@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

@article {pmid38612369,
year = {2024},
author = {Silva, FG and Silva, SR and Pereira, AMF and Cerqueira, JL and Conceição, C},
title = {A Comprehensive Review of Bovine Colostrum Components and Selected Aspects Regarding Their Impact on Neonatal Calf Physiology.},
journal = {Animals : an open access journal from MDPI},
volume = {14},
number = {7},
pages = {},
pmid = {38612369},
issn = {2076-2615},
support = {UIDB/00772/2020//Fundação para a Ciência e Tecnologia/ ; UIDB/05183/2020//Fundação para a Ciência e Tecnologia/ ; UI/BD/150834/2021//Fundação para a Ciência e Tecnologia/ ; },
abstract = {Colostrum contains macro- and micronutrients necessary to meet the nutritional and energy requirements of the neonatal calf, bioactive components that intervene in several physiological aspects, and cells and microorganisms that modulate the calf's immune system and gut microbiome. Colostrum is sometimes mistaken as transition milk, which, although more nutritive than whole milk, has a distinct biochemical composition. Furthermore, most research about colostrum quality and colostrum management focuses on the transfer of maternal IgG to the newborn calf. The remaining components of colostrum and transition milk have not received the same attention, despite their importance to the newborn animal. In this narrative review, a large body of literature on the components of bovine colostrum was reviewed. The variability of these components was summarized, emphasizing specific components that warrant deeper exploration. In addition, the effects of each component present in colostrum and transition milk on several key physiological aspects of the newborn calf are discussed.},
}

@article {pmid38612237,
year = {2024},
author = {Li, B and Wu, K and Duan, G and Yin, W and Lei, M and Yan, Y and Ren, Y and Zhang, C},
title = {Folic Acid and Taurine Alleviate the Impairment of Redox Status, Immunity, Rumen Microbial Composition and Fermentation of Lambs under Heat Stress.},
journal = {Animals : an open access journal from MDPI},
volume = {14},
number = {7},
pages = {},
pmid = {38612237},
issn = {2076-2615},
support = {SXBYKY2021037//Shanxi Province Outstanding Doctor Award Fund/ ; 2020BQ53//Science and Technology Innovation Program of Shanxi Agricultural University/ ; J202011313//"1331 Project" Key Disciplines of Animal Sciences, Shanxi Province/ ; 2023CYJSTX14//earmarked fund for Modern Agro-industry Technology Research System in Shanxi Province/ ; },
abstract = {The aim of this study was to investigate if the supplementation of folic acid and taurine can relieve the adverse effects of different levels of heat stress (HS) on growth performance, physiological indices, antioxidative capacity, immunity, rumen fermentation and microbiota. A total of 24 Dorper × Hu crossbred lambs (27.51 ± 0.96 kg) were divided into four groups: control group (C, 25 °C), moderate HS group (MHS, 35 °C), severe HS group (SHS, 40 °C), and the treatment group, under severe HS (RHS, 40 °C, 4 and 40 mg/kg BW/d coated folic acid and taurine, respectively). Results showed that, compared with Group C, HS significantly decreased the ADG of lambs (p < 0.05), and the ADG in the RHS group was markedly higher than in the MHS and SHS group (p < 0.05). HS had significant detrimental effects on physiological indices, antioxidative indices and immune status on the 4th day (p < 0.05). The physiological indices, such as RR and ST, increased significantly (p < 0.05) with the HS level and were significantly decreased in the RHS group, compared to the SHS group (p < 0.05). HS induced the significant increase of MDA, TNF-α, and IL-β, and the decrease of T-AOC, SOD, GPx, IL-10, IL-13, IgA, IgG, and IgM (p < 0.05). However, there was a significant improvement in these indices after the supplementation of folic acid and taurine under HS. Moreover, there were a significant increase in Quinella and Succinivibrio, and an evident decrease of the genera Rikenellaceae_RC9_gut_group and Asteroleplasma under HS (p < 0.05). The LEfSe analysis showed that the genera Butyrivibrio, Eubacterium_ventriosum_group, and f_Bifidobacteriaceae were enriched in the MHS, SHS and RHS groups, respectively. Correlated analysis indicated that the genus Rikenellaceae_RC9_gut_group was positively associated with MDA, while it was negatively involved in IL-10, IgA, IgM, and SOD (p < 0.05); The genus Anaeroplasma was positively associated with the propionate and valerate, while the genus Succinivibrio was negatively involved in TNF-α (p < 0.05). In conclusion, folic acid and taurine may alleviate the adverse effects of HS on antioxidant capacity, immunomodulation, and rumen fermentation of lambs by inducing changes in the microbiome that improve animal growth performance.},
}

@article {pmid38611776,
year = {2024},
author = {Szulc, J and Okrasa, M and Nowak, A and Ryngajłło, M and Nizioł, J and Kuźniar, A and Ruman, T and Gutarowska, B},
title = {Uncontrolled Post-Industrial Landfill-Source of Metals, Potential Toxic Compounds, Dust, and Pathogens in Environment-A Case Study.},
journal = {Molecules (Basel, Switzerland)},
volume = {29},
number = {7},
pages = {},
pmid = {38611776},
issn = {1420-3049},
support = {Phase IV of the National Program "Safety and working conditions improvement"//Ministry of Science and Higher Education and the National Centre for Research and Development/ ; 726/BN/D/2019-2021//Regional Found for Environmental Protection and Water Management in Lodz/ ; },
mesh = {Humans ; *Dust ; Caco-2 Cells ; Metals ; *Mercury ; Soil ; },
abstract = {The aim of this case study was the evaluation of the selected metals' concentration, potential toxic compound identification, cytotoxicity analysis, estimation of the airborne dust concentration, biodiversity, and number of microorganisms in the environment (leachate, soil, air) of the biggest uncontrolled post-industrial landfills in Poland. Based on the results obtained, preliminary solutions for the future management of post-industrial objects that have become an uncontrolled landfill were indicated. In the air, the PM1 fraction dominated, constituting 78.1-98.2% of the particulate matter. Bacterial counts were in the ranges of 9.33 × 10[1]-3.21 × 10[3] CFU m[-3] (air), 1.87 × 10[5]-2.30 × 10[6] CFU mL[-1] (leachates), and 8.33 × 10[4]-2.69 × 10[6] CFU g[-1] (soil). In the air, the predominant bacteria were Cellulosimicrobium and Stenotrophomonas. The predominant fungi were Mycosphaerella, Cladosporium, and Chalastospora. The main bacteria in the leachates and soils were Acinetobacter, Mortierella, Proteiniclasticum, Caloramator, and Shewanella. The main fungi in the leachates and soils were Lindtneria. Elevated concentrations of Pb, Zn, and Hg were detected. The soil showed the most pronounced cytotoxic potential, with rates of 36.55%, 63.08%, and 100% for the A-549, Caco-2, and A-549 cell lines. Nine compounds were identified which may be responsible for this cytotoxic effect, including 2,4,8-trimethylquinoline, benzo(f)quinoline, and 1-(m-tolyl)isoquinoline. The microbiome included bacteria and fungi potentially metabolizing toxic compounds and pathogenic species.},
}

Humans
*Dust
Caco-2 Cells
Metals
*Mercury
Soil

@article {pmid38611483,
year = {2024},
author = {Rojas-Sánchez, B and Castelán-Sánchez, H and Garfias-Zamora, EY and Santoyo, G},
title = {Diversity of the Maize Root Endosphere and Rhizosphere Microbiomes Modulated by the Inoculation with Pseudomonas fluorescens UM270 in a Milpa System.},
journal = {Plants (Basel, Switzerland)},
volume = {13},
number = {7},
pages = {},
pmid = {38611483},
issn = {2223-7747},
abstract = {Milpa is an agroecological production system based on the polyculture of plant species, with corn featuring as a central component. Traditionally, the milpa system does not require the application of chemicals, and so pest attacks and poor growth in poor soils can have adverse effects on its production. Therefore, the application of bioinoculants could be a strategy for improving crop growth and health; however, the effect of external inoculant agents on the endemic microbiota associated with corn has not been extensively studied. Here, the objective of this work was to fertilize a maize crop under a milpa agrosystem with the PGPR Pseudomonas fluorescens UM270, evaluating its impact on the diversity of the rhizosphere (rhizobiome) and root endophytic (root endobiome) microbiomes of maize plants. The endobiome of maize roots was evaluated by 16S rRNA and internal transcribed spacer region (ITS) sequencing, and the rhizobiome was assessed by metagenomic sequencing upon inoculation with the strain UM270. The results showed that UM270 inoculation of the rhizosphere of P. fluorescens UM270 did not increase alpha diversity in either the monoculture or milpa, but it did alter the endophytic microbiome of maize plant roots by stimulating the presence of bacterial operational taxonomic units (OTUs) of the genera Burkholderia and Pseudomonas (in a monoculture), whereas, in the milpa system, the PGPR stimulated greater endophytic diversity and the presence of genera such as Burkholderia, Variovorax, and N-fixing rhizobia genera, including Rhizobium, Mesorhizobium, and Bradyrhizobium. No clear association was found between fungal diversity and the presence of strain UM270, but beneficial fungi, such as Rizophagus irregularis and Exophiala pisciphila, were detected in the Milpa system. In addition, network analysis revealed unique interactions with species such as Stenotrophomonas sp., Burkholderia xenovorans, and Sphingobium yanoikuyae, which could potentially play beneficial roles in the plant. Finally, the UM270 strain does not seem to have a strong impact on the microbial diversity of the rhizosphere, but it does have a strong impact on some functions, such as trehalose synthesis, ammonium assimilation, and polyamine metabolism. The inoculation of UM270 biofertilizer in maize plants modifies the rhizo- and endophytic microbiomes with a high potential for stimulating plant growth and health in agroecological crop models.},
}

@article {pmid38611432,
year = {2024},
author = {Papadimitriou, K and Georgalaki, M and Anastasiou, R and Alexandropoulou, AM and Manolopoulou, E and Zoumpopoulou, G and Tsakalidou, E},
title = {Study of the Microbiome of the Cretan Sour Cream Staka Using Amplicon Sequencing and Shotgun Metagenomics and Isolation of Novel Strains with an Important Antimicrobial Potential.},
journal = {Foods (Basel, Switzerland)},
volume = {13},
number = {7},
pages = {},
pmid = {38611432},
issn = {2304-8158},
abstract = {Staka is a traditional Greek sour cream made mostly from spontaneously fermented sheep milk or a mixture of sheep and goat milk. At the industrial scale, cream separators and starter cultures may also be used. Staka is sometimes cooked with flour to absorb most of the fat. In this study, we employed culture-based techniques, amplicon sequencing, and shotgun metagenomics to analyze the Staka microbiome for the first time. The samples were dominated by Lactococcus or Leuconostoc spp. Most other bacteria were lactic acid bacteria (LAB) from the Streptococcus and Enterococcus genera or Gram-negative bacteria from the Buttiauxella, Pseudomonas, Enterobacter, Escherichia-Shigella, and Hafnia genera. Debaryomyces, Kluyveromyces, or Alternaria were the most prevalent genera in the samples, followed by other yeasts and molds like Saccharomyces, Penicillium, Aspergillus, Stemphylium, Coniospotium, or Cladosporium spp. Shotgun metagenomics allowed the species-level identification of Lactococcus lactis, Lactococcus raffinolactis, Streptococcus thermophilus, Streptococcus gallolyticus, Escherichia coli, Hafnia alvei, Streptococcus parauberis, and Enterococcus durans. Binning of assembled shotgun reads followed by recruitment plot analysis of single reads could determine near-complete metagenome assembled genomes (MAGs). Culture-dependent and culture-independent analyses were in overall agreement with some distinct differences. For example, lactococci could not be isolated, presumably because they had entered a viable but not culturable (VBNC) state or because they were dead. Finally, several LAB, Hafnia paralvei, and Pseudomonas spp. isolates exhibited antimicrobial activities against oral or other pathogenic streptococci, and certain spoilage and pathogenic bacteria establishing their potential role in food bio-protection or new biomedical applications. Our study may pave the way for additional studies concerning artisanal sour creams to better understand the factors affecting their production and the quality.},
}

@article {pmid38611393,
year = {2024},
author = {Li, Y and Wang, H and Leng, X and Gao, J and Li, C and Huang, D},
title = {Polysaccharides from Eucommia ulmoides Oliv. Leaves Alleviate Acute Alcoholic Liver Injury by Modulating the Microbiota-Gut-Liver Axis in Mice.},
journal = {Foods (Basel, Switzerland)},
volume = {13},
number = {7},
pages = {},
pmid = {38611393},
issn = {2304-8158},
support = {20232ACB215010//Natural Science Foundation of Jiangxi Province/ ; 32260563//National Natural Science Foundation of China/ ; 2023YFD2201300//National Key Research and Development Program of China/ ; },
abstract = {The interplay among gut microbiota, intestines, and liver is crucial in preventing acute alcoholic liver injury. In this study, the hepatoprotective potential of polysaccharides from Eucommia ulmoides Oliv. leaves (EULP) on acute alcoholic liver injury in Kunming male mice was investigated. The structural features suggested that the EULP appeared as a heterogeneous mixture of polysaccharides with a molecular weight of 186132 Da. A 14-day pretreatment of EULP ameliorated acute alcoholic-induced hepatic inflam mation (TNF-α, IL-6, and IL-10), oxidative stress (GSH, SOD, and T-AOC), and liver damage (ALT and AST) via enhancing intestinal barrier (Occludin, Claudin 1, and ZO-1) and modulating microbiome, which subsequently inhibiting endotoxemia and balancing the homeostasis of the gut-liver axis. EULP restored the composition of intestinal flora with an increase in the relative abundance of Lactobacillaceae and a decrease in Lachnospiraceae and Verrucomicrobiaceae. Notably, prolonged EULP pretreatment (14 days) but no single gavage of EULP achieved excellent hepatoprotection. These findings endorsed the potential of EULP as a functional food for mitigating acute alcoholic-induce d liver damage, attributed to its anti-inflammatory, antioxidant, and prebiotic properties facilitated by the microbiota-gut-liver axis.},
}

@article {pmid38611345,
year = {2024},
author = {Ariaee, A and Wardill, HR and Wignall, A and Prestidge, CA and Joyce, P},
title = {The Degree of Inulin Polymerization Is Important for Short-Term Amelioration of High-Fat Diet (HFD)-Induced Metabolic Dysfunction and Gut Microbiota Dysbiosis in Rats.},
journal = {Foods (Basel, Switzerland)},
volume = {13},
number = {7},
pages = {},
pmid = {38611345},
issn = {2304-8158},
support = {2022-CF-EMCR-004-25314//Hospital Research Foundation/ ; },
abstract = {Inulin, a non-digestible polysaccharide, has gained attention for its prebiotic properties, particularly in the context of obesity, a condition increasingly understood as a systemic inflammatory state linked to gut microbiota composition. This study investigates the short-term protective effects of inulin with different degrees of polymerization (DPn) against metabolic health deterioration and gut microbiota alterations induced by a high-fat diet (HFD) in Sprague Dawley rats. Inulin treatments with an average DPn of 7, 14, and 27 were administered at 1 g/kg of bodyweight to HFD-fed rats over 21 days. Body weight, systemic glucose levels, and proinflammatory markers were measured to assess metabolic health. Gut microbiota composition was analyzed through 16S rRNA gene sequencing. The results showed that inulin27 significantly reduced total weight gain and systemic glucose levels, suggesting a DPn-specific effect on metabolic health. The study also observed shifts in gut microbial populations, with inulin7 promoting several beneficial taxa from the Bifidobacterium genera, whilst inducing a unique microbial composition compared to medium-chain (DPn 14) and long-chain inulin (DPn: 27). However, the impact of inulin on proinflammatory markers and lipid metabolism parameters was not statistically significant, possibly due to the short study duration. Inulin with a higher DPn has a more pronounced effect on mitigating HFD-induced metabolic health deterioration, whilst inulin7 is particularly effective at inducing healthy microbial shifts. These findings highlight the benefits of inulin as a dietary adjuvant in obesity management and the importance of DPn in optimizing performance.},
}

@article {pmid38611328,
year = {2024},
author = {Tsouggou, N and Slavko, A and Tsipidou, O and Georgoulis, A and Dimov, SG and Yin, J and Vorgias, CE and Kapolos, J and Papadelli, M and Papadimitriou, K},
title = {Investigation of the Microbiome of Industrial PDO Sfela Cheese and Its Artisanal Variants Using 16S rDNA Amplicon Sequencing and Shotgun Metagenomics.},
journal = {Foods (Basel, Switzerland)},
volume = {13},
number = {7},
pages = {},
pmid = {38611328},
issn = {2304-8158},
support = {MIS 5047289//European Union and Greek national funds/ ; },
abstract = {Sfela is a white brined Greek cheese of protected designation of origin (PDO) produced in the Peloponnese region from ovine, caprine milk, or a mixture of the two. Despite the PDO status of Sfela, very few studies have addressed its properties, including its microbiology. For this reason, we decided to investigate the microbiome of two PDO industrial Sfela cheese samples along with two non-PDO variants, namely Sfela touloumotiri and Xerosfeli. Matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS), 16S rDNA amplicon sequencing and shotgun metagenomics analysis were used to identify the microbiome of these traditional cheeses. Cultured-based analysis showed that the most frequent species that could be isolated from Sfela cheese were Enterococcus faecium, Lactiplantibacillus plantarum, Levilactobacillus brevis, Pediococcus pentosaceus and Streptococcus thermophilus. Shotgun analysis suggested that in industrial Sfela 1, Str. thermophilus dominated, while industrial Sfela 2 contained high levels of Lactococcus lactis. The two artisanal samples, Sfela touloumotiri and Xerosfeli, were dominated by Tetragenococcus halophilus and Str. thermophilus, respectively. Debaryomyces hansenii was the only yeast species with abundance > 1% present exclusively in the Sfela touloumotiri sample. Identifying additional yeast species in the shotgun data was challenging, possibly due to their low abundance. Sfela cheese appears to contain a rather complex microbial ecosystem and thus needs to be further studied and understood. This might be crucial for improving and standardizing both its production and safety measures.},
}

@article {pmid38611081,
year = {2024},
author = {Jones, AN and Scheurlen, KM and Macleod, A and Simon, HL and Galandiuk, S},
title = {Obesity and Inflammatory Factors in the Progression of Early-Onset Colorectal Cancer.},
journal = {Cancers},
volume = {16},
number = {7},
pages = {},
pmid = {38611081},
issn = {2072-6694},
abstract = {Metabolic dysfunction associated with obesity leads to a chronic pro-inflammatory state with systemic effects, including the alteration of macrophage metabolism. Tumor-associated macrophages have been linked to the formation of cancer through the production of metabolites such as itaconate. Itaconate downregulates peroxisome proliferator-activated receptor gamma as a tumor-suppressing factor and upregulates anti-inflammatory cytokines in M2-like macrophages. Similarly, leptin and adiponectin also influence macrophage cytokine expression and contribute to the progression of colorectal cancer via changes in gene expression within the PI3K/AKT pathway. This pathway influences cell proliferation, differentiation, and tumorigenesis. This work provides a review of obesity-related hormones and inflammatory mechanisms leading to the development and progression of early-onset colorectal cancer (EOCRC). A literature search was performed using the PubMed and Cochrane databases to identify studies related to obesity and EOCRC, with keywords including 'EOCRC', 'obesity', 'obesity-related hormones', 'itaconate', 'adiponectin', 'leptin', 'M2a macrophage', and 'microbiome'. With this concept of pro-inflammatory markers contributing to EOCRC, increased use of chemo-preventative agents such as aspirin may have a protective effect. Elucidating this association between obesity-related, hormone/cytokine-driven inflammatory effects with EOCRC may help lead to new therapeutic targets in preventing and treating EOCRC.},
}

@article {pmid38610937,
year = {2024},
author = {Osazuwa-Peters, OL and Deveaux, A and Muehlbauer, MJ and Ilkayeva, O and Bain, JR and Keku, T and Berchuck, A and Huang, B and Ward, K and Gates Kuliszewski, M and Akinyemiju, T},
title = {Racial Differences in Vaginal Fluid Metabolites and Association with Systemic Inflammation Markers among Ovarian Cancer Patients: A Pilot Study.},
journal = {Cancers},
volume = {16},
number = {7},
pages = {},
pmid = {38610937},
issn = {2072-6694},
support = {R37CA233777/NH/NIH HHS/United States ; },
abstract = {The vaginal microbiome differs by race and contributes to inflammation by directly producing or consuming metabolites or by indirectly inducing host immune response, but its potential contributions to ovarian cancer (OC) disparities remain unclear. In this exploratory cross-sectional study, we examine whether vaginal fluid metabolites differ by race among patients with OC, if they are associated with systemic inflammation, and if such associations differ by race. Study participants were recruited from the Ovarian Cancer Epidemiology, Healthcare Access, and Disparities Study between March 2021 and September 2022. Our study included 36 study participants with ovarian cancer who provided biospecimens; 20 randomly selected White patients and all 16 eligible Black patients, aged 50-70 years. Acylcarnitines (n = 45 species), sphingomyelins (n = 34), and ceramides (n = 21) were assayed on cervicovaginal fluid, while four cytokines (IL-1β, IL-10, TNF-α, and IL-6) were assayed on saliva. Seven metabolites showed >2-fold differences, two showed significant differences using the Wilcoxon rank-sum test (p < 0.05; False Discovery Rate > 0.05), and 30 metabolites had coefficients > ±0.1 in a Penalized Discriminant Analysis that achieved two distinct clusters by race. Arachidonoylcarnitine, the carnitine adduct of arachidonic acid, appeared to be consistently different by race. Thirty-eight vaginal fluid metabolites were significantly correlated with systemic inflammation biomarkers, irrespective of race. These findings suggest that vaginal fluid metabolites may differ by race, are linked with systemic inflammation, and hint at a potential role for mitochondrial dysfunction and sphingolipid metabolism in OC disparities. Larger studies are needed to verify these findings and further establish specific biological mechanisms that may link the vaginal microbiome with OC racial disparities.},
}

@article {pmid38610738,
year = {2024},
author = {Sawaid, IO and Samson, AO},
title = {Proton Pump Inhibitors and Cancer Risk: A Comprehensive Review of Epidemiological and Mechanistic Evidence.},
journal = {Journal of clinical medicine},
volume = {13},
number = {7},
pages = {},
pmid = {38610738},
issn = {2077-0383},
support = {Ginsberg Foundation q//Ginsberg Foundation/ ; Katz foundation 1//Katz foundation/ ; },
abstract = {Background: Proton pump inhibitors (PPIs) are commonly prescribed long-acting drugs used to treat acid reflux, gastroesophageal reflux disease (GERD), and peptic ulcers. Recently, concerns have been raised about their safety, particularly due to the association between long-term PPI use and cancer development. Multiple comprehensive studies have consistently suggested a noteworthy link between prolonged PPI usage and an increased risk of developing gastric, esophageal, colorectal, and pancreatic cancers, yet the precise underlying mechanism remains elusive. Methods: First, we review the extensive body of research that investigates the intricate relationship between cancer and PPIs. Then, we predict PPI toxicity using the prodrug structures with the ProTox-II webserver. Finally, we predict the relative risk of cancer for each PPI, using PubMed citation counts of each drug and keywords related to cancer. Results: Our review indicates that prolonged PPI use (exceeding three months) is significantly associated with an elevated risk of cancer, while shorter-term usage (less than three months) appears to pose a comparatively lower risk. Our review encompasses various proposed mechanisms, such as pH and microbiome alterations, vitamin and mineral malabsorption, hypergastrinemia, and enterochromaffin-like cell proliferation, while ProTox-II also suggests aryl hydrocarbon receptor binding. Potentially, the PubMed citations count suggests that the PPIs omeprazole and lansoprazole are more associated with cancer than pantoprazole and esomeprazole. In comparison, the H2R blocker, famotidine, is potentially less associated with cancer than PPIs, and may serve as a safer alternative treatment for periods beyond 3 months. Conclusions: Despite the well-established cancer risk associated with PPIs, it is notable that these medications continue to be widely prescribed for periods longer than 3 months. Thus, it is of paramount importance for clinicians and patients to thoughtfully evaluate the potential risks and benefits of long-term PPI usage and explore alternative treatments before making informed decisions regarding their medical management.},
}

@article {pmid38610709,
year = {2024},
author = {Kim, GH and Kim, BR and Yoon, HJ and Jeong, JH},
title = {Alterations in Gut Microbiota and Their Correlation with Brain Beta-Amyloid Burden Measured by [18]F-Florbetaben PET in Mild Cognitive Impairment Due to Alzheimer's Disease.},
journal = {Journal of clinical medicine},
volume = {13},
number = {7},
pages = {},
pmid = {38610709},
issn = {2077-0383},
support = {HU21C0016//Korea Health Industry Development Institute/Republic of Korea ; CRC22011-600//national research council of science and technology/ ; NRF-2020M3E5D2A01084721//National Research Foundation of Korea/ ; NRF-2021R1A2C1093636 and NRF No. RS-2023-00302458//National Research Foundation of South Korea/ ; },
abstract = {(1) Background: This study investigated changes in the gut microbial composition of individuals with mild cognitive impairment (MCI) due to Alzheimer's disease (AD) and their relationship with positron emission tomography (PET) amyloid accumulation. (2) Methods: In total, 17 cognitively normal individuals without amyloid-beta (Aβ) accumulation (Aβ[-]NC) and 24 with Aβ-positive mild cognitive impairment (Aβ[+]MCI) who underwent [18]F-florbetaben PET and fecal bacterial 16S ribosomal RNA gene sequencing were enrolled. The taxonomic compositions of the Aβ[-]NC and Aβ[+]MCI groups were compared. The abundance of taxa was correlated with the standardized uptake value ratio (SUVR), using generalized linear models. (3) Results: There were significant differences in microbiome richness (ACE, p = 0.034 and Chao1, p = 0.024), alpha diversity (Shannon, p = 0.039), and beta diversity (Bray-Curtis, p = 0.018 and Generalized UniFrac, p = 0.034) between the Aβ[-]NC and Aβ[+]MCI groups. The global SUVR was positively correlated with the genus Intestinibacter (q = 0.006) and negatively correlated with the genera Roseburia (q = 0.008) and Agathobaculum (q = 0.029). (4) Conclusions: In this study, we identified significant changes in the gut microbiota composition that occur in individuals with MCI due to AD. In particular, the correlation analysis results between PET amyloid burden and gut microbial abundance showed that amyloid deposition is associated with a reduction in specific taxa involved in butyrate production.},
}

@article {pmid38610032,
year = {2024},
author = {Yang, F and Su, Y and Yan, C and Chen, T and Cheung, PCK},
title = {Attenuation of inflammatory bowel disease by oral administration of mucoadhesive polydopamine-coated yeast β-glucan via ROS scavenging and gut microbiota regulation.},
journal = {Journal of nanobiotechnology},
volume = {22},
number = {1},
pages = {166},
pmid = {38610032},
issn = {1477-3155},
mesh = {Animals ; Mice ; Saccharomyces cerevisiae ; *Gastrointestinal Microbiome ; Reactive Oxygen Species ; *Inflammatory Bowel Diseases/drug therapy ; *Colitis/chemically induced/drug therapy ; Administration, Oral ; *Indoles ; *Polymers ; },
abstract = {Treatment for inflammatory bowel disease (IBD) is challenging since current anti-inflammatory and immunosuppressive therapies do not address the underlying causes of the illness, which include increased levels of reactive oxygen species (ROS) and dysbiosis of the gut commensal microbiota. Additionally, these treatments often have systemic off-target effects and adverse side effects. In this study, we have developed a prebiotic yeast β-glucan nanocomplex coated with bio-adhesive polydopamine (YBNs@PDA) to effectively prolong their retention time in the gastrointestinal (GI) tract. The oral administration of YBNs@PDA restored the epithelium barriers, reduced ROS levels, and minimized systemic drug exposure while improved therapeutic efficacy in an acute colitis mouse model. Furthermore, 16S ribosomal RNA genes sequencing demonstrated a higher richness and diversity in gut microflora composition following the treatments. In particular, YBNs@PDA markedly augmented the abundance of Lachnospiraceae NK4A136 and Bifidobacterium, both of which are probiotics with crucial roles in relieving colitis via retaining gut homeostasis. Cumulatively, these results demonstrate that the potential of YBNs@PDA as a novel drug-free, ROS-scavenging and gut microbiota regulation nanoplatform for the treatment of GI disorders.},
}

Animals
Mice
Saccharomyces cerevisiae
*Gastrointestinal Microbiome
Reactive Oxygen Species
*Inflammatory Bowel Diseases/drug therapy
*Colitis/chemically induced/drug therapy
Administration, Oral
*Indoles
*Polymers

@article {pmid38609866,
year = {2024},
author = {Gargallo-Garriga, A and Sardans, J and Llusià, J and Peguero, G and Ayala-Roque, M and Courtois, EA and Stahl, C and Urban, O and Klem, K and Nolis, P and Pérez-Trujillo, M and Parella, T and Richter, A and Janssens, IA and Peñuelas, J},
title = {Different profiles of soil phosphorous compounds depending on tree species and availability of soil phosphorus in a tropical rainforest in French Guiana.},
journal = {BMC plant biology},
volume = {24},
number = {1},
pages = {278},
pmid = {38609866},
issn = {1471-2229},
support = {CZ.02.1.01/0.0/0.0/16_019/0000797//SustES/ ; CZ.02.1.01/0.0/0.0/16_019/0000797//SustES/ ; CZ.02.1.01/0.0/0.0/16_019/0000797//SustES/ ; ERC-2013-SyG-610028 IMBALANCE-P//ERC/ ; ERC-2013-SyG-610028 IMBALANCE-P//ERC/ ; ERC-2013-SyG-610028 IMBALANCE-P//ERC/ ; ERC-2013-SyG-610028 IMBALANCE-P//ERC/ ; ERC-2013-SyG-610028 IMBALANCE-P//ERC/ ; ERC-2013-SyG-610028 IMBALANCE-P//ERC/ ; ERC-2013-SyG-610028 IMBALANCE-P//ERC/ ; ERC-2013-SyG-610028 IMBALANCE-P//ERC/ ; ERC-2013-SyG-610028 IMBALANCE-P//ERC/ ; ERC-2013-SyG-610028 IMBALANCE-P//ERC/ ; ERC-2013-SyG-610028 IMBALANCE-P//ERC/ ; ERC-2013-SyG-610028 IMBALANCE-P//ERC/ ; },
mesh = {*Phosphorus ; Rainforest ; Trees ; French Guiana ; Phosphates ; *Microbiota ; Soil ; },
abstract = {BACKGROUND: The availability of soil phosphorus (P) often limits the productivities of wet tropical lowland forests. Little is known, however, about the metabolomic profile of different chemical P compounds with potentially different uses and about the cycling of P and their variability across space under different tree species in highly diverse tropical rainforests.

RESULTS: We hypothesised that the different strategies of the competing tree species to retranslocate, mineralise, mobilise, and take up P from the soil would promote distinct soil [31]P profiles. We tested this hypothesis by performing a metabolomic analysis of the soils in two rainforests in French Guiana using [31]P nuclear magnetic resonance (NMR). We analysed [31]P NMR chemical shifts in soil solutions of model P compounds, including inorganic phosphates, orthophosphate mono- and diesters, phosphonates, and organic polyphosphates. The identity of the tree species (growing above the soil samples) explained > 53% of the total variance of the [31]P NMR metabolomic profiles of the soils, suggesting species-specific ecological niches and/or species-specific interactions with the soil microbiome and soil trophic web structure and functionality determining the use and production of P compounds. Differences at regional and topographic levels also explained some part of the the total variance of the [31]P NMR profiles, although less than the influence of the tree species. Multivariate analyses of soil [31]P NMR metabolomics data indicated higher soil concentrations of P biomolecules involved in the active use of P (nucleic acids and molecules involved with energy and anabolism) in soils with lower concentrations of total soil P and higher concentrations of P-storing biomolecules in soils with higher concentrations of total P.

CONCLUSIONS: The results strongly suggest "niches" of soil P profiles associated with physical gradients, mostly topographic position, and with the specific distribution of species along this gradient, which is associated with species-specific strategies of soil P mineralisation, mobilisation, use, and uptake.},
}

*Phosphorus
Rainforest
Trees
French Guiana
Phosphates
*Microbiota
Soil

@article {pmid38609782,
year = {2024},
author = {Han, N and Chang, HJ and Yeo, HY and Kim, BC and Kim, B and Park, SC and Kim, J and Park, JW and Oh, JH},
title = {Association of gut microbiome with immune microenvironment in surgically treated colorectal cancer patients.},
journal = {Pathology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.pathol.2024.01.010},
pmid = {38609782},
issn = {1465-3931},
abstract = {This study explored the relationship between faecal microbiota distribution and local or systemic immune response in patients with colorectal cancer (CRC). The study population included 114 surgically treated CRC patients. Faeces were analysed using 16S rRNA gene sequencing. The immune score in tumour microenvironment was evaluated using CD3 and CD8 immunohistochemistry. Genetic alterations, microsatellite instability status and five systemic inflammatory markers were also analysed. Thirty of 114 (26.3%) CRC patients were categorised as the 'immune type' with a high density of T-cells. The immune type CRC cases showed lower angiolymphatic invasion and longer overall survival. Of the 123 selected bacterial species, Bacteroides fragilis and Collinsella aerofaciens were prevalent in immune CRC cases, whereas Odoribacter splanchnicus and Phascolarctobacterium succinatutens were prevalent in non-immune CRC patients. Bacteroides fragilis was associated with shorter disease free survival in univariable and multivariable survival analyses. Regarding systemic immunity, a high prevalence of C. aerofaciens was associated with a high modified Glasgow prognostic score. This study revealed a potential relationship among the gut microbiome, immune microenvironment, and disease progression in patients with CRC. Our findings suggest that abundant B. fragilis in patients with CRC is associated with a 'cold immune' tumour microenvironment.},
}

@article {pmid38609760,
year = {2024},
author = {Mullish, BH and Merrick, B and Quraishi, MN and Bak, A and Green, CA and Moore, DJ and Porter, RJ and Elumogo, NT and Segal, JP and Sharma, N and Marsh, B and Kontkowski, G and Manzoor, SE and Hart, AL and Settle, C and Keller, JJ and Hawkey, P and Iqbal, TH and Goldenberg, SD and Williams, HRT},
title = {The use of faecal microbiota transplant as treatment for recurrent or refractory Clostridioides difficile infection and other potential indications: second edition of joint British Society of Gastroenterology (BSG) and Healthcare Infection Society (HIS) guidelines.},
journal = {The Journal of hospital infection},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jhin.2024.03.001},
pmid = {38609760},
issn = {1532-2939},
abstract = {The first British Society of Gastroenterology (BSG) and Healthcare Infection Society (HIS)-endorsed faecal microbiota transplant (FMT) guidelines were published in 2018. Over the past 5 years, there has been considerable growth in the evidence base (including publication of outcomes from large national FMT registries), necessitating an updated critical review of the literature and a second edition of the BSG/HIS FMT guidelines. These have been produced in accordance with National Institute for Health and Care Excellence-accredited methodology, thus have particular relevance for UK-based clinicians, but are intended to be of pertinence internationally. This second edition of the guidelines have been divided into recommendations, good practice points and recommendations against certain practices. With respect to FMT for Clostridioides difficile infection (CDI), key focus areas centred around timing of administration, increasing clinical experience of encapsulated FMT preparations and optimising donor screening. The latter topic is of particular relevance given the COVID-19 pandemic, and cases of patient morbidity and mortality resulting from FMT-related pathogen transmission. The guidelines also considered emergent literature on the use of FMT in non-CDI settings (including both gastrointestinal and non-gastrointestinal indications), reviewing relevant randomised controlled trials. Recommendations are provided regarding special areas (including compassionate FMT use), and considerations regarding the evolving landscape of FMT and microbiome therapeutics.},
}

@article {pmid38609525,
year = {2024},
author = {Tsugawa, H and Ishihara, T and Ogasa, K and Iwanami, S and Hori, A and Takahashi, M and Yamada, Y and Satoh-Takayama, N and Ohno, H and Minoda, A and Arita, M},
title = {A lipidome landscape of aging in mice.},
journal = {Nature aging},
volume = {},
number = {},
pages = {},
pmid = {38609525},
issn = {2662-8465},
support = {JPMJER2101//MEXT | JST | Exploratory Research for Advanced Technology (ERATO)/ ; JPMJER2101//MEXT | JST | Exploratory Research for Advanced Technology (ERATO)/ ; 21K18216//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; 22K11718//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; 15H05897//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; 15H05898//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; 20H00495//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; JP15dm0207001//Japan Agency for Medical Research and Development (AMED)/ ; JP22zf0127007//Japan Agency for Medical Research and Development (AMED)/ ; 22ae0121036h0002//Japan Agency for Medical Research and Development (AMED)/ ; 21wm0325036h0001//Japan Agency for Medical Research and Development (AMED)/ ; JPMJND2305//MEXT | JST | National Bioscience Database Center (NBDC)/ ; },
abstract = {Understanding the molecular mechanisms of aging is crucial for enhancing healthy longevity. We conducted untargeted lipidomics across 13 biological samples from mice at various life stages (2, 12, 19 and 24 months) to explore the potential link between aging and lipid metabolism, considering sex (male or female) and microbiome (specific pathogen-free or germ-free) dependencies. By analyzing 2,704 molecules from 109 lipid subclasses, we characterized common and tissue-specific lipidome alterations associated with aging. For example, the levels of bis(monoacylglycero)phosphate containing polyunsaturated fatty acids increased in various organs during aging, whereas the levels of other phospholipids containing saturated and monounsaturated fatty acids decreased. In addition, we discovered age-dependent sulfonolipid accumulation, absent in germ-free mice, correlating with Alistipes abundance determined by 16S ribosomal RNA gene amplicon sequencing. In the male kidney, glycolipids such as galactosylceramides, galabiosylceramides (Gal2Cer), trihexosylceramides (Hex3Cer), and mono- and digalactosyldiacylglycerols were detected, with two lipid classes-Gal2Cer and Hex3Cer-being significantly enriched in aged mice. Integrated analysis of the kidney transcriptome revealed uridine diphosphate galactosyltransferase 8A (UGT8a), alkylglycerone phosphate synthase and fatty acyl-coenzyme A reductase 1 as potential enzymes responsible for the male-specific glycolipid biosynthesis in vivo, which would be relevant to sex dependency in kidney diseases. Inhibiting UGT8 reduced the levels of these glycolipids and the expression of inflammatory cytokines in the kidney. Our study provides a valuable resource for clarifying potential links between lipid metabolism and aging.},
}

@article {pmid38609443,
year = {2024},
author = {Kholousi Adab, F and Mehdi Yaghoobi, M and Gharechahi, J},
title = {Enhanced crystalline cellulose degradation by a novel metagenome-derived cellulase enzyme.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {8560},
pmid = {38609443},
issn = {2045-2322},
mesh = {Animals ; Metagenome ; Camelus ; *Microbiota ; *Cellulase/genetics ; Cellulose ; },
abstract = {Metagenomics has revolutionized access to genomic information of microorganisms inhabiting the gut of herbivorous animals, circumventing the need for their isolation and cultivation. Exploring these microorganisms for novel hydrolytic enzymes becomes unattainable without utilizing metagenome sequencing. In this study, we harnessed a suite of bioinformatic analyses to discover a novel cellulase-degrading enzyme from the camel rumen metagenome. Among the protein-coding sequences containing cellulase-encoding domains, we identified and subsequently cloned and purified a promising candidate cellulase enzyme, Celcm05-2, to a state of homogeneity. The enzyme belonged to GH5 subfamily 4 and exhibited robust enzymatic activity under acidic pH conditions. It maintained hydrolytic activity under various environmental conditions, including the presence of metal ions, non-ionic surfactant Triton X-100, organic solvents, and varying temperatures. With an optimal temperature of 40 °C, Celcm05-2 showcased remarkable efficiency when deployed on crystalline cellulose (> 3.6 IU/mL), specifically Avicel, thereby positioning it as an attractive candidate for a myriad of biotechnological applications spanning biofuel production, paper and pulp processing, and textile manufacturing. Efficient biodegradation of waste paper pulp residues and the evidence of biopolishing suggested that Celcm05-2 can be used in the bioprocessing of cellulosic craft fabrics in the textile industry. Our findings suggest that the camel rumen microbiome can be mined for novel cellulase enzymes that can find potential applications across diverse biotechnological processes.},
}

Animals
Metagenome
Camelus
*Microbiota
*Cellulase/genetics
Cellulose

@article {pmid38609432,
year = {2024},
author = {Kut, P and Garcia-Pichel, F},
title = {Nimble vs. torpid responders to hydration pulse duration among soil microbes.},
journal = {Communications biology},
volume = {7},
number = {1},
pages = {455},
pmid = {38609432},
issn = {2399-3642},
mesh = {RNA, Ribosomal, 16S/genetics ; Chemical Phenomena ; Heart Rate ; *Microbiota ; Soil ; },
abstract = {Environmental parameters vary in time, and variability is inherent in soils, where microbial activity follows precipitation pulses. The expanded pulse-reserve paradigm (EPRP) contends that arid soil microorganisms have adaptively diversified in response to pulse regimes differing in frequency and duration. To test this, we incubate Chihuahuan Desert soil microbiomes under separate treatments in which 60 h of hydration was reached with pulses of different pulse duration (PD), punctuated by intervening periods of desiccation. Using 16S rRNA gene amplicon data, we measure treatment effects on microbiome net growth, growth efficiency, diversity, and species composition, tracking the fate of 370 phylotypes (23% of those detected). Consistent with predictions, microbial diversity is a direct, saturating function of PD. Increasingly larger shifts in community composition are detected with decreasing PD, as specialist phylotypes become more prominent. One in five phylotypes whose fate was tracked responds consistently to PD, some preferring short pulses (nimble responders; NIRs) and some longer pulses (torpid responders; TORs). For pulses shorter than a day, microbiome growth efficiency is an inverse function of PD, as predicted. We conclude that PD in pulsed soil environments constitutes a major driver of microbial community assembly and function, largely consistent with the EPRP predictions.},
}

RNA, Ribosomal, 16S/genetics
Chemical Phenomena
Heart Rate
*Microbiota
Soil

@article {pmid38609223,
year = {2024},
author = {Ma, J and Qian, C and Hu, Q and Zhang, J and Gu, G and Liang, X and Zhang, L},
title = {The bacteriome-coupled phage communities continuously contract and shift to orchestrate the traditional rice vinegar fermentation.},
journal = {Food research international (Ottawa, Ont.)},
volume = {184},
number = {},
pages = {114244},
doi = {10.1016/j.foodres.2024.114244},
pmid = {38609223},
issn = {1873-7145},
mesh = {Humans ; *Oryza ; Acetic Acid ; Fermentation ; *Bacteriophages/genetics ; *Microbiota/genetics ; },
abstract = {Amounts of microbiome studies have uncovered the microbial communities of traditional food fermentations, while in which the phageome development with time is poorly understood. Here, we conducted a study to decipher both phageome and bacteriome of the traditional rice vinegar fermentation. The vinegar phageomes showed significant differences in the alpha diversity, network density and clustering coefficient over time. Peduoviridae had the highest relative abundance. Moreover, the phageome negatively correlated to the cognate bacteriome in alpha diversity, and undergone constantly contracting and shifting across the temporal scale. Nevertheless, 257 core virial clusters (VCs) persistently occurred with time whatever the significant impacts imposed by the varied physiochemical properties. Glycoside hydrolase (GH) and glycosyltransferase (GT) families genes displayed the higher abundances across all samples. Intriguingly, diversely structuring of toxin-antitoxin systems (TAs) and CRISPR-Cas arrays were frequently harbored by phage genomes. Their divergent organization and encoding attributes underlie the multiple biological roles in modulation of network and/or contest of phage community as well as bacterial host community. This phageome-wide mapping will fuel the current insights of phage community ecology in other traditional fermented ecosystems that are challenging to decipher.},
}

Humans
*Oryza
Acetic Acid
Fermentation
*Bacteriophages/genetics
*Microbiota/genetics

@article {pmid38609165,
year = {2024},
author = {Mullish, BH and Merrick, B and Quraishi, MN and Bak, A and Green, CA and Moore, DJ and Porter, RJ and Elumogo, NT and Segal, JP and Sharma, N and Marsh, B and Kontkowski, G and Manzoor, SE and Hart, AL and Settle, C and Keller, JJ and Hawkey, P and Iqbal, TH and Goldenberg, SD and Williams, HRT},
title = {The use of faecal microbiota transplant as treatment for recurrent or refractory Clostridioides difficile infection and other potential indications: second edition of joint British Society of Gastroenterology (BSG) and Healthcare Infection Society (HIS) guidelines.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2023-331550},
pmid = {38609165},
issn = {1468-3288},
abstract = {The first British Society of Gastroenterology (BSG) and Healthcare Infection Society (HIS)-endorsed faecal microbiota transplant (FMT) guidelines were published in 2018. Over the past 5 years, there has been considerable growth in the evidence base (including publication of outcomes from large national FMT registries), necessitating an updated critical review of the literature and a second edition of the BSG/HIS FMT guidelines. These have been produced in accordance with National Institute for Health and Care Excellence-accredited methodology, thus have particular relevance for UK-based clinicians, but are intended to be of pertinence internationally. This second edition of the guidelines have been divided into recommendations, good practice points and recommendations against certain practices. With respect to FMT for Clostridioides difficile infection (CDI), key focus areas centred around timing of administration, increasing clinical experience of encapsulated FMT preparations and optimising donor screening. The latter topic is of particular relevance given the COVID-19 pandemic, and cases of patient morbidity and mortality resulting from FMT-related pathogen transmission. The guidelines also considered emergent literature on the use of FMT in non-CDI settings (including both gastrointestinal and non-gastrointestinal indications), reviewing relevant randomised controlled trials. Recommendations are provided regarding special areas (including compassionate FMT use), and considerations regarding the evolving landscape of FMT and microbiome therapeutics.},
}

@article {pmid38608996,
year = {2024},
author = {Akintola, AA and Hwang, UW},
title = {Microbiome Profile of South Korean Vector Mosquitoes.},
journal = {Acta tropica},
volume = {},
number = {},
pages = {107213},
doi = {10.1016/j.actatropica.2024.107213},
pmid = {38608996},
issn = {1873-6254},
abstract = {This research offers a comprehensive exploration of the microbial communities associated with vector mosquitoes from South Korea. Aedes albopictus, Anopheles sinensis, and Culex molestus are vectors of pathogens, and understanding the intricacies of their microbiome profile is paramount for unraveling their roles in disease transmission dynamics. In this study, we characterized the microbiome of the midguts of adult female vector mosquitoes collected from different locations in South Korea. After DNA extraction from dissected mosquito midguts, we used the Illumina MiSeq next-generation sequencing to obtain sequences spanning the V4 hypervariable region of the bacteria 16S rRNA. Morphological and molecular characterization using 506-bp mitochondrial 16S rRNA was used to identify the mosquito species before amplicon sequencing. Across the three vector mosquitoes surveyed, 21 bacteria genera belonging to 20 families and 5 phyla were discovered. Proteobacteria and Bacteriodota were the major phyla of bacteria associated with the three mosquito species. There were significant differences in the gut microbiome genera composition between the species and little variation in the gut microbiome between individuals of the same mosquito species. Wolbachia is the most dominant genus in Aedes while Aeromonas, Acinetobacter, and unassigned taxa are the most common in An. sinensis. In addition to that, Chromobacterium, Chryseobacterium, and Aeromonas are dominant in Cx. molestus. This study sheds light on the complex interactions between mosquitoes and their microbiome, revealing potential implications for vector competence, disease transmission, and vector control strategies.},
}

@article {pmid38608958,
year = {2024},
author = {Li, SY and Tong, MM and Li, L and Hui, F and Meng, FZ and Zhao, YL and Guo, YM and Guo, XY and Shi, BL and Yan, SM},
title = {Rectal microbiomes and serum metabolomics reveal the improved effect of Artemisia ordosica crude polysaccharides on the lactation performance, antioxidant and immune responses of lactating donkeys.},
journal = {Journal of dairy science},
volume = {},
number = {},
pages = {},
doi = {10.3168/jds.2023-24570},
pmid = {38608958},
issn = {1525-3198},
abstract = {This study is aimed at investigating the effects of dietary supplementation with Artemisia ordosica crude polysaccharides (AOCP) on lactation performance, antioxidant status, and immune status of lactating donkeys and analyzing rectal microbiomes and serum metabolomes. Fourteen lactating Dezhou donkeys with similar age (6.16 ± 0.67 years of BW ± SD), weight (250.06 ± 25.18 kg), days in milk (39.11 ± 7.42 d), and averaged parity of 3 were randomly allocated into 2 treatments: a control group (CON, basal diet) and an AOCP group (AOCP, basal diet with 1.0 g/kg DM AOCP). Ten weeks were allotted for the experiment, 2 weeks for adaptation, and 8 weeks for collecting data and samples. The results showed that supplementation of donkey diets with AOCP increased lactation performance, including dry matter intake, milking yield, estimated milk yield, solids-corrected milk, energy-corrected milk, milk fat yield, milk protein yield, milk lactose yield, milk total solids yield, and milk solid not fat yield. The digestibility of dry matter, crude protein, acid detergent fiber, and neutral detergent fiber was increased in the AOCP group compared with the CON group. The AOCP group increased the concentrations of immunoglobulin A, immunoglobulin G, and immunoglobulin M, the activities of the superoxide dismutase, catalase and total antioxidant capacity in the serum. AOCP decreased the concentrations of tumor necrosis factor-α, nitric oxide, reactive oxygen species, and malondialdehyde in the serum. Compared with the CON group, AOCP increased propionate, butyrate, isovalerate, and total VFA concentrations in rectal feces (P < 0.05). The addition of AOCP to increased diversity (Shannon index) and altered structure of the rectal microflora. As a result of AOCP supplementation, there has been a significant improvement in the colonization of beneficial bacteria, including Lactobacillus, Unclassified_f_Prevotellacea, Ruminococcus, and Fibrobacter genera. In contrast, a decrease in the colonization of the Clostridium_sensu_stricto_1 bacterial genus and other pathogenic bacteria was observed. Meanwhile, metabolomics analysis found that AOCP supplementation upregulated metabolites L-tyrosine content while downregulating 9(S)-HODE, choline, sucrose, LysoPC (18:0), LysoPC (18:1(9Z), and LysoPC (20:2(11Z,14Z)) concentrations. These altered metabolites were involved in the PPAR signaling pathway, prolactin signaling pathway, glycerophospholipid metabolism, carbohydrate digestion and absorption, and tyrosine metabolism pathways, which were mainly related to antioxidant capacity, immune responses, and protein metabolism in the lactating donkeys. As a consequence of feeding AOCP diets, beneficial bacteria were abundant, and antioxidant and protein metabolism-related pathways were enriched, which may enhance lactation performance in donkeys. Therefore, supplementing AOCP diets is a desirable dietary strategy to improve donkey health and lactation performance.},
}

@article {pmid38608876,
year = {2024},
author = {Kan, L and Zheng, Z and Fu, W and Ma, Y and Wang, W and Qian, H and Xu, L},
title = {Recent progress on engineered micro/nanomaterials mediated modulation of gut microbiota for treating inflammatory bowel disease.},
journal = {Journal of controlled release : official journal of the Controlled Release Society},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jconrel.2024.04.014},
pmid = {38608876},
issn = {1873-4995},
abstract = {Inflammatory bowel disease (IBD) is a type of chronic recurrent inflammation disease that mainly includes Crohn's disease and ulcerative colitis. Currently, the treatments for IBD remain highly challenging, with clinical treatment drugs showing limited efficacy and adverse side effects. Thus, developing drug candidates with comprehensive therapeutic effects, high efficiency, and low toxicity is urgently needed. Recently, micro/nanomaterials have attracted considerable interest because of their bioavailability, multitarget and efficient effects on IBD. In addition, gut modulation plays a substantial role in restoring intestinal homeostasis. Therefore, efficient microbiota-based strategies modulating gut microenvironment have great potential in remarkably treating IBD. With the development of micro- and nanomaterials for the treatment of IBD and more in-depth studies of their therapeutic mechanisms, it has been found that these treatments also have a tendency to positively regulate the intestinal flora, resulting in an increase in the beneficial flora and a decrease in the level of pathogenic bacteria, thus regulating the composition of the intestinal flora to a normal state. In this review, we first present the interactions among the immune system, intestinal barrier, and gut microbiome. In addition, recent advances in administration routes and methods that positively arouse the regulation of intestinal flora for IBD using probiotics, prebiotics, and redox-active micro/nanomaterials have been reviewed. Finally, the key challenges and critical perspectives of gut microbiota-based micro/nanomaterial treatment are also discussed.},
}

@article {pmid38608842,
year = {2024},
author = {Sun, Z and Ning, Z and Figeys, D},
title = {The Landscape and Perspectives of the Human Gut Metaproteomics.},
journal = {Molecular & cellular proteomics : MCP},
volume = {},
number = {},
pages = {100763},
doi = {10.1016/j.mcpro.2024.100763},
pmid = {38608842},
issn = {1535-9484},
abstract = {The human gut microbiome is closely associated with human health and diseases. Metaproteomics has emerged as a valuable tool for studying the functionality of the gut microbiome by analyzing the entire proteins present in microbial communities. Recent advancements in liquid chromatography and tandem mass spectrometry (LC-MS/MS) techniques have expanded the detection range of metaproteomics. However, the overall coverage of the proteome in metaproteomics is still limited. While metagenomics studies have revealed substantial microbial diversity and functional potential of the human gut microbiome, few studies have summarized and studied the human gut microbiome landscape revealed with metaproteomics. In this paper, we present the current landscape of human gut metaproteomics studies by re-analyzing the identification results from fifteen published studies. We quantified the limited proteome coverage in metaproteomics and revealed a high proportion of annotation coverage of metaproteomics-identified proteins. We conducted a preliminary comparison between the metaproteomics view and the metagenomics view of the human gut microbiome, identifying key areas of consistency and divergence. Based on the current landscape of human gut metaproteomics, we discuss the feasibility of using metaproteomics to study functionally unknown proteins and propose a whole workflow peptide-centric analysis. Additionally, we suggest enhancing metaproteomics analysis by refining taxonomic classification and calculating confidence scores, as well as developing tools for analyzing the interaction between taxonomy and function.},
}

@article {pmid38608681,
year = {2024},
author = {Maier, L and Stein-Thoeringer, C and Ley, RE and Brötz-Oesterhelt, H and Link, H and Ziemert, N and Wagner, S and Peschel, A},
title = {Integrating research on bacterial pathogens and commensals to fight infections-an ecological perspective.},
journal = {The Lancet. Microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/S2666-5247(24)00049-1},
pmid = {38608681},
issn = {2666-5247},
abstract = {The incidence of antibiotic-resistant bacterial infections is increasing, and development of new antibiotics has been deprioritised by the pharmaceutical industry. Interdisciplinary research approaches, based on the ecological principles of bacterial fitness, competition, and transmission, could open new avenues to combat antibiotic-resistant infections. Many facultative bacterial pathogens use human mucosal surfaces as their major reservoirs and induce infectious diseases to aid their lateral transmission to new host organisms under some pathological states of the microbiome and host. Beneficial bacterial commensals can outcompete specific pathogens, thereby lowering the capacity of the pathogens to spread and cause serious infections. Despite the clinical relevance, however, the understanding of commensal-pathogen interactions in their natural habitats remains poor. In this Personal View, we highlight directions to intensify research on the interactions between bacterial pathogens and commensals in the context of human microbiomes and host biology that can lead to the development of innovative and sustainable ways of preventing and treating infectious diseases.},
}

@article {pmid38608580,
year = {2024},
author = {Benrahla, DE and Mohan, S and Trickovic, M and Castelli, FA and Alloul, G and Sobngwi, A and Abdiche, R and Kieser, S and Demontant, V and Trawinski, E and Chollet, C and Rodriguez, C and Kitagishi, H and Fenaille, F and Trajkovski, M and Motterlini, R and Foresti, R},
title = {An orally active carbon monoxide-releasing molecule enhances beneficial gut microbial species to combat obesity in mice.},
journal = {Redox biology},
volume = {72},
number = {},
pages = {103153},
doi = {10.1016/j.redox.2024.103153},
pmid = {38608580},
issn = {2213-2317},
abstract = {Carbon monoxide (CO), a gaseous signaling molecule, has shown promise in preventing body weight gain and metabolic dysfunction induced by high fat diet (HFD), but the mechanisms underlying these effects are largely unknown. An essential component in response to HFD is the gut microbiome, which is significantly altered during obesity and represents a target for developing new therapeutic interventions to fight metabolic diseases. Here, we show that CO delivered to the gut by oral administration with a CO-releasing molecule (CORM-401) accumulates in faeces and enriches a variety of microbial species that were perturbed by a HFD regimen. Notably, Akkermansia muciniphila, which exerts salutary metabolic effects in mice and humans, was strongly depleted by HFD but was the most abundant gut species detected after CORM-401 treatment. Analysis of bacterial transcripts revealed a restoration of microbial functional activity, with partial or full recovery of the Krebs cycle, β-oxidation, respiratory chain and glycolysis. Mice treated with CORM-401 exhibited normalization of several plasma and fecal metabolites that were disrupted by HFD and are dependent on Akkermansia muciniphila's metabolic activity, including indoles and tryptophan derivatives. Finally, CORM-401 treatment led to an improvement in gut morphology as well as reduction of inflammatory markers in colon and cecum and restoration of metabolic profiles in these tissues. Our findings provide therapeutic insights on the efficacy of CO as a potential prebiotic to combat obesity, identifying the gut microbiota as a crucial target for CO-mediated pharmacological activities against metabolic disorders.},
}

@article {pmid38608440,
year = {2024},
author = {Zhang, W and Ling, J and Xu, B and Wang, J and Chen, Z and Li, G},
title = {Gut microbiome-mediated monocytes promote liver metastasis.},
journal = {International immunopharmacology},
volume = {133},
number = {},
pages = {111877},
doi = {10.1016/j.intimp.2024.111877},
pmid = {38608440},
issn = {1878-1705},
abstract = {The gut microbiome plays an important role in tumor growth by regulating immune cell function. However, the role of the gut microbiome-mediated monocytes in liver metastasis remains unclear. In this study, we found that fecal microbiome transplantation (FMT) from the stool of patients with liver metastasis (LM) significantly promoted liver metastasis compared with healthy donors (HD). Monocytes were upregulated in liver tissues by the CCL2/CCR2 axis in LM patients' stool transplanted mouse model. CCL2/CCR2 inhibition and monocyte depletion significantly suppress liver metastasis. FMT using LM patients' stool enhanced the plasma lipopolysaccharides (LPS) concentration. The LPS/TLR4 signaling pathway is crucial for gut microbiome-mediated liver metastasis. These results indicated that monocytes contribute to liver metastasis via the CCL2/CCR2 axis.},
}

@article {pmid38608404,
year = {2024},
author = {Shennon, I and Wilson, BC and Behling, AH and Portlock, T and Haque, R and Forrester, T and Nelson, CA and O'Sullivan, JM and , },
title = {The infant gut microbiome and cognitive development in malnutrition.},
journal = {Clinical nutrition (Edinburgh, Scotland)},
volume = {43},
number = {5},
pages = {1181-1189},
doi = {10.1016/j.clnu.2024.03.029},
pmid = {38608404},
issn = {1532-1983},
abstract = {Malnutrition affects 195 million children under the age of five worldwide with long term effects that include impaired cognitive development. Brain development occurs rapidly over the first 36 months of life. Whilst seemingly independent, changes to the brain and gut microbiome are linked by metabolites, hormones, and neurotransmitters as part of the gut-brain axis. In the context of severe malnutrition, the composition of the gut microbiome and the repertoire of biochemicals exchanged via the gut-brain axis vary when compared to healthy individuals. These effects are primarily due to the recognized interacting determinants, macro- and micronutrient deficiencies, infection, infestations and toxins related to poor sanitation, and a dearth of psycho-social stimulation. The standard of care for the treatment of severe acute malnutrition is focused on nutritional repletion and weight restoration through the provision of macro- and micronutrients, the latter usually in excess of recommended dietary allowances (RDA). However, existing formulations and supplements have not been designed to specifically address key recovery requirements for brain and gut microbiome development. Animal model studies indicate that treatments targeting the gut microbiome could improve brain development. Despite this, research on humans targeting the gut microbiome with the aim of restoring brain functionality are scarce. We conclude that there is a need for assessment of cognition and the use of various tools that permit visualization of the brain anatomy and function (e.g., Magnetic resonance imaging (MRI), functional near-infrared spectroscopy (fNIRS), electroencephalogram (EEG)) to understand how interventions targeting the gut microbiome impact brain development.},
}

@article {pmid38607765,
year = {2024},
author = {Dorsey, ER and De Miranda, BR and Horsager, J and Borghammer, P},
title = {The Body, the Brain, the Environment, and Parkinson's Disease.},
journal = {Journal of Parkinson's disease},
volume = {},
number = {},
pages = {},
doi = {10.3233/JPD-240019},
pmid = {38607765},
issn = {1877-718X},
abstract = {The brain- and body-first models of Lewy body disorders predict that aggregated alpha-synuclein pathology usually begins in either the olfactory system or the enteric nervous system. In both scenarios the pathology seems to arise in structures that are closely connected to the outside world. Environmental toxicants, including certain pesticides, industrial chemicals, and air pollution are therefore plausible trigger mechanisms for Parkinson's disease and dementia with Lewy bodies. Here, we propose that toxicants inhaled through the nose can lead to pathological changes in alpha-synuclein in the olfactory system that subsequently spread and give rise to a brain-first subtype of Lewy body disease. Similarly, ingested toxicants can pass through the gut and cause alpha-synuclein pathology that then extends via parasympathetic and sympathetic pathways to ultimately produce a body-first subtype. The resulting spread can be tracked by the development of symptoms, clinical assessments, in vivo imaging, and ultimately pathological examination. The integration of environmental exposures into the brain-first and body-first models generates testable hypotheses, including on the prevalence of the clinical conditions, their future incidence, imaging patterns, and pathological signatures. The proposed link, though, has limitations and leaves many questions unanswered, such as the role of the skin, the influence of the microbiome, and the effects of ongoing exposures. Despite these limitations, the interaction of exogenous factors with the nose and the gut may explain many of the mysteries of Parkinson's disease and open the door toward the ultimate goal -prevention.},
}

@article {pmid38607737,
year = {2024},
author = {Wang, Y and Qu, Z and Chu, J and Hun, S},
title = {Aging Gut Microbiome in Healthy and Unhealthy Aging.},
journal = {Aging and disease},
volume = {},
number = {},
pages = {},
doi = {10.14336/AD.2024.0331},
pmid = {38607737},
issn = {2152-5250},
abstract = {The characteristics of human aging manifest in tissue and organ function decline, heightening susceptibility to age-related ailments, thereby presenting novel challenges to fostering and sustaining healthy longevity. In recent years, an abundance of research on human aging has surfaced. Intriguingly, evidence suggests a pervasive correlation among gut microbiota, bodily functions, and chronic diseases. From infancy to later stages of adulthood, healthy individuals witness dynamic shifts in gut microbiota composition. This microbial community is associated with tissue and organ function deterioration (e.g., brain, bones, muscles, immune system, vascular system) and heightened risk of age-related diseases. Thus, we present a narrative review of the aging gut microbiome in both healthy and unhealthy aging contexts. Additionally, we explore the potential for adjustments to physical health based on gut microbiome analysis and how targeting the gut microbiome can potentially slow down the aging process.},
}

@article {pmid38606974,
year = {2024},
author = {Cardoso, PM and Hill, LJ and Villela, HDM and Vilela, CLS and Assis, JM and Rosado, PM and Rosado, JG and Chacon, MA and Majzoub, ME and Duarte, GAS and Thomas, T and Peixoto, RS},
title = {Localization and symbiotic status of probiotics in the coral holobiont.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0026124},
doi = {10.1128/msystems.00261-24},
pmid = {38606974},
issn = {2379-5077},
abstract = {UNLABELLED: Corals establish symbiotic relationships with microorganisms, especially endosymbiotic photosynthetic algae. Although other microbes have been commonly detected in coral tissues, their identity and beneficial functions for their host are unclear. Here, we confirm the beneficial outcomes of the inoculation of bacteria selected as probiotics and use fluorescence in situ hybridization (FISH) to define their localization in the coral Pocillopora damicornis. Our results show the first evidence of the inherent presence of Halomonas sp. and Cobetia sp. in native coral tissues, even before their inoculation. Furthermore, the relative enrichment of these coral tissue-associated bacteria through their inoculation in corals correlates with health improvements, such as increases in photosynthetic potential, and productivity. Our study suggests the symbiotic status of Halomonas sp. and Cobetia sp. in corals by indicating their localization within coral gastrodermis and epidermis and correlating their increased relative abundance through active inoculation with beneficial outcomes for the holobiont. This knowledge is crucial to facilitate the screening and application of probiotics that may not be transient members of the coral microbiome.

IMPORTANCE: Despite the promising results indicating the beneficial outcomes associated with the application of probiotics in corals and some scarce knowledge regarding the identity of bacterial cells found within the coral tissue, the correlation between these two aspects is still missing. This gap limits our understanding of the actual diversity of coral-associated bacteria and whether these symbionts are beneficial. Some researchers, for example, have been suggesting that probiotic screening should only focus on the very few known tissue-associated bacteria, such as Endozoicomonas sp., assuming that the currently tested probiotics are not tissue-associated. Here, we provide specific FISH probes for Halomonas sp. and Cobetia sp., expand our knowledge of the identity of coral-associated bacteria and confirm the probiotic status of the tested probiotics. The presence of these beneficial microorganisms for corals (BMCs) inside host tissues and gastric cavities also supports the notion that direct interactions with the host may underpin their probiotic role. This is a new breakthrough; these results argue against the possibility that the positive effects of BMCs are due to factors that are not related to a direct symbiotic interaction, for example, that the host simply feeds on inoculated bacteria or that the bacteria change the water quality.},
}

@article {pmid38606662,
year = {2024},
author = {Mach, N},
title = {The forecasting power of the mucin-microbiome interplay in livestock respiratory diseases.},
journal = {The veterinary quarterly},
volume = {44},
number = {1},
pages = {1-18},
doi = {10.1080/01652176.2024.2340003},
pmid = {38606662},
issn = {1875-5941},
abstract = {Complex respiratory diseases are a significant challenge for the livestock industry worldwide. These diseases considerably impact animal health and welfare and cause severe economic losses. One of the first lines of pathogen defense combines the respiratory tract mucus, a highly viscous material primarily composed of mucins, and a thriving multi-kingdom microbial ecosystem. The microbiome-mucin interplay protects from unwanted substances and organisms, but its dysfunction may enable pathogenic infections and the onset of respiratory disease. Emerging evidence also shows that noncoding regulatory RNAs might modulate the structure and function of the microbiome-mucin relationship. This opinion paper unearths the current understanding of the triangular relationship between mucins, the microbiome, and noncoding RNAs in the context of respiratory infections in animals of veterinary interest. There is a need to look at these molecular underpinnings that dictate distinct health and disease outcomes to implement effective prevention, surveillance, and timely intervention strategies tailored to the different epidemiological contexts.},
}

@article {pmid38606551,
year = {2024},
author = {Luise, D and Correa, F and Cestonaro, G and Sattin, E and Mele, M and Conte, G and Archetti, I and Virdis, S and Negrini, C and Galasso, I and Stefanelli, C and Mazzoni, M and Nataloni, L and Trevisi, P and Costanzo, E},
title = {Effect of different doses of camelina cake inclusion as a substitute of dietary soybean meal on growth performance and gut health of weaned pigs.},
journal = {The British journal of nutrition},
volume = {},
number = {},
pages = {1-36},
doi = {10.1017/S0007114524000722},
pmid = {38606551},
issn = {1475-2662},
abstract = {Camelina cake (CAM) is a co-product proposed as an alternative protein source; however, piglet data are still limited. This study aimed to evaluate the effect of different doses of CAM in substitution of soybean meal on the growth, health and gut health of weaned pigs. At 14 days post-weaning (d0), 64 piglets were assigned either to a standard diet or to a diet with 4%, 8% or 12% of CAM. Piglets were weighed weekly. At d7 and d28, faeces were collected for microbiota and polyamine and blood for reactive oxygen metabolites (ROMs) and thyroxine analysis. At d28, pigs were slaughtered; organs were weighed, pH was recorded on gut, colon was analysed for volatile fatty acid (VFAs) and jejunum was used for morphological and gene expression analysis. Data analysis was carried out using a mixed model including diet, pen and litter as factors; linear and quadratic contrasts were tested. CAM linearly reduced the average daily gain from d0-d7, d0-d14, d0-d21and d0-d28 (P≤0.01). From d0-d7 increasing CAM linearly decreased feed intake (P=0.04) and increased linearly the feed to gain (P=0.004). CAM increased linearly the liver weight (P<0.0001) and affected the cadaverine (P<0.001). The diet did not affect the ROMs, thyroxine, intestinal pH, VFAs and morphology. All doses of CAM increased the alpha diversity indices at d28 (P<0.05). CAM at 4% promoted the abundance of Butyricicoccaceae_UCG-008. Feeding with CAM enhanced resilience in the gut microbiome and can be evaluated as a potential alternative protein source with dose-dependent limitations on piglet growth performance.},
}

@article {pmid38606523,
year = {2024},
author = {Dentand, AL and Schubert, MG and Krayenbuehl, PA},
title = {Current iron therapy in the light of regulation, intestinal microbiome, and toxicity: are we prescribing too much iron?.},
journal = {Critical reviews in clinical laboratory sciences},
volume = {},
number = {},
pages = {1-13},
doi = {10.1080/10408363.2024.2331477},
pmid = {38606523},
issn = {1549-781X},
abstract = {Iron deficiency is a widespread global health concern with varying prevalence rates across different regions. In developing countries, scarcity of food and chronic infections contribute to iron deficiency, while in industrialized nations, reduced food intake and dietary preferences affect iron status. Other causes that can lead to iron deficiency are conditions and diseases that result in reduced intestinal iron absorption and blood loss. In addition, iron absorption and its bioavailability are influenced by the composition of the diet. Individuals with increased iron needs, including infants, adolescents, and athletes, are particularly vulnerable to deficiency. Severe iron deficiency can lead to anemia with performance intolerance or shortness of breath. In addition, even without anemia, iron deficiency leads to mental and physical fatigue, which points to the fundamental biological importance of iron, especially in mitochondrial function and the respiratory chain. Standard oral iron supplementation often results in gastrointestinal side effects and poor compliance. Low-dose iron therapy seems to be a valid and reasonable therapeutic option due to reduced hepatic hepcidin formation, facilitating efficient iron resorption, replenishment of iron storage, and causing significantly fewer side effects. Elevated iron levels influence gut microbiota composition, favoring pathogenic bacteria and potentially disrupting metabolic and immune functions. Protective bacteria, such as bifidobacteria and lactobacilli, are particularly susceptible to increased iron levels. Dysbiosis resulting from iron supplementation may contribute to gastrointestinal disorders, inflammatory bowel disease, and metabolic disturbances. Furthermore, gut microbiota alterations have been linked to mental health issues. Future iron therapy should consider low-dose supplementation to mitigate adverse effects and the impact on the gut microbiome. A comprehensive understanding of the interplay between iron intake, gut microbiota, and human health is crucial for optimizing therapeutic approaches and minimizing potential risks associated with iron supplementation.},
}

@article {pmid38606451,
year = {2024},
author = {Nguyen, TTH and Bez, C and Bertani, I and Nguyen, MH and Nguyen, TKN and Venturi, V and Dinh, HT},
title = {Microbiome Analysis Revealed Acholeplasma as a Possible Factor Influencing the Susceptibility to Bacterial Leaf Blight Disease of Two Domestic Rice Cultivars in Vietnam.},
journal = {The plant pathology journal},
volume = {40},
number = {2},
pages = {225-332},
doi = {10.5423/PPJ.NT.12.2023.0167},
pmid = {38606451},
issn = {1598-2254},
support = {VINIF.2021.TS.111//Vingroup Innovation Foundation/ ; },
abstract = {The microbiomes of two important rice cultivars in Vietnam which differ by their susceptibility to the bacterial leaf blight (BLB) disease were analyzed through 16S rRNA amplicon technology. A higher number of operational taxonomic units and alpha-diversity indices were shown in the BLB-resistant LA cultivar than in the BLB-susceptible TB cultivar. The BLB pathogen Xanthomonas was scantly found (0.003%) in the LA cultivar, whereas was in a significantly higher ratio in the TB cultivar (1.82%), reflecting the susceptibility to BLB of these cultivars. Of special interest was the genus Acholeplasma presented in the BLB-resistant LA cultivar at a high relative abundance (22.32%), however, was minor in the BLB-sensitive TB cultivar (0.09%), raising a question about its roles in controlling the Xanthomonas low in the LA cultivar. It is proposed that Acholeplasma once entered the host plant would hamper other phytopathogens, i.e. Xanthomonas, by yet unknown mechanisms, of which the triggering of the host plants to produce secondary metabolites against pathogens could be a testable hypothesis.},
}

@article {pmid38606356,
year = {2024},
author = {Monger, XC and Saucier, L and Guay, F and Turcotte, A and Lemieux, J and Pouliot, E and Fournaise, S and Vincent, AT},
title = {Effect of a probiotic and an antibiotic on the mobilome of the porcine microbiota.},
journal = {Frontiers in genetics},
volume = {15},
number = {},
pages = {1355134},
pmid = {38606356},
issn = {1664-8021},
abstract = {Introduction: To consider the growing health issues caused by antibiotic resistance from a "one health" perspective, the contribution of meat production needs to be addressed. While antibiotic resistance is naturally present in microbial communities, the treatment of farm animals with antibiotics causes an increase in antibiotic resistance genes (ARG) in the gut microbiome. Pigs are among the most prevalent animals in agriculture; therefore, reducing the prevalence of antibiotic-resistant bacteria in the pig gut microbiome could reduce the spread of antibiotic resistance. Probiotics are often studied as a way to modulate the microbiome and are, therefore, an interesting way to potentially decrease antibiotic resistance. Methods: To assess the efficacy of a probiotic to reduce the prevalence of ARGs in the pig microbiome, six pigs received either treatment with antibiotics (tylvalosin), probiotics (Pediococcus acidilactici MA18/5M; Biopower[®] PA), or a combination of both. Their faeces and ileal digesta were collected and DNA was extracted for whole genome shotgun sequencing. The reads were compared with taxonomy and ARG databases to identify the taxa and resistance genes in the samples. Results: The results showed that the ARG profiles in the faeces of the antibiotic and combination treatments were similar, and both were different from the profiles of the probiotic treatment (p < 0.05). The effects of the treatments were different in the digesta and faeces. Many macrolide resistance genes were detected in a higher proportion in the microbiome of the pigs treated with antibiotics or the combination of probiotics and antibiotics. Resistance-carrying conjugative plasmids and horizontal transfer genes were also amplified in faeces samples for the antibiotic and combined treatments. There was no effect of treatment on the short chain fatty acid content in the digesta or the faeces. Conclusion: There is no positive effect of adding probiotics to an antibiotic treatment when these treatments are administered simultaneously.},
}

@article {pmid38606343,
year = {2024},
author = {Su, C and Xie, T and Jiang, L and Wang, Y and Wang, Y and Nie, R and Zhao, Y and He, B and Ma, J and Yang, Q and Hao, J},
title = {Host genetics and larval host plant modulate microbiome structure and evolution underlying the intimate insect-microbe-plant interactions in Parnassius species on the Qinghai-Tibet Plateau.},
journal = {Ecology and evolution},
volume = {14},
number = {4},
pages = {e11218},
pmid = {38606343},
issn = {2045-7758},
abstract = {Insects harbor a remarkable diversity of gut microbiomes critical for host survival, health, and fitness, but the mechanism of this structured symbiotic community remains poorly known, especially for the insect group consisting of many closely related species that inhabit the Qinghai-Tibet Plateau. Here, we firstly analyzed population-level 16S rRNA microbial dataset, comprising 11 Parnassius species covering 5 subgenera, from 14 populations mostly sampled in mountainous regions across northwestern-to-southeastern China, and meanwhile clarified the relative importance of multiple factors on gut microbial community structure and evolution. Our findings indicated that both host genetics and larval host plant modulated gut microbial diversity and community structure. Moreover, the effect analysis of host genetics and larval diet on gut microbiomes showed that host genetics played a critical role in governing the gut microbial beta diversity and the symbiotic community structure, while larval host plant remarkably influenced the functional evolution of gut microbiomes. These findings of the intimate insect-microbe-plant interactions jointly provide some new insights into the correlation among the host genetic background, larval host plant, the structure and evolution of gut microbiome, as well as the mechanisms of high-altitude adaptation in closely related species of this alpine butterfly group.},
}

@article {pmid38606003,
year = {2023},
author = {Tsetseri, MN and Silman, AJ and Keene, DJ and Dakin, SG},
title = {The role of the microbiome in rheumatoid arthritis: a review.},
journal = {Rheumatology advances in practice},
volume = {7},
number = {2},
pages = {rkad034},
pmid = {38606003},
issn = {2514-1775},
abstract = {The close bidirectional relationship between the microbiome and the immune system is well supported, and a role of gut dysbiosis has been implied in many systemic autoimmune diseases. This review aims to provide a critical summary and appraisal of 6 murine studies and 16 clinical studies. The findings of the literature review suggest that gut dysbiosis precedes arthritis and that local intestinal inflammation leads to systemic inflammation in genetically predisposed individuals. However, the exact mechanism by which microorganisms provoke immune responses at distal sites remains to be elucidated. Although a characteristic RA microbiome was not identified, there were some common findings among studies: overabundance of Prevotella copri in early RA patients, and proliferation of the genus Collinsela and some Lactobacillus species. Three mechanisms by which microbiota might contribute to RA pathogenesis were proposed: inflammatory responses (P. copri and Lactobacillus), molecular mimicry (P. copri) and loss of intestinal barrier integrity (Collinsella). Larger longitudinal studies are required in order to shed light on the mechanisms involved and unravel the therapeutic potential of the microbiome, and clinical trials are needed to evaluate the safety and efficacy of the implied therapeutic interventions.},
}

@article {pmid38605969,
year = {2024},
author = {Stallmach, A and Quickert, S and Puta, C and Reuken, PA},
title = {The gastrointestinal microbiota in the development of ME/CFS: a critical view and potential perspectives.},
journal = {Frontiers in immunology},
volume = {15},
number = {},
pages = {1352744},
pmid = {38605969},
issn = {1664-3224},
abstract = {Like other infections, a SARS-CoV-2 infection can also trigger Post-Acute Infection Syndromes (PAIS), which often progress into myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS). ME/CFS, characterized by post-exercise malaise (PEM), is a severe multisystemic disease for which specific diagnostic markers or therapeutic concepts have not been established. Despite numerous indications of post-infectious neurological, immunological, endocrinal, and metabolic deviations, the exact causes and pathophysiology remain unclear. To date, there is a paucity of data, that changes in the composition and function of the gastrointestinal microbiota have emerged as a potential influencing variable associated with immunological and inflammatory pathways, shifts in ME/CFS. It is postulated that this dysbiosis may lead to intestinal barrier dysfunction, translocation of microbial components with increased oxidative stress, and the development or progression of ME/CFS. In this review, we detailed discuss the findings regarding alterations in the gastrointestinal microbiota and its microbial mediators in ME/CFS. When viewed critically, there is currently no evidence indicating causality between changes in the microbiota and the development of ME/CFS. Most studies describe associations within poorly defined patient populations, often combining various clinical presentations, such as irritable bowel syndrome and fatigue associated with ME/CFS. Nevertheless, drawing on analogies with other gastrointestinal diseases, there is potential to develop strategies aimed at modulating the gut microbiota and/or its metabolites as potential treatments for ME/CFS and other PAIS. These strategies should be further investigated in clinical trials.},
}

@article {pmid38605957,
year = {2024},
author = {Kopczyńska, J and Kowalczyk, M},
title = {The potential of short-chain fatty acid epigenetic regulation in chronic low-grade inflammation and obesity.},
journal = {Frontiers in immunology},
volume = {15},
number = {},
pages = {1380476},
pmid = {38605957},
issn = {1664-3224},
abstract = {Obesity and chronic low-grade inflammation, often occurring together, significantly contribute to severe metabolic and inflammatory conditions like type 2 diabetes (T2D), cardiovascular disease (CVD), and cancer. A key player is elevated levels of gut dysbiosis-associated lipopolysaccharide (LPS), which disrupts metabolic and immune signaling leading to metabolic endotoxemia, while short-chain fatty acids (SCFAs) beneficially regulate these processes during homeostasis. SCFAs not only safeguard the gut barrier but also exert metabolic and immunomodulatory effects via G protein-coupled receptor binding and epigenetic regulation. SCFAs are emerging as potential agents to counteract dysbiosis-induced epigenetic changes, specifically targeting metabolic and inflammatory genes through DNA methylation, histone acetylation, microRNAs (miRNAs), and long non-coding RNAs (lncRNAs). To assess whether SCFAs can effectively interrupt the detrimental cascade of obesity and inflammation, this review aims to provide a comprehensive overview of the current evidence for their clinical application. The review emphasizes factors influencing SCFA production, the intricate connections between metabolism, the immune system, and the gut microbiome, and the epigenetic mechanisms regulated by SCFAs that impact metabolism and the immune system.},
}

@article {pmid38605920,
year = {2024},
author = {Santiago-Rodriguez, TM},
title = {Comparative oncology using domesticated dogs and their microbiome.},
journal = {Frontiers in veterinary science},
volume = {11},
number = {},
pages = {1378551},
pmid = {38605920},
issn = {2297-1769},
}

@article {pmid38605718,
year = {2024},
author = {Wang, S and Gong, X and Xiao, F and Yang, Y},
title = {Recent advances in host-focused molecular tools for investigating host-gut microbiome interactions.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1335036},
pmid = {38605718},
issn = {1664-302X},
abstract = {Microbial communities in the human gut play a significant role in regulating host gene expression, influencing a variety of biological processes. To understand the molecular mechanisms underlying host-microbe interactions, tools that can dissect signaling networks are required. In this review, we discuss recent advances in molecular tools used to study this interplay, with a focus on those that explore how the microbiome regulates host gene expression. These tools include CRISPR-based whole-body genetic tools for deciphering host-specific genes involved in the interaction process, Cre-loxP based tissue/cell-specific gene editing approaches, and in vitro models of host-derived organoids. Overall, the application of these molecular tools is revolutionizing our understanding of how host-microbiome interactions contribute to health and disease, paving the way for improved therapies and interventions that target microbial influences on the host.},
}

@article {pmid38605646,
year = {2024},
author = {Heston, SM and Hurst, JH and Kelly, MS},
title = {Understanding the influence of the microbiome on childhood infections.},
journal = {Expert review of anti-infective therapy},
volume = {},
number = {},
pages = {1-17},
doi = {10.1080/14787210.2024.2340664},
pmid = {38605646},
issn = {1744-8336},
abstract = {INTRODUCTION: The microbiome is known to have a substantial impact on human health and disease. However, the impacts of the microbiome on immune system development, susceptibility to infectious diseases, and vaccine-elicited immune responses are emerging areas of interest.

AREAS COVERED: In this review, we provide an overview of development of the microbiome during childhood. We highlight available data suggesting that the microbiome is critical to maturation of the immune system and modifies susceptibility to a variety of infections during childhood and adolescence, including respiratory tract infections, Clostridioides difficile infection, and sexually transmitted infections. We discuss currently available and investigational therapeutics that have the potential to modify the microbiome to prevent or treat infections among children. Finally, we review the accumulating evidence that the gut microbiome influences vaccine-elicited immune responses among children.

EXPERT OPINION: Recent advances in sequencing technologies have led to an explosion of studies associating the human microbiome with the risk and severity of infectious diseases. As our knowledge of the extent to which the microbiome influences childhood infections continues to grow, microbiome-based diagnostics and therapeutics will increasingly be incorporated into clinical practice to improve the prevention, diagnosis, and treatment of infectious diseases among children.},
}

@article {pmid38605228,
year = {2024},
author = {Karakousi, T and Mudianto, T and Lund, AW},
title = {Lymphatic vessels in the age of cancer immunotherapy.},
journal = {Nature reviews. Cancer},
volume = {},
number = {},
pages = {},
pmid = {38605228},
issn = {1474-1768},
abstract = {Lymphatic transport maintains homeostatic health and is necessary for immune surveillance, and yet lymphatic growth is often associated with solid tumour development and dissemination. Although tumour-associated lymphatic remodelling and growth were initially presumed to simply expand a passive route for regional metastasis, emerging research puts lymphatic vessels and their active transport at the interface of metastasis, tumour-associated inflammation and systemic immune surveillance. Here, we discuss active mechanisms through which lymphatic vessels shape their transport function to influence peripheral tissue immunity and the current understanding of how tumour-associated lymphatic vessels may both augment and disrupt antitumour immune surveillance. We end by looking forward to emerging areas of interest in the field of cancer immunotherapy in which lymphatic vessels and their transport function are likely key players: the formation of tertiary lymphoid structures, immune surveillance in the central nervous system, the microbiome, obesity and ageing. The lessons learnt support a working framework that defines the lymphatic system as a key determinant of both local and systemic inflammatory networks and thereby a crucial player in the response to cancer immunotherapy.},
}

@article {pmid38605016,
year = {2024},
author = {Sha, H and Lu, J and Chen, J and Xiong, J},
title = {Rationally designed probiotics prevent shrimp white feces syndrome via the probiotics-gut microbiome-immunity axis.},
journal = {NPJ biofilms and microbiomes},
volume = {10},
number = {1},
pages = {40},
pmid = {38605016},
issn = {2055-5008},
support = {32071549, 32371596//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Increasing evidence infers that some complex diseases are attributed to co-infection with multiple pathogens, such as shrimp white feces syndrome (WFS); however, there is a lack of experimental evidence to validate such causal link. This deficiency further impedes rational design of probiotics to elicit desired benefits to shrimp WFS resistance. Herein, we validated the causal roles of Vibrio fluvialis, V. coralliilyticus and V. tubiashii (in a ratio of 7:2:1) in shrimp WFS etiology, which fully satisfied Koch's postulates. Correspondingly, we precisely designed four antagonistic strains: Ruegeria lacuscaerulensis, Nioella nitratireducens, Bacillus subtilis and Streptomyces euryhalinus in a ratio of 4:3:2:1, which efficiently guarded against WFS. Dietary supplementation of the probiotics stimulated beneficial gut populations, streptomycin, short chain fatty acids, taurine metabolism potentials, network stability, tight junction, and host selection, while reducing turnover rate and average variation degree of gut microbiota, thereby facilitating ecological and mechanical barriers against pathogens. Additionally, shrimp immune pathways, such as Fcγ R-mediated phagocytosis, Toll-like receptor and RIG-I-like receptor signaling pathways conferring immune barrier, were activated by probiotics supplementation. Collectively, we establish an updated framework for precisely validating co-infection with multiple pathogens and rationally designing antagonistic probiotics. Furthermore, our findings uncover the underlying beneficial mechanisms of designed probiotics from the probiotics-gut microbiome-host immunity axis.},
}

@article {pmid38605009,
year = {2024},
author = {Zorea, A and Pellow, D and Levin, L and Pilosof, S and Friedman, J and Shamir, R and Mizrahi, I},
title = {Plasmids in the human gut reveal neutral dispersal and recombination that is overpowered by inflammatory diseases.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {3147},
pmid = {38605009},
issn = {2041-1723},
support = {866530//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; ISF 1947/19//Israel Science Foundation (ISF)/ ; },
abstract = {Plasmids are pivotal in driving bacterial evolution through horizontal gene transfer. Here, we investigated 3467 human gut microbiome samples across continents and disease states, analyzing 11,086 plasmids. Our analyses reveal that plasmid dispersal is predominantly stochastic, indicating neutral processes as the primary driver of their wide distribution. We find that only 20-25% of plasmid DNA is being selected in various disease states, constraining its distribution across hosts. Selective pressures shape specific plasmid segments with distinct ecological functions, influenced by plasmid mobilization lifestyle, antibiotic usage, and inflammatory gut diseases. Notably, these elements are more commonly shared within groups of individuals with similar health conditions, such as Inflammatory Bowel Disease (IBD), regardless of geographic location across continents. These segments contain essential genes such as iron transport mechanisms- a distinctive gut signature of IBD that impacts the severity of inflammation. Our findings shed light on mechanisms driving plasmid dispersal and selection in the human gut, highlighting their role as carriers of vital gene pools impacting bacterial hosts and ecosystem dynamics.},
}

@article {pmid38604998,
year = {2024},
author = {Chen, Y and Li, Z and Bai, L and Lu, B and Peng, Y and Xu, P and Song, X and Bian, Y and Wang, X and Zhao, S},
title = {Glycyrrhiza polysaccharides may have an antitumor effect in γδT cells through gut microbiota and TLRs/NF-κB pathway in mice.},
journal = {FEBS open bio},
volume = {},
number = {},
pages = {},
doi = {10.1002/2211-5463.13800},
pmid = {38604998},
issn = {2211-5463},
support = {81873100//National Natural Science Foundation of China/ ; 82305332//National Natural Science Foundation of China/ ; },
abstract = {Tumor immunotherapy can be a suitable cancer treatment option in certain instances. Here we investigated the potential immunomodulatory effect of oral glycyrrhiza polysaccharides (GCP) on the antitumor function of γδT cells in intestinal epithelial cells in mice. We found that GCP can inhibit tumor growth and was involved in the regulation of systemic immunosuppression. GCP administration also promoted the differentiation of gut epithelia γδT cells into IFN-γ-producing subtype through regulation of local cytokines in gut mucosa. GCP administration increased local cytokine levels through gut microbiota and the gut mucosa Toll-like receptors / nuclear factor kappa-B pathway. Taken together, our results suggest that GCP might be a suitable candidate for tumor immunotherapy, although further clinical research, including clinical trials, are required to validate these results.},
}

@article {pmid38604961,
year = {2024},
author = {Jia, W and Liu, M and Zhou, Z and Li, J and Wu, S and Shen, X and He, F and Cheng, R},
title = {[Relationship between gut microbiome and neurodevelopment in early life].},
journal = {Wei sheng yan jiu = Journal of hygiene research},
volume = {53},
number = {2},
pages = {250-256},
doi = {10.19813/j.cnki.weishengyanjiu.2024.02.012},
pmid = {38604961},
issn = {1000-8020},
abstract = {OBJECTIVE: To compare the differences in gut microbiome composition between children with good neurodevelopment and those with delayed neurodevelopment, and to analyze the relationship between gut microbiome and the neurodevelopment status of infants in early life.

METHODS: The mothers were included at the Second West China Hospital from November 2020 to April 2021. Their infant stools were collected on day 0 and day 90 after birth, and the follow-up questionnaires at the corresponding time points were completed. Additionally, the Ages and Stages Questionnaires-Third Edition(ASQ-3) were completed by mothers at 12 months of age. The structure and diversity of gut microbiota were examined by 16S rRNA sequencing, and the relationship between gut microbiome and ASQ-3 questionnaire scores in early life was analyzed.

RESULTS: According to the ASQ-3 scores, mothers and infants into neurodevelopment good group(G group, n=18) and neurodevelopmental delay group(D group, n=10). Compared with the D group, the relative abundance of the Firmicutes was significantly higher in the G group at day 0(P<0.05), while the level of the Proteobacteria was lower(P<0.05). At day 90 after birth, the relative abundance of the Actinobacteria, Bifidobacteriaceae and Enterococcaceae was significantly higher in the G group(P<0.05). In addition, alpha diversity was not statistically different between the two groups. Spearman's correlation analysis showed that Clostridiaceae of the postnatal day 0 infants was positively correlated with the communication domain score, but negatively associated with gross motor domain score in children at 12 months of age, whereas the relative abundance of Proteobacteria and Enterobacteriaceae of children at postnatal day 90 was negatively associated with communication development, while the relative abundance of Erysipelatoclostridiaceae showed a negative correlation with gross motor domain scores.

CONCLUSION: The structure of the gut microbiome in early life between neurodevelopment good and delayed infants, and were associated with the development of communication and gross motor domain in infants at 12 months of age, suggesting that gut microbiome in early life may be related to the level of neurodevelopment in infants.},
}

@article {pmid38604888,
year = {2024},
author = {Taylor, SL and Rogers, GB},
title = {The evolving focus of cystic fibrosis microbiome research.},
journal = {Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jcf.2024.03.014},
pmid = {38604888},
issn = {1873-5010},
}

@article {pmid38604562,
year = {2024},
author = {Song, G and Shin, D and Kim, JS},
title = {Microbiome changes in Akanthomyces attenuatus JEF-147-infected two-spotted spider mites.},
journal = {Journal of invertebrate pathology},
volume = {204},
number = {},
pages = {108102},
doi = {10.1016/j.jip.2024.108102},
pmid = {38604562},
issn = {1096-0805},
abstract = {The two-spotted spider mite (Tetranychus urticae Koch) is an agriculturally serious polyphagous pest that has acquired strong resistance against acaricides because of its short life cycle and continuous exposure to acaricides. As an alternative, mite-pathogenic fungi with different modes of action could be used to control the mites. The spider mite has symbiotic microorganisms that could be involved in the physiological and ecological adaptations to biotic stresses. In this study, mite-pathogenic fungi were used to control female adults, and the microbiomes changes in the fungus-infected mites were analyzed. The acaricidal activity of 77 fungal isolates was tested, and Akanthomyces attenuatus JEF-147 exhibited the highest acaricidal activity. Subsequently a dose-response assay and morphological characterization was undertaken For microbiome analysis in female adults infected with A. attenuatus JEF-147, 16S rDNA and ITS1 were sequenced using Illumina Miseq. Infected mite showed a higher Shannon index in bacterial diversity but lower index in fungal diversity. In beta diversity using principal component analysis, JEF-147-treated mites were significantly different from non-treated controls in both bacteria and fungi. Particularly in bacterial abundance, arthropod defense-related Rickettsia increased, but arthropod reproduction-associated Wolbachia decreased. The change in major bacterial abundance in the infected mites could be explained by a trade-off between reproduction and immunity against the early stage of fungal attack. In fungal abundance, Akanthomyces showed up as expected. Foremost, this work reports microbiome changes in a fungus-infected mite and suggests a possible trade-off in mites against fungal pathogens. Future studies will focus on gene-based investigations related to this topic.},
}

@article {pmid38604559,
year = {2024},
author = {Kesbiç, OS and Acar, Ü and Kesbiç, FI and Yılmaz, S},
title = {Growth performance, health status, gut microbiome, and expression of immune and growth-related genes of rainbow trout (Oncorhynchus mykiss) fed diets with pea protein replacement of fish meal.},
journal = {Comparative biochemistry and physiology. Part B, Biochemistry & molecular biology},
volume = {},
number = {},
pages = {110968},
doi = {10.1016/j.cbpb.2024.110968},
pmid = {38604559},
issn = {1879-1107},
abstract = {The need for fish meal constrains fish farming and significantly impacts sustainability of the aquaculture industry. Hence, it is important to investigate the use of plant-based protein sources in fish diets. The present study was conducted to determine the effects of different levels of fish meal (FM) replacement by pea protein (PP) in a 60-day feeding experiment in rainbow trout, Oncorhynchus mykiss. Effects on growth performance, body composition, hematology, serum biochemistry and immunology, and immune (TNF-α, IL1-ß and Il-8) and growth-related (GH and IGFI) gene expression were investigated. Five experimental diets (45% protein and 20% lipid) differed in replacement level of FM by PP at rates of 0% (control (PP0)), 25% (PP25), 50%(PP50), 75%(PP75) and 100%(PP100). Fish were fed with experimental diets in triplicate twice daily. The best growth performance was obtained in PP0 and PP25 groups. While fat ratios of fish fillets significantly differed (p < 0.05), there was no significant effects on protein ratios (p < 0.05). There was no significant change in the hematological values of fish, except those fed the PP100 diets, which displayed a reduction in eyrthocyte counts, hemoglobin content and hematocrit. As PP supplementation increased fish showed elevated serum glucose, total protein, cholesterol and myeloperoxidase activity and decreased glutamic pyruvic transaminase and alkaline phosphatase activity. Fish fed diets with between 25 and 75% replacement showed a decline in lactic acid bacteria in the gut. Significant increases in expression were observed in the liver of the PP25 fish relative to the 0% control for all immune and growth-related genes except for IL1-ß. These data suggest that up to 25% of FM can be replaced by PP without any adverse effects on rainbow trout.},
}

@article {pmid38604402,
year = {2024},
author = {Khadka, VD and Markey, L and Boucher, M and Lieberman, TD},
title = {Commensal skin bacteria exacerbate inflammation and delay skin barrier repair.},
journal = {The Journal of investigative dermatology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jid.2024.03.033},
pmid = {38604402},
issn = {1523-1747},
abstract = {The skin microbiome can both trigger beneficial immune stimulation and pose a potential infection threat. Previous studies have shown that colonization of mouse skin with the model human skin commensal Staphylococcus epidermidis is protective against subsequent excisional wound or pathogen challenge. However, less is known about concurrent skin damage and exposure to commensal microbes, despite growing interest in interventional probiotic therapy. Here, we address this open question by applying commensal skin bacteria at a high dose to abraded skin. While depletion of the skin microbiome via antibiotics delayed repair from damage, probiotic-like application of commensals-- including the mouse commensal Staphylococcus xylosus, three distinct isolates of S. epidermidis, and all other tested human skin commensals-- also significantly delayed barrier repair. Increased inflammation was observed within four hours of S. epidermidis exposure and persisted through day four, at which point the skin displayed a chronic wound-like inflammatory state with increased neutrophil infiltration, increased fibroblast activity, and decreased monocyte differentiation. Transcriptomic analysis suggested that the prolonged upregulation of early canonical proliferative pathways inhibited the progression of barrier repair. These results highlight the nuanced role of members of the skin microbiome in modulating barrier integrity and indicate the need for caution in their development as probiotics.},
}

@article {pmid38604398,
year = {2024},
author = {Hsu, JE and Matsen, FA and Whitson, AJ and Waalkes, A and Almazan, J and Bourassa, LA and Salipante, SJ and Long, DR},
title = {2023 Neer Award for Basic Science: Genetics of Cutibacterium acnes in Revision Shoulder Arthroplasty: A Large-Scale Bacterial Whole-Genome Sequencing Study.},
journal = {Journal of shoulder and elbow surgery},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jse.2024.02.039},
pmid = {38604398},
issn = {1532-6500},
abstract = {BACKGROUND: Cutibacterium acnes is the bacterium most commonly responsible for shoulder periprosthetic joint infection (PJI) and is often cultured from samples obtained at the time of revision for failed shoulder arthroplasty. We sought to determine whether these bacteria originate from the patient or from exogenous sources. We also sought to identify which C. acnes genetic traits were associated with the development of shoulder PJI.

METHODS: We performed bacterial whole-genome sequencing of C. acnes from a single-institution repository of cultures obtained before or during primary and revision shoulder arthroplasty and correlated the molecular epidemiology and genetic content of strains with clinical features of infection.

RESULTS: A total of 341 isolates collected over a four-year period from 88 patients were sequenced. C. acnes cultured from surgical specimens demonstrated significant similarity to the strains colonizing the skin of the same patient (p<0.001). Infrequently, there was evidence of strains shared across unrelated patients, suggesting that exogenous sources of C. acnes culture-positivity were uncommon. Phylotypes IB and II were modestly associated with clinical features of PJI, but all phylotypes appeared inherently capable of causing disease. Chronic shoulder PJI was associated with the absence of common C. acnes genes involved in bacterial quorum-sensing (luxS, tqsA).

CONCLUSION: C. acnes strains cultured from deep intraoperative sources during revision shoulder arthroplasty demonstrate strong genetic similarity to the strains colonizing a patient's skin. Some phylotypes of C. acnes commonly colonizing human skin are modestly more virulent than others, but all phylotypes have a capacity for PJI. C. acnes cultured from cases of PJI commonly demonstrated genetic hallmarks associated with adaptation from acute to chronic phases of infection. This is the strongest evidence to date supporting the role of the patient's own, cutaneous C. acnes strains in the pathogenesis of shoulder arthroplasty infection. Our findings support the importance of further research focused on perioperative decolonization and management of endogenous bacteria that are likely to be introduced into the arthroplasty wound at the time of skin incision.},
}

@article {pmid38604200,
year = {2024},
author = {Porcari, S and Fusco, W and Spivak, I and Fiorani, M and Gasbarrini, A and Elinav, E and Cammarota, G and Ianiro, G},
title = {Fine-tuning the gut ecosystem: the current landscape and outlook of artificial microbiome therapeutics.},
journal = {The lancet. Gastroenterology & hepatology},
volume = {9},
number = {5},
pages = {460-475},
doi = {10.1016/S2468-1253(23)00357-6},
pmid = {38604200},
issn = {2468-1253},
abstract = {The gut microbiome is acknowledged as a key determinant of human health, and technological progress in the past two decades has enabled the deciphering of its composition and functions and its role in human disorders. Therefore, manipulation of the gut microbiome has emerged as a promising therapeutic option for communicable and non-communicable disorders. Full exploitation of current therapeutic microbiome modulators (including probiotics, prebiotics, and faecal microbiota transplantation) is hindered by several factors, including poor precision, regulatory and safety issues, and the impossibility of providing reproducible and targeted treatments. Artificial microbiota therapeutics (which include a wide range of products, such as microbiota consortia, bacteriophages, bacterial metabolites, and engineered probiotics) have appeared as an evolution of current microbiota modulators, as they promise safe and reproducible effects, with variable levels of precision via different pathways. We describe the landscape of artificial microbiome therapeutics, from those already on the market to those still in the pipeline, and outline the major challenges for positioning these therapeutics in clinical practice.},
}

@article {pmid38604121,
year = {2024},
author = {C, BG and Zhou, P and Wu, C},
title = {Fusobacterium nucleatum subsp. animalis comes to the spotlight in oral diseases.},
journal = {Cell host & microbe},
volume = {32},
number = {4},
pages = {443-444},
doi = {10.1016/j.chom.2024.03.009},
pmid = {38604121},
issn = {1934-6069},
support = {R01 DE030895/DE/NIDCR NIH HHS/United States ; },
abstract = {Krieger et al.'s study in this issue of Cell Host & Microbe reveals that Fusobacterium nucleatum subsp. animalis strains, previously underestimated, are significant in disease-affected oral areas. This challenges the long-held notion of the dominance of Fusobacterium nucleatum subsp. nucleatum, reshaping our understanding of Fusobacterium distribution in the oral microbiome.},
}

@article {pmid38604013,
year = {2024},
author = {Zhuang, Y and Wang, H and Tan, F and Wu, B and Liu, L and Qin, H and Yang, Z and He, M},
title = {Rhizosphere metabolic cross-talk from plant-soil-microbe tapping into agricultural sustainability: Current advance and perspectives.},
journal = {Plant physiology and biochemistry : PPB},
volume = {210},
number = {},
pages = {108619},
doi = {10.1016/j.plaphy.2024.108619},
pmid = {38604013},
issn = {1873-2690},
abstract = {Rhizosphere interactions from plant-soil-microbiome occur dynamically all the time in the "black microzone" underground, where we can't see intuitively. Rhizosphere metabolites including root exudates and microbial metabolites act as various chemical signalings involving in rhizosphere interactions, and play vital roles on plant growth, development, disease suppression and resistance to stress conditions as well as proper soil health. Although rhizosphere metabolites are a mixture from plant roots and soil microbes, they often are discussed alone. As a rapid appearance of various omics platforms and analytical methods, it offers possibilities and opportunities for exploring rhizosphere interactions in unprecedented breadth and depth. However, our comprehensive understanding about the fine-tuning mechanisms of rhizosphere interactions mediated by these chemical compounds still remain clear. Thus, this review summarizes recent advances systemically including the features of rhizosphere metabolites and their effects on rhizosphere ecosystem, and looks forward to the future research perspectives, which contributes to facilitating better understanding of biochemical communications belowground and helping identify novel rhizosphere metabolites. We also address challenges for promoting the understanding about the roles of rhizosphere metabolites in different environmental stresses.},
}

@article {pmid38603815,
year = {2024},
author = {Bai, H and He, LY and Gao, FZ and Yao, KS and Zhang, M and Qiao, LK and Chen, ZY and He, LX and Liu, YS and Zhao, JL and Ying, GG},
title = {Airborne antibiotic resistome and microbiome in pharmaceutical factories.},
journal = {Environment international},
volume = {186},
number = {},
pages = {108639},
doi = {10.1016/j.envint.2024.108639},
pmid = {38603815},
issn = {1873-6750},
abstract = {Antimicrobial resistance is considered to be one of the biggest public health problems, and airborne transmission is an important but under-appreciated pathway for the spread of antibiotic resistance genes (ARGs) in the environment. Previous research has shown pharmaceutical factories to be a major source of ARGs and antibiotic resistant bacteria (ARB) in the surrounding receiving water and soil environments. Pharmaceutical factories are hotspots of antibiotic resistance, but the atmospheric transmission and its environmental risk remain more concerns. Here, we conducted a metagenomic investigation into the airborne microbiome and resistome in three pharmaceutical factories in China. Soil (average: 38.45%) and wastewater (average: 28.53%) were major contributors of airborne resistome. ARGs (vanR/vanS, blaOXA, and CfxA) conferring resistance to critically important clinically used antibiotics were identified in the air samples. The wastewater treatment area had significantly higher relative abundances of ARGs (average: 0.64 copies/16S rRNA). Approximately 28.2% of the detected airborne ARGs were found to be associated with plasmids, and this increased to about 50% in the wastewater treatment area. We have compiled a list of high-risk airborne ARGs found in pharmaceutical factories. Moreover, A total of 1,043 viral operational taxonomic units were identified and linked to 47 family-group taxa. Different CRISPR-Cas immune systems have been identified in bacterial hosts in response to phage infection. Similarly, higher phage abundance (average: 2451.70 PPM) was found in the air of the wastewater treatment area. Our data provide insights into the antibiotic resistance gene profiles and microbiome (bacterial and non-bacterial) in pharmaceutical factories and reveal the potential role of horizontal transfer in the spread of airborne ARGs, with implications for human and animal health.},
}

@article {pmid38603812,
year = {2024},
author = {Li, Y and Jin, L and Wu, M and Wang, B and Qu, N and Zhou, H and Chen, T and Liu, G and Yue, M and Zhang, G},
title = {Forest management positively reshapes the phyllosphere bacterial community and improves community stability.},
journal = {Environment international},
volume = {186},
number = {},
pages = {108611},
doi = {10.1016/j.envint.2024.108611},
pmid = {38603812},
issn = {1873-6750},
abstract = {Research has shown that forest management can improve the post-drought growth and resilience of Qinghai spruce in the eastern Qilian Mountains, located on the northeastern Tibetan Plateau. However, the impact of such management on the tree-associated phyllosphere microbiome is not yet fully understood. This study provides new evidence of positive forest management effects on the phyllosphere microbiome after extreme drought, from the perspectives of community diversity, structure, network inference, keystone species, and assembly processes. In managed Qinghai spruce forest, the α-diversity of the phyllosphere bacterial communities increased, whereas the β-diversity decreased. In addition, the phyllosphere bacterial community became more stable and resistant, yet less complex, following forest management. Keystone species inferred from a bacterial network also changed under forest management. Furthermore, forest management mediated changes in community assembly processes, intensifying the influence of determinacy, while diminishing that of stochasticity. These findings support the hypothesis that management can re-assemble the phyllosphere bacterial community, enhance community stability, and ultimately improve tree growth. Overall, the study highlights the importance of forest management on the phyllosphere microbiome and furnishes new insights into forest conservation from the perspective of managing microbial processes and effects.},
}

@article {pmid38603714,
year = {2024},
author = {Goforth, M and Obergh, V and Park, R and Porchas, M and Crosby, KM and Jifon, JL and Ravishankar, S and Brierley, P and Leskovar, DL and Turini, TA and Schultheis, J and Coolong, T and Miller, R and Koiwa, H and Patil, BS and Cooper, MA and Huynh, S and Parker, CT and Guan, W and Cooper, KK},
title = {Bacterial diversity and composition on the rinds of specific melon cultivars and hybrids from across different growing regions in the United States.},
journal = {PloS one},
volume = {19},
number = {4},
pages = {e0293861},
pmid = {38603714},
issn = {1932-6203},
abstract = {The goal of this study was to characterize the bacterial diversity on different melon varieties grown in different regions of the US, and determine the influence that region, rind netting, and variety of melon has on the composition of the melon microbiome. Assessing the bacterial diversity of the microbiome on the melon rind can identify antagonistic and protagonistic bacteria for foodborne pathogens and spoilage organisms to improve melon safety, prolong shelf-life, and/or improve overall plant health. Bacterial community composition of melons (n = 603) grown in seven locations over a four-year period were used for 16S rRNA gene amplicon sequencing and analysis to identify bacterial diversity and constituents. Statistically significant differences in alpha diversity based on the rind netting and growing region (p < 0.01) were found among the melon samples. Principal Coordinate Analysis based on the Bray-Curtis dissimilarity distance matrix found that the melon bacterial communities clustered more by region rather than melon variety (R2 value: 0.09 & R2 value: 0.02 respectively). Taxonomic profiling among the growing regions found Enterobacteriaceae, Bacillaceae, Microbacteriaceae, and Pseudomonadaceae present on the different melon rinds at an abundance of ≥ 0.1%, but no specific core microbiome was found for netted melons. However, a core of Pseudomonadaceae, Bacillaceae, and Exiguobacteraceae were found for non-netted melons. The results of this study indicate that bacterial diversity is driven more by the region that the melons were grown in compared to rind netting or melon type. Establishing the foundation for regional differences could improve melon safety, shelf-life, and quality as well as the consumers' health.},
}

@article {pmid38603577,
year = {2024},
author = {Cao, D and Lin, Y and Lin, C and Xu, M and Wang, J and Zeng, Z and Wang, P and Li, Q and Wang, X and Wang, W and Luo, L and Zhao, Y and Shi, Y and Gao, Z and Kang, X and Wang, S and Zhang, Y and Xu, X and Liu, SL and Liu, H},
title = {Cannabidiol Inhibits Epithelial Ovarian Cancer: Role of Gut Microbiome.},
journal = {Journal of natural products},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jnatprod.3c00782},
pmid = {38603577},
issn = {1520-6025},
abstract = {Epithelial ovarian cancer is among the deadliest gynecological tumors worldwide. Clinical treatment usually consists of surgery and adjuvant chemo- and radiotherapies. Due to the high rate of recurrence and rapid development of drug resistance, the current focus of research is on finding effective natural products with minimal toxic side effects for treating epithelial ovarian tumors. Cannabidiol is among the most abundant cannabinoids and has a non-psychoactive effect compared to tetrahydrocannabinol, which is a key advantage for clinical application. Studies have shown that cannabidiol has antiproliferative, pro-apoptotic, cytotoxic, antiangiogenic, anti-inflammatory, and immunomodulatory properties. However, its therapeutic value for epithelial ovarian tumors remains unclear. This study aims to investigate the effects of cannabidiol on epithelial ovarian tumors and to elucidate the underlying mechanisms. The results showed that cannabidiol has a significant inhibitory effect on epithelial ovarian tumors. In vivo experiments demonstrated that cannabidiol could inhibit tumor growth by modulating the intestinal microbiome and increasing the abundance of beneficial bacteria. Western blot assays showed that cannabidiol bound to EGFR/AKT/MMPs proteins and suppressed EGFR/AKT/MMPs expression in a dose-dependent manner. Network pharmacology and molecular docking results suggested that cannabidiol could affect the EGFR/AKT/MMPs signaling pathway.},
}

@article {pmid38602593,
year = {2024},
author = {Maslin, M and Paix, B and van der Windt, N and Ambo-Rappe, R and Debitus, C and Gaertner-Mazouni, N and Ho, R and de Voogd, NJ},
title = {Prokaryotic communities of the French Polynesian sponge Dactylospongia metachromia display a site-specific and stable diversity during an aquaculture trial.},
journal = {Antonie van Leeuwenhoek},
volume = {117},
number = {1},
pages = {65},
pmid = {38602593},
issn = {1572-9699},
support = {08858/VP/DRMM//Direction des Ressources Marines/ ; 08858/VP/DRMM//Direction des Ressources Marines/ ; 08858/VP/DRMM//Direction des Ressources Marines/ ; 3299/MTF//Government of French Polynesia/ ; 3299/MTF//Government of French Polynesia/ ; 16.161.301//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; 16.161.301//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; },
mesh = {Animals ; *Porifera ; Aquaculture ; Agriculture ; *Microbiota ; Polynesia ; },
abstract = {Dynamics of microbiomes through time are fundamental regarding survival and resilience of their hosts when facing environmental alterations. As for marine species with commercial applications, such as marine sponges, assessing the temporal change of prokaryotic communities allows us to better consider the adaptation of sponges to aquaculture designs. The present study aims to investigate the factors shaping the microbiome of the sponge Dactylospongia metachromia, in a context of aquaculture development in French Polynesia, Rangiroa, Tuamotu archipelago. A temporal approach targeting explants collected during farming trials revealed a relative high stability of the prokaryotic diversity, meanwhile a complementary biogeographical study confirmed a spatial specificity amongst samples at different longitudinal scales. Results from this additional spatial analysis confirmed that differences in prokaryotic communities might first be explained by environmental changes (mainly temperature and salinity), while no significant effect of the host phylogeny was observed. The core community of D. metachromia is thus characterized by a high spatiotemporal constancy, which is a good prospect for the sustainable exploitation of this species towards drug development. Indeed, a microbiome stability across locations and throughout the farming process, as evidenced by our results, should go against a negative influence of sponge translocation during in situ aquaculture.},
}

Animals
*Porifera
Aquaculture
Agriculture
*Microbiota
Polynesia

@article {pmid38602577,
year = {2024},
author = {Ślusarczyk, A},
title = {ASO Author Reflections: Changes in the Urinary Microbiome After Transurethral Resection of Nonmuscle-Invasive Bladder Cancer: Insights from a Prospective Observational Study.},
journal = {Annals of surgical oncology},
volume = {},
number = {},
pages = {},
pmid = {38602577},
issn = {1534-4681},
}

@article {pmid38602449,
year = {2024},
author = {Brandt, E and Koivisto, A and Pereira, P and Mustanoja, E and Auvinen, P and Saari, T and Lehtola, JM and Hannonen, S and Rusanen, M and Leinonen, V and Scheperjans, F and Kärkkäinen, V},
title = {Gut Microbiome Changes in Patients With Idiopathic Normal Pressure Hydrocephalus.},
journal = {Alzheimer disease and associated disorders},
volume = {},
number = {},
pages = {},
pmid = {38602449},
issn = {1546-4156},
abstract = {BACKGROUND: The gut microbiome is a complex system within the human gastrointestinal tract. The bacteria play a significant role in human health, and some can promote inflammation and pathologic processes through chemical interactions or metabolites. Gut microbiome dysbiosis has been linked to some neurological and other diseases. Here we aimed to examine microbiome differences between patients with a progressive neurological disorder, idiopathic normal pressure hydrocephalus (iNPH), compared with healthy controls (CO).

METHODS: We recruited 37 neurologically healthy CO and 10 patients with shunted iNPH. We evaluated these participants' cognition using the CERAD-NB test battery and CDR test, and collected a variety of information, including about dietary habits and health. We also collected fecal samples, which were subjected to 16S amplicon sequencing to analyze differences in gut microbiome composition.

RESULTS: We found that the iNPH group exhibited significantly different abundances of 10 bacterial genera compared with the CO group. The Escherichia/Shigella and Anaeromassilibacillus genera were most remarkably increased. Other increased genera were Butyrivibrio, Duncaniella, and an unidentified genus. The decreased genera were Agathobaculum, Paramuribaculum, Catenibacterium, and 2 unidentified genera.

CONCLUSIONS: Here we report the first identified microbiome differences in iNPH patients compared with healthy controls.},
}

@article {pmid38602350,
year = {2024},
author = {Lu, S and Cheng, D and Yao, H and Wen, Y and Yu, Y and Li, H and Wang, J and Sun, B},
title = {Cascade Microbial Metabolism of Ferulic Acid In Vitro Fermented by the Human Fecal Inoculum.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.3c09782},
pmid = {38602350},
issn = {1520-5118},
abstract = {Ferulic acid (FA), predominantly existing in most cereals, can modulate the gut microbiome, but the influences of its metabolites on the microbial population and FA-transforming microorganisms are still unclear. In this study, FA and its potential phenolic metabolites were fermented in vitro for 24 h with the human fecal inoculum. A comparable short chain fatty acid (SCFA) production trend was observed in the presence and absence of substrates, suggesting limited contribution of FA mechanism to SCFA formation. Dihydroferulic acid, 3-(3,4-dihydroxyphenyl)propionic acid, and 3-(3-hydroxyphenyl)propionic acid were ascertained to be successive metabolites of FA, by tracking the intermediate variation. FA remarkably promoted the absolute abundances of total bacteria, while different metabolites affected bacterial growth of selective genera. Specific genera were identified as quantitatively correlating to the content of FA and its metabolites. Ultimately, FA-mediated gut microbiota modulation involves both the action of metabolizing microbes and the regulation effects of metabolites on bacterial growth.},
}

@article {pmid38602133,
year = {2024},
author = {Schoonakker, MP and van Peet, PG and van den Burg, EL and Numans, ME and Ducarmon, QR and Pijl, H and Wiese, M},
title = {Impact of dietary carbohydrate, fat, or protein restriction on the human gut microbiome: a systematic review.},
journal = {Nutrition research reviews},
volume = {},
number = {},
pages = {1-47},
doi = {10.1017/S0954422424000131},
pmid = {38602133},
issn = {1475-2700},
abstract = {Restriction of dietary carbohydrates, fat, and/or protein is often used to reduce body weight and/or treat (metabolic) diseases. Since diet is a key modulator of the human gut microbiome, which plays an important role in health and disease, this review aims to provide an overview of current knowledge of the effects of macronutrient-restricted diets on gut microbial composition and metabolites. A structured search strategy was performed in several databases. After screening for in-and exclusion criteria, 36 articles could be included. Data are included in the results only when supported by at least three independent studies to enhance the reliability of our conclusions. Low-carbohydrate (<30 energy%) diets tended to induce a decrease in the relative abundance of several health-promoting bacteria, such as Bifidobacterium, as well as a reduction in short-chain fatty acid (SCFA) levels in faeces. In contrast, low-fat diets (<30 energy%) increased alpha diversity, faecal SCFA levels, and abundance of some beneficial bacteria, including F. prausnitzii. There was insufficient data to draw conclusions concerning the effects of low-protein (<10 energy%) diets on gut microbiota. Although the data of included studies unveils possible benefits of low-fat and potential drawbacks of low-carbohydrate diets for human gut microbiota, the diversity in study designs made it difficult to draw firm conclusions. Using a more uniform methodology in design, sample processing and sharing raw sequence data could foster our understanding of the effects of macronutrient restriction on gut microbiota composition and metabolic dynamics relevant to health. This systematic review was registered at https://www.crd.york.ac.uk/prospero as CRD42020156929.},
}

@article {pmid38602003,
year = {2024},
author = {Kang, M and Kang, M and Yoo, J and Lee, J and Lee, S and Yun, B and Song, M and Kim, JM and Kim, HW and Yang, J and Kim, Y and Oh, S},
title = {Dietary supplementation with Lacticaseibacillus rhamnosus IDCC3201 alleviates sarcopenia by modulating the gut microbiota and metabolites in dexamethasone-induced models.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d3fo05420a},
pmid = {38602003},
issn = {2042-650X},
abstract = {Probiotics can exert direct or indirect influences on various aspects of health claims by altering the composition of the gut microbiome and producing bioactive metabolites. The aim of this study was to examine the effect of Lacticaseibacillus rhamnosus IDCC3201 on skeletal muscle atrophy in dexamethasone-induced C2C12 cells and a mouse animal model. Dexamethasone treatment significantly reduced C2C12 muscle cell viability, myotube diameter, and levels of muscle atrophic markers (Atrogin-1 and MuRF-1). These effects were alleviated by conditioned media (CM) and cell extract (EX) derived from L. rhamnosus IDCC3201. In addition, we assessed the in vivo therapeutic effect of L. rhamnosus IDCC3201 in a mouse model of dexamethasone (DEX)-induced muscle atrophy. Supplementation with IDCC3201 resulted in significant enhancements in body composition, particularly in lean mass, muscle strength, and myofibril size, in DEX-induced muscle atrophy mice. In comparison to the DEX-treatment group, the normal and DEX + L. rhamnosus IDCC3201 groups showed a higher transcriptional level of myosin heavy chain family genes (MHC1, MHC1b, MHC2A, 2bB, and 2X) and a reduction in atrophic muscle makers. These analyses revealed that L. rhamnosus IDCC3201 supplementation led to increased production of branched-chain amino acids (BCAAs) and improved the Allobaculum genus within the gut microbiota of muscle atrophy-induced groups. Taken together, our findings suggest that L. rhamnosus IDCC3201 represents a promising dietary supplement with the potential to alleviate sarcopenia by modulating the gut microbiome and metabolites.},
}

@article {pmid38601989,
year = {2024},
author = {Zheng, G and Zhang, Y and Ou, F and Chang, Q and Ji, C and Yang, H and Chen, L and Xia, Y and Zhao, Y},
title = {Sugar types, genetic predictors of the gut microbiome, and the risk of chronic kidney disease: a prospective cohort study.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d4fo00724g},
pmid = {38601989},
issn = {2042-650X},
abstract = {Background: Emerging studies suggest that focusing on the intake of specific types or sources of sugars may yield greater benefits in preventing chronic kidney disease (CKD). Objective: We aimed to investigate the associations between free and non-free sugar intakes and CKD risk as well as the potential sugar type-gut microbiome interactions. Methods: A total of 138 064 participants from the UK Biobank were included in this prospective study. The free and non-free sugar intakes were assessed using repeated web-based 24-hour dietary recalls. A cause-specific competing risk model was used to estimate hazard ratios (HRs) and the corresponding confidence intervals (CIs) of incident CKD, treating deaths before incident CKD as competing events. Results: During a median follow-up of 10.5 years, 2,923 participants (2.1%) developed CKD. The free sugar intake was positively associated with the risk of CKD (HRquartile 4 vs. quartile 1 = 1.32, 95% CI = 1.18, 1.47), with a nonlinear relationship (P for nonlinearity = 0.01, the risk increased rapidly after free sugars made up 10% of the total energy). The non-free sugar intake was inversely associated with CKD risk (HRquartile 4 vs. quartile 1 = 0.68, 95% CI = 0.60, 0.77), with an L-shaped nonlinear curve (p for nonlinearity = 0.01, the turning point was at 13.5% of the total energy). We found that the associations between free sugar and non-free sugar intakes and CKD risk were more pronounced in participants with high genetically predicted gut microbial abundance. Furthermore, a significant interaction was observed between the genetically predicted gut microbial abundance and non-free sugar intake (P for interaction = 0.04). Conclusion: A higher intake of free sugars was associated with an elevated risk of CKD, whereas a higher intake of non-free sugars was associated with a reduced risk of CKD. The impact of free sugar intake and non-free sugar intake may be modified by the gut microbial abundance.},
}

@article {pmid38601973,
year = {2024},
author = {Alsulami, KA and Bakr, AA and Alshehri, AA and Aodah, AH and Almughem, FA and Alamer, AA and Alharbi, LA and Alsuwayeh, DS and Halwani, AA and Alamoudi, AA and Alfassam, HA and Tawfik, EA},
title = {Fabrication and evaluation of ribavirin-loaded electrospun nanofibers as an antimicrobial wound dressing.},
journal = {Saudi pharmaceutical journal : SPJ : the official publication of the Saudi Pharmaceutical Society},
volume = {32},
number = {5},
pages = {102058},
pmid = {38601973},
issn = {1319-0164},
abstract = {BACKGROUND: Skin is regarded as an essential first line of defense against harmful pathogens and it hosts an ecosystem of microorganisms that create a widely diverse skin microbiome. In chronic wounds, alterations in the host-microbe interactions occur forming polymicrobial biofilms that hinder the process of wound healing. Ribavirin, an antiviral drug, possesses antimicrobial activity, especially against Pseudomonas aeruginosa and Candida albicans, which are known as the main opportunistic pathogens in chronic wounds.

RATIONALE: In this study, electrospun nanofiber systems loaded with ribavirin were developed as a potential wound dressing for topical application in chronic wounds. Ribavirin was chosen in this study owing to the emerging cases of antimicrobial (antibiotics and antifungal) resistance and the low attempts to discover new antimicrobial agents, which encouraged the repurposing use of current medication as an alternative solution in case of resistance to the available agents. Additionally, the unique mechanism of action of ribavirin, i.e., perturbing the bacterial virulence system without killing or stopping their growth and rendering the pathogens disarmed, might be a promising choice to prevent drug resistance. Cyclodextrin (CD) was utilized to formulate ribavirin as an electrospun nanofibers delivery system to enhance the absorption and accelerate the release of ribavirin for topical use.

RESULTS: The results demonstrated a successful ribavirin nanofibers fabrication that lacked beads and pores on the nanofibrous surfaces. Ribavirin underwent a physical transformation from crystalline to amorphous form, as confirmed by X-ray diffraction analysis. This change occurred due to the molecular dispersion after the electrospinning process. Additionally, the CD enhanced the encapsulation efficiency of ribavirin in the nanofibers as observed from the drug-loading results. Polyvinylpyrrolidone (PVP) and CD increased ribavirin released into the solution and the disintegration of fibrous mats which shrank and eventually dissolved into a gel-like substance as the ribavirin-loaded fibers began to break down from their border toward the midpoint. Cytotoxicity of ribavirin and CD was evaluated against human dermal fibroblasts (HFF-1) and the results showed a relatively safe profile of ribavirin upon 24-hour cell exposure, while CD was safe within 24- and 48-hour.

CONCLUSION: This study provides valuable insights into the potential application of our nanofibrous system for treating chronic wounds; however, further antimicrobial and in-vivo studies are required to confirm its safety and effectiveness.},
}

@article {pmid38601942,
year = {2024},
author = {Ahmad, W and Din, AU and Khan, TM and Rehman, MU and Hassan, A and Aziz, T and Alharbi, M and Wu, J},
title = {Lacticaseibacillusparacasei BNCC345679 revolutionizes DSS-induced colitis and modulates gut microbiota.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1343891},
pmid = {38601942},
issn = {1664-302X},
abstract = {The gut microbiota plays an important role in the disease progression of inflammatory bowel disease. Although probiotics are effective against IBD, not many studies have investigated their effects on gut microbiota composition and immunomodulation in mouse colitis models. Our study aimed at the therapeutic effects of Lacticaseibacillus paracasei BNCC345679 for the first time and explored its impact on gut microbiome dysbiosis, inflammatory cytokines, related miRNAs, VCAM-1, oxidative stress, intestinal integrity, and mucus barrier. We found that oral intervention of L. paracasei BNCC345679 affects recovering beneficial microbial taxa, including lactobacillus spp. and akkermansia spp., followed by improved body weight, DAI score, and inflammatory cytokines. L. paracasei BNCC345679 mitigated oxidative stress and increased the expression of intestinal integrity proteins MUC2 and ZO-1. These results suggested that L. paracasei BNCC345679 has the capacity to reduce DSS-induced colitis and has the potential as a supplement for the mitigation of IBD.},
}

@article {pmid38601940,
year = {2024},
author = {Sohaib, H and Fays, M and Khatib, A and Rivière, J and El Aouad, N and Desoignies, N},
title = {Contribution to the characterization of the seed endophyte microbiome of Argania spinosa across geographical locations in Central Morocco using metagenomic approaches.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1310395},
pmid = {38601940},
issn = {1664-302X},
abstract = {Microbial endophytes are microorganisms that live inside plants, and some of them play important yet understudied roles in plant health, growth, and adaptation to environmental conditions. Their diversity within plants has traditionally been underestimated due to the limitations of culture-dependent techniques. Metagenomic profiling provides a culture-independent approach to characterize entire microbial communities. The argan tree (Argania spinosa) is ecologically and economically important in Morocco, yet its seed endophyte microbiome remains unexplored. This study aimed to compare the bacterial and fungal endophyte communities associated with argan seeds collected from six sites across Morocco using Illumina MiSeq sequencing of the 16S rRNA gene and ITS regions, respectively. Bacterial DNA was extracted from surface-sterilized seeds and amplified using universal primers, while fungal DNA was isolated directly from seeds. Bioinformatics analysis of sequencing data identified taxonomic profiles at the phylum to genus levels. The results indicated that bacterial communities were dominated by the genus Rhodoligotrophos, while fungal communities exhibited varying degrees of dominance between Ascomycota and Basidiomycota depending on site, with Penicillium being the most abundant overall. Distinct site-specific profiles were observed, with Pseudomonas, Bacillus, and Aspergillus present across multiple locations. Alpha diversity indices revealed variation in endophyte richness between seed sources. In conclusion, this first exploration of the argan seed endophyte microbiome demonstrated environmental influence on community structure. While facing limitations due to small sample sizes and lack of ecological metadata, it provides a foundation for future mechanistic investigations into how specific endophyte-host interactions shape argan adaptation across Morocco's diverse landscapes.},
}

@article {pmid38601932,
year = {2024},
author = {Guo, H and Liu, W and Xie, Y and Wang, Z and Huang, C and Yi, J and Yang, Z and Zhao, J and Yu, X and Sibirina, LA},
title = {Soil microbiome of shiro reveals the symbiotic relationship between Tricholoma bakamatsutake and Quercus mongolica.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1361117},
pmid = {38601932},
issn = {1664-302X},
abstract = {Tricholoma bakamatsutake is a delicious and nutritious ectomycorrhizal fungus. However, its cultivation is hindered owing to limited studies on its symbiotic relationships. The symbiotic relationship between T. bakamatsutake and its host is closely related to the shiro, a complex network composed of mycelium, mycorrhizal roots, and surrounding soil. To explore the symbiotic relationship between T. bakamatsutake and its host, soil samples were collected from T. bakamatsutake shiro (Tb) and corresponding Q. mongolica rhizosphere (CK) in four cities in Liaoning Province, China. The physicochemical properties of all the soil samples were then analyzed, along with the composition and function of the fungal and bacterial communities. The results revealed a significant increase in total potassium, available nitrogen, and sand in Tb soil compared to those in CK soil, while there was a significant decrease in pH, total nitrogen, total phosphorus, available phosphorus, and silt. The fungal community diversity in shiro was diminished, and T. bakamatsutake altered the community structure of its shiro by suppressing other fungi, such as Russula (ectomycorrhizal fungus) and Penicillium (phytopathogenic fungus). The bacterial community diversity in shiro increased, with the aggregation of mycorrhizal-helper bacteria, such as Paenibacillus and Bacillus, and plant growth-promoting bacteria, such as Solirubrobacter and Streptomyces, facilitated by T. bakamatsutake. Microbial functional predictions revealed a significant increase in pathways associated with sugar and fat catabolism within the fungal and bacterial communities of shiro. The relative genetic abundance of carboxylesterase and gibberellin 2-beta-dioxygenase in the fungal community was significantly increased, which suggested a potential symbiotic relationship between T. bakamatsutake and Q. mongolica. These findings elucidate the microbial community and relevant symbiotic environment to better understand the relationship between T. bakamatsutake and Q. mongolica.},
}

@article {pmid38601914,
year = {2024},
author = {Hao, P and Yang, X and Yin, W and Wang, X and Ling, Y and Zhu, M and Yu, Y and Chen, S and Yuan, Y and Quan, X and Xu, Z and Zhang, J and Zhao, W and Zhang, Y and Song, C and Xu, Q and Qin, S and Wu, Y and Shu, X and Wei, K},
title = {A study on the treatment effects of Crataegus pinnatifida polysaccharide on non-alcoholic fatty liver in mice by modulating gut microbiota.},
journal = {Frontiers in veterinary science},
volume = {11},
number = {},
pages = {1383801},
pmid = {38601914},
issn = {2297-1769},
abstract = {The objective of this study was to investigate the protective effect of Crataegus pinnatifida polysaccharide (CPP) on non-alcoholic fatty liver disease (NAFLD) induced by a high-fat diet (HFD) in mice. The findings demonstrated that CPP improved free fatty acid (FFA)-induced lipid accumulation in HepG2 cells and effectively reduced liver steatosis and epididymal fat weight in NAFLD mice, as well as decreased serum levels of TG, TC, AST, ALT, and LDL-C. Furthermore, CPP exhibited inhibitory effects on the expression of fatty acid synthesis genes FASN and ACC while activating the expression of fatty acid oxidation genes CPT1A and PPARα. Additionally, CPP reversed disturbances in intestinal microbiota composition caused by HFD consumption. CPP decreased the firmicutes/Bacteroidetes ratio, increased Akkermansia abundance, and elevated levels of total short-chain fatty acid (SCFA) content specifically butyric acid and acetic acid. Our results concluded that CPP may intervene in the development of NAFLD by regulating of intes-tinal microbiota imbalance and SCFAs production. Our study highlights that CPP has a potential to modulate lipid-related pathways via alterations to gut microbiome composition thereby ex-erting inhibitory effects on obesity and NAFLD development.},
}

@article {pmid38601772,
year = {2023},
author = {Colonetti, T and Saggioratto, MC and Grande, AJ and Colonetti, L and Junior, JCD and Ceretta, LB and Roever, L and Silva, FR and da Rosa, MI},
title = {Gut and Vaginal Microbiota in the Endometriosis: Systematic Review and Meta-Analysis.},
journal = {BioMed research international},
volume = {2023},
number = {},
pages = {2675966},
pmid = {38601772},
issn = {2314-6141},
mesh = {Female ; Humans ; *Endometriosis/pathology ; *Microbiota ; Vagina/pathology ; *Gastrointestinal Microbiome/physiology ; Reproduction ; },
abstract = {BACKGROUND: Endometriosis is a clinical condition associated with genetic, endocrine, and immunological factors, present in 6 to 10% of women of reproductive age. Currently, the human microbiota has been studied and associated with the evolution of diseases due to its influence on pathogenesis, indicating that changes in the colonization of microorganisms in the genitourinary and gastrointestinal systems can promote physiological changes that can trigger inflammatory and immunological processes and hormonal dysregulation, which can be linked to endometriosis. Thus, this systematic review and meta-analysis evaluated microbiota changes in women with endometriosis.

METHODS: The following electronic databases were searched up to April 2022: Medline, Embase, Web of Science, Cochrane Library, and gray literature (Google Scholar), using the keywords "dysbiosis", "microbiome" and "endometriosis", combined with their synonyms. The observational studies conducted with women diagnosed with endometriosis and women without endometriosis as controls were included. For the analyses, a standard mean difference with a 95% confidence interval was used using RevMan software (version 5.4), and for methodological quality assessment, the Newcastle-Ottawa scale was used.

RESULTS: A total of 16 studies were found in the literature assessing the composition of the microbiota in women with endometriosis, and no significant difference were found for changes in alpha diversity analysis in gut microbiota (SMD = -0.28; 95% CI = -0.70 to 0.14; P = 0.19; I[2] = 52%; four studies, 357 participants) or vaginal microbiota (SMD = -0.68; 95% CI = -1.72 to 0.35; P = 0.19; I[2] = 66%; two studies, 49 participants).

CONCLUSION: In intestinal and vaginal samples from women with endometriosis, alpha-diversity did not present a significant difference when compared to the control population. However, each study individually showed a possible relationship between the female microbiota and endometriosis. This trial is registered with CRD42021260972.},
}

Female
Humans
*Endometriosis/pathology
*Microbiota
Vagina/pathology
*Gastrointestinal Microbiome/physiology
Reproduction

@article {pmid38601755,
year = {2024},
author = {Vilhais, G and Alpuim Costa, D and Fontes-Sousa, M and Ribeiro, PC and Martinho, F and Botelho de Sousa, C and Santos, CR and Negreiros, I and Canastra, A and Borralho, P and Guia Pereira, A and Marçal, C and Germano Sousa, J and Chaleira, R and Rocha, JC and Calhau, C and Faria, A},
title = {Case report: Primary CDK4/6 inhibitor and endocrine therapy in locally advanced breast cancer and its effect on gut and intratumoral microbiota.},
journal = {Frontiers in oncology},
volume = {14},
number = {},
pages = {1360737},
pmid = {38601755},
issn = {2234-943X},
abstract = {Locally advanced breast cancer poses significant challenges to the multidisciplinary team, in particular with hormone receptor (HR) positive, HER2-negative tumors that classically yield lower pathological complete responses with chemotherapy. The increasingly significant use of CDK 4/6 inhibitors (CDK4/6i) plus endocrine therapy (ET) in different breast cancer settings has led to clinical trials focusing on this strategy as a primary treatment, with promising results. The impact of the microbiota on cancer, and vice-versa, is an emerging topic in oncology. The authors report a clinical case of a postmenopausal female patient with an invasive breast carcinoma of the right breast, Luminal B-like, staged as cT4cN3M0 (IIIB). Since the lesion was considered primarily inoperable, the patient started letrozole and ribociclib. Following 6 months of systemic therapy, the clinical response was significant, and surgery with curative intent was performed. The final staging was ypT3ypN2aM0, R1, and the patient started adjuvant letrozole and radiotherapy. This case provides important insights on primary CDK4/6i plus ET in locally advanced unresectable HR+/HER2- breast cancer and its potential implications in disease management further ahead. The patient's gut microbiota was analyzed throughout the disease course and therapeutic approach, evidencing a shift in gut microbial dominance from Firmicutes to Bacteroidetes and a loss of microbial diversity following 6 months of systemic therapy. The analysis of the intratumoral microbiota from the surgical specimen revealed high microbial dissimilarity between the residual tumor and respective margins.},
}

@article {pmid38601267,
year = {2024},
author = {Willits, AB and Kader, L and Eller, O and Roberts, E and Bye, B and Strope, T and Freudenthal, BD and Umar, S and Chintapalli, S and Shankar, K and Pei, D and Christianson, J and Baumbauer, KM and Young, EE},
title = {Spinal cord injury-induced neurogenic bowel: A role for host-microbiome interactions in bowel pain and dysfunction.},
journal = {Neurobiology of pain (Cambridge, Mass.)},
volume = {15},
number = {},
pages = {100156},
pmid = {38601267},
issn = {2452-073X},
abstract = {BACKGROUND AND AIMS: Spinal cord injury (SCI) affects roughly 300,000 Americans with 17,000 new cases added annually. In addition to paralysis, 60% of people with SCI develop neurogenic bowel (NB), a syndrome characterized by slow colonic transit, constipation, and chronic abdominal pain. The knowledge gap surrounding NB mechanisms after SCI means that interventions are primarily symptom-focused and largely ineffective. The goal of the present studies was to identify mechanism(s) that initiate and maintain NB after SCI as a critical first step in the development of evidence-based, novel therapeutic treatment options.

METHODS: Following spinal contusion injury at T9, we observed alterations in bowel structure and function reflecting key clinical features of NB. We then leveraged tissue-specific whole transcriptome analyses (RNAseq) and fecal 16S rRNA amplicon sequencing in combination with histological, molecular, and functional (Ca[2+] imaging) approaches to identify potential mechanism(s) underlying the generation of the NB phenotype.

RESULTS: In agreement with prior reports focused on SCI-induced changes in the skin, we observed a rapid and persistent increase in expression of calcitonin gene-related peptide (CGRP) expression in the colon. This is suggestive of a neurogenic inflammation-like process engaged by antidromic activity of below-level primary afferents following SCI. CGRP has been shown to disrupt colon homeostasis and negatively affect peristalsis and colon function. As predicted, contusion SCI resulted in increased colonic transit time, expansion of lymphatic nodules, colonic structural and genomic damage, and disruption of the inner, sterile intestinal mucus layer corresponding to increased CGRP expression in the colon. Gut microbiome colonization significantly shifted over 28 days leading to the increase in Anaeroplasma, a pathogenic, gram-negative microbe. Moreover, colon specific vagal afferents and enteric neurons were hyperresponsive after SCI to different agonists including fecal supernatants.

CONCLUSIONS: Our data suggest that SCI results in overexpression of colonic CGRP which could alter colon structure and function. Neurogenic inflammatory-like processes and gut microbiome dysbiosis can also sensitize vagal afferents, providing a mechanism for visceral pain despite the loss of normal sensation post-SCI. These data may shed light on novel therapeutic interventions targeting this process to prevent NB development in patients.},
}

@article {pmid38601060,
year = {2024},
author = {Imdad, S and Kim, JH and So, B and Jang, J and Park, J and Lim, W and Lee, YK and Shin, WS and Hillyer, T and Kang, C},
title = {Effect of aerobic exercise and particulate matter exposure duration on the diversity of gut microbiota.},
journal = {Animal cells and systems},
volume = {28},
number = {1},
pages = {137-151},
pmid = {38601060},
issn = {1976-8354},
abstract = {Inhalation of ambient particulate matter (PM) can disrupt the gut microbiome, while exercise independently influences the gut microbiome by promoting beneficial bacteria. In this study, we analyzed changes in gut microbial diversity and composition in response to combined interventions of PM exposure and aerobic exercise, extending up to 12 weeks. This investigation was conducted using mice, categorized into five groups: control group (Con), exercise group (EXE), exercise group followed by 3-day exposure to PM (EXE + 3-day PM), particulate matter exposure (PM), and PM exposure with concurrent treadmill exercise (PME). Notably, the PM group exhibited markedly lower alpha diversity and richness compared to the Con group and our analysis of beta diversity revealed significant variations among the intervention groups. Members of the Lachnospiraceae family showed significant enhancement in the exercise intervention groups (EXE and PME) compared to the Con and PM groups. The biomarker Lactobacillus, Coriobacteraceae, and Anaerofustis were enriched in the EXE group, while Desulfovibrionaceae, Mucispirillum schaedleri, Lactococcus and Anaeroplasma were highly enriched in the PM group. Differential abundance analysis revealed that Paraprevotella, Bacteroides, and Blautia were less abundant in the 12-week PM exposure group than in the 3-day PM exposure group. Moreover, both the 3-day and 12-week PM exposure groups exhibited a reduced relative abundance of Bacteroides uniformis, SMB53, and Staphylococcus compared to non-PM exposure groups. These findings will help delineate the possible roles and associations of altered microbiota resulting from the studied interventions, paving the way for future mechanistic research.},
}

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

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

@article {pmid38600460,
year = {2024},
author = {Weatherspoon, DJ and Kirk, GD and Piggott, DA and Thumbigere-Math, V and Dye, BA and Macek, MD},
title = {Baltimore oral epidemiology, disease effects, and HIV evaluation study (BEEHIVE) study protocol: a prospective cohort study.},
journal = {BMC oral health},
volume = {24},
number = {1},
pages = {439},
pmid = {38600460},
issn = {1472-6831},
support = {R01 DE029643/DE/NIDCR NIH HHS/United States ; R01DE029643/DE/NIDCR NIH HHS/United States ; },
mesh = {Humans ; *HIV Infections/epidemiology/drug therapy ; Prospective Studies ; Baltimore/epidemiology ; Risk Factors ; *Mouth Diseases/epidemiology ; *Periodontitis ; },
abstract = {BACKGROUND: As antiretroviral therapy has become widely available and highly effective, HIV has evolved to a manageable, chronic disease. Despite this health advancement, people living with HIV (PLWH) are at an increased risk for age-related non-communicable diseases (NCDs) compared to HIV-uninfected individuals. Similarly, PLWH are at an increased risk for selected oral diseases. PLWH with a history of injecting drugs experience an even greater burden of disease than their counterparts. The overall objective of the Baltimore Oral Epidemiology, Disease Effects, and HIV Evaluation (BEEHIVE) study is to determine the combined effects of HIV infection and NCDs on oral health status. The specific aims of the study are to: (1) determine to what extent HIV status influences access to and utilization of oral health care services; (2) determine to what extent HIV status affects self-reported and clinical oral health status; (3) determine to what extent HIV status influences the progression of periodontitis; and (4) determine to what extent HIV status impacts the periodontitis-associated oral microbiome signature.

METHODS: The BEEHIVE study uses a prospective cohort study design to collect data from participants at baseline and at a 24-month follow-up visit. Data are collected through questionnaire assessments, clinical examinations, and evaluation of oral microbiological samples to determine the drivers of oral disease among a high-risk population of PLWH with a history of injection drug use and prevalent comorbid NCDs. The established AIDS Linked to the Intravenous Experience (ALIVE) cohort serves as the source of participants for the BEEHIVE Study.

DISCUSSION: Upon completion of the BEEHIVE study, the knowledge gained will be important in informing future clinical and preventive interventions that can be implemented into medical and dental practice to ultimately help eliminate long-standing oral health inequities that PLWH experience.},
}

Humans
*HIV Infections/epidemiology/drug therapy
Prospective Studies
Baltimore/epidemiology
Risk Factors
*Mouth Diseases/epidemiology
*Periodontitis

@article {pmid38600293,
year = {2024},
author = {Jiang, MZ and Liu, C and Xu, C and Jiang, H and Wang, Y and Liu, SJ},
title = {Gut microbial interactions based on network construction and bacterial pairwise cultivation.},
journal = {Science China. Life sciences},
volume = {},
number = {},
pages = {},
pmid = {38600293},
issn = {1869-1889},
abstract = {Association networks are widely applied for the prediction of bacterial interactions in studies of human gut microbiomes. However, the experimental validation of the predicted interactions is challenging due to the complexity of gut microbiomes and the limited number of cultivated bacteria. In this study, we addressed this challenge by integrating in vitro time series network (TSN) associations and co-cultivation of TSN taxon pairs. Fecal samples were collected and used for cultivation and enrichment of gut microbiome on YCFA agar plates for 13 days. Enriched cells were harvested for DNA extraction and metagenomic sequencing. A total of 198 metagenome-assembled genomes (MAGs) were recovered. Temporal dynamics of bacteria growing on the YCFA agar were used to infer microbial association networks. To experimentally validate the interactions of taxon pairs in networks, we selected 24 and 19 bacterial strains from this study and from the previously established human gut microbial biobank, respectively, for pairwise co-cultures. The co-culture experiments revealed that most of the interactions between taxa in networks were identified as neutralism (51.67%), followed by commensalism (21.67%), amensalism (18.33%), competition (5%) and exploitation (3.33%). Genome-centric analysis further revealed that the commensal gut bacteria (helpers and beneficiaries) might interact with each other via the exchanges of amino acids with high biosynthetic costs, short-chain fatty acids, and/or vitamins. We also validated 12 beneficiaries by adding 16 additives into the basic YCFA medium and found that the growth of 66.7% of these strains was significantly promoted. This approach provides new insights into the gut microbiome complexity and microbial interactions in association networks. Our work highlights that the positive relationships in gut microbial communities tend to be overestimated, and that amino acids, short-chain fatty acids, and vitamins are contributed to the positive relationships.},
}

@article {pmid38600101,
year = {2024},
author = {Ma, X and Wen, G and Zhao, Z and Lu, L and Li, T and Gao, N and Han, G},
title = {Alternations in the human skin, gut and vaginal microbiomes in perimenopausal or postmenopausal Vulvar lichen sclerosus.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {8429},
pmid = {38600101},
issn = {2045-2322},
support = {YN2021QX02//Peking University International Hospital/ ; },
mesh = {Female ; Humans ; *Vulvar Lichen Sclerosus/pathology ; Postmenopause ; Perimenopause ; Quality of Life ; *Microbiota ; Arrhythmias, Cardiac ; Vagina/pathology ; },
abstract = {Vulvar lichen sclerosus (VLS) is a chronic and progressive dermatologic condition that can cause physical dysfunction, disfigurement, and impaired quality of life. However, the etiology of VLS remains unknown. The vulvar skin, intestinal and vaginal microbiomes have been postulated to play important roles in the pathogenesis of this disease. The aim of this study was to compare the compositional characteristics of the vulvar skin, vagina, and gut microbiota between perimenopausal or postmenopausal VLS patients and healthy controls. The study involved six perimenopausal or postmenopausal VLS patients which were based on characteristic clinical manifestations and histologic confirmation and five healthy controls. The pruritus severity of each patient was evaluated using the NRS scale, and the dermatology-specific health-related quality of life was assessed using the Skindex-16. Metagenomic sequencing was performed, and the results were analyzed for alpha and beta diversity. LEfSe analysis were used to investigate the microbial alterations in vulvar skin, gut and vagina. KEGG databases were used to analyze differences in functional abundance. The study found significant differences in alpha diversity between the two groups in stool and vaginal samples (P < 0.05). Patients with VLS had a higher abundance of Enterobacter cloacae, Flavobacterium_branchiophilum, Mediterranea_sp._An20, Parabacteroides_johnsoniiand Streptococcus_bovimastitidis on the vulvar skin, while Corynebacterium_sp._zg-913 was less abundant compared to the control group. The relative abundance of Sphingomonas_sp._SCN_67_18, Sphingobium_sp._Ant17, and Pontibacter_sp_BT213 was significantly higher in the gut samples of patients with VLS.Paenibacillus_popilliae,Gemella_asaccharolytica, and Coriobacteriales_bacterium_DNF00809 compared to the control group. Additionally, the vaginal samples of patients with VLS exhibited a significantly lower relative abundance of Bacteroidales_bacterium_43_8, Bacteroides_sp._CAG:20, Blautia_sp._AM28-10, Fibrobacter_sp._UWB16, Lachnospiraceae_bacterium_AM25-39, Holdemania_filiformis, Lachnospiraceae_bacterium_GAM79, and Tolumonas_sp. Additionally, the butyrate-producing bacterium SS3/4 showed a significant difference compared to the controls. The study found a negative relationship between Sphingobium_sp._Ant17 in stool and Skindex-16 (P < 0.05), while Mediterranea_sp._An20 had a positive correlation with Skindex-16 (P < 0.05) in the skin. Additionally, our functional analysis revealed alterations in Aminoacyl_tRNA_biosynthesis, Glutathione_metabolism, the pentose phosphate pathway, and Alanine__aspartate_and_glutamate_metabolism in the VLS patient group. The study suggests that perimenopausal or postmenopausal patients with VLS have a modified microbiome in the vulvar skin, gut, and vagina. This modification is linked to abnormal energy metabolism, increased oxidative stress, and abnormal amino acid metabolism.},
}

Female
Humans
*Vulvar Lichen Sclerosus/pathology
Postmenopause
Perimenopause
Quality of Life
*Microbiota
Arrhythmias, Cardiac
Vagina/pathology

@article {pmid38599548,
year = {2024},
author = {McCoubrey, LE and Seegobin, N and Sangfuang, N and Moens, F and Duyvejonck, H and Declerck, E and Dierick, A and Marzorati, M and Basit, AW},
title = {The colon targeting efficacies of mesalazine medications and their impacts on the gut microbiome.},
journal = {Journal of controlled release : official journal of the Controlled Release Society},
volume = {369},
number = {},
pages = {630-641},
doi = {10.1016/j.jconrel.2024.04.016},
pmid = {38599548},
issn = {1873-4995},
abstract = {Successful treatment of ulcerative colitis (UC) is highly dependent on several parameters, including dosing regimen and the ability to deliver drugs to the disease site. In this study two strategies for delivering mesalazine (5-aminosalicylic acid, 5-ASA) to the colon were compared in an advanced in vitro model of the human gastrointestinal (GI) tract, the SHIME® system. Herein, a prodrug strategy employing bacteria-mediated drug release (sulfasalazine, Azulfidine®) was evaluated alongside a formulation strategy that utilised pH and bacteria-mediated release (5-ASA, Octasa® 1600 mg). SHIME® experiments were performed simulating both the GI physiology and colonic microbiota under healthy and inflammatory bowel disease (IBD) conditions, to study the impact of the disease state and ileal pH variability on colonic 5-ASA delivery. In addition, the effects of the products on the colonic microbiome were investigated by monitoring bacterial growth and metabolites. Results demonstrated that both the prodrug and formulation approaches resulted in a similar percentage of 5-ASA recovery under healthy conditions. On the contrary, during experiments simulating the GI physiology and microbiome of IBD patients (the target population) the formulation strategy resulted in a higher proportion of 5-ASA delivery to the colonic region as compared to the prodrug approach (P < 0.0001). Interestingly, the two products had distinct effects on the synthesis of key bacterial metabolites, such as lactate and short chain fatty acids, which varied according to disease state and ileal pH variability. Further, both 5-ASA and sulfasalazine significantly reduced the growth of the faecal microbiota sourced from six healthy humans. The findings support that the approach selected for colonic drug delivery could significantly influence the effectiveness of UC treatment, and highlight that drugs licensed for UC may differentially impact the growth and functioning of the colonic microbiota.},
}

@article {pmid38599390,
year = {2024},
author = {Ota, Y and Yasunaga, K and Mahazu, S and Prah, I and Nagai, S and Hayashi, T and Suzuki, M and Yoshida, M and Hoshino, Y and Akeda, Y and Suzuki, T and Gu, Y and Saito, R},
title = {Comparative evaluation of analytical pipelines for illumina short- and nanopore long-read 16S rRNA gene amplicon sequencing with mock microbial communities.},
journal = {Journal of microbiological methods},
volume = {},
number = {},
pages = {106929},
doi = {10.1016/j.mimet.2024.106929},
pmid = {38599390},
issn = {1872-8359},
abstract = {Utility of a recently developed long-read pipeline, Emu, was assessed using an expectation-maximization algorithm for accurate read classification. We compared it to conventional short- and long-read pipelines, using well-characterized mock bacterial samples. Our findings highlight the necessity of appropriate data-processing for taxonomic descriptions, expanding our understanding of the precise microbiome.},
}

@article {pmid38599367,
year = {2024},
author = {Svačina, MKR and Gao, T and Sprenger-Svačina, A and Lin, J and Ganesh, BP and Lee, J and McCullough, LD and Sheikh, KA and Zhang, G},
title = {Rejuvenating fecal microbiota transplant enhances peripheral nerve repair in aged mice by modulating endoneurial inflammation.},
journal = {Experimental neurology},
volume = {376},
number = {},
pages = {114774},
doi = {10.1016/j.expneurol.2024.114774},
pmid = {38599367},
issn = {1090-2430},
abstract = {Peripheral nerve injury (PNI) resulting from trauma or neuropathies can cause significant disability, and its prognosis deteriorates with age. Emerging evidence suggests that gut dysbiosis and reduced fecal short-chain fatty acids (SCFAs) contribute to an age-related systemic hyperinflammation (inflammaging), which hinders nerve recovery after injury. This study thus aimed to evaluate the pro-regenerative effects of a rejuvenating fecal microbiota transplant (FMT) in a preclinical PNI model using aged mice. Aged C57BL/6 mice underwent bilateral crush injuries to their sciatic nerves. Subsequently, they either received FMT from young donors at three and four days after the injury or retained their aged gut microbiota. We analyzed gut microbiome composition and SCFA concentrations in fecal samples. The integrity of the ileac mucosal barrier was assessed by immunofluorescence staining of Claudin-1. Flow cytometry was utilized to examine immune cells and cytokine production in the ileum, spleen, and sciatic nerve. Various assessments, including behavioural tests, electrophysiological studies, and morphometrical analyses, were conducted to evaluate peripheral nerve function and repair following injury. Rejuvenating FMT reversed age-related gut dysbiosis by increasing Actinobacteria, especially Bifidobacteriales genera. This intervention also led to an elevation of gut SCFA levels and mitigated age-related ileac mucosal leakiness in aged recipients. Additionally, it augmented the number of T-helper 2 (Th2) and regulatory T (Treg) cells in the ileum and spleen, with the majority being positive for anti-inflammatory interleukin-10 (IL-10). In sciatic nerves, rejuvenating FMT resulted in increased M2 macrophage counts and a higher IL-10 production by IL-10[+]TNF-α[-] M2 macrophage subsets. Ultimately, restoring a youthful gut microbiome in aged mice led to improved nerve repair and enhanced functional recovery after PNI. Considering that FMT is already a clinically available technique, exploring novel translational strategies targeting the gut microbiome to enhance nerve repair in the elderly seems promising and warrants further evaluation.},
}

@article {pmid38599211,
year = {2024},
author = {Battaglia, TW and Mimpen, IL and Traets, JJH and van Hoeck, A and Zeverijn, LJ and Geurts, BS and de Wit, GF and Noë, M and Hofland, I and Vos, JL and Cornelissen, S and Alkemade, M and Broeks, A and Zuur, CL and Cuppen, E and Wessels, L and van de Haar, J and Voest, E},
title = {A pan-cancer analysis of the microbiome in metastatic cancer.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2024.03.021},
pmid = {38599211},
issn = {1097-4172},
abstract = {Microbial communities are resident to multiple niches of the human body and are important modulators of the host immune system and responses to anticancer therapies. Recent studies have shown that complex microbial communities are present within primary tumors. To investigate the presence and relevance of the microbiome in metastases, we integrated mapping and assembly-based metagenomics, genomics, transcriptomics, and clinical data of 4,160 metastatic tumor biopsies. We identified organ-specific tropisms of microbes, enrichments of anaerobic bacteria in hypoxic tumors, associations between microbial diversity and tumor-infiltrating neutrophils, and the association of Fusobacterium with resistance to immune checkpoint blockade (ICB) in lung cancer. Furthermore, longitudinal tumor sampling revealed temporal evolution of the microbial communities and identified bacteria depleted upon ICB. Together, we generated a pan-cancer resource of the metastatic tumor microbiome that may contribute to advancing treatment strategies.},
}

@article {pmid38599089,
year = {2024},
author = {Ding, MQ and Ding, J and Zhang, ZR and Li, MX and Cui, CH and Pang, JW and Xing, DF and Ren, NQ and Wu, WM and Yang, SS},
title = {Biodegradation of various grades of polyethylene microplastics by Tenebrio molitor and Tenebrio obscurus larvae: Effects on their physiology.},
journal = {Journal of environmental management},
volume = {358},
number = {},
pages = {120832},
doi = {10.1016/j.jenvman.2024.120832},
pmid = {38599089},
issn = {1095-8630},
abstract = {Polyethylene (PE) is the most productive plastic product and includes three major polymers including high-density polyethylene (HDPE), linear low-density polyethylene (LLDPE) and low-density polyethylene (LDPE) variation in the PE depends on the branching of the polymer chain and its crystallinity. Tenebrio obscurus and Tenebrio molitor larvae biodegrade PE. We subsequently tested larval physiology, gut microbiome, oxidative stress, and PE degradation capability and degradation products under high-purity HDPE, LLDPE, and LDPE powders (<300 μm) diets for 21 days at 65 ± 5% humidity and 25 ± 0.5 °C. Our results demonstrated the specific PE consumption rates by T. molitor was 8.04-8.73 mg PE ∙ 100 larvae[-1]⋅day[-1] and by T. obscurus was 7.68-9.31 for LDPE, LLDPE and HDPE, respectively. The larvae digested nearly 40% of the ingested three PE and showed similar survival rates and weight changes but their fat content decreased by 30-50% over 21-day period. All the PE-fed groups exhibited adverse effects, such as increased benzoquinone concentrations, intestinal tissue damage and elevated oxidative stress indicators, compared with bran-fed control. In the current study, the digestive tract or gut microbiome exhibited a high level of adaptability to PE exposure, altering the width of the gut microbial ecological niche and community diversity, revealing notable correlations between Tenebrio species and the physical and chemical properties (PCPs) of PE-MPs, with the gut microbiome and molecular weight change due to biodegradation. An ecotoxicological simulation by T.E.S.T. confirmed that PE degradation products were little ecotoxic to Daphnia magna and Rattus norvegicus providing important novel insights for future investigations into the environmentally-friendly approach of insect-mediated biodegradation of persistent plastics.},
}

@article {pmid38599014,
year = {2024},
author = {Bock, JM and Johnson, S and Kashyap, PC and Somers, VK and Cheung, J},
title = {Impact of PAP on the gut microbiome in OSA: A pilot study.},
journal = {Sleep medicine},
volume = {118},
number = {},
pages = {39-42},
doi = {10.1016/j.sleep.2024.03.042},
pmid = {38599014},
issn = {1878-5506},
abstract = {OBJECTIVE/BACKGROUND: Microbes within the gastrointestinal tract have emerged as modulators of the host's health. Obstructive sleep apnea (OSA) is characterized by intermittent partial, or complete, airway closure during sleep and is associated with increased risk of non-communicable diseases as well as dysbiosis of the gut microbiome. Thus, we investigated if improving nocturnal airway patency via positive airway pressure (PAP) therapy improves gut microbial diversity in recently diagnosed patients with moderate-to-severe OSA (apnea-hypopnea index ≥15.0 events/hr).

PATIENTS/METHODS: Eight subjects (3 F, 56±9yrs, 33.5 ± 7.7 kg/m[2], 45.0 ± 38.4 events/hr) provided stool samples before, and two months after, PAP therapy (mean adherence of 95 ± 6%, residual apnea-hypopnea index of 4.7 ± 4.6 events/hr).

RESULTS: While the Shannon diversity index tended to increase following PAP (3.96 ± 0.52 to 4.18 ± 0.56, p = 0.08), there were no changes in the Observed (1,088 ± 237 to 1,136 ± 289, p = 0.28) nor Inverse-Simpson (22.4 ± 12.99 to 26.6 ± 18.23, p = 0.28) alpha diversity indices. There were also no changes in beta diversity assessed using the Bray-Curtis (p = 0.98), Jaccard (p = 0.99), WUniFrac (p = 0.98), GUniFrac (p = 0.98), or UniFrac (p = 0.98) methods. No changes in differential abundance taxa were found using a false discovery rate threshold of <0.20.

CONCLUSIONS: Our data are the first to report that PAP therapy may not offset, or reverse, gut dysbiosis in patients with OSA. Accordingly, interventions which improve gut microbial health should be explored as potential adjunctive treatment options in patients with OSA to reduce their risk of developing non-communicable diseases.},
}

@article {pmid38598655,
year = {2024},
author = {Pérez-Prieto, I and Rodríguez-Santisteban, A and Altmäe, S},
title = {Beyond the reproductive tract: gut microbiome and its influence on gynecological health.},
journal = {Current opinion in clinical nutrition and metabolic care},
volume = {},
number = {},
pages = {},
pmid = {38598655},
issn = {1473-6519},
abstract = {PURPOSE OF REVIEW: The analysis of microbiome in association with female health is today a "hot topic" with the main focus on microbes in the female reproductive tract. Nevertheless, recent studies are providing novel information of the possible influence of the gut microbiome on gynecological health outcomes, especially as we start to understand that the gut microbiome is an extended endocrine organ influencing female hormonal levels. This review summarizes the current knowledge of the gut microbes in association with gynecological health.

RECENT FINDINGS: The gut microbiome has been associated with endometriosis, polycystic ovary syndrome, gynecological cancers, and infertility, although there is a lack of consistency and consensus among studies due to different study designs and protocols used, and the studies in general are underpowered.

SUMMARY: The interconnection between the gut microbiome and reproductive health is complex and further research is warranted. The current knowledge in the field emphasizes the link between the microbiome and gynecological health outcomes, with high potential for novel diagnostic and treatment tools via modulation of the microenvironment.},
}

@article {pmid38598636,
year = {2024},
author = {Sizemore, N and Oliphant, K and Zheng, R and Martin, CR and Claud, EC and Chattopadhyay, I},
title = {A digital twin of the infant microbiome to predict neurodevelopmental deficits.},
journal = {Science advances},
volume = {10},
number = {15},
pages = {eadj0400},
pmid = {38598636},
issn = {2375-2548},
mesh = {Infant ; Humans ; Infant, Newborn ; Infant, Premature ; Artificial Intelligence ; *Gastrointestinal Microbiome/genetics ; *Microbiota ; Feces ; },
abstract = {Despite the recognized gut-brain axis link, natural variations in microbial profiles between patients hinder definition of normal abundance ranges, confounding the impact of dysbiosis on infant neurodevelopment. We infer a digital twin of the infant microbiome, forecasting ecosystem trajectories from a few initial observations. Using 16S ribosomal RNA profiles from 88 preterm infants (398 fecal samples and 32,942 abundance estimates for 91 microbial classes), the model (Q-net) predicts abundance dynamics with R[2] = 0.69. Contrasting the fit to Q-nets of typical versus suboptimal development, we can reliably estimate individual deficit risk (Mδ) and identify infants achieving poor future head circumference growth with ≈76% area under the receiver operator characteristic curve, 95% ± 1.8% positive predictive value at 98% specificity at 30 weeks postmenstrual age. We find that early transplantation might mitigate risk for ≈45.2% of the cohort, with potentially negative effects from incorrect supplementation. Q-nets are generative artificial intelligence models for ecosystem dynamics, with broad potential applications.},
}

Infant
Humans
Infant, Newborn
Infant, Premature
Artificial Intelligence
*Gastrointestinal Microbiome/genetics
*Microbiota
Feces

@article {pmid38598617,
year = {2024},
author = {Gilbert, JA and Alverdy, J},
title = {Where do the pathogens that cause surgical site infections come from?.},
journal = {Science translational medicine},
volume = {16},
number = {742},
pages = {eado1449},
doi = {10.1126/scitranslmed.ado1449},
pmid = {38598617},
issn = {1946-6242},
mesh = {Humans ; *Surgical Wound Infection/drug therapy ; Anti-Bacterial Agents/pharmacology/therapeutic use ; *Microbiota ; },
abstract = {A study from Long et al. shows that many pathogens that cause surgical site infections during spine surgery come from the patient's own microbiome, suggesting a paradigm shift in the understanding of surgical site infections that questions the effectiveness of current enhanced sterility and antibiotic protocols.},
}

Humans
*Surgical Wound Infection/drug therapy
Anti-Bacterial Agents/pharmacology/therapeutic use
*Microbiota

@article {pmid38598612,
year = {2024},
author = {Long, DR and Bryson-Cahn, C and Waalkes, A and Holmes, EA and Penewit, K and Tavolaro, C and Bellabarba, C and Zhang, F and Chan, JD and Fang, FC and Lynch, JB and Salipante, SJ},
title = {Contribution of the patient microbiome to surgical site infection and antibiotic prophylaxis failure in spine surgery.},
journal = {Science translational medicine},
volume = {16},
number = {742},
pages = {eadk8222},
doi = {10.1126/scitranslmed.adk8222},
pmid = {38598612},
issn = {1946-6242},
mesh = {Humans ; *Surgical Wound Infection/prevention & control/drug therapy/microbiology ; Antibiotic Prophylaxis ; Skin ; *Anti-Infective Agents ; Anti-Bacterial Agents/pharmacology/therapeutic use ; },
abstract = {Despite modern antiseptic techniques, surgical site infection (SSI) remains a leading complication of surgery. However, the origins of SSI and the high rates of antimicrobial resistance observed in these infections are poorly understood. Using instrumented spine surgery as a model of clean (class I) skin incision, we prospectively sampled preoperative microbiomes and postoperative SSI isolates in a cohort of 204 patients. Combining multiple forms of genomic analysis, we correlated the identity, anatomic distribution, and antimicrobial resistance profiles of SSI pathogens with those of preoperative strains obtained from the patient skin microbiome. We found that 86% of SSIs, comprising a broad range of bacterial species, originated endogenously from preoperative strains, with no evidence of common source infection among a superset of 1610 patients. Most SSI isolates (59%) were resistant to the prophylactic antibiotic administered during surgery, and their resistance phenotypes correlated with the patient's preoperative resistome (P = 0.0002). These findings indicate the need for SSI prevention strategies tailored to the preoperative microbiome and resistome present in individual patients.},
}

Humans
*Surgical Wound Infection/prevention & control/drug therapy/microbiology
Antibiotic Prophylaxis
Skin
*Anti-Infective Agents
Anti-Bacterial Agents/pharmacology/therapeutic use

@article {pmid38598334,
year = {2024},
author = {Wei, X and Tsai, MS and Liang, L and Jiang, L and Hung, CJ and Jelliffe-Pawlowski, L and Rand, L and Snyder, M and Jiang, C},
title = {Vaginal microbiomes show ethnic evolutionary dynamics and positive selection of Lactobacillus adhesins driven by a long-term niche-specific process.},
journal = {Cell reports},
volume = {43},
number = {4},
pages = {114078},
doi = {10.1016/j.celrep.2024.114078},
pmid = {38598334},
issn = {2211-1247},
abstract = {The vaginal microbiome's composition varies among ethnicities. However, the evolutionary landscape of the vaginal microbiome in the multi-ethnic context remains understudied. We perform a systematic evolutionary analysis of 351 vaginal microbiome samples from 35 multi-ethnic pregnant women, in addition to two validation cohorts, totaling 462 samples from 90 women. Microbiome alpha diversity and community state dynamics show strong ethnic signatures. Lactobacillaceae have a higher ratio of non-synonymous to synonymous polymorphism and lower nucleotide diversity than non-Lactobacillaceae in all ethnicities, with a large repertoire of positively selected genes, including the mucin-binding and cell wall anchor genes. These evolutionary dynamics are driven by the long-term evolutionary process unique to the human vaginal niche. Finally, we propose an evolutionary model reflecting the environmental niches of microbes. Our study reveals the extensive ethnic signatures in vaginal microbial ecology and evolution, highlighting the importance of studying the host-microbiome ecosystem from an evolutionary perspective.},
}