupont, CL and Freire, M},
title = {Host-microbiome associations in saliva predict COVID-19 severity.},
journal = {PNAS nexus},
volume = {3},
number = {4},
pages = {pgae126},
pmid = {38617584},
issn = {2752-6542},
abstract = {Established evidence indicates that oral microbiota plays a crucial role in modulating host immune responses to viral infection. Following severe acute respiratory syndrome coronavirus 2, there are coordinated microbiome and inflammatory responses within the mucosal and systemic compartments that are unknown. The specific roles the oral microbiota and inflammatory cytokines play in the pathogenesis of coronavirus disease 2019 (COVID-19) are yet to be explored. Here, we evaluated the relationships between the salivary microbiome and host parameters in different groups of COVID-19 severity based on their oxygen requirement. Saliva and blood samples (n = 80) were collected from COVID-19 and from noninfected individuals. We characterized the oral microbiomes using 16S ribosomal RNA gene sequencing and evaluated saliva and serum cytokines and chemokines using multiplex analysis. Alpha diversity of the salivary microbial community was negatively associated with COVID-19 severity, while diversity increased with health. Integrated cytokine evaluations of saliva and serum showed that the oral host response was distinct from the systemic response. The hierarchical classification of COVID-19 status and respiratory severity using multiple modalities separately (i.e. microbiome, salivary cytokines, and systemic cytokines) and simultaneously (i.e. multimodal perturbation analyses) revealed that the microbiome perturbation analysis was the most informative for predicting COVID-19 status and severity, followed by the multimodal. Our findings suggest that oral microbiome and salivary cytokines may be predictive of COVID-19 status and severity, whereas atypical local mucosal immune suppression and systemic hyperinflammation provide new cues to understand the pathogenesis in immunologically compromised populations.},
}

@article {pmid38617537,
year = {2024},
author = {Yu, X and Li, W and Li, Z and Wu, Q and Sun, S},
title = {Influence of Microbiota on Tumor Immunotherapy.},
journal = {International journal of biological sciences},
volume = {20},
number = {6},
pages = {2264-2294},
pmid = {38617537},
issn = {1449-2288},
mesh = {Humans ; Immunotherapy ; *Microbiota ; *Probiotics/therapeutic use ; *Neoplasms/therapy ; },
abstract = {The role of the microbiome in immunotherapy has recently garnered substantial attention, with molecular studies and clinical trials providing emerging evidence on the pivotal influence of the microbiota in enhancing therapeutic outcomes via immune response modulation. However, the impact of microbial communities can considerably vary across individuals and different immunotherapeutic approaches, posing prominent challenges in harnessing their potential. In this comprehensive review, we outline the current research applications in tumor immunotherapy and delve into the possible mechanisms through which immune function is influenced by microbial communities in various body sites, encompassing those in the gut, extraintestinal barrier, and intratumoral environment. Furthermore, we discuss the effects of diverse microbiome-based strategies, including probiotics, prebiotics, fecal microbiota transplantation, and the targeted modulation of specific microbial taxa, and antibiotic treatments on cancer immunotherapy. All these strategies potentially have a profound impact on immunotherapy and pave the way for personalized therapeutic approaches and predictive biomarkers.},
}

Humans
Immunotherapy
*Microbiota
*Probiotics/therapeutic use
*Neoplasms/therapy

@article {pmid38617453,
year = {2024},
author = {Chen, SJ and Zhang, DY and Wu, X and Zhang, FM and Cui, BT and Huang, YH and Zhang, ZL and Wang, R and Bai, FH},
title = {Washed microbiota transplantation for Crohn's disease: A metagenomic, metatranscriptomic, and metabolomic-based study.},
journal = {World journal of gastroenterology},
volume = {30},
number = {11},
pages = {1572-1587},
pmid = {38617453},
issn = {2219-2840},
mesh = {Humans ; Amino Acids ; *Antifibrinolytic Agents ; *Crohn Disease/diagnosis/therapy ; Escherichia coli ; Metagenome ; *Microbiota ; Prospective Studies ; },
abstract = {BACKGROUND: Fecal microbiota transplantation (FMT) is a promising therapeutic approach for treating Crohn's disease (CD). The new method of FMT, based on the automatic washing process, was named as washed microbiota transplantation (WMT). Most existing studies have focused on observing the clinical phenomena. However, the mechanism of action of FMT for the effective management of CD-particularly in-depth multi-omics analysis involving the metagenome, metatranscriptome, and metabolome-has not yet been reported.

AIM: To assess the efficacy of WMT for CD and explore alterations in the microbiome and metabolome in response to WMT.

METHODS: We conducted a prospective, open-label, single-center clinical study. Eleven CD patients underwent WMT. Their clinical responses (defined as a decrease in their CD Activity Index score of > 100 points) and their microbiome (metagenome, metatranscriptome) and metabolome profiles were evaluated three months after the procedure.

RESULTS: Seven of the 11 patients (63.6%) showed an optimal clinical response three months post-WMT. Gut microbiome diversity significantly increased after WMT, consistent with improved clinical symptoms. Comparison of the metagenome and metatranscriptome analyses revealed consistent alterations in certain strains, such as Faecalibacterium prausnitzii, Roseburia intestinalis, and Escherichia coli. In addition, metabolomics analyses demonstrated that CD patients had elevated levels of various amino acids before treatment compared to the donors. However, levels of vital amino acids that may be associated with disease progression (e.g., L-glutamic acid, gamma-glutamyl-leucine, and prolyl-glutamine) were reduced after WMT.

CONCLUSION: WMT demonstrated therapeutic efficacy in CD treatment, likely due to the effective reconstruction of the patient's microbiome. Multi-omics techniques can effectively help decipher the potential mechanisms of WMT in treating CD.},
}

Humans
Amino Acids
*Antifibrinolytic Agents
*Crohn Disease/diagnosis/therapy
Escherichia coli
Metagenome
*Microbiota
Prospective Studies

@article {pmid38617439,
year = {2024},
author = {Ogaya, Y and Kadota, T and Hamada, M and Nomura, R and Nakano, K},
title = {Characterization of the unique oral microbiome of children harboring Helicobacter pylori in the oral cavity.},
journal = {Journal of oral microbiology},
volume = {16},
number = {1},
pages = {2339158},
pmid = {38617439},
issn = {2000-2297},
abstract = {OBJECTIVE: Helicobacter pylori infection is acquired in childhood via the oral cavity, although its relationship with the characteristics of the oral microbiome has not been elucidated. In this study, we performed comprehensive analysis of the oral microbiome in children and adults with or without H. pylori in the oral cavity.

METHODS: Bacterial DNA was extracted from 41 adult and 21 child saliva specimens, and H. pylori was detected using PCR. 16S rRNA gene amplification was performed for next-generation sequencing. Bioinformatic analyses were conducted using Quantitative Insights into Microbial Ecology 2 (QIIME 2).

RESULTS: Faith's phylogenetic diversity analysis showed a significant difference between H. pylori-negative adult and child specimens in terms of α-diversity (p < 0.05), while no significant difference was observed between H. pylori-positive adult and child specimens. There was also a significant difference in β-diversity between H. pylori-positive and negative child specimens (p < 0.05). Taxonomic analysis at the genus level revealed that Porphyromonas was the only bacterium that was significantly more abundant in both H. pylori-positive adults and children than in corresponding negative specimens (p < 0.01 and p < 0.05, respectively).

CONCLUSION: These results suggest unique oral microbiome characteristics in children with H. pylori infection in the oral cavity.},
}

@article {pmid38617281,
year = {2024},
author = {Han, L and Pendleton, A and Singh, A and Xu, R and Scott, SA and Palma, JA and Diebold, P and Malarney, KP and Brito, IL and Chang, PV},
title = {Chemoproteomic profiling of substrate specificity in gut microbiota-associated bile salt hydrolases.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.04.01.587558},
pmid = {38617281},
abstract = {The gut microbiome possesses numerous biochemical enzymes that biosynthesize metabolites that impact human health. Bile acids comprise a diverse collection of metabolites that have important roles in metabolism and immunity. The gut microbiota-associated enzyme that is responsible for the gateway reaction in bile acid metabolism is bile salt hydrolase (BSH), which controls the host's overall bile acid pool. Despite the critical role of these enzymes, the ability to profile their activities and substrate preferences remains challenging due to the complexity of the gut microbiota, whose metaproteome includes an immense diversity of protein classes. Using a systems biochemistry approach employing activity-based probes, we have identified gut microbiota-associated BSHs that exhibit distinct substrate preferences, revealing that different microbes contribute to the diversity of the host bile acid pool. We envision that this chemoproteomic approach will reveal how secondary bile acid metabolism controlled by BSHs contributes to the etiology of various inflammatory diseases.},
}

@article {pmid38617212,
year = {2024},
author = {Nixon, MP and Gloor, GB and Silverman, JD},
title = {Beyond Normalization: Incorporating Scale Uncertainty in Microbiome and Gene Expression Analysis.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.04.01.587602},
pmid = {38617212},
abstract = {Though statistical normalizations are often used in differential abundance or differential expression analysis to address sample-to-sample variation in sequencing depth, we offer a better alternative. These normalizations often make strong, implicit assumptions about the scale of biological systems (e.g., microbial load). Thus, analyses are susceptible to even slight errors in these assumptions, leading to elevated rates of false positives and false negatives. We introduce scale models as a generalization of normalizations so researchers can model potential errors in assumptions about scale. By incorporating scale models into the popular ALDEx2 software, we enhance the reproducibility of analyses while often drastically decreasing false positive and false negative rates. We design scale models that are guaranteed to reduce false positives compared to equivalent normalizations. At least in the context of ALDEx2, we recommend using scale models over normalizations in all practical situations.},
}

@article {pmid38617041,
year = {2024},
author = {Awe, T and Fasawe, A and Sawe, C and Ogunware, A and Jamiu, AT and Allen, M},
title = {The modulatory role of gut microbiota on host behavior: exploring the interaction between the brain-gut axis and the neuroendocrine system.},
journal = {AIMS neuroscience},
volume = {11},
number = {1},
pages = {49-62},
pmid = {38617041},
issn = {2373-7972},
abstract = {The brain-gut axis refers to the communication between the central nervous system and the gastrointestinal tract, with the gut microbiome playing a crucial role. While our understanding of the interaction between the gut microbiome and the host's physiology is still in its nascent stage, evidence suggests that the gut microbiota can indeed modulate host behavior. Understanding the specific mechanisms by which the gut microbiota community modulates the host's behavior remains the focus of present and future neuro-gastroenterology studies. This paper reviews several pieces of evidence from the literature on the impact of gut microbiota on host behavior across animal taxa. We explore the different pathways through which this modulation occurs, with the aim of deepening our understanding of the fascinating relationship between the gut microbiome and the central nervous system.},
}

@article {pmid38617000,
year = {2024},
author = {Zhao, L and Hou, X and Feng, Y and Zhang, Y and Shao, S and Wu, X and Zhang, JJ and Zhang, Z},
title = {A chronic stress-induced microbiome perturbation, highly enriched in Ruminococcaceae_UCG-014, promotes colorectal cancer growth and metastasis.},
journal = {International journal of medical sciences},
volume = {21},
number = {5},
pages = {882-895},
pmid = {38617000},
issn = {1449-1907},
mesh = {Humans ; Animals ; Mice ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; *Gastrointestinal Microbiome ; Disease Models, Animal ; Inflammation ; *Colorectal Neoplasms ; },
abstract = {Purpose: Mounting evidence indicates that psychological stress adversely affects cancer progression including tumor growth and metastasis. The aim of this study was to investigate the role of chronic stress-induced microbiome perturbation in colorectal cancer (CRC) progression. Methods: Chronic restraint stress (CRS) was used to establish the chronic stress mouse model, behavioral tests were used for the CRS model evaluation. Subcutaneous xenograft model and lung metastasis model were established to investigate the growth and metastasis of CRC promoted by CRS exposure. 16S rRNA gene sequencing and liquid chromatograph-mass spectrometer (LC-MS) were applied to observe the effects of CRS exposure on the alteration of the gut microbiome and microbial metabolites. Bioinformatics analysis and correlation analyses were applied to analyse the changes in the frequency of body mass, tumor volume, inflammatory factors, neuroendocrine hormones and metabolites of the gut microbiota. Results: In this study, we identifed that CRS exposure model was appropriately constructed by achieving expected increases in disease activity index and enhanced depressive-like behaviors. CRS exposure can promote growth and metastasis of CRC. Besides, the data indicated that CRS exposure not only increased the neuro- and immune-inflammation, but also weakened the gut mucosal immunological function. The 16s rRNA gene sequencing data showed that CRS exposure increased the abundance of g_Ruminococcaceae_UCG_014. Furthermore, the LC-MS data indicated that with only 2 exceptions of carpaine and DG (15:0/20:4(5Z,8Z,11Z,14Z)/0:0), the majority of these 24 metabolites were less abundant in CRS-exposed mice. Bioinformatics analysis and correlation analyses indicated that only Ruminoscoccaceae-UCG-014 was significantly associated with inflammation (IL-6), neurotransmission (5-HT), and microbial metabolism (PS). Conclusion: CRS exposure altered diversity, composition and metabolites of the gut microbiome, with Ruminococcaceae_UCG-014 perturbation consistently correlated to inflammatory responses, suggesting a particular role of this bacterial genus in CRC growth and metastasis.},
}

Humans
Animals
Mice
RNA, Ribosomal, 16S/genetics
*Microbiota
*Gastrointestinal Microbiome
Disease Models, Animal
Inflammation
*Colorectal Neoplasms

@article {pmid38616877,
year = {2023},
author = {An, J and Kim, Y and Song, M and Choi, J and Oh, H and Chang, S and Song, D and Cho, H and Park, S and Jeon, K and Park, Y and Park, G and Oh, S and Kim, Y and Choi, N and Kim, J and Kim, H and Cho, J},
title = {Effects of different levels of organic chromium and selenomethionine cocktails in broilers.},
journal = {Journal of animal science and technology},
volume = {65},
number = {6},
pages = {1226-1241},
pmid = {38616877},
issn = {2055-0391},
abstract = {Selenium (Se) is an essential trace mineral that plays an important role in physiological processes by regulating the antioxidant defense system and enhancing immunity. Chromium is an essential mineral involved in carbohydrate and lipid metabolism and also plays a role in maintaining normal insulin function. Based on these advantages, we hypothesized that the addition of selenomethionine (SeMet) and organic chromium (OC) to broiler diets would increase Se deposition, antioxidant capacity and immune response in meat. Therefore, this study analyzed the effects of OC and SeMet on growh performance, nutrients digestibility, blood profiles, intestinal morphology, meat quality characteristics, and taxonomic analysis of broilers. A total of 168 one-day-old broiler chicken (Arbor Acres) were randomly allotted to 3 groups based on the initial body weight of 37.33 ± 0.24 g with 7 replicate per 8 birds (mixed sex). The experiments period was 28 days. Dietary treatments were folloewd: Basal diets based on corn-soybean meal (CON), basal diet supplemented with 0.2 ppm OC and 0.2 ppm SeMet (CS4), and basal diet supplemented with 0.4 ppm OC and 0.4 ppm SeMet (CS8). Supplementation of OC and SeMet did not affect on growth performance, nutrient digestibility. However, CS8 supplementation increased in duodenum villus height and villus height : crypt depth, and increased in breast meat Se deposition. In addition, CS8 group showed higher uric acid and total antioxidant status than CON group. Taxonomic analysis at phylum level revealed that Proteobacteria and Firmicutes of CS4 and CS8 were lower than CON group. In genus level, the relative abundance of fecal Lactobacillus and Enterococcus of CS4 and CS8 groups were higher than CON group. In short, 0.4 ppm OC and 0.4 ppm SeMet supplementation to broiler diet supporitng positive gut microbiome change, also enhancing antioxidant capacity, and Se deposition in breast meat.},
}

@article {pmid38616572,
year = {2024},
author = {Cain, CL and White, E and Citron, LE and Zheng, Q and Morris, DO and Grice, EA and Bradley, CW},
title = {Longitudinal evaluation of the cutaneous and rectal microbiota of German shepherd dogs with perianal fistulas undergoing therapy with ciclosporin and ketoconazole.},
journal = {Veterinary dermatology},
volume = {},
number = {},
pages = {},
doi = {10.1111/vde.13249},
pmid = {38616572},
issn = {1365-3164},
support = {//National Institutes of Health/Boehringer Ingelheim Summer Research Program/ ; T32-AR007465//National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases/ ; P30-AR069589//Penn Skin Biology and Diseases Resource-based Center, funded by NIH/NIAMS grant/ ; //PennVet Center for Host-Microbial Interactions/ ; },
abstract = {BACKGROUND: Perianal fistulas are painful ulcers or sinus tracts that disproportionately affect German shepherd dogs and are proposed as a spontaneous animal model of fistulising Crohn's disease.

OBJECTIVES: To characterise the rectal and cutaneous microbiota in German shepherd dogs with perianal fistulas and to investigate longitudinal shifts with lesion resolution during immunomodulatory therapy.

ANIMALS: Eleven German shepherd dogs with perianal fistulas and 15 healthy German shepherd dogs.

MATERIALS AND METHODS: Affected dogs were evaluated and swabbed at three visits, 30 days apart, while undergoing treatment with ciclosporin and ketoconazole. Healthy German shepherd dogs were contemporaneously sampled. Sites included the rectum, perianal skin and axilla. The microbiome was evaluated following sequencing of the V4 hypervariable region of the 16S ribosomal RNA (rRNA) gene.

RESULTS: Alpha diversity was not significantly different between healthy and affected dogs at each of the three body sites (p > 0.5), yet rectal and perianal beta diversities from affected dogs differed significantly from those of healthy dogs at Day 0 (p = 0.004). Rectal and perianal relative abundance of Prevotella spp. increased and perianal Staphylococcus spp. relative abundance decreased in affected dogs over time, coincident with lesion resolution.

Changes in lesional cutaneous and rectal microbiota occur in German shepherd dogs with perianal fistulas and shift over time with lesion resolution during immunomodulatory therapy. Further investigations of the role of cutaneous and enteric microbiota in the pathogenesis of perianal fistulas, and whether manipulation of microbial populations may ameliorate disease, are needed.},
}

@article {pmid38616557,
year = {2024},
author = {Gill, SK and Hernaiz-Leonardo, JC and Edens, TJ and Pascual, A and Tang, C and Fan, J and Thamboo, A and Mullings, W and Alsaleh, S and Alim, BM and Javer, AR and Manges, AR},
title = {SinoNasal Microbiota Transfer to treat recalcitrant chronic rhinosinusitis: A case series.},
journal = {International forum of allergy & rhinology},
volume = {},
number = {},
pages = {},
doi = {10.1002/alr.23352},
pmid = {38616557},
issn = {2042-6984},
support = {CIHR/CAPMC/CIHR/Canada ; FRN-171447/CAPMC/CIHR/Canada ; PJT-183766/CAPMC/CIHR/Canada ; },
abstract = {SinoNasal Microbiota Transfer (SNMT) was safe with immediate benefit in all recipients, with sustained improvement in two of three recipients for up to 180 days. The addition of antimicrobial photodynamic therapy worsened chronic rhinosinusitis. These promising SNMT results warrant further study of safety and efficacy.},
}

@article {pmid38616524,
year = {2024},
author = {Hardison, EA and Eliason, EJ},
title = {Diet effects on ectotherm thermal performance.},
journal = {Biological reviews of the Cambridge Philosophical Society},
volume = {},
number = {},
pages = {},
doi = {10.1111/brv.13081},
pmid = {38616524},
issn = {1469-185X},
support = {//University of California, Santa Barbara (Eliason Lab Start Up Funds)/ ; OCE-9982105//National Science Foundation (Santa Barbara Coastal Long Term Ecological Research program) under awards/ ; OCE-0620276//National Science Foundation (Santa Barbara Coastal Long Term Ecological Research program) under awards/ ; OCE-1232779//National Science Foundation (Santa Barbara Coastal Long Term Ecological Research program) under awards/ ; OCE-1831937//National Science Foundation (Santa Barbara Coastal Long Term Ecological Research program) under awards/ ; },
abstract = {The environment is changing rapidly, and considerable research is aimed at understanding the capacity of organisms to respond. Changes in environmental temperature are particularly concerning as most animals are ectothermic, with temperature considered a key factor governing their ecology, biogeography, behaviour and physiology. The ability of ectotherms to persist in an increasingly warm, variable, and unpredictable future will depend on their nutritional status. Nutritional resources (e.g. food availability, quality, options) vary across space and time and in response to environmental change, but animals also have the capacity to alter how much they eat and what they eat, which may help them improve their performance under climate change. In this review, we discuss the state of knowledge in the intersection between animal nutrition and temperature. We take a mechanistic approach to describe nutrients (i.e. broad macronutrients, specific lipids, and micronutrients) that may impact thermal performance and discuss what is currently known about their role in ectotherm thermal plasticity, thermoregulatory behaviour, diet preference, and thermal tolerance. We finish by describing how this topic can inform ectotherm biogeography, behaviour, and aquaculture research.},
}

@article {pmid38616224,
year = {2024},
author = {Zalewska, M and Błażejewska, A and Szadziul, M and Ciuchciński, K and Popowska, M},
title = {Effect of composting and storage on the microbiome and resistome of cattle manure from a commercial dairy farm in Poland.},
journal = {Environmental science and pollution research international},
volume = {},
number = {},
pages = {},
pmid = {38616224},
issn = {1614-7499},
support = {2017/25/Z/NZ7/03026//Narodowe Centrum Nauki/ ; },
abstract = {Manure from food-producing animals, rich in antibiotic-resistant bacteria and antibiotic resistance genes (ARGs), poses significant environmental and healthcare risks. Despite global efforts, most manure is not adequately processed before use on fields, escalating the spread of antimicrobial resistance. This study examined how different cattle manure treatments, including composting and storage, affect its microbiome and resistome. The changes occurring in the microbiome and resistome of the treated manure samples were compared with those of raw samples by high-throughput qPCR for ARGs tracking and sequencing of the V3-V4 variable region of the 16S rRNA gene to indicate bacterial community composition. We identified 203 ARGs and mobile genetic elements (MGEs) in raw manure. Post-treatment reduced these to 76 in composted and 51 in stored samples. Notably, beta-lactam, cross-resistance to macrolides, lincosamides and streptogramin B (MLSB), and vancomycin resistance genes decreased, while genes linked to MGEs, integrons, and sulfonamide resistance increased after composting. Overall, total resistance gene abundance significantly dropped with both treatments. During composting, the relative abundance of genes was lower midway than at the end. Moreover, higher biodiversity was observed in samples after composting than storage. Our current research shows that both composting and storage effectively reduce ARGs in cattle manure. However, it is challenging to determine which method is superior, as different groups of resistance genes react differently to each treatment, even though a notable overall reduction in ARGs is observed.},
}

@article {pmid38616077,
year = {2024},
author = {Yaşar, A and Ryu, HJ and Esen, E and Sarıoğlan, İ and Deemer, D and Çetin, B and Yoo, SH and Lindemann, SR and Lee, BH and Tunçil, YE},
title = {The branching ratio of enzymatically synthesized α-glucans impacts microbiome and metabolic outcomes of in vitro fecal fermentation.},
journal = {Carbohydrate polymers},
volume = {335},
number = {},
pages = {122087},
doi = {10.1016/j.carbpol.2024.122087},
pmid = {38616077},
issn = {1879-1344},
mesh = {Fermentation ; RNA, Ribosomal, 16S/genetics ; *1,4-alpha-Glucan Branching Enzyme ; Glucans ; *Microbiota ; },
abstract = {The aim of this study was to evaluate the impacts of enzymatically synthesized α-glucans possessing α-1,4- and α-1,6-glucose linkages, and varying in branching ratio, on colonic microbiota composition and metabolic function. Four different α-glucans varying in branching ratio were synthesized by amylosucrase from Neisseria polysaccharea and glycogen branching enzyme from Rhodothermus obamensis. The branching ratios were found to range from 0 % to 2.8 % using GC/MS. In vitro fecal fermentation analyses (n = 8) revealed that the branching ratio dictates the short-chain fatty acid (SCFA) generation by fecal microbiota. Specifically, slightly branched (0.49 %) α-glucan resulted in generation of significantly (P < 0.05) higher amounts of propionate, compared to more-branched counterparts. In addition, the amount of butyrate generated from this α-glucan was statistically (P > 0.05) indistinguishable than those observed in resistant starches. 16S rRNA sequencing revealed that enzymatically synthesized α-glucans stimulated Lachnospiraceae and Ruminococcus related OTUs. Overall, the results demonstrated metabolic function of colonic microbiota can be manipulated by altering the branching ratio of enzymatically synthesized α-glucans, providing insights into specific structure-function relationships between dietary fibers and the colonic microbiome. Furthermore, the slightly branched α-glucans could be used as functional carbohydrates to stimulate the beneficial microbiota and SCFAs in the colon.},
}

Fermentation
RNA, Ribosomal, 16S/genetics
*1,4-alpha-Glucan Branching Enzyme
Glucans
*Microbiota

@article {pmid38616048,
year = {2024},
author = {Winters, TA and Marzella, L and Molinar-Inglis, O and Price, PW and Han, NC and Cohen, JE and Wang, SJ and Fotenos, AF and Sullivan, JM and Esker, J and Lapinskas, PJ and DiCarlo, AL},
title = {Gastrointestinal Acute Radiation Syndrome: Mechanisms, Models, Markers, and Medical Countermeasures.},
journal = {Radiation research},
volume = {},
number = {},
pages = {},
doi = {10.1667/RADE-23-00196.1},
pmid = {38616048},
issn = {1938-5404},
abstract = {There have been a number of reported human exposures to high dose radiation, resulting from accidents at nuclear power plants (e.g., Chernobyl), atomic bombings (Hiroshima and Nagasaki), and mishaps in industrial and medical settings. If absorbed radiation doses are high enough, evolution of acute radiation syndromes (ARS) will likely impact both the bone marrow as well as the gastrointestinal (GI) tract. Damage incurred in the latter can lead to nutrient malabsorption, dehydration, electrolyte imbalance, altered microbiome and metabolites, and impaired barrier function, which can lead to septicemia and death. To prepare for a medical response should such an incident arise, the National Institute of Allergy and Infectious Diseases (NIAID) funds basic and translational research to address radiation-induced GI-ARS, which remains a critical and prioritized unmet need. Areas of interest include identification of targets for damage and mitigation, animal model development, and testing of medical countermeasures (MCMs) to address GI complications resulting from radiation exposure. To appropriately model expected human responses, it is helpful to study analogous disease states in the clinic that resemble GI-ARS, to inform on best practices for diagnosis and treatment, and translate them back to inform nonclinical drug efficacy models. For these reasons, the NIAID partnered with two other U.S. government agencies (the Biomedical Advanced Research and Development Authority, and the Food and Drug Administration), to explore models, biomarkers, and diagnostics to improve understanding of the complexities of GI-ARS and investigate promising treatment approaches. A two-day workshop was convened in August 2022 that comprised presentations from academia, industry, healthcare, and government, and highlighted talks from 26 subject matter experts across five scientific sessions. This report provides an overview of information that was presented during the conference, and important discussions surrounding a broad range of topics that are critical for the research, development, licensure, and use of MCMs for GI-ARS.},
}

@article {pmid38615875,
year = {2024},
author = {Zhang, J and Wang, P and Wang, J and Wei, X and Wang, M},
title = {Unveiling intratumoral microbiota: an emerging force for colorectal cancer diagnosis and therapy.},
journal = {Pharmacological research},
volume = {},
number = {},
pages = {107185},
doi = {10.1016/j.phrs.2024.107185},
pmid = {38615875},
issn = {1096-1186},
abstract = {Microbes, including bacteria, viruses, fungi, and other eukaryotic organisms, are commonly present in multiple organs of the human body and contribute significantly to both physiological and pathological processes. Nowadays, the development of sequencing technology has revealed the presence and composition of the intratumoral microbiota, which includes Fusobacterium, Bifidobacteria, and Bacteroides, and has shed light on the significant involvement in the progression of colorectal cancer (CRC). Here, we summarized the current understanding of the intratumoral microbiota in CRC and outline the potential translational and clinical applications in the diagnosis, prevention, and treatment of CRC. We focused on reviewing the development of microbial therapies targeting the intratumoral microbiota to improve the efficacy and safety of chemotherapy and immunotherapy for CRC and to identify biomarkers for the diagnosis and prognosis of CRC. Finally, we emphasized the obstacles and potential solutions to translating the knowledge of the intratumoral microbiota into clinical practice.},
}

@article {pmid38615754,
year = {2024},
author = {Li, W and Guan, S and Hu, X and Zhao, H and Cai, J and Li, X and Zhang, X and Zhu, W and Pan, X and Li, S and Tian, J},
title = {Lysimachia capillipes Hemsl. saponins ameliorate colorectal cancer in mice via regulating gut microbiota and restoring metabolic profiles.},
journal = {Fitoterapia},
volume = {},
number = {},
pages = {105959},
doi = {10.1016/j.fitote.2024.105959},
pmid = {38615754},
issn = {1873-6971},
abstract = {Lysimachia capillipes Hemsl., a traditional Chinese medicine (TCM), is commonly prescribed for its anti-inflammatory and anti-tumor properties. Pharmacological studies have demonstrated that Lysimachia capillipes Hemsl. saponins (LCS) are the primary bioactive component. However, its mechanism for treating colorectal cancer (CRC) is still unknown. Increasing evidence suggests a close relationship between CRC, intestinal flora, and host metabolism. Thus, this study aims to investigate the mechanism of LCS amelioration of CRC from the perspective of the gut microbiome and metabolome. As a result, seven gut microbiotas and fourteen plasma metabolites were significantly altered between the control and model groups. Among them, one gut microbiota genera (Monoglobus) and six metabolites (Ureidopropionic acid, Cytosine, L-Proline, 3-hydroxyanthranilic acid, Cyclic AMP and Suberic acid) showed the most pronounced callback trend after LCS administration. Subsequently, the correlation analysis revealed significant associations between 68 pairs of associated metabolites and gut microbes, with 13 pairs of strongly associated metabolites regulated by the LCS. Taken together, these findings indicate that the amelioration of CRC by LCS is connected to the regulation of intestinal flora and the recasting of metabolic abnormalities. These insights highlight the potential of LCS as a candidate drug for the treatment of CRC.},
}

@article {pmid38615703,
year = {2024},
author = {Fei, S and Kang, J and Ou, M and Liu, H and Zhang, X and Luo, Q and Li, K and Chen, K and Zhao, J},
title = {Effects of essential amino acids supplementation in a low-protein diet on growth performance, intestinal health and microbiota of juvenile blotched snakehead (Channa maculata).},
journal = {Fish & shellfish immunology},
volume = {149},
number = {},
pages = {109555},
doi = {10.1016/j.fsi.2024.109555},
pmid = {38615703},
issn = {1095-9947},
abstract = {Developing a low-protein feed is important for the sustainable advancement of aquaculture. The aim of this study was to investigate the effects of essential amino acid (EAA) supplementation in a low-protein diet on the growth, intestinal health, and microbiota of the juvenile blotched snakehead, Channa maculata in an 8-week trial conducted in a recirculating aquaculture system. Three isoenergetic diets were formulated to include a control group (48.66 % crude protein (CP), HP), a low protein group (42.54 % CP, LP), and a low protein supplementation EAA group (44.44 % CP, LP-AA). The results showed that significantly lower weight gain (WG), specific growth rate (SGR), protein efficiency ratio (PER), and feed efficiency ratio (FER) were observed in fish that were fed LP than in the HP and LP-AA groups (P < 0.05). The HP and LP-AA groups exhibited a significant increase in intestinal villus length, villus width, and muscular thickness compared to the LP group (P < 0.05). Additionally, the HP and LP-AA groups demonstrated significantly higher levels of intestinal total antioxidant capacity (T-AOC), catalase (CAT), and superoxide dismutase (SOD) and lower levels of malondialdehyde (MDA) compared to the LP group (P < 0.05). The apoptosis rate of intestinal cells in the LP group was significantly higher than those in the LP and HP groups (P < 0.05). The mRNA expression levels of superoxide dismutase (sod), nuclear factor kappa B p65 subunit (nfκb-p65), heat shock protein 70 (hsp70), and inhibitor of NF-κBα (iκba) in the intestine were significantly higher in the LP group than those in the HP and LP-AA groups (P < 0.05). The 16s RNA analysis indicated that EAA supplementation significantly increased the growth of Desulfovibrio and altered the intestinal microflora. The relative abundances of Firmicutes and Cyanobacteria were positively correlated with antioxidant parameters (CAT and T-AOC), whereas Desulfobacterota was negatively correlated with sod and T-AOC. The genera Bacillus, Bacteroides, and Rothia were associated with the favorable maintenance of gut health. In conclusion, dietary supplementation with EAAs to achieve a balanced amino acid profile could potentially reduce the dietary protein levels from 48.66 % to 44.44 % without adversely affecting the growth and intestinal health of juvenile blotched snakeheads.},
}

@article {pmid38615449,
year = {2024},
author = {Jatkowska, A and Gkikas, K and Nichols, B and Short, B and Rizou, VK and Kapranos, P and Gunnewiek, JK and Christina, E and Svolos, V and Quince, C and Gerasimidis, K},
title = {Dose-dependent effects of enteral nutrition on the faecal microbiota and short chain fatty acids.},
journal = {Clinical nutrition (Edinburgh, Scotland)},
volume = {43},
number = {5},
pages = {1200-1207},
doi = {10.1016/j.clnu.2024.04.010},
pmid = {38615449},
issn = {1532-1983},
abstract = {INTRODUCTION: Enteral nutrition (EN) involves replacing all or part of a person's habitual diet with a nutritional formula. The impact of varying doses of EN on the gut microbiome remains understudied.

METHODS: Healthy adults replaced all (100% EN) or part (85% EN, 50% EN and 20% EN) of their energy requirements with EN for 7 days. Faecal samples were collected before and on day 7 of interventions. Faecal pH, short chain fatty acids (SCFAs), branched-chain fatty acids (BCFAs) and 16S rRNA sequencing were performed. Dietary assessment was performed with 7-day food diaries.

RESULTS: Sixty-one participants (31 females; median (IQR) age: 24.7 (23.0-27.8) years) were recruited. A dose-dependent impact of EN on faecal microbiota, SCFAs, BCFAs) and pH was observed, with changes detectable at EN intakes of at least 50% of energy requirements. 100% and 85% EN reduced the abundance of fibre-fermenting taxa such as Agathobacter, Faecalibaterium, Succinivibrio and Acidaminococcus. In parallel, potentially harmful organisms like Eubacterium, Actinomyces, and Klebsiella increased. In the 50% EN group, adherence to a diet high in fish, vegetables, potatoes, non-alcoholic beverages, and fat spreads, and low in cereal products, milk, and meat negatively correlated with changes in microbiota structure (r = -0.75, P = 0.025). This signal was not observed when using compositional tools for microbiota analysis.

CONCLUSIONS: EN detrimentally influences the faecal microbiota and diet-related bacterial metabolites in a dose-dependent manner, particularly at doses of at least 50%. The findings of this study have implications for the dietary management and counselling of patients receiving high volume EN.},
}

@article {pmid38614959,
year = {2024},
author = {Boyang, H and Yanjun, Y and Jing, Z and Chenxin, Y and Ying, M and Shuwen, H and Qiang, Y},
title = {Investigating the influence of the gut microbiome on cholelithiasis: unveiling insights through sequencing and predictive modeling.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxae096},
pmid = {38614959},
issn = {1365-2672},
abstract = {BACKGROUND: Cholelithiasis is one of the most common disorders of hepatobiliary system. Gut bacteria may be involved in the process of gallstone formation and are therefore considered as potential targets for cholelithiasis prediction.

OBJECTIVE: To reveal the correlation between cholelithiasis and gut bacteria.

METHODS: Stool samples were collected from 100 cholelithiasis and 250 healthy individuals from Huzhou Central Hospital; The 16S rRNA of gut bacteria in the stool samples was sequenced using the third-generation Pacbio sequencing platform; Mothur v.1.21.1 was used to analyze the diversity of gut bacteria; Wilcoxon rank-sum test and linear discriminant analysis of effect sizes (LEfSe) were used to analyze differences in gut bacteria between patients suffering from cholelithiasis and healthy individuals; Chord diagram and Plot related heat maps were used to analyze the correlation between cholelithiasis and gut bacteria; Six machine algorithms were used to construct models to predict cholelithiasis.

RESULTS: There were differences in the abundance of gut bacteria between cholelithiasis and healthy individuals, but there were no differences in their community diversity. Increased abundance of Costridia, Escherichia flexneri, and Klebsiella pneumonae were found in cholelithiasis, while Bacteroidia, Phocaeicola, and Phocaeicola vulgatus were more abundant in healthy individuals. The top 4 bacteria that were most closely associated with cholelithiasis were Escherichia flexneri, Escherichia dysenteriae, Streptococcus salivarius and Escherichiadysenteriae. The cholelithiasis model based on CatBoost algorithm had the best prediction effect (sensitivity: 90.48%, specificity: 88.32%, AUC: 0.962).

CONCLUSION: The identification of characteristic gut bacteria may provide new predictive targets for gallstone screening. As being screened by the predictive model, people at high risk of cholelithiasis can determine the need for further testing, thus enabling early warning of cholelithiasis.},
}

@article {pmid38614956,
year = {2024},
author = {Lee, S and Tejesvi, MV and Hurskainen, E and Aasmets, O and Plaza-Díaz, J and Franks, S and Morin-Papunen, L and Tapanainen, JS and Ruuska, TS and Altmäe, S and Org, E and Salumets, A and Arffman, RK and Piltonen, TT},
title = {Gut bacteriome and mood disorders in women with PCOS.},
journal = {Human reproduction (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/humrep/deae073},
pmid = {38614956},
issn = {1460-2350},
support = {//European Union's Horizon 2020 Research and Innovation Programme/ ; },
abstract = {STUDY QUESTION: How does the gut bacteriome differ based on mood disorders (MDs) in women with polycystic ovary syndrome (PCOS), and how can the gut bacteriome contribute to the associations between these two conditions?

SUMMARY ANSWER: Women with PCOS who also have MDs exhibited a distinct gut bacteriome with reduced alpha diversity and a significantly lower abundance of Butyricicoccus compared to women with PCOS but without MDs.

WHAT IS KNOWN ALREADY: Women with PCOS have a 4- to 5-fold higher risk of having MDs compared to women without PCOS. The gut bacteriome has been suggested to influence the pathophysiology of both PCOS and MDs.

STUDY DESIGN, SIZE, DURATION: This population-based cohort study was derived from the Northern Finland Birth Cohort 1966 (NFBC1966), which includes all women born in Northern Finland in 1966. Women with PCOS who donated a stool sample at age 46 years (n = 102) and two BMI-matched controls for each case (n = 205), who also responded properly to the MD criteria scales, were included.

A total of 102 women with PCOS and 205 age- and BMI-matched women without PCOS were included. Based on the validated MD criteria, the subjects were categorized into MD or no-MD groups, resulting in the following subgroups: PCOS no-MD (n = 84), PCOS MD (n = 18), control no-MD (n = 180), and control MD (n = 25). Clinical characteristics were assessed at age 31 years and age 46 years, and stool samples were collected from the women at age 46 years, followed by the gut bacteriome analysis using 16 s rRNA sequencing. Alpha diversity was assessed using observed features and Shannon's index, with a focus on genera, and beta diversity was characterized using principal components analysis (PCA) with Bray-Curtis Dissimilarity at the genus level. Associations between the gut bacteriome and PCOS-related clinical features were explored by Spearman's correlation coefficient. A P-value for multiple testing was adjusted with the Benjamini-Hochberg false discovery rate (FDR) method.

We observed changes in the gut bacteriome associated with MDs, irrespective of whether the women also had PCOS. Similarly, PCOS MD cases showed a lower alpha diversity (Observed feature, PCOS no-MD, median 272; PCOS MD, median 208, FDR = 0.01; Shannon, PCOS no-MD, median 5.95; PCOS MD, median 5.57, FDR = 0.01) but also a lower abundance of Butyricicoccus (log-fold changeAnalysis of Compositions of Microbiomes with Bias Correction (ANCOM-BC)=-0.90, FDRANCOM-BC=0.04) compared to PCOS no-MD cases. In contrast, in the controls, the gut bacteriome did not differ based on MDs. Furthermore, in the PCOS group, Sutterella showed positive correlations with PCOS-related clinical parameters linked to obesity (BMI, r2=0.31, FDR = 0.01; waist circumference, r2=0.29, FDR = 0.02), glucose metabolism (fasting glucose, r2=0.46, FDR < 0.001; fasting insulin, r2=0.24, FDR = 0.05), and gut barrier integrity (zonulin, r2=0.25, FDR = 0.03).

Although this was the first study to assess the link between the gut bacteriome and MDs in PCOS and included the largest PCOS dataset for the gut microbiome analysis, the number of subjects stratified by the presence of MDs was limited when contrasted with previous studies that focused on MDs in a non-selected population.

The main finding is that gut bacteriome is associated with MDs irrespective of the PCOS status, but PCOS may also modulate further the connection between the gut bacteriome and MDs.

This research was funded by the European Union's Horizon 2020 Research and Innovation Programme under the Marie Sklodowska-Curie Grant Agreement (MATER, No. 813707), the Academy of Finland (project grants 315921, 321763, 336449), the Sigrid Jusélius Foundation, Novo Nordisk Foundation (NNF21OC0070372), grant numbers PID2021-12728OB-100 (Endo-Map) and CNS2022-135999 (ROSY) funded by MCIN/AEI/10.13039/501100011033 and ERFD A Way of Making Europe. The study was also supported by EU QLG1-CT-2000-01643 (EUROBLCS) (E51560), NorFA (731, 20056, 30167), USA/NIH 2000 G DF682 (50945), the Estonian Research Council (PRG1076, PRG1414), EMBO Installation (3573), and Horizon 2020 Innovation Grant (ERIN, No. EU952516). The funders did not participate in any process of the study. We have no conflicts of interest to declare.

TRIAL REGISTRATION NUMBER: N/A.},
}

@article {pmid38614639,
year = {2023},
author = {Masood, B and Moorthy, M},
title = {Causes of obesity: a review.},
journal = {Clinical medicine (London, England)},
volume = {23},
number = {4},
pages = {284-291},
doi = {10.7861/clinmed.2023-0168},
pmid = {38614639},
issn = {1473-4893},
mesh = {Humans ; *Obesity/epidemiology ; *Ethnicity ; },
abstract = {Obesity research is advancing swiftly, but the increase in obesity prevalence is faster. Over the past three decades, researchers have found that biopsychosocial factors determine weight gain much more than personal choices and responsibility. Various genes have found to predispose people to obesity by interacting with our obesogenic environment. In this review, we discuss the impact of physical inactivity, excessive caloric intake, intrauterine environment, postnatal influences, insufficient sleep, drugs, medical conditions, socioeconomic status, ethnicity, psychosocial stress, endocrine disrupting chemicals and the gastrointestinal microbiome, on the occurrence of obesity.},
}

Humans
*Obesity/epidemiology
*Ethnicity

@article {pmid38614408,
year = {2024},
author = {Wu, ZJ and Zhao, YY and Hao, SJ and Dong, BB and Zheng, YX and Liu, B and Li, J},
title = {Combining fecal 16 S rRNA sequencing and spinal cord metabolomics analysis to explain the modulatory effect of PPARα on neuropathic pain.},
journal = {Brain research bulletin},
volume = {211},
number = {},
pages = {110943},
doi = {10.1016/j.brainresbull.2024.110943},
pmid = {38614408},
issn = {1873-2747},
abstract = {BACKGROUND: Existing evidence suggests that the composition of the gut microbiota is associated with neuropathic pain (NP), but the mechanistic link is elusive. Peroxisome proliferator-activated receptor α (PPARα) has been shown to be a pharmacological target for the treatment of metabolic disorders, and its expression is also involved in inflammatory regulation. The aim of this study was to investigate the important modulatory effects of PPARα on gut microbiota and spinal cord metabolites in mice subjected to chronic constriction injury.

METHODS: We analyzed fecal microbiota and spinal cord metabolic alterations in mice from the sham, CCI, GW7647 (PPARα agonist) and GW6471 (PPARα antagonist) groups by 16 S rRNA amplicon sequencing and untargeted metabolomics analysis. On this basis, the intestinal microbiota and metabolites that were significantly altered between treatment groups were analyzed in a combined multiomics analysis. We also investigated the effect of PPARα on the polarization fractionation of spinal microglia.

RESULTS: PPARα agonist significantly reduce paw withdrawal threshold and paw withdrawal thermal latency, while PPARα antagonist significantly increase paw withdrawal threshold and paw withdrawal thermal latency. 16 S rRNA gene sequencing showed that intraperitoneal injection of GW7647 or GW6471 significantly altered the abundance, homogeneity and composition of the gut microbiome. Analysis of the spinal cord metabolome showed that the levels of spinal cord metabolites were shifted after exposure to GW7647 or GW6471. Alterations in the composition of gut microbiota were significantly associated with the abundance of various spinal cord metabolites. The abundance of Licheniformes showed a significant positive correlation with nicotinamide, benzimidazole, eicosanoids, and pyridine abundance. Immunofluorescence results showed that intraperitoneal injection of GW7647 or GW6471 altered microglial activation and polarization levels.

CONCLUSION: Our study shows that PPARα can promote M2-type microglia polarization, as well as alter gut microbiota and metabolites in CCI mice. This study enhances our understanding of the mechanism of PPARα in the treatment of neuropathic pain.},
}

@article {pmid38614349,
year = {2024},
author = {Urbaniak, M and Mierzejewska-Sinner, E and Bednarek, A and Krauze, K and Włodarczyk-Marciniak, R},
title = {Microbial response to Nature-Based Solutions in urban soils: A comprehensive analysis using Biolog® EcoPlates™.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {172360},
doi = {10.1016/j.scitotenv.2024.172360},
pmid = {38614349},
issn = {1879-1026},
abstract = {The study presents a comprehensive examination of changes in soil microbial functional diversity (hereafter called microbial activity) following the implementation of Nature-Based Solutions (NBS) in urban areas. Utilizing the Biolog® EcoPlates™ technique, the study explored variations in microbial diversity in urban soil under NBSs implementation across timespan of two years. Significant differences in microbial activity were observed between control location and those with NBS implementations, with seasonal variations playing a crucial role. NBS positively impacted soil microbial activity especially at two locations: infiltration basin and wild flower meadow showing the most substantial increase after NBS implementation. The study links rainfall levels to microbial functional diversity, highlighting the influence of climatic conditions on soil microbiome. The research investigates also the utilization of different carbon sources by soil microorganisms, shedding light on the specificity of substrate utilization across seasons and locations. The results demonstrate that NBSs implementations lead to changes in substrate utilization patterns, emphasizing the positive influence of NBS on soil microbial communities. Likewise, biodiversity indices, such as Shannon-Weaver diversity (H'), Shannon Evenness Index (E), and substrate richness index (S), exhibit significant variations in response to NBS. Notably, NBS implementation positively impacted H' and E indexes, especially in infiltration basin and wild flower meadow, underlining the benefits of NBS for enhancing microbial diversity. The obtained results demonstrated valuable insight into the dynamic interactions between NBS implementation and soil microbial activity. The findings underscore the potential of NBS to positively influence soil microbial diversity in urban environments, contributing to urban sustainability and soil health. The study emphasizes the importance of monitoring soil microbial activity to assess the effectiveness of NBS interventions and guides sustainable urban development practices.},
}

@article {pmid38614202,
year = {2024},
author = {Yu, H and Liu, Y},
title = {Sheep dung deposition disrupted the soil microbiome in degraded grassland but not in non-degraded grassland.},
journal = {Environmental research},
volume = {},
number = {},
pages = {118922},
doi = {10.1016/j.envres.2024.118922},
pmid = {38614202},
issn = {1096-0953},
abstract = {Grazing is the most extensive land use in grassland worldwide, wherein the soil microbiome is known to support multiple ecosystem functions. Yet, the experimental impact of livestock grazing and dung deposits on the soil microbiome in degraded grassland remains poorly understood. We examined the effects of sheep dung depositions on the bacterial and fungal microbiome of two grasslands: non-degraded and degraded (long-term overgrazing) in northern China. Specifically, sheep dung was experimentally added to the soil and its effects on the soil microbial community were determined 3 months later (corresponding to livestock excreta deposited throughout the entire growing season of grassland, June to September). Our results showed that sheep dung additions showed negative effects on the soil microbiome of already degraded grassland, while with a diminished impact on the non-degraded grassland. In particular, dung deposition decreased soil microbial Shannon index, notably significantly reducing fungal diversity in degraded grassland. Moreover, sheep dung deposition modifies soil bacterial community structure and diminishes bacterial community network complexity. The alteration of soil pH caused by sheep dung deposition partially explains the decline in microbial diversity in degraded grassland. However, sheep dung did not alter the relative abundance and community composition of bacterial and fungal dominant phyla either in the non-degraded or in the degraded grassland. In conclusion, the short-term deposition of sheep dung exerted a detrimental influence on the microbial community in degraded grassland soil. It contributes new experimental evidence regarding the adverse effects of livestock grazing, particularly through dung deposition, on the soil microbiome in degraded grassland. This knowledge is crucial for guiding managers in conserving the soil microbiome in grazed grasslands.},
}

@article {pmid38614128,
year = {2024},
author = {Li, C and Guo, X and He, Y and Wang, J and Hao, J and Liu, X},
title = {Cohabiting with ulcerative colitis patients decreases differences of gut microbiome between healthy individuals and the patients.},
journal = {Annals of medicine},
volume = {56},
number = {1},
pages = {2337712},
pmid = {38614128},
issn = {1365-2060},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Colitis, Ulcerative/genetics ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; Inflammation ; },
abstract = {Background: Ulcerative colitis (UC), which is characterized by chronic relapsing inflammation of the colon, results from a complex interaction of factors involving the host, environment, and microbiome. The present study aimed to investigate the gut microbial composition and metabolic variations in patients with UC and their spouses. Materials and Methods: Fecal samples were collected from 13 healthy spouses and couples with UC. 16S rRNA gene amplicon sequencing and metagenomics sequencing were used to analyze gut microbiota composition, pathways, gene expression, and enzyme activity, followed by the Kyoto Encyclopedia of Genes and Genomes. Results: We found that the microbiome diversity of couples with UC decreased, especially that of UC patients. Bacterial composition, such as Firmicutes, was altered between UC patients and healthy controls, but was not significantly different between UC patients and their spouses. This has also been observed in pathways, such as metabolism, genetic information processing, organismal systems, and human diseases. However, the genes and enzymes of spouses with UC were not significantly different from those of healthy individuals. Furthermore, the presence of Faecalibacterium correlated with oxidative phosphorylation, starch and sucrose metabolism, amino sugar and nucleotide sugar metabolism, and the bacterial secretion system, showed a marked decline in the UC group compared with their spouses, but did not vary between healthy couples. Conclusion: Our study revealed that cohabitation with UC patients decreased differences in the gut microbiome between healthy individuals and patients. Not only was the composition and diversity of the microbiota diminished, but active pathways also showed some decline. Furthermore, Firmicutes, Faecalibacterium, and the four related pathways may be associated with the pathological state of the host rather than with human behavior.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Colitis, Ulcerative/genetics
RNA, Ribosomal, 16S/genetics
*Microbiota
Inflammation

@article {pmid38613781,
year = {2024},
author = {Gheorghe, CE and Leigh, SJ and Tofani, GSS and Bastiaanssen, TFS and Lyte, JM and Gardellin, E and Govindan, A and Strain, C and Martinez-Herrero, S and Goodson, MS and Kelley-Loughnane, N and Cryan, JF and Clarke, G},
title = {The microbiota drives diurnal rhythms in tryptophan metabolism in the stressed gut.},
journal = {Cell reports},
volume = {43},
number = {4},
pages = {114079},
doi = {10.1016/j.celrep.2024.114079},
pmid = {38613781},
issn = {2211-1247},
abstract = {Chronic stress disrupts microbiota-gut-brain axis function and is associated with altered tryptophan metabolism, impaired gut barrier function, and disrupted diurnal rhythms. However, little is known about the effects of acute stress on the gut and how it is influenced by diurnal physiology. Here, we used germ-free and antibiotic-depleted mice to understand how microbiota-dependent oscillations in tryptophan metabolism would alter gut barrier function at baseline and in response to an acute stressor. Cecal metabolomics identified tryptophan metabolism as most responsive to a 15-min acute stressor, while shotgun metagenomics revealed that most bacterial species exhibiting rhythmicity metabolize tryptophan. Our findings highlight that the gastrointestinal response to acute stress is dependent on the time of day and the microbiome, with a signature of stress-induced functional alterations in the ileum and altered tryptophan metabolism in the colon.},
}

@article {pmid38613648,
year = {2024},
author = {Hs, A},
title = {The Impact of Prevotella on Neurobiology in Aging: Deciphering Dendritic Cell Activity and Inflammatory Dynamics.},
journal = {Molecular neurobiology},
volume = {},
number = {},
pages = {},
pmid = {38613648},
issn = {1559-1182},
abstract = {Prevotella species, notably Prevotella copri, significantly populate the human gut. In particular, P. copri is prevalent among non-Western populations with diets high in fiber. These species show complex relationships with diverse health aspects, associating with beneficial outcomes, including reduced visceral fat and improved glucose tolerance. Studies implicate various Prevotella species in specific diseases. Prevotella nigrescens and Porphyromonas gingivalis were linked to periodontal disease, promoting immune responses and influencing T helper type 17 (Th17) cells. Prevotella bivia was associated with bacterial vaginosis and a specific increase in activated cells in the vaginal mucosa. In contrast, they have shown substantial potential for inducing connective tissue degradation and alveolar bone resorption. Prevotella's role in neuroinflammatory disorders and autoinflammatory conditions such as Alzheimer's disease and Parkinson's disease has also been noted. The complex relationship between Prevotella and age-related conditions further extends to neurobiological changes in aging, with varying associations with Alzheimer's, Parkinson's, and other inflammatory conditions. Studies have also identified Prevotella to be implicated in cognitive decline in middle aged and the elderly. Future directions in this research area are anticipated to explore Prevotella-associated inflammatory mechanisms and therapeutic interventions. Investigating specific drug targets and immunomodulatory measures could lead to novel therapeutic strategies. Understanding how Prevotella-induced inflammation interacts with aging diseases would offer promising insights for treatments and interventions. This review urges ongoing research to discover therapeutic targets and mechanisms for moderating Prevotella-associated inflammation to further enhance our understanding and improve health outcomes.},
}

@article {pmid38613180,
year = {2024},
author = {McKenna, MC and Choi, IY and Schousboe, A},
title = {Preface: Special issue: 14[th] International Conference on Brain Energy Metabolism: Energy substrates and microbiome govern brain bioenergetics and cognitive function with aging.},
journal = {Journal of neurochemistry},
volume = {},
number = {},
pages = {},
doi = {10.1111/jnc.16094},
pmid = {38613180},
issn = {1471-4159},
support = {1R13 AG067693-01/AG/NIA NIH HHS/United States ; },
abstract = {This Preface introduces the Special Issue entitled, "Energy Substrates and Microbiome Govern Brain Bioenergetics and Cognitive Function with Aging", which is comprised of manuscripts contributed by invited speakers and program/organizing committee members who participated in the 14th International Conference on Brain Energy Metabolism (ICBEM) held on October 24-27, 2022 in Santa Fe, New Mexico, USA. The conference covered the latest developments in research related to neuronal energetics, emerging roles for glycogen in higher brain functions, the impact of dietary intervention on aging, memory, and Alzheimer's disease, roles of the microbiome in gut-brain signaling, astrocyte-neuron interactions related to cognition and memory, novel roles for mitochondria and their metabolites, and metabolic neuroimaging in aging and neurodegeneration. The special issue contains 25 manuscripts on these topics plus three tributes to outstanding scientists who have made important contributions to brain energy metabolism and participated in numerous ICBEM conferences. In addition, two of the manuscripts describe important directions and the rationale for future research in many thematic areas covered by the conference.},
}

@article {pmid38613113,
year = {2024},
author = {Leonard, LM and Simpson, AMR and Li, S and Reddivari, L and Cross, TL},
title = {A Gnotobiotic Mouse Model with Divergent Equol-Producing Phenotypes: Potential for Determining Microbial-Driven Health Impacts of Soy Isoflavone Daidzein.},
journal = {Nutrients},
volume = {16},
number = {7},
pages = {},
pmid = {38613113},
issn = {2072-6643},
support = {Agricultural Science and Extension for Economic Development (AgSeed) program by the College of Agriculture//Purdue University West Lafayette/ ; },
mesh = {Humans ; Female ; Male ; Animals ; Mice ; *Equol ; *Isoflavones ; Disease Models, Animal ; Ketones ; Phenotype ; },
abstract = {The implications of soy consumption on human health have been a subject of debate, largely due to the mixed evidence regarding its benefits and potential risks. The variability in responses to soy has been partly attributed to differences in the metabolism of soy isoflavones, compounds with structural similarities to estrogen. Approximately one-third of humans possess gut bacteria capable of converting soy isoflavone daidzein into equol, a metabolite produced exclusively by gut microbiota with significant estrogenic potency. In contrast, lab-raised rodents are efficient equol producers, except for those raised germ-free. This discrepancy raises concerns about the applicability of traditional rodent models to humans. Herein, we designed a gnotobiotic mouse model to differentiate between equol producers and non-producers by introducing synthetic bacterial communities with and without the equol-producing capacity into female and male germ-free mice. These gnotobiotic mice display equol-producing phenotypes consistent with the capacity of the gut microbiota received. Our findings confirm the model's efficacy in mimicking human equol production capacity, offering a promising tool for future studies to explore the relationship between endogenous equol production and health outcomes like cardiometabolic health and fertility. This approach aims to refine dietary guidelines by considering individual microbiome differences.},
}

Humans
Female
Male
Animals
Mice
*Equol
*Isoflavones
Disease Models, Animal
Ketones
Phenotype

@article {pmid38613109,
year = {2024},
author = {Byerley, LO and Lorenzen, B and Chang, HM and Hartman, WG and Keenan, MJ and Page, R and Luo, M and Dowd, SE and Taylor, CM},
title = {Gut Microbial Dysbiosis Differs in Two Distinct Cachectic Tumor-Bearing Models Consuming the Same Diet.},
journal = {Nutrients},
volume = {16},
number = {7},
pages = {},
pmid = {38613109},
issn = {2072-6643},
support = {no number//American Institute for Cancer Research/ ; no number//California Walnut Commission/ ; },
mesh = {Male ; Animals ; Rats ; Cachexia/etiology ; Dysbiosis ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; Diet ; *Sarcoma ; *Juglans ; },
abstract = {The impact of cancer cachexia on the colonic microbiota is poorly characterized. This study assessed the effect of two cachectic-producing tumor types on the gut microbiota to determine if a similar dysbiosis could be found. In addition, it was determined if a diet containing an immunonutrient-rich food (walnuts) known to promote the growth of probiotic bacteria in the colon could alter the dysbiosis and slow cachexia. Male Fisher 344 rats were randomly assigned to a semi-purified diet with or without walnuts. Then, within each diet group, rats were further assigned randomly to a treatment group: tumor-bearing ad libitum fed (TB), non-tumor-bearing ad libitum fed (NTB-AL), and non-tumor-bearing group pair-fed to the TB (NTB-PF). The TB group was implanted either with the Ward colon carcinoma or MCA-induced sarcoma, both transplantable tumor lines. Fecal samples were collected after the development of cachexia, and bacteria species were identified using 16S rRNA gene analysis. Both TB groups developed cachexia but had a differently altered gut microbiome. Beta diversity was unaffected by treatment (NTB-AL, TB, and NTB-PF) regardless of tumor type but was affected by diet. Also, diet consistently changed the relative abundance of several bacteria taxa, while treatment and tumor type did not. The control diet increased the abundance of A. Anaeroplasma, while the walnut diet increased the genus Ruminococcus. There were no common fecal bacterial changes characteristic of cachexia found. Diet consistently changed the gut microbiota, but these changes were insufficient to slow the progression of cachexia, suggesting cancer cachexia is more complex than a few gut microbiota shifts.},
}

Male
Animals
Rats
Cachexia/etiology
Dysbiosis
*Gastrointestinal Microbiome
RNA, Ribosomal, 16S/genetics
Diet
*Sarcoma
*Juglans

@article {pmid38613108,
year = {2024},
author = {Schoenthaler, SJ and Prescott, SL and Logan, AC},
title = {Homicide or Happiness: Did Folate Fortification and Public Health Campaigns Influence Homicide Rates and the Great American Crime Decline?.},
journal = {Nutrients},
volume = {16},
number = {7},
pages = {},
pmid = {38613108},
issn = {2072-6643},
mesh = {*Homicide ; *Happiness ; Retrospective Studies ; Folic Acid ; Health Promotion ; },
abstract = {The last several years have witnessed a remarkable growth in research directed at nutrition and behavior, with increased interest in the field of nutritional criminology. It is becoming clear that dietary patterns and specific nutrients play an important role in cognition and behavior, including those related to aggression, violence, and antisocial activity. Included in this expanding knowledge base is the recognition that folate, through multiple pathways, including enzymatic reactions and gut microbiome ecology, plays a critical role in central nervous system functioning. These mechanistic advances allow for a retrospective analysis of a topic that remains unexplained-the sudden and unpredicted drop in homicide and other violent crime rates in the United States and other nations in the 1990s. Here, we revisit this marked reduction in homicide rates through the lens of the coincident public health campaign (and subsequent mandatory fortification) to increase folic acid intake. Based on objectively measured blood folate levels through the National Health and Nutrition Examination Surveys, there is little doubt that tissue folate witnessed a dramatic rise at the national level from 1988 through 2000. Drawing from accumulated and emerging research on the neurobehavioral aspects of folate, it is our contention that this relatively sudden and massive increase in tissue folate levels may have contributed to reductions in violent crime in the United States.},
}

*Homicide
*Happiness
Retrospective Studies
Folic Acid
Health Promotion

@article {pmid38613107,
year = {2024},
author = {Yu, J and Zhang, Y and Wells, JCK and Wei, Z and Bajaj-Elliott, M and Nielsen, DS and Fewtrell, MS},
title = {A Stress Reduction Intervention for Lactating Mothers Alters Maternal Gut, Breast Milk, and Infant Gut Microbiomes: Data from a Randomized Controlled Trial.},
journal = {Nutrients},
volume = {16},
number = {7},
pages = {},
pmid = {38613107},
issn = {2072-6643},
support = {private research account//Prof. Mary Fewtrell's research account/ ; },
mesh = {Female ; Infant ; Humans ; Milk, Human ; *Gastrointestinal Microbiome ; Mothers ; Breast ; *Microbiota ; },
abstract = {BACKGROUND: This secondary analysis of data from a randomized controlled trial (RCT) investigated how the maternal gut, breast milk, and infant gut microbiomes may contribute to the effects of a relaxation intervention, which reduced maternal stress and promoted infant weight gain.

METHODS: An RCT was undertaken in healthy Chinese primiparous mother-infant pairs (34[0/7]-37[6/7]gestation weeks). Mothers were randomly allocated to either the intervention group (IG, listening to relaxation meditation) or the control group (CG). Outcomes were the differences in microbiome composition and the diversity in the maternal gut, breast milk, and infant gut at 1 (baseline) and 8 weeks (post-intervention) between IG and CG, assessed using 16S rRNA gene amplicon sequencing of fecal and breastmilk samples.

RESULTS: In total, 38 mother-infant pairs were included in this analysis (IG = 19, CG = 19). The overall microbiome community structure in the maternal gut was significantly different between the IG and CG at 1 week, with the difference being more significant at 8 weeks (Bray-Curtis distance R[2] = 0.04 vs. R[2] = 0.13). Post-intervention, a significantly lower α-diversity was observed in IG breast milk (observed features: CG = 295 vs. IG = 255, p = 0.032); the Bifidobacterium genera presented a higher relative abundance. A significantly higher α-diversity was observed in IG infant gut (observed features: CG = 73 vs. IG = 113, p < 0.001).

CONCLUSIONS: The findings were consistent with the hypothesis that the microbiome might mediate observed relaxation intervention effects via gut-brain axis and entero-mammary pathways; but confirmation is required.},
}

Female
Infant
Humans
Milk, Human
*Gastrointestinal Microbiome
Mothers
Breast
*Microbiota

@article {pmid38613104,
year = {2024},
author = {Hamamah, S and Hajnal, A and Covasa, M},
title = {Influence of Bariatric Surgery on Gut Microbiota Composition and Its Implication on Brain and Peripheral Targets.},
journal = {Nutrients},
volume = {16},
number = {7},
pages = {},
pmid = {38613104},
issn = {2072-6643},
mesh = {Humans ; *Gastrointestinal Microbiome ; Dopamine ; Brain ; *Bariatric Surgery ; Obesity/surgery ; *Gastrointestinal Hormones ; *Obesity, Morbid ; },
abstract = {Obesity remains a significant global health challenge, with bariatric surgery remaining as one of the most effective treatments for severe obesity and its related comorbidities. This review highlights the multifaceted impact of bariatric surgery beyond mere physical restriction or nutrient malabsorption, underscoring the importance of the gut microbiome and neurohormonal signals in mediating the profound effects on weight loss and behavior modification. The various bariatric surgery procedures, such as Roux-en-Y gastric bypass (RYGB) and sleeve gastrectomy (SG), act through distinct mechanisms to alter the gut microbiome, subsequently impacting metabolic health, energy balance, and food reward behaviors. Emerging evidence has shown that bariatric surgery induces profound changes in the composition of the gut microbiome, notably altering the Firmicutes/Bacteroidetes ratio and enhancing populations of beneficial bacteria such as Akkermansia. These microbiota shifts have far-reaching effects beyond gut health, influencing dopamine-mediated reward pathways in the brain and modulating the secretion and action of key gut hormones including ghrelin, leptin, GLP-1, PYY, and CCK. The resultant changes in dopamine signaling and hormone levels contribute to reduced hedonic eating, enhanced satiety, and improved metabolic outcomes. Further, post-bariatric surgical effects on satiation targets are in part mediated by metabolic byproducts of gut microbiota like short-chain fatty acids (SCFAs) and bile acids, which play a pivotal role in modulating metabolism and energy expenditure and reducing obesity-associated inflammation, as well as influencing food reward pathways, potentially contributing to the regulation of body weight and reduction in hedonic eating behaviors. Overall, a better understanding of these mechanisms opens the door to developing non-surgical interventions that replicate the beneficial effects of bariatric surgery on the gut microbiome, dopamine signaling, and gut hormone regulation, offering new avenues for obesity treatment.},
}

Humans
*Gastrointestinal Microbiome
Dopamine
Brain
*Bariatric Surgery
Obesity/surgery
*Gastrointestinal Hormones
*Obesity, Morbid

@article {pmid38613087,
year = {2024},
author = {Dziedzic, A and Maciak, K and Bliźniewska-Kowalska, K and Gałecka, M and Kobierecka, W and Saluk, J},
title = {The Power of Psychobiotics in Depression: A Modern Approach through the Microbiota-Gut-Brain Axis: A Literature Review.},
journal = {Nutrients},
volume = {16},
number = {7},
pages = {},
pmid = {38613087},
issn = {2072-6643},
mesh = {Humans ; *Brain-Gut Axis ; Depression/therapy ; *Gastrointestinal Microbiome ; Brain ; Dysbiosis ; },
abstract = {The microbiota-gut-brain (MGB) axis is a complex communication network linking the gut, microbiota, and brain, influencing various aspects of health and disease. Dysbiosis, a disturbance in the gut microbiome equilibrium, can significantly impact the MGB axis, leading to alterations in microbial composition and function. Emerging evidence highlights the connection between microbiota alterations and neurological and psychiatric disorders, including depression. This review explores the potential of psychobiotics in managing depressive disorders, emphasizing their role in restoring microbial balance and influencing the MGB axis. Psychobiotics exhibit positive effects on the intestinal barrier, immune response, cortisol levels, and the hypothalamic-pituitary-adrenal (HPA) axis. Studies suggest that probiotics may serve as an adjunct therapy for depression, especially in treatment-resistant cases. This review discusses key findings from studies on psychobiotics interventions, emphasizing their impact on the gut-brain axis and mental health. The increasing acceptance of the expanded concept of the MGB axis underscores the importance of microorganisms in mental well-being. As our understanding of the microbiome's role in health and disease grows, probiotics emerge as promising agents for addressing mental health issues, providing new avenues for therapeutic interventions in depressive disorders.},
}

Humans
*Brain-Gut Axis
Depression/therapy
*Gastrointestinal Microbiome
Brain
Dysbiosis

@article {pmid38613066,
year = {2024},
author = {Dijk, S and Jarman, M and Zhang, Z and Lawley, M and Ahmad, M and Suarez, R and Rossi, L and Chen, M and Wu, J and Carroll, MW and Otley, A and Sherlock, M and Mack, DR and Jacobson, K and deBruyn, JC and El-Matary, W and Deslandres, C and Rashid, M and Church, PC and Walters, TD and Huynh, HQ and Surette, MG and Griffiths, AM and Wine, E and , },
title = {Pre-Diagnosis Diet Predicts Response to Exclusive Enteral Nutrition and Correlates with Microbiome in Pediatric Crohn Disease.},
journal = {Nutrients},
volume = {16},
number = {7},
pages = {},
pmid = {38613066},
issn = {2072-6643},
support = {426160/CAPMC/CIHR/Canada ; },
mesh = {Animals ; Male ; Child ; Humans ; Enteral Nutrition ; *Crohn Disease/therapy ; Tumor Necrosis Factor Inhibitors ; *Microbiota ; *Diet, Mediterranean ; },
abstract = {Exclusive enteral nutrition (EEN) is effective in inducing remission in pediatric Crohn disease (CD). EEN alters the intestinal microbiome, but precise mechanisms are unknown. We hypothesized that pre-diagnosis diet establishes a baseline gut microbiome, which then mediates response to EEN. We analyzed prospectively recorded food frequency questionnaires (FFQs) for pre-diagnosis dietary patterns. Fecal microbiota were sequenced (16SrRNA) at baseline and through an 18-month follow-up period. Dietary patterns, Mediterranean diet adherence, and stool microbiota were associated with EEN treatment outcomes, disease flare, need for anti-tumor necrosis factor (TNF)-α therapy, and long-term clinical outcomes. Ninety-eight patients were included. Baseline disease severity and microbiota were associated with diet. Four dietary patterns were identified by FFQs; a "mature diet" high in fruits, vegetables, and fish was linked to increased baseline microbial diversity, which was associated with fewer disease flares (p < 0.05) and a trend towards a delayed need for anti-TNF therapy (p = 0.086). Baseline stool microbial taxa were increased (Blautia and Faecalibacterium) or decreased (Ruminococcus gnavus group) with the mature diet compared to other diets. Surprisingly, a "pre-packaged" dietary pattern (rich in processed foods) was associated with delayed flares in males (p < 0.05). Long-term pre-diagnosis diet was associated with outcomes of EEN therapy in pediatric CD; diet-microbiota and microbiota-outcome associations may mediate this relationship.},
}

Animals
Male
Child
Humans
Enteral Nutrition
*Crohn Disease/therapy
Tumor Necrosis Factor Inhibitors
*Microbiota
*Diet, Mediterranean

@article {pmid38613058,
year = {2024},
author = {Lombardi, M and Troisi, J and Motta, BM and Torre, P and Masarone, M and Persico, M},
title = {Gut-Liver Axis Dysregulation in Portal Hypertension: Emerging Frontiers.},
journal = {Nutrients},
volume = {16},
number = {7},
pages = {},
pmid = {38613058},
issn = {2072-6643},
mesh = {Humans ; *Esophageal and Gastric Varices ; Gastrointestinal Hemorrhage ; *Hypertension, Portal/etiology ; Ascites ; },
abstract = {Portal hypertension (PH) is a complex clinical challenge with severe complications, including variceal bleeding, ascites, hepatic encephalopathy, and hepatorenal syndrome. The gut microbiota (GM) and its interconnectedness with human health have emerged as a captivating field of research. This review explores the intricate connections between the gut and the liver, aiming to elucidate how alterations in GM, intestinal barrier function, and gut-derived molecules impact the development and progression of PH. A systematic literature search, following PRISMA guidelines, identified 12 original articles that suggest a relationship between GM, the gut-liver axis, and PH. Mechanisms such as dysbiosis, bacterial translocation, altered microbial structure, and inflammation appear to orchestrate this relationship. One notable study highlights the pivotal role of the farnesoid X receptor axis in regulating the interplay between the gut and liver and proposes it as a promising therapeutic target. Fecal transplantation experiments further emphasize the pathogenic significance of the GM in modulating liver maladies, including PH. Recent advancements in metagenomics and metabolomics have expanded our understanding of the GM's role in human ailments. The review suggests that addressing the unmet need of identifying gut-liver axis-related metabolic and molecular pathways holds potential for elucidating pathogenesis and directing novel therapeutic interventions.},
}

Humans
*Esophageal and Gastric Varices
Gastrointestinal Hemorrhage
*Hypertension, Portal/etiology
Ascites

@article {pmid38613035,
year = {2024},
author = {Angima, G and Qu, Y and Park, SH and Dallas, DC},
title = {Prebiotic Strategies to Manage Lactose Intolerance Symptoms.},
journal = {Nutrients},
volume = {16},
number = {7},
pages = {},
pmid = {38613035},
issn = {2072-6643},
support = {NA//BUILD Dairy/ ; NA//the Oregon Dairy Nutrition Council/ ; NA//the USDA Multistate Workgroup W4002/ ; },
mesh = {Humans ; *Lactose Intolerance/genetics ; Lactose ; Lactase/genetics ; Abdominal Pain ; Biological Evolution ; Prebiotics ; },
abstract = {Lactose intolerance, which affects about 65-75% of the world's population, is caused by a genetic post-weaning deficiency of lactase, the enzyme required to digest the milk sugar lactose, called lactase non-persistence. Symptoms of lactose intolerance include abdominal pain, bloating and diarrhea. Genetic variations, namely lactase persistence, allow some individuals to metabolize lactose effectively post-weaning, a trait thought to be an evolutionary adaptation to dairy consumption. Although lactase non-persistence cannot be altered by diet, prebiotic strategies, including the consumption of galactooligosaccharides (GOSs) and possibly low levels of lactose itself, may shift the microbiome and mitigate symptoms of lactose consumption. This review discusses the etiology of lactose intolerance and the efficacy of prebiotic approaches like GOSs and low-dose lactose in symptom management.},
}

Humans
*Lactose Intolerance/genetics
Lactose
Lactase/genetics
Abdominal Pain
Biological Evolution
Prebiotics

@article {pmid38613022,
year = {2024},
author = {Wang, Y and Wymond, B and Tandon, H and Belobrajdic, DP},
title = {Swapping White for High-Fibre Bread Increases Faecal Abundance of Short-Chain Fatty Acid-Producing Bacteria and Microbiome Diversity: A Randomized, Controlled, Decentralized Trial.},
journal = {Nutrients},
volume = {16},
number = {7},
pages = {},
pmid = {38613022},
issn = {2072-6643},
support = {n/a//Bakers Delight/ ; },
mesh = {Adult ; Humans ; *Bread ; *Microbiota ; Fatty Acids, Volatile ; Butyrates ; Bacteria ; Prebiotics ; },
abstract = {A low-fibre diet leads to gut microbiota imbalance, characterized by low diversity and reduced ability to produce beneficial metabolites, such as short-chain fatty acids (SCFAs). This imbalance is associated with poor gastrointestinal and metabolic health. We aimed to determine whether one dietary change, substitution of white bread with high-fibre bread, improves gut microbiota diversity and SCFA-producing capability. Twenty-two healthy adults completed a two-phase randomized, cross-over trial. The participants consumed three slices of a high-fibre bread (Prebiotic Cape Seed Loaf with BARLEYmax[®]) or control white bread as part of their usual diet for 2 weeks, with the treatment periods separated by a 4-week washout. High-fibre bread consumption increased total dietary fibre intake to 40 g/d, which was double the amount of fibre consumed at baseline or during the white bread intervention. Compared to white bread, the high-fibre bread intervention resulted in higher faecal alpha diversity (Shannon, p = 0.014) and relative abundance of the Lachnospiracae ND3007 group (p < 0.001, FDR = 0.019) and tended to increase the butyrate-producing capability (p = 0.062). In conclusion, substituting white bread with a high-fibre bread improved the diversity of gut microbiota and specific microbes involved in SCFA production and may enhance the butyrate-producing capability of gut microbiota in healthy adults. These findings suggest that a single dietary change involving high-fibre bread provides a practical way for adults to exceed recommended dietary fibre intake levels that improve gut microbiota composition and support gastrointestinal and metabolic health.},
}

Adult
Humans
*Bread
*Microbiota
Fatty Acids, Volatile
Butyrates
Bacteria
Prebiotics

@article {pmid38613011,
year = {2024},
author = {Feng, Q and Lin, J and Niu, Z and Wu, T and Shen, Q and Hou, D and Zhou, S},
title = {A Comparative Analysis between Whole Chinese Yam and Peeled Chinese Yam: Their Hypolipidemic Effects via Modulation of Gut Microbiome in High-Fat Diet-Fed Mice.},
journal = {Nutrients},
volume = {16},
number = {7},
pages = {},
pmid = {38613011},
issn = {2072-6643},
support = {SPKX-202203//China Agricultural University and Wilmar (Shanghai) Biotechnology Research & Development Center Co., Ltd., Discipline construction - Food Science and Engineering/ ; QNJJ2022-18//Research Foundation for Youth Scholars of Beijing Technology and Business University/ ; },
mesh = {Male ; Animals ; Mice ; Diet, High-Fat/adverse effects ; *Gastrointestinal Microbiome ; *Dioscorea ; RNA, Ribosomal, 16S/genetics ; Obesity ; *Hyperlipidemias ; Lipids ; },
abstract = {Chinese yam is a "medicine food homology" food with medical properties, but little is known about its health benefits on hyperlipidemia. Furthermore, the effect of peeling processing on the efficacy of Chinese yam is still unclear. In this study, the improvement effects of whole Chinese yam (WY) and peeled Chinese yam (PY) on high-fat-diet (HFD)-induced hyperlipidemic mice were explored by evaluating the changes in physiological, biochemical, and histological parameters, and their modulatory effects on gut microbiota were further illustrated. The results show that both WY and PY could significantly attenuate the HFD-induced obesity phenotype, accompanied by the mitigative effect on epididymis adipose damage and hepatic tissue injury. Except for the ameliorative effect on TG, PY retained the beneficial effects of WY on hyperlipemia. Furthermore, 16S rRNA sequencing revealed that WY and PY reshaped the gut microbiota composition, especially the bloom of several beneficial bacterial strains (Akkermansia, Bifidobacterium, and Faecalibaculum) and the reduction in some HFD-dependent taxa (Mucispirillum, Coriobacteriaceae_UCG-002, and Candidatus_Saccharimonas). PICRUSt analysis showed that WY and PY could significantly regulate lipid transport and metabolism-related pathways. These findings suggest that Chinese yam can alleviate hyperlipidemia via the modulation of the gut microbiome, and peeling treatment had less of an effect on the lipid-lowering efficacy of yam.},
}

Male
Animals
Mice
Diet, High-Fat/adverse effects
*Gastrointestinal Microbiome
*Dioscorea
RNA, Ribosomal, 16S/genetics
Obesity
*Hyperlipidemias
Lipids

@article {pmid38612992,
year = {2024},
author = {Teng, Q and Lv, H and Peng, L and Ren, Z and Chen, J and Ma, L and Wei, H and Wan, C},
title = {Lactiplantibacillus plantarum ZDY2013 Inhibits the Development of Non-Alcoholic Fatty Liver Disease by Regulating the Intestinal Microbiota and Modulating the PI3K/Akt Pathway.},
journal = {Nutrients},
volume = {16},
number = {7},
pages = {},
pmid = {38612992},
issn = {2072-6643},
support = {20212BAB205027//National Nature Science Foundation of Jiangxi Province/ ; YC2022-s004//Jiangxi Provincial Postgraduate Innovation Special Fund/ ; },
mesh = {Humans ; Male ; Animals ; Mice ; Mice, Inbred C57BL ; *Non-alcoholic Fatty Liver Disease/drug therapy/prevention & control ; *Gastrointestinal Microbiome ; Phosphatidylinositol 3-Kinases ; Proto-Oncogene Proteins c-akt ; *Insulin Resistance ; Fructose ; *Hypercholesterolemia ; Inflammation/drug therapy ; *Lactobacillus plantarum ; },
abstract = {Non-alcoholic fatty liver disease (NAFLD) is a common chronic hepatic condition whose impact on human health is increasingly significant. The imbalance of the gut microbiome, linked to insulin resistance, heightened intestinal permeability, and pro-inflammatory reactions, may be the linchpin in the development of NAFLD. In our research, the impact of Lactiplantibacillus plantarum ZDY2013 administration for 12 weeks on gut microbiota dysbiosis induced by a high-fat, high-fructose, high-cholesterol (FHHC) diet in male C57BL/6n mice was investigated. Research results presented that the intervention of L. plantarum ZDY2013 in mice fed with the FHHC diet could restore their liver function and regulate oxidative stress. Compared to mice in the model group, the intervention of L. plantarum ZDY2013 significantly regulated the gut microbiota, inhibited the LPS/NF-κB pathway, and led to a lower level of colonic inflammation in the mice administered with L. plantarum ZDY2013. It also improved insulin resistance to regulate the PI3K/Akt pathway and lipid metabolism, thereby resulting in reduced fat accumulation in the liver. The above results suggest that the intervention of L. plantarum ZDY2013 can hinder the progression of diet-induced NAFLD by reducing inflammation to regulate the PI3K/Akt pathway and regulating gut microbiota disturbance.},
}

Humans
Male
Animals
Mice
Mice, Inbred C57BL
*Non-alcoholic Fatty Liver Disease/drug therapy/prevention & control
*Gastrointestinal Microbiome
Phosphatidylinositol 3-Kinases
Proto-Oncogene Proteins c-akt
*Insulin Resistance
Fructose
*Hypercholesterolemia
Inflammation/drug therapy
*Lactobacillus plantarum

@article {pmid38612976,
year = {2024},
author = {Fagunwa, O and Davies, K and Bradbury, J},
title = {The Human Gut and Dietary Salt: The Bacteroides/Prevotella Ratio as a Potential Marker of Sodium Intake and Beyond.},
journal = {Nutrients},
volume = {16},
number = {7},
pages = {},
pmid = {38612976},
issn = {2072-6643},
support = {FMoH/PTDF//Federal Government of Nigeria/ ; NA//University of Huddersfield/ ; publishing//Queen's University Belfast/ ; },
mesh = {Humans ; *Sodium Chloride, Dietary ; *Microbiota ; Bacteroides ; Bacteroidetes ; Firmicutes ; Prevotella ; Sodium ; },
abstract = {The gut microbiota is a dynamic ecosystem that plays a pivotal role in maintaining host health. The perturbation of these microbes has been linked to several health conditions. Hence, they have emerged as promising targets for understanding and promoting good health. Despite the growing body of research on the role of sodium in health, its effects on the human gut microbiome remain under-explored. Here, using nutrition and metagenomics methods, we investigate the influence of dietary sodium intake and alterations of the human gut microbiota. We found that a high-sodium diet (HSD) altered the gut microbiota composition with a significant reduction in Bacteroides and inverse increase in Prevotella compared to a low-sodium diet (LSD). However, there is no clear distinction in the Firmicutes/Bacteroidetes (F/B) ratio between the two diet types. Metabolic pathway reconstruction revealed the presence of sodium reabsorption genes in the HSD, but not LSD. Since it is currently difficult in microbiome studies to confidently associate the F/B ratio with what is considered healthy (e.g., low sodium) or unhealthy (e.g., high sodium), we suggest that the use of a genus-based ratio such as the Bacteroides/Prevotella (B/P) ratio may be more beneficial for the application of microbiome studies in health.},
}

Humans
*Sodium Chloride, Dietary
*Microbiota
Bacteroides
Bacteroidetes
Firmicutes
Prevotella
Sodium

@article {pmid38612971,
year = {2024},
author = {Vesci, L and Tundo, G and Soldi, S and Galletti, S and Stoppoloni, D and Bernardini, R and Modolea, AB and Luberto, L and Marra, E and Giorgi, F and Marini, S},
title = {A Novel Lactobacillus brevis Fermented with a Vegetable Substrate (AL0035) Counteracts TNBS-Induced Colitis by Modulating the Gut Microbiota Composition and Intestinal Barrier.},
journal = {Nutrients},
volume = {16},
number = {7},
pages = {},
pmid = {38612971},
issn = {2072-6643},
mesh = {Humans ; Animals ; Mice ; *Gastrointestinal Microbiome ; *Levilactobacillus brevis ; Vegetables ; RNA, Ribosomal, 16S ; *Colitis/chemically induced ; Inflammation ; Cytokines ; Tight Junction Proteins/genetics ; },
abstract = {Crohn's and ulcerative colitis are common conditions associated with inflammatory bowel disease as well as intestinal flora and epithelial barrier dysfunction. A novel fermented Lactobacillus brevis (AL0035) herein assayed in a trinitro benzene sulfonic acid (TNBS)-induced colitis mice model after oral administration significantly counteracted the body weight loss and improves the disease activity index and histological injury scores. AL0035 significantly decreased the mRNA and protein expression of different pro-inflammatory cytokines (TNFalpha, IL-1beta, IL-6, IL-12, IFN-gamma) and enhanced the expression of IL-10. In addition, the probiotic promoted the expression of tight junction proteins, such as ZO-1, keeping the intestinal mucosal barrier function to attenuate colitis symptoms in mice. Markers of inflammation cascade such as myeloperoxidase (MPO) and PPAR-gamma measured in the colon were also modified by AL0035 treatment. AL0035 was also able to reduce different lymphocyte markers' infiltration in the colon (GATA-3, T-Bet, NK1.1) and monocyte chemoattractant protein-1 (MCP-1/CCL2), a key chemokine involved in the migration and infiltration of monocytes/macrophages in the immunological surveillance of tissues and inflammation. In colonic microbiota profile analysis through 16S rRNA sequencing, AL0035 increased the microbial diversity depleted by TNBS administration and the relative abundance of the Lactobacillaceae and Lachnospiraceae families, whereas it decreased the abundance of Proteobacteria. Altogether, these data indicated that AL0035 could lower the severity of colitis induced by TNBS by regulating inflammatory cytokines, increasing the expression of tight junction proteins and modulating intestinal microbiota, thus preventing tissue damage induced by colitis.},
}

Humans
Animals
Mice
*Gastrointestinal Microbiome
*Levilactobacillus brevis
Vegetables
RNA, Ribosomal, 16S
*Colitis/chemically induced
Inflammation
Cytokines
Tight Junction Proteins/genetics

@article {pmid38612969,
year = {2024},
author = {Alvernaz, SA and Wenzel, ES and Nagelli, U and Pezley, LB and LaBomascus, B and Gilbert, JA and Maki, PM and Tussing-Humphreys, L and Peñalver Bernabé, B},
title = {Inflammatory Dietary Potential Is Associated with Vitamin Depletion and Gut Microbial Dysbiosis in Early Pregnancy.},
journal = {Nutrients},
volume = {16},
number = {7},
pages = {},
pmid = {38612969},
issn = {2072-6643},
support = {U24 DK131617/DK/NIDDK NIH HHS/United States ; R03HD095056/NH/NIH HHS/United States ; K12HD101373/NH/NIH HHS/United States ; R03 HD095056/HD/NICHD NIH HHS/United States ; 1U24DK131617-01/NH/NIH HHS/United States ; K12 HD101373/HD/NICHD NIH HHS/United States ; UL1 TR002003/TR/NCATS NIH HHS/United States ; },
mesh = {Infant, Newborn ; Female ; Pregnancy ; Humans ; Dysbiosis ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S ; *Premature Birth ; *Avitaminosis ; Diet ; Vitamins ; Inflammation ; },
abstract = {Pregnancy alters many physiological systems, including the maternal gut microbiota. Diet is a key regulator of this system and can alter the host immune system to promote inflammation. Multiple perinatal disorders have been associated with inflammation, maternal metabolic alterations, and gut microbial dysbiosis, including gestational diabetes mellitus, pre-eclampsia, preterm birth, and mood disorders. However, the effects of high-inflammatory diets on the gut microbiota during pregnancy have yet to be fully explored. We aimed to address this gap using a system-based approach to characterize associations among dietary inflammatory potential, a measure of diet quality, and the gut microbiome during pregnancy. Forty-seven pregnant persons were recruited prior to 16 weeks of gestation. Participants completed a food frequency questionnaire (FFQ) and provided fecal samples. Dietary inflammatory potential was assessed using the Dietary Inflammatory Index (DII) from the FFQ data. Fecal samples were analyzed using 16S rRNA amplicon sequencing. Differential taxon abundances with respect to the DII score were identified, and the microbial metabolic potential was predicted using PICRUSt2. Inflammatory diets were associated with decreased vitamin and mineral intake and a dysbiotic gut microbiota structure and predicted metabolism. Gut microbial compositional differences revealed a decrease in short-chain fatty acid producers such as Faecalibacterium, and an increase in predicted vitamin B12 synthesis, methylglyoxal detoxification, galactose metabolism, and multidrug efflux systems in pregnant individuals with increased DII scores. Dietary inflammatory potential was associated with a reduction in the consumption of vitamins and minerals and predicted gut microbiota metabolic dysregulation.},
}

Infant, Newborn
Female
Pregnancy
Humans
Dysbiosis
*Gastrointestinal Microbiome
RNA, Ribosomal, 16S
*Premature Birth
*Avitaminosis
Diet
Vitamins
Inflammation

@article {pmid38612951,
year = {2024},
author = {Czarnowski, P and Bałabas, A and Kułaga, Z and Kulecka, M and Goryca, K and Pyśniak, K and Unrug-Bielawska, K and Kluska, A and Bagińska-Drabiuk, K and Głowienka-Stodolak, M and Piątkowska, M and Dąbrowska, M and Żeber-Lubecka, N and Wierzbicka-Rucińska, A and Kotowska, A and Więckowski, S and Mikula, M and Kapuśniak, J and Socha, P and Ostrowski, J},
title = {Effects of Soluble Dextrin Fiber from Potato Starch on Body Weight and Associated Gut Dysbiosis Are Evident in Western Diet-Fed Mice but Not in Overweight/Obese Children.},
journal = {Nutrients},
volume = {16},
number = {7},
pages = {},
pmid = {38612951},
issn = {2072-6643},
support = {POIR.04.01.02-00-0102/17-00 (PreSTFibre4kids)//National Centre for Research and Development/ ; },
mesh = {Child ; Humans ; Male ; Female ; Animals ; Mice ; Dextrins ; *Solanum tuberosum ; Diet, Western ; Dysbiosis ; Overweight ; *Pediatric Obesity ; RNA, Ribosomal, 16S/genetics ; Body Weight ; Starch/pharmacology ; Fruit ; },
abstract = {BACKGROUND: The study investigated the impact of starch degradation products (SDexF) as prebiotics on obesity management in mice and overweight/obese children.

METHODS: A total of 48 mice on a normal diet (ND) and 48 on a Western diet (WD) were divided into subgroups with or without 5% SDexF supplementation for 28 weeks. In a human study, 100 overweight/obese children were randomly assigned to prebiotic and control groups, consuming fruit and vegetable mousse with or without 10 g of SDexF for 24 weeks. Stool samples were analyzed for microbiota using 16S rRNA gene sequencing, and short-chain fatty acids (SCFA) and amino acids (AA) were assessed.

RESULTS: Results showed SDexF slowed weight gain in female mice on both diets but only temporarily in males. It altered bacterial diversity and specific taxa abundances in mouse feces. In humans, SDexF did not influence weight loss or gut microbiota composition, showing minimal changes in individual taxa. The anti-obesity effect observed in mice with WD-induced obesity was not replicated in children undergoing a weight-loss program.

CONCLUSIONS: SDexF exhibited sex-specific effects in mice but did not impact weight loss or microbiota composition in overweight/obese children.},
}

Child
Humans
Male
Female
Animals
Mice
Dextrins
*Solanum tuberosum
Diet, Western
Dysbiosis
Overweight
*Pediatric Obesity
RNA, Ribosomal, 16S/genetics
Body Weight
Starch/pharmacology
Fruit

@article {pmid38612871,
year = {2024},
author = {Wang, L and Koelink, PJ and Garssen, J and Folkerts, G and Henricks, PAJ and Braber, S},
title = {Gut Microbiome and Transcriptomic Changes in Cigarette Smoke-Exposed Mice Compared to COPD and CD Patient Datasets.},
journal = {International journal of molecular sciences},
volume = {25},
number = {7},
pages = {},
pmid = {38612871},
issn = {1422-0067},
support = {201706170055//Chinese Scholarship Council/ ; },
mesh = {Humans ; Animals ; Mice ; *Gastrointestinal Microbiome ; *Crohn Disease/genetics ; *Cigarette Smoking/adverse effects ; RNA, Ribosomal, 16S ; Gene Expression Profiling ; *Pulmonary Disease, Chronic Obstructive/genetics ; Membrane Glycoproteins ; },
abstract = {Chronic obstructive pulmonary disease (COPD) patients and smokers have a higher incidence of intestinal disorders. The aim of this study was to gain insight into the transcriptomic changes in the lungs and intestines, and the fecal microbial composition after cigarette smoke exposure. Mice were exposed to cigarette smoke and their lung and ileum tissues were analyzed by RNA sequencing. The top 15 differentially expressed genes were investigated in publicly available gene expression datasets of COPD and Crohn's disease (CD) patients. The murine microbiota composition was determined by 16S rRNA sequencing. Increased expression of MMP12, GPNMB, CTSK, CD68, SPP1, CCL22, and ITGAX was found in the lungs of cigarette smoke-exposed mice and COPD patients. Changes in the intestinal expression of CD79B, PAX5, and FCRLA were observed in the ileum of cigarette smoke-exposed mice and CD patients. Furthermore, inflammatory cytokine profiles and adhesion molecules in both the lungs and intestines of cigarette smoke-exposed mice were profoundly changed. An altered intestinal microbiota composition and a reduction in bacterial diversity was observed in cigarette smoke-exposed mice. Altered gene expression in the murine lung was detected after cigarette smoke exposure, which might simulate COPD-like alterations. The transcriptomic changes in the intestine of cigarette smoke-exposed mice had some similarities with those of CD patients and were associated with changes in the intestinal microbiome. Future research could benefit from investigating the specific mechanisms underlying the observed gene expression changes due to cigarette smoke exposure, focusing on identifying potential therapeutic targets for COPD and CD.},
}

Humans
Animals
Mice
*Gastrointestinal Microbiome
*Crohn Disease/genetics
*Cigarette Smoking/adverse effects
RNA, Ribosomal, 16S
Gene Expression Profiling
*Pulmonary Disease, Chronic Obstructive/genetics
Membrane Glycoproteins

@article {pmid38612860,
year = {2024},
author = {Marrella, V and Nicchiotti, F and Cassani, B},
title = {Microbiota and Immunity during Respiratory Infections: Lung and Gut Affair.},
journal = {International journal of molecular sciences},
volume = {25},
number = {7},
pages = {},
pmid = {38612860},
issn = {1422-0067},
support = {20223X2JYJ//Governo Italiano/ ; },
mesh = {Animals ; Humans ; *Respiratory Tract Infections ; Antibodies, Monoclonal, Humanized ; *Bacteriophages ; *Microbiota ; Lung ; },
abstract = {Bacterial and viral respiratory tract infections are the most common infectious diseases, leading to worldwide morbidity and mortality. In the past 10 years, the importance of lung microbiota emerged in the context of pulmonary diseases, although the mechanisms by which it impacts the intestinal environment have not yet been fully identified. On the contrary, gut microbial dysbiosis is associated with disease etiology or/and development in the lung. In this review, we present an overview of the lung microbiome modifications occurring during respiratory infections, namely, reduced community diversity and increased microbial burden, and of the downstream consequences on host-pathogen interaction, inflammatory signals, and cytokines production, in turn affecting the disease progression and outcome. Particularly, we focus on the role of the gut-lung bidirectional communication in shaping inflammation and immunity in this context, resuming both animal and human studies. Moreover, we discuss the challenges and possibilities related to novel microbial-based (probiotics and dietary supplementation) and microbial-targeted therapies (antibacterial monoclonal antibodies and bacteriophages), aimed to remodel the composition of resident microbial communities and restore health. Finally, we propose an outlook of some relevant questions in the field to be answered with future research, which may have translational relevance for the prevention and control of respiratory infections.},
}

Animals
Humans
*Respiratory Tract Infections
Antibodies, Monoclonal, Humanized
*Bacteriophages
*Microbiota
Lung

@article {pmid38612834,
year = {2024},
author = {Barathan, M and Ng, SL and Lokanathan, Y and Ng, MH and Law, JX},
title = {The Profound Influence of Gut Microbiome and Extracellular Vesicles on Animal Health and Disease.},
journal = {International journal of molecular sciences},
volume = {25},
number = {7},
pages = {},
pmid = {38612834},
issn = {1422-0067},
support = {DIP-2023-011//National University of Malaysia/ ; FF-2023-264//National University of Malaysia/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome ; *Extracellular Vesicles ; Brain-Gut Axis ; *Microbiota ; *Exosomes ; },
abstract = {The animal gut microbiota, comprising a diverse array of microorganisms, plays a pivotal role in shaping host health and physiology. This review explores the intricate dynamics of the gut microbiome in animals, focusing on its composition, function, and impact on host-microbe interactions. The composition of the intestinal microbiota in animals is influenced by the host ecology, including factors such as temperature, pH, oxygen levels, and nutrient availability, as well as genetic makeup, diet, habitat, stressors, and husbandry practices. Dysbiosis can lead to various gastrointestinal and immune-related issues in animals, impacting overall health and productivity. Extracellular vesicles (EVs), particularly exosomes derived from gut microbiota, play a crucial role in intercellular communication, influencing host health by transporting bioactive molecules across barriers like the intestinal and brain barriers. Dysregulation of the gut-brain axis has implications for various disorders in animals, highlighting the potential role of microbiota-derived EVs in disease progression. Therapeutic approaches to modulate gut microbiota, such as probiotics, prebiotics, microbial transplants, and phage therapy, offer promising strategies for enhancing animal health and performance. Studies investigating the effects of phage therapy on gut microbiota composition have shown promising results, with potential implications for improving animal health and food safety in poultry production systems. Understanding the complex interactions between host ecology, gut microbiota, and EVs provides valuable insights into the mechanisms underlying host-microbe interactions and their impact on animal health and productivity. Further research in this field is essential for developing effective therapeutic interventions and management strategies to promote gut health and overall well-being in animals.},
}

Animals
*Gastrointestinal Microbiome
*Extracellular Vesicles
Brain-Gut Axis
*Microbiota
*Exosomes

@article {pmid38612738,
year = {2024},
author = {Aronica, TS and Carella, M and Balistreri, CR},
title = {Different Levels of Therapeutic Strategies to Recover the Microbiome to Prevent/Delay Acute Lymphoblastic Leukemia (ALL) or Arrest Its Progression in Children.},
journal = {International journal of molecular sciences},
volume = {25},
number = {7},
pages = {},
pmid = {38612738},
issn = {1422-0067},
mesh = {Infant, Newborn ; Humans ; Child ; *Microbiota ; *Gastrointestinal Microbiome ; *Precursor Cell Lymphoblastic Leukemia-Lymphoma/therapy ; Fetus ; *Hematologic Neoplasms ; },
abstract = {Changes in the components, variety, metabolism, and products of microbiomes, particularly of the gut microbiome (GM), have been revealed to be closely associated with the onset and progression of numerous human illnesses, including hematological neoplasms. Among the latter pathologies, there is acute lymphoblastic leukemia (ALL), the most widespread malignant neoplasm in pediatric subjects. Accordingly, ALL cases present a typical dysfunctional GM during all its clinical stages and resulting inflammation, which contributes to its progression, altered response to therapy, and possible relapses. Children with ALL have GM with characteristic variations in composition, variety, and functions, and such alterations may influence and predict the complications and prognosis of ALL after chemotherapy treatment or stem cell hematopoietic transplants. In addition, growing evidence also reports the ability of GM to influence the formation, growth, and roles of the newborn's hematopoietic system through the process of developmental programming during fetal life as well as its susceptibility to the onset of onco-hematological pathologies, namely ALL. Here, we suggest some therapeutic strategies that can be applied at two levels of intervention to recover the microbiome and consequently prevent/delay ALL or arrest its progression.},
}

Infant, Newborn
Humans
Child
*Microbiota
*Gastrointestinal Microbiome
*Precursor Cell Lymphoblastic Leukemia-Lymphoma/therapy
Fetus
*Hematologic Neoplasms

@article {pmid38612702,
year = {2024},
author = {McDermott, G and Walsh, A and Crispie, F and Frost, S and Greally, P and Cotter, PD and O'Sullivan, O and Renwick, J},
title = {Insights into the Adolescent Cystic Fibrosis Airway Microbiome Using Shotgun Metagenomics.},
journal = {International journal of molecular sciences},
volume = {25},
number = {7},
pages = {},
pmid = {38612702},
issn = {1422-0067},
support = {204814/Z/16/A/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Child ; Humans ; Adolescent ; *Cystic Fibrosis ; Staphylococcus aureus ; Biological Assay ; DNA, Ribosomal ; *Microbiota/genetics ; },
abstract = {Cystic fibrosis (CF) is an inherited genetic disorder which manifests primarily in airway disease. Recent advances in molecular technologies have unearthed the diverse polymicrobial nature of the CF airway. Numerous studies have characterised the genus-level composition of this airway community using targeted 16S rDNA sequencing. Here, we employed whole-genome shotgun metagenomics to provide a more comprehensive understanding of the early CF airway microbiome. We collected 48 sputum samples from 11 adolescents and children with CF over a 12-month period and performed shotgun metagenomics on the Illumina NextSeq platform. We carried out functional and taxonomic analysis of the lung microbiome at the species and strain levels. Correlations between microbial diversity measures and independent demographic and clinical variables were performed. Shotgun metagenomics detected a greater diversity of bacteria than culture-based methods. A large proportion of the top 25 most-dominant species were anaerobes. Samples dominated by Staphylococcus aureus and Prevotella melaninogenica had significantly higher microbiome diversity, while no CF pathogen was associated with reduced microbial diversity. There was a diverse resistome present in all samples in this study, with 57.8% agreement between shotgun metagenomics and culture-based methods for detection of resistance. Pathogenic sequence types (STs) of S. aureus, Pseudomonas aeruginosa, Haemophilus influenzae and Stenotrophomonas maltophilia were observed to persist in young CF patients, while STs of S. aureus were both persistent and shared between patients. This study provides new insight into the temporal changes in strain level composition of the microbiome and the landscape of the resistome in young people with CF. Shotgun metagenomics could provide a very useful one-stop assay for detecting pathogens, emergence of resistance and conversion to persistent colonisation in early CF disease.},
}

Child
Humans
Adolescent
*Cystic Fibrosis
Staphylococcus aureus
Biological Assay
DNA, Ribosomal
*Microbiota/genetics

@article {pmid38612556,
year = {2024},
author = {Kasprzak-Drozd, K and Niziński, P and Kasprzak, P and Kondracka, A and Oniszczuk, T and Rusinek, A and Oniszczuk, A},
title = {Does Resveratrol Improve Metabolic Dysfunction-Associated Steatotic Liver Disease (MASLD)?.},
journal = {International journal of molecular sciences},
volume = {25},
number = {7},
pages = {},
pmid = {38612556},
issn = {1422-0067},
mesh = {Animals ; Humans ; Resveratrol/pharmacology/therapeutic use ; *Metabolic Diseases ; Antioxidants ; *Fatty Liver ; Inflammation ; },
abstract = {Metabolic dysfunction-associated steatotic liver disease (MASLD) is influenced by a variety of factors, including environmental and genetic factors. The most significant outcome is the alteration of free fatty acid and triglyceride metabolism. Lipotoxicity, impaired autophagy, chronic inflammation, and oxidative stress, as well as coexisting insulin resistance, obesity, and changes in the composition of gut microbiota, are also considered crucial factors in the pathogenesis of MASLD. Resveratrol is a polyphenolic compound that belongs to the stilbene subgroup. This review summarises the available information on the therapeutic effects of resveratrol against MASLD. Resveratrol has demonstrated promising antisteatotic, antioxidant, and anti-inflammatory activities in liver cells in in vitro and animal studies. Resveratrol has been associated with inhibiting the NF-κB pathway, activating the SIRT-1 and AMPK pathways, normalizing the intestinal microbiome, and alleviating intestinal inflammation. However, clinical studies have yielded inconclusive results regarding the efficacy of resveratrol in alleviating hepatic steatosis or reducing any of the parameters found in MASLD in human patients. The lack of homogeneity between studies, low bioavailability of resveratrol, and population variability when compared to animal models could be the reasons for this.},
}

Animals
Humans
Resveratrol/pharmacology/therapeutic use
*Metabolic Diseases
Antioxidants
*Fatty Liver
Inflammation

@article {pmid38612468,
year = {2024},
author = {da C Pinaffi-Langley, AC and Melia, E and Hays, FA},
title = {Exploring the Gut-Mitochondrial Axis: p66Shc Adapter Protein and Its Implications for Metabolic Disorders.},
journal = {International journal of molecular sciences},
volume = {25},
number = {7},
pages = {},
pmid = {38612468},
issn = {1422-0067},
support = {R01GM118599/NH/NIH HHS/United States ; },
mesh = {Humans ; Src Homology 2 Domain-Containing, Transforming Protein 1/genetics ; *Metabolic Diseases ; Adaptor Proteins, Signal Transducing ; Forkhead Transcription Factors ; Mitochondria ; },
abstract = {This review investigates the multifaceted role of the p66Shc adaptor protein and the gut microbiota in regulating mitochondrial function and oxidative stress, and their collective impact on the pathogenesis of chronic diseases. The study delves into the molecular mechanisms by which p66Shc influences cellular stress responses through Rac1 activation, Forkhead-type transcription factors inactivation, and mitochondria-mediated apoptosis, alongside modulatory effects of gut microbiota-derived metabolites and endotoxins. Employing an integrative approach, the review synthesizes findings from a broad array of studies, including molecular biology techniques and analyses of microbial metabolites' impacts on host cellular pathways. The results underscore a complex interplay between microbial metabolites, p66Shc activation, and mitochondrial dysfunction, highlighting the significance of the gut microbiome in influencing disease outcomes through oxidative stress pathways. Conclusively, the review posits that targeting the gut microbiota-p66Shc-mitochondrial axis could offer novel therapeutic strategies for mitigating the development and progression of metabolic diseases. This underscores the potential of dietary interventions and microbiota modulation in managing oxidative stress and inflammation, pivotal factors in chronic disease etiology.},
}

Humans
Src Homology 2 Domain-Containing, Transforming Protein 1/genetics
*Metabolic Diseases
Adaptor Proteins, Signal Transducing
Forkhead Transcription Factors
Mitochondria

@article {pmid38612453,
year = {2024},
author = {Tsai, CC and Chiu, MH and Kek, HP and Yang, MC and Su, YT and Liu, HK and Wu, MS and Yeh, YT},
title = {The Reduced Gut Lachnospira Species Is Linked to Liver Enzyme Elevation and Insulin Resistance in Pediatric Fatty Liver Disease.},
journal = {International journal of molecular sciences},
volume = {25},
number = {7},
pages = {},
pmid = {38612453},
issn = {1422-0067},
support = {112-EDN0005//E-Da Hospital/ ; EDAHS112030//E-Da Hospital/ ; EDAHI112002//E-Da Hospital/ ; },
mesh = {Humans ; Child ; *Insulin Resistance ; Clostridiales ; *Flavones ; *Hepatitis A ; *Non-alcoholic Fatty Liver Disease ; Flavonols ; },
abstract = {The objective of this study was to investigate gut dysbiosis and its metabolic and inflammatory implications in pediatric metabolic dysfunction-associated fatty liver disease (MAFLD). This study included 105 children and utilized anthropometric measurements, blood tests, the Ultrasound Fatty Liver Index, and fecal DNA sequencing to assess the relationship between gut microbiota and pediatric MAFLD. Notable decreases in Lachnospira spp., Faecalibacterium spp., Oscillospira spp., and Akkermansia spp. were found in the MAFLD group. Lachnospira spp. was particularly reduced in children with MAFLD and hepatitis compared to controls. Both MAFLD groups showed a reduction in flavone and flavonol biosynthesis sequences. Lachnospira spp. correlated positively with flavone and flavonol biosynthesis and negatively with insulin levels and insulin resistance. Body weight, body mass index (BMI), and total cholesterol levels were inversely correlated with flavone and flavonol biosynthesis. Reduced Lachnospira spp. in children with MAFLD may exacerbate insulin resistance and inflammation through reduced flavone and flavonol biosynthesis, offering potential therapeutic targets.},
}

Humans
Child
*Insulin Resistance
Clostridiales
*Flavones
*Hepatitis A
*Non-alcoholic Fatty Liver Disease
Flavonols