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

Humans
*Gastrointestinal Microbiome
Immunotherapy
Oxygen
*Probiotics/therapeutic use

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

TRIAL REGISTRATION NUMBER: N/A.},
}

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

Humans
*Obesity/epidemiology
*Ethnicity

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

*Homicide
*Happiness
Retrospective Studies
Folic Acid
Health Promotion

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

@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.},
}