@article {pmid39046491,
year = {2024},
author = {Soto-Cortés, E and Marroquín-Rodríguez, M and Basanta, MD and Maldonado-López, Y and Parra-Olea, G and Rebollar, EA},
title = {Host Species and Environment Shape the Skin Microbiota of Mexican Axolotls.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {98},
pmid = {39046491},
issn = {1432-184X},
support = {CF-2019/373914//CONAHCYT/ ; CF-2019/373914//CONAHCYT/ ; CF-2019/373914//CONAHCYT/ ; CF-2019/373914//CONAHCYT/ ; CF-2019/373914//CONAHCYT/ ; CF-2019/373914//CONAHCYT/ ; IN205521//PAPIIT/UNAM/ ; },
mesh = {Animals ; *Skin/microbiology ; *Microbiota ; *Bacteria/classification/genetics/isolation & purification ; Mexico ; *Fungi/classification/isolation & purification/genetics ; Ambystoma mexicanum/microbiology ; Host Specificity ; Environment ; Biodiversity ; },
abstract = {Skin microbiomes in amphibians are complex systems that can be influenced by biotic and abiotic factors. In this study, we examined the effect of host species and environmental conditions on the skin bacterial and fungal microbiota of four obligate paedomorphic salamander species, commonly known as axolotls (Ambystoma andersoni, A. dumerilii, A. mexicanum, and A. taylori), all of them endemic to the Trans-Mexican Volcanic Belt. We found that despite their permanent aquatic lifestyle, these species present a host-specific skin microbiota that is distinct from aquatic communities. We identified skin-associated taxa that were unique to each host species and that differentiated axolotl species based on alpha and beta diversity metrics. Moreover, we identified a set of microbial taxa that were shared across hosts with high relative abundances across skin samples. Specifically, bacterial communities were dominated by Burkholderiales and Pseudomonadales bacterial orders and Capnodiales and Pleosporales fungal orders. Host species and environmental variables collectively explained more microbial composition variation in bacteria (R2 = 0.46) in comparison to fungi (R2 = 0.2). Our results contribute to a better understanding of the factors shaping the diversity and composition of skin microbial communities in Ambystoma. Additional studies are needed to disentangle the effects of specific host associated and environmental factors that could influence the skin microbiome of these endangered species.},
}

Animals
*Skin/microbiology
*Microbiota
*Bacteria/classification/genetics/isolation & purification
Mexico
*Fungi/classification/isolation & purification/genetics
Ambystoma mexicanum/microbiology
Host Specificity
Environment
Biodiversity

@article {pmid39046431,
year = {2024},
author = {Felton, AM and Spitzer, R and Raubenheimer, D and Hedwall, PO and Felton, A and Nichols, RV and O'Connell, BL and Malmsten, J and Löfmarck, E and Wam, HK},
title = {Increased intake of tree forage by moose is associated with intake of crops rich in nonstructural carbohydrates.},
journal = {Ecology},
volume = {},
number = {},
pages = {e4377},
doi = {10.1002/ecy.4377},
pmid = {39046431},
issn = {1939-9170},
support = {2016-01140//Swedish Research Council for Sustainable Development/ ; 5909/2021//Swedish Hunting Association/ ; 13/274//SEPA/ ; 2020-00108//SEPA/ ; //Södra Research Fund/ ; },
abstract = {Animals representing a wide range of taxonomic groups are known to select specific food combinations to achieve a nutritionally balanced diet. The nutrient balancing hypothesis suggests that, when given the opportunity, animals select foods to achieve a particular target nutrient balance, and that balancing occurs between meals and between days. For wild ruminants who inhabit landscapes dominated by human land use, nutritionally imbalanced diets can result from ingesting agricultural crops rich in starch and sugar (nonstructural carbohydrates [NCs]), which can be provided to them by people as supplementary feeds. Here, we test the nutrient balancing hypothesis by assessing potential effects that the ingestion of such crops by Alces alces (moose) may have on forage intake. We predicted that moose compensate for an imbalanced intake of excess NC by selecting tree forage with macro-nutritional content better suited for their rumen microbiome during wintertime. We applied DNA metabarcoding to identify plants in fecal and rumen content from the same moose during winter in Sweden. We found that the concentration of NC-rich crops in feces predicted the presence of Picea abies (Norway spruce) in rumen samples. The finding is consistent with the prediction that moose use tree forage as a nutritionally complementary resource to balance their intake of NC-rich foods, and that they ingested P. abies in particular (normally a forage rarely eaten by moose) because it was the most readily available tree. Our finding sheds new light on the foraging behavior of a model species in herbivore ecology, and on how habitat alterations by humans may change the behavior of wildlife.},
}

@article {pmid39045894,
year = {2024},
author = {D'Accolti, M and Soffritti, I and Bini, F and Mazziga, E and Caselli, E},
title = {Tackling transmission of infectious diseases: A probiotic-based system as a remedy for the spread of pathogenic and resistant microbes.},
journal = {Microbial biotechnology},
volume = {17},
number = {7},
pages = {e14529},
pmid = {39045894},
issn = {1751-7915},
mesh = {*Probiotics ; Humans ; Cross Infection/prevention & control/microbiology ; Sanitation/methods ; Disinfection/methods ; Communicable Diseases/transmission/microbiology/drug therapy ; Disease Transmission, Infectious/prevention & control ; Detergents/pharmacology ; Disinfectants/pharmacology ; },
abstract = {Built environments (BEs) currently represent the areas in which human beings spend most of their life. Consistently, microbes populating BEs mostly derive from human occupants and can be easily transferred from BE to occupants. The hospital microbiome is a paradigmatic example, representing a reservoir for harmful pathogens that can be transmitted to susceptible patients, causing the healthcare-associated infections (HAIs). Environmental cleaning is a crucial pillar in controlling BE pathogens and preventing related infections, and chemical disinfectants have been largely used so far towards this aim. However, despite their immediate effect, chemical-based disinfection is unable to prevent recontamination, has a high environmental impact, and can select/increase antimicrobial resistance (AMR) in treated microbes. To overcome these limitations, probiotic-based sanitation (PBS) strategies were recently proposed, built on the use of detergents added with selected probiotics able to displace surrounding pathogens by competitive exclusion. PBS was reported as an effective and low-impact alternative to chemical disinfection, providing stable rebalance of the BE microbiome and significantly reducing pathogens and HAIs compared to disinfectants, without exacerbating AMR and pollution concerns. This minireview summarizes the most significant results obtained by applying PBS in sanitary and non-sanitary settings, which overall suggest that PBS may effectively tackle the infectious risk meanwhile preventing the further spread of pathogenic and resistant microbes.},
}

*Probiotics
Humans
Cross Infection/prevention & control/microbiology
Sanitation/methods
Disinfection/methods
Communicable Diseases/transmission/microbiology/drug therapy
Disease Transmission, Infectious/prevention & control
Detergents/pharmacology
Disinfectants/pharmacology

@article {pmid39045769,
year = {2024},
author = {Tian, S and Lei, Y and Zhao, F and Che, J and Wu, Y and Lei, P and Kang, YE and Shan, Y},
title = {Improving insulin resistance by sulforaphane via activating the Bacteroides and Lactobacillus SCFAs-GPR-GLP1 signal axis.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d4fo01059k},
pmid = {39045769},
issn = {2042-650X},
abstract = {Background: Insulin resistance (IR) is closely associated with non-alcoholic fatty liver disease (NAFLD), and the gut microbiome contributes to the development of NAFLD. Sulforaphane (SFN) is a phytochemical in cruciferous vegetables that could improve lipid metabolism disorder. However, whether SFN can alleviate IR in NAFLD by regulating the intestinal flora remains unclear. Methods: SFN was administered to high fat diet (HFD)-fed Wistar rats for 10 weeks. Gut microbiota was analysed by 16S rRNA sequencing and the short chain fatty acids (SCFAs) by gas chromatography. The expression of tight junction protein and the numbers of Lactobacillus, Bacteroides and Bifidobacterium were determined by qPCR. The expression of G-protein-coupled receptor 41/43 (GPR41/43) was determined by western blot. A randomized controlled trial (RCT) was conducted in NAFLD patients with broccoli seed tablets (rich in SFN, 42 mg d[-1]) as intervention for 12 weeks. Thirty-six volunteers with abnormal glucose before the broccoli seed tablet treatment were selected in the intervention group to analyze their blood glucose, insulin, homeostasis model assessment-insulin resistance index (HOMA-IRI), homeostasis model assessment-insulin sensitivity index (HOMA-ISI) and glucagon-like peptide (GLP-1). Results: SFN reduced blood glucose and HOMA-IRI while increasing insulin sensitivity in HFD rats. SFN reduced glycogen synthase kinase 3 (GSK-3), phosphoenolpyruvate carboxykinase (PEPCK) activity, and phosphorylation of serine residues of IRS-2 induced by HFD. SFN reshaped the gut microbiota composition of HFD-induced rats and, especially, increased the content of Bacteroidaceae, Lactobacillaceae and Bifidobacteriaceae, which are related to the improvement from SFN of the blood glucose and HOMA-IRI. The increased numbers of Bacteroides and Lactobacillus were the targets of SFN to enhance the expression of tight junction proteins ZO-1 and occludin, thereby lowering lipopolysaccharide content to reduce inflammation, ultimately alleviating IR. Bacteroides and Lactobacillus produced SCFAs, which activated GPR41/43 to secrete GLP1. Moreover, it was also confirmed in RCT that SFN intervention increased the level of GLP1 in NAFLD patients, which was positively correlated with the reduction of blood glucose and HOMA-IR. Conclusions: SFN alleviated IR in NAFLD via the Bacteroides and Lactobacillus SCFAs-GPR41/43-GLP1 axis and protected the intestinal mucosal barrier to decrease inflammation.},
}

@article {pmid39045277,
year = {2024},
author = {Tian, Q and Jin, S and Zhang, G and Liu, Y and Liu, J and Tang, X and Li, Y and Liu, J and Liu, Y and Wang, Z},
title = {Assessing vaginal microbiome through Vaginal Microecology Evaluation System as a predictor for in vitro fertilization outcomes: a retrospective study.},
journal = {Frontiers in endocrinology},
volume = {15},
number = {},
pages = {1380187},
pmid = {39045277},
issn = {1664-2392},
mesh = {Humans ; Female ; *Fertilization in Vitro/methods ; Retrospective Studies ; Pregnancy ; *Vagina/microbiology ; Adult ; *Microbiota ; *Pregnancy Outcome ; *Embryo Transfer/methods ; Infertility, Female/microbiology/therapy ; Pregnancy Rate ; Vaginosis, Bacterial/microbiology/diagnosis ; },
abstract = {OBJECTIVE: This study aims to evaluate the effectiveness of the Vaginal Microecology Evaluation System (VMES) in assessing the dynamics of the vaginal microbiome (VM) throughout the process of in vitro fertilization and embryo transfer (IVF-ET). Furthermore, it seeks to explore the potential correlation between distinct types of VM ecology and the success rate of IVF-ET.

METHODS: This study employed VMES to ascertain the composition of the VM. Data were collected from infertile women who underwent their initial IVF-ET treatment for tubal factor between January 2018 and December 2021. A retrospective analysis of pregnancy outcomes resulting from their fresh embryo transfer was conducted to determine the predictive significance of the vaginal microenvironment.

RESULTS: We demonstrate that VMES is able to predict IVF-ET outcomes in patients diagnosed with Bacterial Vaginosis (BV). Notably, a discernible shift in the VM was observed in a decent subset of patients following Controlled Ovarian Stimulation (COS), though this phenomenon was not universal across all participants. Specifically, there was a noteworthy increase in the proportion of patients exhibiting BV and uncharacterized dysbiosis subsequent to COS. Furthermore, our investigation revealed a significant correlation between VM and both the live birth rate and early miscarriage rate. Employing a multivariable logistic regression model, we identified that VM status pre-COS, VM status post-COS, patient age, and the number of embryos transferred emerged as independent predictors of the live birth rate.

CONCLUSION: Our study suggests that, during IVF-ET treatment, the VMES can effectively detect changes in the VM, which are strongly correlated with the pregnancy outcome of IVF-ET procedures.},
}

Humans
Female
*Fertilization in Vitro/methods
Retrospective Studies
Pregnancy
*Vagina/microbiology
Adult
*Microbiota
*Pregnancy Outcome
*Embryo Transfer/methods
Infertility, Female/microbiology/therapy
Pregnancy Rate
Vaginosis, Bacterial/microbiology/diagnosis

@article {pmid39045090,
year = {2024},
author = {Izzy, S and Yahya, T and Albastaki, O and Cao, T and Schwerdtfeger, LA and Abou-El-Hassan, H and Chopra, K and Ekwudo, MN and Kurdeikaite, U and Verissimo, IM and LeServe, DS and Lanser, TB and Aronchik, M and Oliveira, MG and Moreira, T and Rezende, RM and El Khoury, J and Cox, LM and Weiner, HL and Zafonte, R and Whalen, MJ},
title = {High-salt diet induces microbiome dysregulation, neuroinflammation and anxiety in the chronic period after mild repetitive closed head injury in adolescent mice.},
journal = {Brain communications},
volume = {6},
number = {4},
pages = {fcae147},
pmid = {39045090},
issn = {2632-1297},
abstract = {The associations between human concussions and subsequent sequelae of chronic neuropsychiatric and cardiovascular diseases such as hypertension have been reported; however, little is known about the underlying biological processes. We hypothesized that dietary changes, including a high-salt diet, disrupt the bidirectional gut-brain axis, resulting in worsening neuroinflammation and emergence of cardiovascular and behavioural phenotypes in the chronic period after repetitive closed head injury in adolescent mice. Adolescent mice were subjected to three daily closed head injuries, recovered for 12 weeks and then maintained on a high-salt diet or a normal diet for an additional 12 weeks. Experimental endpoints were haemodynamics, behaviour, microglial gene expression (bulk RNA sequencing), brain inflammation (brain tissue quantitative PCR) and microbiome diversity (16S RNA sequencing). High-salt diet did not affect systemic blood pressure or heart rate in sham or injured mice. High-salt diet increased anxiety-like behaviour in injured mice compared to sham mice fed with high-salt diet and injured mice fed with normal diet. Increased anxiety in injured mice that received a high-salt diet was associated with microgliosis and a proinflammatory microglial transcriptomic signature, including upregulation in interferon-gamma, interferon-beta and oxidative stress-related pathways. Accordingly, we found upregulation of tumour necrosis factor-alpha and interferon-gamma mRNA in the brain tissue of high salt diet-fed injured mice. High-salt diet had a larger effect on the gut microbiome composition than repetitive closed head injury. Increases in gut microbes in the families Lachnospiraceae, Erysipelotrichaceae and Clostridiaceae were positively correlated with anxiety-like behaviours. In contrast, Muribaculaceae, Acholeplasmataceae and Lactobacillaceae were negatively correlated with anxiety in injured mice that received a high-salt diet, a time-dependent effect. The findings suggest that high-salt diet, administered after a recovery period, may affect neurologic outcomes following mild repetitive head injury, including the development of anxiety. This effect was linked to microbiome dysregulation and an exacerbation of microglial inflammation, which may be physiological targets to prevent behavioural sequelae in the chronic period after mild repetitive head injury. The data suggest an important contribution of diet in determining long-term outcomes after mild repetitive head injury.},
}

@article {pmid39044953,
year = {2024},
author = {Ma, F and Liu, Y and Qi, Y and Deng, N and Xiang, H and Qi, C and Peng, P and Jia, L and Zhang, X},
title = {Tree age affects carbon sequestration potential via altering soil bacterial community composition and function.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1379409},
pmid = {39044953},
issn = {1664-302X},
abstract = {Among various factors related to the forest carbon pool, the tree stand age, which interacts with soil organic matter, decomposition rates, and microbial activity, is essential and cannot be disregarded. However, knowledge about how tree phases influence soil carbon sinks is not adequate. This study sampled Larix kaempferi (Japanese larch) plantations with different tree stand ages to investigate the temporal dynamics of soil carbon sink in the forest. Physiochemical analyses and high-throughput sequencing results further revealed the interactions of tree stands and their related rhizosphere microbiome. It was found that microbial composition and metabolic activity were significantly affected by different tree ages, whose structures gradually diversified and became more stable from young to mature forests. Many keystone taxa from the phyla Chloroflexi, Proteobacteria, Acidobacteriota, and Nitrospirota were found to be associated with carbon transformation processes. Interestingly, the carbon resource utilization strategies of microbial groups related to tree ages also differed, with near-mature forest soils showing better labile carbon degradation capacity, and mature forests possessing higher degradation potential of recalcitrant carbon. Age-altered tree growth and physiology were found to interact with its rhizosphere microbiome, which is the driving factor in the formation and stability of forest soil carbon. This study highlighted that the tree age-associated soil microbiomes, which provided insights into their effects on soil carbon transformation, were significant in enhancing the knowledge of carbon sequestration in L. kaempferi plantations.},
}

@article {pmid39044948,
year = {2024},
author = {Han, N and Peng, X and Zhang, T and Qiang, Y and Li, X and Zhang, W},
title = {Temporal dynamics and species-level complexity of Prevotella spp. in the human gut microbiota: implications for enterotypes and health.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1414000},
pmid = {39044948},
issn = {1664-302X},
abstract = {The concept of "enterotypes" in microbiome research has attracted substantial interest, particularly focusing on the abundance of Prevotella spp. in the human gut. In this study, the intricate dynamics of Prevotella spp. in the human gut microbiota was investigated, based on the metagenomic method. First, 239 fecal samples from individuals across four regions of China revealed a bimodal distribution, highlighting the abundance and variability in Prevotella spp. within the Chinese population. Second, the longitudinal cohort study included 184 fecal samples from 52 time points collected from seven individuals who demonstrated either the outbreaks or disappearances of Prevotella spp., emphasizing the transient nature of Prevotella abundance levels and suggesting shifts in Prevotella "enterotypes." Furthermore, a turnover of the dominant Prevotella spp. was observed, indicating the potential presence of diverse subtypes of Prevotella enterotype. Notably, the genomic analysis demonstrated the persistence of specific Prevotella strains within individuals over extended periods, highlighting the enduring presence of Prevotella in the human gut. In conclusion, by integrating the temporal and geographical scales in our research, we gained deeper insights into the dynamics of Prevotella, emphasizing the importance of considering the dynamics at the time and species level in gut microbiota studies and their implications on human health.},
}

@article {pmid39044834,
year = {2024},
author = {Tabrizi, E and Pourteymour Fard Tabrizi, F and Mahmoud Khaled, G and Sestito, MP and Jamie, S and Boone, BA},
title = {Unraveling the gut microbiome's contribution to pancreatic ductal adenocarcinoma: mechanistic insights and therapeutic perspectives.},
journal = {Frontiers in immunology},
volume = {15},
number = {},
pages = {1434771},
pmid = {39044834},
issn = {1664-3224},
mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; *Carcinoma, Pancreatic Ductal/therapy/microbiology/immunology ; *Pancreatic Neoplasms/microbiology/therapy/immunology ; Animals ; Probiotics/therapeutic use ; Fecal Microbiota Transplantation ; Immunotherapy/methods ; Immune Checkpoint Inhibitors/therapeutic use ; },
abstract = {The gut microbiome plays a significant role in the pathogenesis of pancreatic ductal adenocarcinoma (PDAC), influencing oncogenesis, immune responses, and treatment outcomes. Studies have identified microbial species like Porphyromonas gingivalis and Fusobacterium nucleatum, that promote PDAC progression through various mechanisms. Additionally, the gut microbiome affects immune cell activation and response to immunotherapy, including immune checkpoint inhibitors and CAR-T therapy. Specific microbes and their metabolites play a significant role in the effectiveness of immune checkpoint inhibitors (ICIs). Alterations in the gut microbiome can either enhance or diminish responses to PD-1/PD-L1 and CTLA-4 blockade therapy. Additionally, bacterial metabolites like trimethylamine N-oxide (TMAO) and lipopolysaccharide (LPS) impact antitumor immunity, offering potential targets to augment immunotherapy responses. Modulating the microbiome through fecal microbiota transplantation, probiotics, prebiotics, dietary changes, and antibiotics shows promise in PDAC treatment, although outcomes are highly variable. Dietary modifications, particularly high-fiber diets and specific fat consumption, influence microbiome composition and impact cancer risk. Combining microbiome-based therapies with existing treatments holds potential for improving PDAC therapy outcomes, but further research is needed to optimize their effectiveness.},
}

Humans
*Gastrointestinal Microbiome/immunology
*Carcinoma, Pancreatic Ductal/therapy/microbiology/immunology
*Pancreatic Neoplasms/microbiology/therapy/immunology
Animals
Probiotics/therapeutic use
Fecal Microbiota Transplantation
Immunotherapy/methods
Immune Checkpoint Inhibitors/therapeutic use

@article {pmid39044721,
year = {2024},
author = {Connell, JT and Bouras, G and Yeo, K and Fenix, K and Cooksley, C and Bassiouni, A and Vreugde, S and Wormald, PJ and Psaltis, AJ},
title = {Characterising the allergic fungal rhinosinusitis microenvironment using full-length 16S rRNA gene amplicon sequencing and fungal ITS sequencing.},
journal = {Allergy},
volume = {},
number = {},
pages = {},
doi = {10.1111/all.16240},
pmid = {39044721},
issn = {1398-9995},
abstract = {INTRODUCTION: Allergic fungal rhinosinusitis (AFRS) is a severe phenotype of chronic rhinosinusitis with nasal polyposis (CRSwNP), characterised by localised and exaggerated type 2 inflammation. While fungal antigenic stimulation of unregulated Th2-mediated inflammation is the core pathophysiological mechanism, the direct and synergistic role of bacteria in disease modification is a pervasive hypothesis. We set out to define the microenvironment of AFRS to elucidate virulent organisms that may be implicated in the pathophysiology of AFRS.

METHODOLOGY: We undertook a cross-sectional study of AFRS patients and non-fungal CRSwNP patients. Demographics, disease severity, culture and microbiome sequences were analysed. Multimodality microbiome sequencing included short-read next-generation sequencing (NGS) on the Illumina Miseq (16S rRNA and ITS) and full-length 16S rRNA sequencing on the Oxford Nanopore Technologies GridION (ONT).

RESULTS: Thirty-two AFRS and 29 non-fungal CRSwNP patients (NF) were included in this study. Staphylococcus aureus was the dominant organism cultured and sequenced in both AFRS and NF groups (AFRS 27.54%; NF 18.04%; p = .07). Streptococcus pneumoniae (AFRS 12.31%; NF 0.98%; p = .03) and Haemophilus influenzae (AFRS 15.03%; NF 0.24%; p = .005) were significantly more abundant in AFRS. Bacterial diversity (Shannon's index) was considerably lower in AFRS relative to NF (AFRS 0.6; NF 1.0, p = .008). Aspergillus was the most cultured fungus in AFRS (10/32, 31.3%). The AFRS sequenced mycobiome was predominantly represented by Malassezia (43.6%), Curvularia (18.5%) and Aspergillus (16.8%), while the NF mycobiome was nearly exclusively Malassezia (84.2%) with an absence of Aspergillus or dematiaceous fungi.

CONCLUSION: A low diversity, dysbiotic microenvironment dominated by Staphylococcus aureus, Streptococcus pneumoniae and Haemophilus influenzae characterised the bacterial microbiome of AFRS, with a mycobiome abundant in Malassezia, Aspergillus and Curvularia. While Staphylococcus aureus has been previously implicated in AFRS through enterotoxin superantigen potential, Streptococcus pneumoniae and Haemophilus influenzae are novel findings that may represent alternate cross-kingdom pathophysiological mechanisms.},
}

@article {pmid39044706,
year = {2024},
author = {Maurer, M and Kolkhir, P and Pereira, MP and Siebenhaar, F and Witte-Händel, E and Bergmann, KC and Bonnekoh, H and Buttgereit, T and Fluhr, JW and Frischbutter, S and Grekowitz, EM and Herzog, L and Kiefer, LA and Krause, K and Magerl, M and Muñoz, M and Neisinger, S and Nojarov, N and Prins, S and Pyatilova, P and Ramanauskaité, A and Scheffel, J and Terhorst-Molawi, D and Treudler, R and Weller, K and Zuberbier, T and Metz, M},
title = {Disease modification in chronic spontaneous urticaria.},
journal = {Allergy},
volume = {},
number = {},
pages = {},
doi = {10.1111/all.16243},
pmid = {39044706},
issn = {1398-9995},
abstract = {Chronic spontaneous urticaria (CSU) is a debilitating, inflammatory skin condition characterized by infiltrating immune cells. Available treatments are limited to improving the signs and symptoms. There is an unmet need to develop therapies that target disease-driving pathways upstream of mast cell activation to inhibit or delay the progression of CSU and associated comorbidities. Here, we aim to define disease modification due to a treatment intervention and criteria that disease-modifying treatments (DMTs) must meet in CSU. We have defined disease modification in CSU as a favorable treatment-induced change in the underlying pathophysiology and, therefore, the disease course, which is clinically beneficial and enduring. A DMT must fulfil the following criteria: (1) prevents or delays the progression of CSU, (2) induces long-term, therapy-free clinical remission, which is the sustained absence of CSU signs and symptoms without the need for treatment, and (3) affects the underlying mechanism of CSU, as demonstrated by an effect on disease-driving signals and/or a biomarker. DMTs in CSU should slow disease progression, achieve long-lasting disease remission, target disease-driving mechanisms, reduce mast cell-activating IgE autoantibodies, target cytokine profile polarization, and normalize the gut microbiome and barrier. Treating CSU at the immune system level could provide valuable alternatives to pharmacotherapy in CSU management. Specific DMTs in CSU are yet to be developed, but some show potential benefits, such as inhibitors of Bruton's Tyrosine Kinase, IL-4 and IL-13. Future therapies could prevent CSU signs and symptoms, achieve long-term clinical benefits after discontinuing treatment, and prevent associated concomitant disorders.},
}

@article {pmid39044605,
year = {2024},
author = {Xu, H and Zhang, J and Wang, F and Chen, Y and Chen, H and Feng, Y and Hou, G and Zi, J and Zhang, M and Zhou, J and Deng, L and Lin, L and Zhang, X and Liu, S},
title = {Integration of metagenomics and metaproteomics in the intestinal lavage fluids benefits construction of discriminative model and discovery of biomarkers for HBV liver diseases.},
journal = {Proteomics},
volume = {},
number = {},
pages = {e2400002},
doi = {10.1002/pmic.202400002},
pmid = {39044605},
issn = {1615-9861},
support = {2023YFC3402900//National Key Research and Development Program of China/ ; 2022YFA1304500//National Key Research and Development Program of China/ ; 2020YFE0202200//National Key Research and Development Program of China/ ; },
abstract = {Intestinal lavage fluid (IVF) containing the mucosa-associated microbiota instead of fecal samples was used to study the gut microbiota using different omics approaches. Focusing on the 63 IVF samples collected from healthy and hepatitis B virus-liver disease (HBV-LD), a question is prompted whether omics features could be extracted to distinguish these samples. The IVF-related microbiota derived from the omics data was classified into two enterotype sets, whereas the genomics-based enterotypes were poorly overlapped with the proteomics-based one in either distribution of microbiota or of IVFs. There is lack of molecular features in these enterotypes to specifically recognize healthy or HBV-LD. Running machine learning against the omics data sought the appropriate models to discriminate the healthy and HBV-LD IVFs based on selected genes or proteins. Although a single omics dataset is basically workable in such discrimination, integration of the two datasets enhances discrimination efficiency. The protein features with higher frequencies in the models are further compared between healthy and HBV-LD based on their abundance, bringing about three potential protein biomarkers. This study highlights that integration of metaomics data is beneficial for a molecular discriminator of healthy and HBV-LD, and reveals the IVF samples are valuable for microbiome in a small cohort.},
}

@article {pmid39044522,
year = {2024},
author = {Leow, YJ and Wang, JDJ and Vipin, A and Sandhu, GK and Soo, SA and Kumar, D and Mohammed, AA and Zailan, FZB and Lee, FPHE and Ghildiyal, S and Liew, SY and Dang, C and Tanoto, P and Tan, IYZ and Chong, WFW and Kandiah, N},
title = {Biomarkers and Cognition Study, Singapore (BIOCIS): Protocol, Study Design, and Preliminary Findings.},
journal = {The journal of prevention of Alzheimer's disease},
volume = {11},
number = {4},
pages = {1093-1105},
pmid = {39044522},
issn = {2426-0266},
mesh = {Humans ; Singapore/epidemiology ; *Biomarkers ; Longitudinal Studies ; Male ; Aged ; Middle Aged ; Female ; *Cognitive Dysfunction/diagnosis/epidemiology ; Adult ; Aged, 80 and over ; Neuropsychological Tests ; Cognition/physiology ; Neuroimaging ; Dementia/epidemiology/diagnosis ; Research Design ; },
abstract = {BACKGROUND: The focus of medicine is shifting from treatment to preventive care. The expression of biomarkers of dementia and Alzheimer's disease (AD) appear decades before the onset of observable symptoms, and evidence has emerged supporting pharmacological and non-pharmacological interventions to treat modifiable risk factors of dementia. However, there is limited research on the epidemiology, clinical phenotypes, and underlying pathobiology of cognitive diseases in Asian populations.

OBJECTIVES: The objectives of the Biomarkers and Cognition Study, Singapore(BIOCIS) are to characterize the underlying pathobiology of Cognitive Impairment through a longitudinal study incorporating fluid biomarker profiles, neuroimaging, neuropsychological and clinical outcomes in a multi-ethnic Southeast Asian population.

DESIGN, SETTING, PARTICIPANTS: BIOCIS is a 5-year longitudinal study where participants are assessed annually. 2500 participants aged 30 to 95 will be recruited from the community in Singapore. To investigate how pathology presents with or without minimal clinical symptoms and vice versa, CI and unimpaired individuals will be recruited. Participants will undergo assessments to characterise biomarkers of dementia through neuroimaging, fluid biomarkers, cognitive assessments, behavioural and lifestyle profiles, retinal scans and microbiome indicators.

RESULTS: Since commencement of recruitment in February 2022, 1148 participants have been enrolled, comprising 1012 Chinese, 62 Indian, and 35 Malay individuals. Mean age and education is 61.32 years and 14.34 years respectively with 39.8% males. 47.9 % of the cohort are employed and 32.06% have a family history of dementia. The prevalence of cerebral small vessel disease is 90.2% with a mean modified Fazekas white matter hyperintensity score of 4.1.

CONCLUSION: The BIOCIS cohort will help identify novel biomarkers, pathological trajectories, epidemiology of dementia, and reversible risk factors in a Southeast Asian population. Completion of BIOCIS longitudinal data could provide insights into risk-stratification of Asians populations, and potentially inform public healthcare and precision medicine for better patient outcomes in the prevention of Alzheimer's disease and dementia.},
}

Humans
Singapore/epidemiology
*Biomarkers
Longitudinal Studies
Male
Aged
Middle Aged
Female
*Cognitive Dysfunction/diagnosis/epidemiology
Adult
Aged, 80 and over
Neuropsychological Tests
Cognition/physiology
Neuroimaging
Dementia/epidemiology/diagnosis
Research Design

@article {pmid39044244,
year = {2024},
author = {Glendinning, L and Jia, X and Kebede, A and Oyola, SO and Park, JE and Park, W and Assiri, A and Holm, JB and Kristiansen, K and Han, J and Hanotte, O},
title = {Altitude-dependent agro-ecologies impact the microbiome diversity of scavenging indigenous chicken in Ethiopia.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {138},
pmid = {39044244},
issn = {2049-2618},
mesh = {Animals ; *Chickens/microbiology ; Ethiopia ; *Altitude ; *Bacteria/classification/genetics/isolation & purification ; Gastrointestinal Microbiome/genetics ; Metagenome ; Cecum/microbiology ; Microbiota ; Biodiversity ; Phylogeny ; },
abstract = {BACKGROUND: Scavenging indigenous village chickens play a vital role in sub-Saharan Africa, sustaining the livelihood of millions of farmers. These chickens are exposed to vastly different environments and feeds compared to commercial chickens. In this study, we analysed the caecal microbiota of 243 Ethiopian village chickens living in different altitude-dependent agro-ecologies.

RESULTS: Differences in bacterial diversity were significantly correlated with differences in specific climate factors, topsoil characteristics, and supplemental diets provided by farmers. Microbiota clustered into three enterotypes, with one particularly enriched at high altitudes. We assembled 9977 taxonomically and functionally diverse metagenome-assembled genomes. The vast majority of these were not found in a dataset of previously published chicken microbes or in the Genome Taxonomy Database.

CONCLUSIONS: The wide functional and taxonomic diversity of these microbes highlights their importance in the local adaptation of indigenous poultry, and the significant impacts of environmental factors on the microbiota argue for further discoveries in other agro-ecologies. Video Abstract.},
}

Animals
*Chickens/microbiology
Ethiopia
*Altitude
*Bacteria/classification/genetics/isolation & purification
Gastrointestinal Microbiome/genetics
Metagenome
Cecum/microbiology
Microbiota
Biodiversity
Phylogeny

@article {pmid39043743,
year = {2024},
author = {Fregulia, P and Park, T and Li, W and Cersosimo, LM and Zanton, GI},
title = {Microbial inoculum effects on the rumen epithelial transcriptome and rumen epimural metatranscriptome in calves.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {16914},
pmid = {39043743},
issn = {2045-2322},
support = {DE-SC0014664//This research was supported in part by an appointment to the Agricultural Research Service (ARS) Research Participation Program administered by the Oak Ridge Institute for Science and Education (ORISE) through an interagency agreement between the U.S. Department of Energy (DOE) and the U.S. Department of Agriculture (USDA)./ ; 5090-31000-026-00D//USDA, Agricultural Research Service under National Program 101 Food Animal Production Current Research Information System (CRIS) funds/ ; },
mesh = {Animals ; Cattle ; *Rumen/microbiology/metabolism ; *Transcriptome ; Epithelium/metabolism/microbiology ; Male ; Gastrointestinal Microbiome/genetics ; Bacteria/classification/genetics/metabolism ; Gene Expression Profiling/methods ; },
abstract = {Manipulation of the rumen microbial ecosystem in early life may affect ruminal fermentation and enhance the productive performance of dairy cows. The objective of this experiment was to evaluate the effects of dosing three different types of microbial inoculum on the rumen epithelium tissue (RE) transcriptome and the rumen epimural metatranscriptome (REM) in dairy calves. For this objective, 15 Holstein bull calves were enrolled in the study at birth and assigned to three different intraruminal inoculum treatments dosed orally once weekly from three to six weeks of age. The inoculum treatments were prepared from rumen contents collected from rumen fistulated lactating cows and were either autoclaved (control; ARF), processed by differential centrifugation to create the bacterial-enriched inoculum (BE), or through gravimetric separation to create the protozoal-enriched inoculum (PE). Calves were fed 2.5 L/d pasteurized waste milk 3x/d from 0 to 7 weeks of age and texturized starter until euthanasia at 9 weeks of age, when the RE tissues were collected for transcriptome and microbial metatranscriptome analyses, from four randomly selected calves from each treatment. The different types of inoculum altered the RE transcriptome and REM. Compared to ARF, 9 genes were upregulated in the RE of BE and 92 in PE, whereas between BE and PE there were 13 genes upregulated in BE and 114 in PE. Gene ontology analysis identified enriched GO terms in biological process category between PE and ARF, with no enrichment between BE and ARF. The RE functional signature showed different KEGG pathways related to BE and ARF, and no specific KEGG pathway for PE. We observed a lower alpha diversity index for RE microbiome in ARF (observed genera and Chao1 (p < 0.05)). Five microbial genera showed a significant correlation with the changes in host gene expression: Roseburia (25 genes), Entamoeba (two genes); Anaerosinus, Lachnospira, and Succiniclasticum were each related to one gene. sPLS-DA analysis showed that RE microbial communities differ among the treatments, although the taxonomic and functional microbial profiles show different distributions. Co-expression Differential Network Analysis indicated that both BE and PE had an impact on the abundance of KEGG modules related to acyl-CoA synthesis, type VI secretion, and methanogenesis, while PE had a significant impact on KEGGs related to ectoine biosynthesis and D-xylose transport. Our study indicated that artificial dosing with different microbial inocula in early life alters not only the RE transcriptome, but also affects the REM and its functions.},
}

Animals
Cattle
*Rumen/microbiology/metabolism
*Transcriptome
Epithelium/metabolism/microbiology
Male
Gastrointestinal Microbiome/genetics
Bacteria/classification/genetics/metabolism
Gene Expression Profiling/methods

@article {pmid39043687,
year = {2024},
author = {Cai, Z and Yu, T and Tan, W and Zhou, Q and Liu, L and Nian, H and Lian, T},
title = {GmAMT2.1/2.2-dependent ammonium nitrogen and metabolites shape rhizosphere microbiome assembly to mitigate cadmium toxicity.},
journal = {NPJ biofilms and microbiomes},
volume = {10},
number = {1},
pages = {60},
pmid = {39043687},
issn = {2055-5008},
support = {32170115//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {*Cadmium/metabolism/toxicity ; *Rhizosphere ; *Glycine max/microbiology ; *Soil Microbiology ; *Ammonium Compounds/metabolism ; *Nitrogen/metabolism ; *Microbiota/drug effects ; Bacteria/genetics/metabolism/classification/drug effects/isolation & purification ; Cation Transport Proteins/genetics/metabolism ; Fungi/genetics/metabolism/drug effects ; Plant Roots/microbiology ; Plant Proteins/genetics/metabolism ; },
abstract = {Cadmium (Cd), a heavy metal, is negatively associated with plant growth. AMT (ammonium transporter) genes can confer Cd resistance and enhance nitrogen (N) uptake in soybeans. The potential of AMT genes to alleviate Cd toxicity by modulating rhizosphere microbiota remains unkonwn. Here, the rhizosphere microbial taxonomic and metabolic differences in three genotypes, i.e., double knockout and overexpression lines and wild type, were identified. The results showed that GmAMT2.1/2.2 genes could induce soybean to recruit beneficial microorganisms, such as Tumebacillus, Alicyclobacillus, and Penicillium, by altering metabolites. The bacterial, fungal, and cross-kingdom synthetic microbial communities (SynComs) formed by these microorganisms can help soybean resist Cd toxicity. The mechanisms by which SynComs help soybeans resist Cd stress include reducing Cd content, increasing ammonium (NH4[+]-N) uptake and regulating specific functional genes in soybeans. Overall, this study provides valuable insights for the developing microbial formulations that enhance Cd resistance in sustainable agriculture.},
}

*Cadmium/metabolism/toxicity
*Rhizosphere
*Glycine max/microbiology
*Soil Microbiology
*Ammonium Compounds/metabolism
*Nitrogen/metabolism
*Microbiota/drug effects
Bacteria/genetics/metabolism/classification/drug effects/isolation & purification
Cation Transport Proteins/genetics/metabolism
Fungi/genetics/metabolism/drug effects
Plant Roots/microbiology
Plant Proteins/genetics/metabolism

@article {pmid39043677,
year = {2024},
author = {Johnson, KE and Hernandez-Alvarado, N and Blackstad, M and Heisel, T and Allert, M and Fields, DA and Isganaitis, E and Jacobs, KM and Knights, D and Lock, EF and Rudolph, MC and Gale, CA and Schleiss, MR and Albert, FW and Demerath, EW and Blekhman, R},
title = {Human cytomegalovirus in breast milk is associated with milk composition and the infant gut microbiome and growth.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {6216},
pmid = {39043677},
issn = {2041-1723},
support = {R01 HD080444/HD/NICHD NIH HHS/United States ; R01 HD109830/HD/NICHD NIH HHS/United States ; R21 HD099473/HD/NICHD NIH HHS/United States ; L50 HD099866/HD/NICHD NIH HHS/United States ; F32HD105364//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; F32 HD105364/HD/NICHD NIH HHS/United States ; },
mesh = {Humans ; *Milk, Human/virology/microbiology/chemistry ; *Gastrointestinal Microbiome ; Female ; *Cytomegalovirus ; *Cytomegalovirus Infections/transmission/virology ; Infant ; Infant, Newborn ; *Kynurenine/metabolism/analysis ; *Breast Feeding ; Viral Load ; Male ; Adult ; Indoleamine-Pyrrole 2,3,-Dioxygenase/metabolism ; Tryptophan/metabolism/analysis ; Metabolome ; },
abstract = {Human cytomegalovirus (CMV) is a highly prevalent herpesvirus that is often transmitted to the neonate via breast milk. Postnatal CMV transmission can have negative health consequences for preterm and immunocompromised infants, but any effects on healthy term infants are thought to be benign. Furthermore, the impact of CMV on the composition of the hundreds of bioactive factors in human milk has not been tested. Here, we utilize a cohort of exclusively breastfeeding full-term mother-infant pairs to test for differences in the milk transcriptome and metabolome associated with CMV, and the impact of CMV in breast milk on the infant gut microbiome and infant growth. We find upregulation of the indoleamine 2,3-dioxygenase (IDO) tryptophan-to-kynurenine metabolic pathway in CMV+ milk samples, and that CMV+ milk is associated with decreased Bifidobacterium in the infant gut. Our data indicate two opposing CMV-associated effects on infant growth; with kynurenine positively correlated, and CMV viral load negatively correlated, with infant weight-for-length at 1 month of age. These results suggest CMV transmission, CMV-related changes in milk composition, or both may be modulators of full-term infant development.},
}

Humans
*Milk, Human/virology/microbiology/chemistry
*Gastrointestinal Microbiome
Female
*Cytomegalovirus
*Cytomegalovirus Infections/transmission/virology
Infant
Infant, Newborn
*Kynurenine/metabolism/analysis
*Breast Feeding
Viral Load
Male
Adult
Indoleamine-Pyrrole 2,3,-Dioxygenase/metabolism
Tryptophan/metabolism/analysis
Metabolome

@article {pmid39043536,
year = {2024},
author = {Lu, S and Chen, Y and Guo, H and Liu, Z and Du, Y and Duan, L},
title = {Differences in clinical manifestations and the fecal microbiome between irritable bowel syndrome and small intestinal bacterial overgrowth.},
journal = {Digestive and liver disease : official journal of the Italian Society of Gastroenterology and the Italian Association for the Study of the Liver},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.dld.2024.07.011},
pmid = {39043536},
issn = {1878-3562},
abstract = {BACKGROUND: Irritable bowel syndrome (IBS) and small intestinal bacterial overgrowth (SIBO) share similar abdominal symptoms; however, their differentiation remains controversial.

AIMS: To illustrate the differences between the two conditions.

METHODS: Patients and healthy controls completed questionnaires and provided stool samples for analysis.

RESULTS: IBS presented with the most severe symptoms and was specifically characterized by intense abdominal pain and frequent episodes of diarrhea. Patients with IBS displayed more dysregulated taxonomy within the fecal microbiota than SIBO. Opportunistic pathogens, including Lachnoclostridium, Escherichia-Shigella, and Enterobacter were enriched in the IBS group which contributed to increased bacterial pathogenicity and positively correlated with abdominal pain and bloating, meanwhile, Lachnoclostridium and Escherichia-Shigella were found to be associated with metabolites affiliated to bile acids, alcohols and derivatives. Bacteria enriched in SIBO group correlated with constipation. The bacterial co-occurrence network within the SIBO group was the most intricate. Ruminococcaceae Group were defined as core bacteria in SIBO. Differential metabolites affiliated to androstane steroids and phenylacetic acids were associated with core bacteria.

CONCLUSIONS: Our study elucidates the differences between IBS and SIBO in terms of symptoms, microbiota and functions, which provides insights into a better understanding of both diseases and evidence for different treatment strategies.},
}

@article {pmid39043475,
year = {2024},
author = {van Dijk, MT and Talati, A and Barrios, PG and Crandall, AJ and Lugo-Candelas, C},
title = {Prenatal depression outcomes in the next generation: A critical review of recent DOHaD studies and recommendations for future research.},
journal = {Seminars in perinatology},
volume = {},
number = {},
pages = {151948},
doi = {10.1016/j.semperi.2024.151948},
pmid = {39043475},
issn = {1558-075X},
abstract = {Prenatal depression, a common pregnancy-related risk with a prevalence of 10-20 %, may affect in utero development and socioemotional and neurodevelopmental outcomes in the next generation. Although there is a growing body of work that suggests prenatal depression has an independent and long-lasting effect on offspring outcomes, important questions remain, and findings often do not converge. The present review examines work carried out in the last decade, with an emphasis on studies focusing on mechanisms and leveraging innovative technologies and study designs to fill in gaps in research. Overall, the past decade of research continues to suggest that prenatal depression increases risk for offspring socioemotional problems and may alter early brain development by affecting maternal-fetal physiology during pregnancy. However, important limitations remain; lack of diversity in study samples, inconsistent consideration of potential confounders (e.g., genetics, postnatal depression, parenting), and restriction of examination to narrow time windows and single exposures. On the other hand, exciting work has begun uncovering potential mechanisms underlying transmission, including alterations in mitochondria functioning, epigenetics, and the prenatal microbiome. We review the evidence to date, identify limitations, and suggest strategies for the next decade of research to detect mechanisms as well as sources of plasticity and resilience to ensure this work translates into meaningful, actionable science that improves the lives of families.},
}

@article {pmid39043421,
year = {2024},
author = {Fan, C and Li, R and Wang, L and Li, K and Jia, X and Gao, H and Zhang, B and Xu, X and Qian, S},
title = {Fecal Microbiota Transplantation for Severe Infant Botulism, China.},
journal = {Emerging infectious diseases},
volume = {30},
number = {8},
pages = {1732-1734},
doi = {10.3201/eid3008.231702},
pmid = {39043421},
issn = {1080-6059},
mesh = {*Botulism/therapy/microbiology ; Humans ; Infant ; Male ; *Fecal Microbiota Transplantation ; China ; Feces/microbiology ; Gastrointestinal Microbiome ; Treatment Outcome ; },
abstract = {Infant botulism in a 4-month-old boy in China who continued to excrete toxins for over a month despite antitoxin therapy was further treated with fecal microbiota transplantation. After treatment, we noted increased gut microbial diversity and altered fecal metabolites, which may help reduce intestinal pH and enhance anti-inflammatory capabilities.},
}

*Botulism/therapy/microbiology
Humans
Infant
Male
*Fecal Microbiota Transplantation
China
Feces/microbiology
Gastrointestinal Microbiome
Treatment Outcome

@article {pmid39043386,
year = {2024},
author = {Duller, S and Moissl-Eichinger, C},
title = {Archaea in the Human Microbiome and Potential Effects on Human Infectious Disease.},
journal = {Emerging infectious diseases},
volume = {30},
number = {8},
pages = {},
doi = {10.3201/eid3008.240181},
pmid = {39043386},
issn = {1080-6059},
mesh = {Humans ; *Archaea/genetics ; *Microbiota ; Communicable Diseases/microbiology ; },
abstract = {Archaea represent a separate domain of life, next to bacteria and eukarya. As components of the human microbiome, archaea have been associated with various diseases, including periodontitis, endodontic infections, small intestinal bacterial overgrowth, and urogenital tract infections. Archaea are generally considered nonpathogenic; the reasons are speculative because of limited knowledge and gene annotation challenges. Nevertheless, archaeal syntrophic principles that shape global microbial networks aid both archaea and potentially pathogenic bacteria. Evaluating archaea interactions remains challenging, requiring clinical studies on inflammatory potential and the effects of archaeal metabolism. Establishing a culture collection is crucial for investigating archaea functions within the human microbiome, which could improve health outcomes in infectious diseases. We summarize potential reasons for archaeal nonpathogenicity, assess the association with infectious diseases in humans, and discuss the necessary experimental steps to enable mechanistic studies involving archaea.},
}

Humans
*Archaea/genetics
*Microbiota
Communicable Diseases/microbiology

@article {pmid39043353,
year = {2024},
author = {Thacharodi, A and Hassan, S and Ahmed, ZHT and Singh, P and Maqbool, M and Meenatchi, R and Pugazhendhi, A and Sharma, A},
title = {The ruminant gut microbiome vs enteric methane emission: The essential microbes may help to mitigate the global methane crisis.},
journal = {Environmental research},
volume = {},
number = {},
pages = {119661},
doi = {10.1016/j.envres.2024.119661},
pmid = {39043353},
issn = {1096-0953},
abstract = {Ruminants release enteric methane into the atmosphere, significantly increasing greenhouse gas emissions and degrading the environment. A common focus of traditional mitigation efforts is on dietary management and manipulation, which may have limits in sustainability and efficacy, exploring the potential of essential microorganisms as a novel way to reduce intestinal methane emissions in ruminants; a topic that has garnered increased attention in recent years. Fermentation and feed digestion are significantly aided by essential microbes found in the rumen, such as bacteria, fungi, and archaea. The practical implications of the findings reported in various studies conducted on rumen gut concerning methane emissions may pave the way to understanding the mechanisms of CH4 production in the rumen to enhance cattle feed efficiency and mitigate CH4 emissions from livestock. This review discussed using essential bacteria to reduce intestinal methane emissions in ruminants. It investigates how particular microbial strains or consortia can alter rumen fermentation pathways to lower methane output while preserving the health and productivity of animals. We also describe the role of probiotics and prebiotics in managing methane emissions using microbial feed additives, some recent studies involving microbial interventions have been discussed. The use of new methods involving functional metagenomics and meta-transcriptomics for exploring the rumen microbiome structure has been highlighted. This review also emphasizes the challenges faced in altering the gut microbiome and future directions in this area.},
}

@article {pmid39043190,
year = {2024},
author = {Chen, Y and Chaudhari, SN and Harris, DA and Roberts, CF and Moscalu, A and Mathur, V and Zhao, L and Tavakkoli, A and Devlin, AS and Sheu, EG},
title = {A small intestinal bile acid modulates the gut microbiome to improve host metabolic phenotypes following bariatric surgery.},
journal = {Cell host & microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2024.06.014},
pmid = {39043190},
issn = {1934-6069},
abstract = {Bariatric surgical procedures such as sleeve gastrectomy (SG) provide effective type 2 diabetes (T2D) remission in human patients. Previous work demonstrated that gastrointestinal levels of the bacterial metabolite lithocholic acid (LCA) are decreased after SG in mice and humans. Here, we show that LCA worsens glucose tolerance and impairs whole-body metabolism. We also show that taurodeoxycholic acid (TDCA), which is the only bile acid whose concentration increases in the murine small intestine post-SG, suppresses the bacterial bile acid-inducible (bai) operon and production of LCA both in vitro and in vivo. Treatment of diet-induced obese mice with TDCA reduces LCA levels and leads to microbiome-dependent improvements in glucose handling. Moreover, TDCA abundance is decreased in small intestinal tissue from T2D patients. This work reveals that TDCA is an endogenous inhibitor of LCA production and suggests that TDCA may contribute to the glucoregulatory effects of bariatric surgery.},
}

@article {pmid39043054,
year = {2024},
author = {Perdomo, A and Calle, A},
title = {Assessment of microbial communities in a dairy farm from a food safety perspective.},
journal = {International journal of food microbiology},
volume = {423},
number = {},
pages = {110827},
doi = {10.1016/j.ijfoodmicro.2024.110827},
pmid = {39043054},
issn = {1879-3460},
abstract = {Microbial communities associated with dairy farm operations have a significant influence on food safety, dairy product quality, and animal health. This study aimed to create a microbial mapping at a dairy farm to learn about their bacterial diversity, distribution, and potential dissemination pathways. The investigation included the detection of key zoonotic pathogens, enumeration of Staphylococcus aureus and Escherichia coli as indicators of typical bacterial loads in a dairy production environment, and a microbiome analysis using metagenomics. A total of 160 samples (environmental, udder swabs, feed, feces, raw milk, and water) were collected during winter (N = 80) and spring (N = 80). In winter, Cronobacter spp. were detected in four feed and two water samples; L. monocytogenes was identified in two samples, one from feces and one from a cattle mat; E. coli O157:H7 was found in two feed samples. On the other hand, during spring, Cronobacter spp. were present in four feed samples and one hallway drain, with only one feed sample testing positive for E. coli O157:H7, while L. monocytogenes was absent during the spring season. Regarding microbial counts, there was no significant difference between the two seasons (p = 0.068) for S. aureus; however, a significant difference (p = 0.025) was observed for E. coli. Environmental microbiome analysis showed the presence of Proteobacteria (46.0 %) and Firmicutes (27.2 %) as the dominant phyla during both seasons. Moraxellaceae (11.8 %) and Pseudomonadaceae (10.62 %) were notable during winter, while Lactobacillaceae (13.0 %) and Enterobacteriaceae (12.6 %) were prominent during spring. These findings offer valuable insights into microbial distribution within a dairy farm and potential risks to animal and human health through environmental cross-contamination.},
}

@article {pmid39042929,
year = {2024},
author = {Leclercq, S},
title = {Involvement of the gut microbiome-brain axis in alcohol use disorder.},
journal = {Alcohol and alcoholism (Oxford, Oxfordshire)},
volume = {59},
number = {5},
pages = {},
doi = {10.1093/alcalc/agae050},
pmid = {39042929},
issn = {1464-3502},
support = {//Fonds de la Recherche Scientifique - FNRS/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Brain-Gut Axis/physiology ; *Alcoholism/microbiology/therapy ; *Probiotics/therapeutic use ; *Fecal Microbiota Transplantation ; Prebiotics ; Animals ; Brain/metabolism ; },
abstract = {The human intestine is colonized by a variety of microorganisms that influence the immune system, the metabolic response, and the nervous system, with consequences for brain function and behavior. Unbalance in this microbial ecosystem has been shown to be associated with psychiatric disorders, and altered gut microbiome composition related to bacteria, viruses, and fungi has been well established in patients with alcohol use disorder. This review describes the gut microbiome-brain communication pathways, including the ones related to the vagus nerve, the inflammatory cytokines, and the gut-derived metabolites. Finally, the potential benefits of microbiota-based therapies for the management of alcohol use disorder, such as probiotics, prebiotics, and fecal microbiota transplantation, are also discussed.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Brain-Gut Axis/physiology
*Alcoholism/microbiology/therapy
*Probiotics/therapeutic use
*Fecal Microbiota Transplantation
Prebiotics
Animals
Brain/metabolism

@article {pmid39042424,
year = {2024},
author = {Coutry, N and Gasmi, I and Herbert, F and Jay, P},
title = {Mechanisms of intestinal dysbiosis: new insights into tuft cell functions.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2379624},
pmid = {39042424},
issn = {1949-0984},
mesh = {*Dysbiosis/microbiology ; Humans ; *Gastrointestinal Microbiome ; Animals ; *Paneth Cells/metabolism ; Symbiosis ; Bacteria/classification/metabolism/genetics ; Inflammatory Bowel Diseases/microbiology/metabolism ; Intestinal Mucosa/microbiology/metabolism ; Tuft Cells ; },
abstract = {Symbiosis between the host and intestinal microbial communities is essential for human health. Disruption in this symbiosis is linked to gastrointestinal diseases, including inflammatory bowel diseases, as well as extra-gastrointestinal diseases. Unbalanced gut microbiome or gut dysbiosis contributes in multiple ways to disease frequency, severity and progression. Microbiome taxonomic profiling and metabolomics approaches greatly improved our understanding of gut dysbiosis features; however, the precise mechanisms involved in gut dysbiosis establishment still need to be clarified. The aim of this review is to present new actors and mechanisms underlying gut dysbiosis formation following parasitic infection or in a context of altered Paneth cells, revealing the existence of a critical crosstalk between Paneth and tuft cells to control microbiome composition.},
}

*Dysbiosis/microbiology
Humans
*Gastrointestinal Microbiome
Animals
*Paneth Cells/metabolism
Symbiosis
Bacteria/classification/metabolism/genetics
Inflammatory Bowel Diseases/microbiology/metabolism
Intestinal Mucosa/microbiology/metabolism
Tuft Cells

@article {pmid39042309,
year = {2024},
author = {Hussan, H and Ali, MR and Lyo, V and Webb, A and Pietrzak, M and Zhu, J and Choueiry, F and Li, H and Cummings, BP and Marco, ML and Medici, V and Clinton, SK},
title = {Bariatric Surgery Is Associated with Lower Concentrations of Fecal Secondary Bile Acids and Their Metabolizing Microbial Enzymes: A Pilot Study.},
journal = {Obesity surgery},
volume = {},
number = {},
pages = {},
pmid = {39042309},
issn = {1708-0428},
support = {R35GM133510/GM/NIGMS NIH HHS/United States ; },
abstract = {INTRODUCTION: Excess body fat elevates colorectal cancer risk. While bariatric surgery (BRS) induces significant weight loss, its effects on the fecal stream and colon biology are poorly understood. Specifically, limited data exist on the impact of bariatric surgery (BRS) on fecal secondary bile acids (BA), including lithocholic acid (LCA), a putative promotor of colorectal carcinogenesis.

METHODS: This cross-sectional case-control study included 44 patients with obesity; 15 pre-BRS (controls) vs. 29 at a median of 24.1 months post-BRS. We examined the fecal concentrations of 11 BA by liquid chromatography and gene abundance of BA-metabolizing bacterial enzymes through fecal metagenomic sequencing. Differences were quantified using non-parametric tests for BA levels and linear discriminant analysis (LDA) effect size (LEfSe) for genes encoding BA-metabolizing enzymes.

RESULTS: Total fecal secondary BA concentrations trended towards lower levels post- vs. pre-BRS controls (p = 0.07). Individually, fecal LCA concentrations were significantly lower post- vs. pre-BRS (8477.0 vs. 11,914.0 uM/mg, p < 0.008). Consistent with this finding, fecal bacterial genes encoding BA-metabolizing enzymes, specifically 3-betahydroxycholanate-3-dehydrogenase (EC 1.1.1.391) and 3-alpha-hydroxycholanate dehydrogenase (EC 1.1.1.52), were also lower post- vs. pre-BRS controls (LDA of - 3.32 and - 2.64, respectively, adjusted p < 0.0001). Post-BRS fecal BA concentrations showed significant inverse correlations with weight loss, a healthy diet quality, and increased physical activity.

CONCLUSIONS: Concentrations of LCA, a secondary BA, and bacterial genes needed for BA metabolism are lower post-BRS. These changes can impact health and modulate the colorectal cancer cascade. Further research is warranted to examine how surgical alterations and the associated dietary changes impact bile acid metabolism.},
}

@article {pmid39042197,
year = {2024},
author = {Fine, H and Bonthu, A and Kogan, M},
title = {Integrative Geriatric Oncology: A Review of Current Practices.},
journal = {Current oncology reports},
volume = {},
number = {},
pages = {},
pmid = {39042197},
issn = {1534-6269},
abstract = {PURPOSE OF REVIEW: This article aims to offer a comprehensive review of optimal integrative medicine practices for geriatric oncology patients. Given the aging population and the global rise in cancer incidence, it is crucial to identify evidence-based modalities and employ an integrated approach to enhance cancer outcomes and quality of life in older adults.

RECENT FINDINGS: It has been predicted that 20.5% (6.9 million) of new cancer cases in 2050 will occur in adults over 80 years old.[1] The increasing focus on lifestyle factors in healthy aging has shed light on various overlooked areas of significance. Notably, anti-inflammatory diets and the promotion of a healthy gut microbiome have demonstrated significant impacts on overall health outcomes, bolstering the body's innate capacity to combat disease. This review delves into further evidence and extrapolation concerning integrative approaches and their influence on cancer outcomes and older adults quality of life. The complexity and unique nature of cancer in older adults requires a wide range of support from medical providers. Incorporating various integrative techniques as part of cancer treatment and side effect support can improve health outcomes and patient's quality of life. Familiarity with the lifestyle interventions and other topics explored in this review equips healthcare providers to offer tailored and holistic care to geriatric patients navigating cancer.},
}

@article {pmid39042150,
year = {2024},
author = {Dejonckheere, CS and Layer, JP and Schmeel, LC and Gkika, E},
title = {Identification of the skin microbiome as an emerging and modifiable risk factor for radiation dermatitis in breast cancer.},
journal = {Supportive care in cancer : official journal of the Multinational Association of Supportive Care in Cancer},
volume = {32},
number = {8},
pages = {538},
pmid = {39042150},
issn = {1433-7339},
mesh = {Humans ; *Breast Neoplasms/radiotherapy ; Female ; *Microbiota ; Risk Factors ; *Radiodermatitis/etiology ; *Skin/microbiology ; Middle Aged ; },
}

Humans
*Breast Neoplasms/radiotherapy
Female
*Microbiota
Risk Factors
*Radiodermatitis/etiology
*Skin/microbiology
Middle Aged

@article {pmid39041890,
year = {2024},
author = {Fu, E and Qian, M and He, N and Yin, Y and Liu, Y and Han, Z and Han, Z and Zhao, Q and Cao, X and Li, Z},
title = {Biomimetic Supramolecular Assembly with IGF-1C Delivery Ameliorates Inflammatory Bowel Disease (IBD) by Restoring Intestinal Barrier Integrity.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e2403075},
doi = {10.1002/advs.202403075},
pmid = {39041890},
issn = {2198-3844},
support = {U2004126//National Natural Science Foundation of China/ ; 82330066//National Natural Science Foundation of China/ ; 82270565//National Natural Science Foundation of China/ ; 81925021//National Natural Science Foundation of China/ ; 2017YFA0103200//National Key Research and Development Program of China/ ; NKYKD202203//Nankai University Eye Institute/ ; BKJ21J016//Research Project on Skin Injury & Repair/ ; TJYXZDXK-043A//Tianjin Key Medical Discipline (Specialty) Construction Project/ ; 22JCZXJC00170//Natural Science Foundation of Tianjin Municipal Science and Technology Commission/ ; 21JCZDJC00070//Natural Science Foundation of Tianjin Municipal Science and Technology Commission/ ; },
abstract = {The management of dysfunctional intestinal epithelium by promoting mucosal healing and modulating the gut microbiota represents a novel therapeutic strategy for inflammatory bowel disease (IBD). As a convenient and well-tolerated method of drug delivery, intrarectal administration may represent a viable alternative to oral administration for the treatment of IBD. Here, a biomimetic supramolecular assembly of hyaluronic acid (HA) and β-cyclodextrin (HA-β-CD) for the delivery of the C domain peptide of insulin-like growth factor-1 (IGF-1C), which gradually releases IGF-1C, is developed. It is identified that the supramolecular assembly of HA-β-CD enhances the stability and prolongs the release of IGF-1C. Furthermore, this biomimetic supramolecular assembly potently inhibits the inflammatory response, thereby restoring intestinal barrier integrity. Following HA-β-CD-IGF-1C administration, 16S rDNA sequencing reveals a significant increase in the abundance of the probiotic Akkermansia, suggesting enhanced intestinal microbiome homeostasis. In conclusion, the findings demonstrate the promise of the HA-based mimicking peptide delivery platform as a therapeutic approach for IBD. This biomimetic supramolecular assembly effectively ameliorates intestinal barrier function and intestinal microbiome homeostasis, suggesting its potential for treating IBD.},
}

@article {pmid39041801,
year = {2024},
author = {Gapp, C and Dijamentiuk, A and Mangavel, C and Callon, C and Theil, S and Revol-Junelles, A-M and Chassard, C and Borges, F},
title = {Serial fermentation in milk generates functionally diverse community lineages with different degrees of structure stabilization.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0044524},
doi = {10.1128/msystems.00445-24},
pmid = {39041801},
issn = {2379-5077},
abstract = {UNLABELLED: Microbial communities offer considerable potential for tackling environmental challenges by improving the functioning of ecosystems. Top-down community engineering is a promising strategy that could be used to obtain communities of desired function. However, the ecological factors that control the balance between community shaping and propagation are not well understood. Dairy backslopping, which consists of using part of the previous production to inoculate a new one, can be used as a model engineering approach to investigate community dynamics during serial propagations. In this study, 26 raw milk samples were serially propagated 6 times each, giving rise to 26 community lineages. Bacterial community structures were analyzed by metabarcoding, and acidification was recorded by pH monitoring. The results revealed that different types of community lineages could be obtained in terms of taxonomic composition and dynamics. Five lineages reached a repeatable community structure in a few propagation steps, with little variation between the final generations, giving rise to stable acidification kinetics. Moreover, these stabilized communities presented a high variability of structure and diverse acidification properties between community lineages. Besides, the other lineages were characterized by different levels of dynamics leading to parallel or divergent trajectories. The functional properties and dynamics of the communities were mainly related to the relative abundance and the taxonomic composition of lactic acid bacteria within the communities. These findings highlight that short-term schemes of serial fermentation can produce communities with a wide range of dynamics and that the balance between community shaping and propagation is intimately linked to community structure.

IMPORTANCE: Microbiome applications require approaches for shaping and propagating microbial communities. Shaping allows the selection of communities with desired taxonomic and functional properties, while propagation allows the production of the biomass required to inoculate the engineered communities in the target ecosystem. In top-down community engineering, where communities are obtained from a pool of mixed microorganisms by acting on environmental variables, a major challenge is to master the balance between shaping and propagation. However, the ecological factors that favor high dynamics of community structure and, conversely, those that favor stability during propagation are not well understood. In this work, short-term dairy backslopping was used to investigate the key role of the taxonomic composition and structure of bacterial communities on their dynamics. The results obtained open up interesting prospects for the biotechnological use of microbiomes, particularly in the field of dairy fermentation, to diversify approaches for injecting microbial biodiversity into cheesemaking processes.},
}

@article {pmid39041797,
year = {2024},
author = {Peña-Montenegro, TD and Kleindienst, S and Allen, AE and Eren, AM and McCrow, JP and Arnold, J and Joye, SB},
title = {Metatranscriptomic response of deep ocean microbial populations to infusions of oil and/or synthetic chemical dispersant.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0108324},
doi = {10.1128/aem.01083-24},
pmid = {39041797},
issn = {1098-5336},
abstract = {Oil spills are a frequent perturbation to the marine environment that has rapid and significant impacts on the local microbiome. Previous studies have shown that exposure to synthetic dispersant alone did not enhance heterotrophic microbial activity or oxidation rates of specific hydrocarbon components but increased the abundance of some taxa (e.g., Colwellia). In contrast, exposure to oil, but not dispersants, increased the abundance of other taxa (e.g., Marinobacter) and stimulated hydrocarbon oxidation rates. Here, we advance these findings by interpreting metatranscriptomic data from this experiment to explore how and why specific components of the microbial community responded to distinct organic carbon exposure regimes. Dispersant alone was selected for a unique community and for dominant organisms that reflected treatment- and time-dependent responses. Dispersant amendment also led to diverging functional profiles among the different treatments. Similarly, oil alone was selected for a community that was distinct from treatments amended with dispersants. The presence of oil and dispersants with added nutrients led to substantial differences in microbial responses, likely suggesting increased fitness driven by the presence of additional inorganic nutrients. The oil-only additions led to a marked increase in the expression of phages, prophages, transposable elements, and plasmids (PPTEPs), suggesting that aspects of microbial community response to oil are driven by the "mobilome," potentially through viral-associated regulation of metabolic pathways in ciliates and flagellates that would otherwise throttle the microbial community through grazing.IMPORTANCEMicrocosm experiments simulated the April 2010 Deepwater Horizon oil spill by applying oil and synthetic dispersants (Corexit EC9500A and EC9527A) to deep ocean water samples. The exposure regime revealed severe negative alterations in the treatments' heterotrophic microbial activity and hydrocarbon oxidation rates. We expanded these findings by exploring metatranscriptomic signatures of the microbial communities during the chemical amendments in the microcosm experiments. Here we report how dominant organisms were uniquely associated with treatment- and time-dependent trajectories during the exposure regimes; nutrient availability was a significant factor in driving changes in metatranscriptomic responses. Remarkable signals associated with PPTEPs showed the potential role of mobilome and viral-associated survival responses. These insights underscore the time-dependent environmental perturbations of fragile marine environments under oil and anthropogenic stress.},
}

@article {pmid39041354,
year = {2024},
author = {Wang, X and Xu, H and Qin, L and Wang, H and Jiang, Y and Liu, H and Zhang, M and Pang, R and Wu, W and Li, W},
title = {Metagenomic next-generation sequencing of cerebrospinal fluid reveals etiological and microbiological features in patients with various central nervous system infections.},
journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology},
volume = {38},
number = {14},
pages = {e23812},
doi = {10.1096/fj.202400792R},
pmid = {39041354},
issn = {1530-6860},
support = {SBGJ2018077//Health Commission of Henan Province ()/ ; },
mesh = {Humans ; Male ; Female ; Middle Aged ; *High-Throughput Nucleotide Sequencing/methods ; Adult ; *Metagenomics/methods ; Aged ; *Central Nervous System Infections/cerebrospinal fluid/microbiology/diagnosis ; Adolescent ; Biomarkers/cerebrospinal fluid ; Child ; Young Adult ; Cerebrospinal Fluid/microbiology ; Aged, 80 and over ; Child, Preschool ; Metagenome ; },
abstract = {The application of metagenomic next-generation sequencing (mNGS) in pathogens detection of cerebrospinal fluid (CSF) is limited because clinical, microbiological, and biological information are not well connected. We analyzed the 428 enrolled patients' clinical features, pathogens diagnostic efficiency of mNGS in CSF, microbial community structure and composition in CSF, and correlation of microbial and clinical biomarkers in CSF. General characteristics were unspecific but helpful in formulating a differential diagnosis. CSF mNGS has a higher detection rate (34.6%) compared to traditional methods (5.4%). mNGS detection rate was higher when the time from onset to CSF collection was ≤20 days, the CSF leukocytes count was >200 × 10[6]/L, the CSF protein concentration was >1.3 g/L, or CSF glucose concentration was ≤2.5 mmol/L in non-postoperative bacterial CNS infections (CNSi). CSF was not strictly a sterile environment, and the potential pathogens may contribute to the dysbiosis of CSF microbiome. Furthermore, clinical biomarkers were significantly relevant to CNS pathogens. Clinical data are helpful in choosing a proper opportunity to obtain an accurate result of mNGS, and can speculate whether the mNGS results are correct or not. Our study is a pioneering study exploring the CSF microbiome in different CNSIs.},
}

Humans
Male
Female
Middle Aged
*High-Throughput Nucleotide Sequencing/methods
Adult
*Metagenomics/methods
Aged
*Central Nervous System Infections/cerebrospinal fluid/microbiology/diagnosis
Adolescent
Biomarkers/cerebrospinal fluid
Child
Young Adult
Cerebrospinal Fluid/microbiology
Aged, 80 and over
Child, Preschool
Metagenome

@article {pmid39041321,
year = {2024},
author = {Liukkonen, M and Muriel, J and Martínez-Padilla, J and Nord, A and Pakanen, VM and Rosivall, B and Tilgar, V and van Oers, K and Grond, K and Ruuskanen, S},
title = {Seasonal and environmental factors contribute to the variation in the gut microbiome: A large-scale study of a small bird.},
journal = {The Journal of animal ecology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1365-2656.14153},
pmid = {39041321},
issn = {1365-2656},
support = {2020-04686//Vetenskapsrådet/ ; //Emil Aaltonen Foundation/ ; },
abstract = {Environmental variation can shape the gut microbiome, but broad/large-scale data on among and within-population heterogeneity in the gut microbiome and the associated environmental factors of wild populations is lacking. Furthermore, previous studies have limited taxonomical coverage, and knowledge about wild avian gut microbiomes is still scarce. We investigated large-scale environmental variation in the gut microbiome of wild adult great tits across the species' European distribution range. We collected fecal samples to represent the gut microbiome and used the 16S rRNA gene sequencing to characterize the bacterial gut microbiome. Our results show that gut microbiome diversity is higher during winter and that there are compositional differences between winter and summer gut microbiomes. During winter, individuals inhabiting mixed forest habitat show higher gut microbiome diversity, whereas there was no similar association during summer. Also, temperature was found to be a small contributor to compositional differences in the gut microbiome. We did not find significant differences in the gut microbiome among populations, nor any association between latitude, rainfall and the gut microbiome. The results suggest that there is a seasonal change in wild avian gut microbiomes, but that there are still many unknown factors that shape the gut microbiome of wild bird populations.},
}

@article {pmid39041052,
year = {2024},
author = {Ezenabor, EH and Adeyemi, AA and Adeyemi, OS},
title = {Gut Microbiota and Metabolic Syndrome: Relationships and Opportunities for New Therapeutic Strategies.},
journal = {Scientifica},
volume = {2024},
number = {},
pages = {4222083},
pmid = {39041052},
issn = {2090-908X},
abstract = {Since its discovery, numerous studies have shown the role of the microbiota in well-being and disease. The gut microbiota represents an essential factor that plays a multidirectional role that affects not just the gut but also other parts of the body, including the brain, endocrine system, humoral system, immune system, and metabolic pathways, as well as host-microbiome interactions. Through a comprehensive analysis of existing literature using the desktop research methodology, this review elucidates the mechanisms by which gut microbiota dysbiosis contributes to metabolic dysfunction, including obesity, dyslipidaemia, hypertension, atherosclerosis, hyperuricemia, and hyperglycaemia. Furthermore, it examines the bidirectional communication pathways between gut microbiota and host metabolism, highlighting the role of microbial-derived metabolites, immune modulation, and gut barrier integrity in shaping metabolic homeostasis. Importantly, the review identifies promising therapeutic strategies targeting the gut microbiota as potential interventions for metabolic syndrome, including probiotics, prebiotics, symbiotics, dietary modifications, and faecal microbiota transplantation. By delineating the bidirectional interactions between gut microbiota and metabolic syndrome, the review not only advances our understanding of disease pathophysiology but also underscores the potential for innovative microbiota-based interventions to mitigate the global burden of metabolic syndrome and its associated complications.},
}

@article {pmid39041015,
year = {2024},
author = {Brame, JE and Liddicoat, C and Abbott, CA and Cando-Dumancela, C and Fickling, NW and Robinson, JM and Breed, MF},
title = {Urban sports fields support higher levels of soil butyrate and butyrate-producing bacteria than urban nature parks.},
journal = {Ecology and evolution},
volume = {14},
number = {7},
pages = {e70057},
pmid = {39041015},
issn = {2045-7758},
abstract = {Butyrate-producing bacteria colonise the gut of humans and non-human animals, where they produce butyrate, a short-chain fatty acid with known health benefits. Butyrate-producing bacteria also reside in soils and soil bacteria can drive the assembly of airborne bacterial communities (the aerobiome). Aerobiomes in urban greenspaces are important reservoirs of butyrate-producing bacteria as they supplement the human microbiome, but soil butyrate producer communities have rarely been examined in detail. Here, we studied soil metagenome taxonomic and functional profiles and soil physicochemical data from two urban greenspace types: sports fields (n = 11) and nature parks (n = 22). We also developed a novel method to quantify soil butyrate and characterised the in situ activity of butyrate-producing bacteria. We show that soil butyrate was higher in sports fields than nature parks and that sports fields also had significantly higher relative abundances of the terminal butyrate production genes buk and butCoAT than nature parks. Soil butyrate positively correlated with buk gene abundance (but not butCoAT). Soil moisture (r = .50), calcium (r = -.62), iron (ρ = .54), ammonium nitrogen (ρ = .58) and organic carbon (r = .45) had the strongest soil abiotic effects on soil butyrate concentrations and iron (ρ = .56) and calcium (ρ = -.57) had the strongest soil abiotic effects on buk read abundances. Overall, our findings contribute important new insights into the role of sports fields as key exposure reservoirs of butyrate producing bacteria, with important implications for the provision of microbiome-mediated human health benefits via butyrate.},
}

@article {pmid39041013,
year = {2024},
author = {Henry, LP and Fernandez, M and Wolf, S and Abhyankar, V and Ayroles, JF},
title = {Wolbachia impacts microbiome diversity and fitness-associated traits for Drosophila melanogaster in a seasonally fluctuating environment.},
journal = {Ecology and evolution},
volume = {14},
number = {7},
pages = {e70004},
pmid = {39041013},
issn = {2045-7758},
abstract = {The microbiome contributes to many different host traits, but its role in host adaptation remains enigmatic. The fitness benefits of the microbiome often depend on ecological conditions, but theory suggests that fluctuations in both the microbiome and environment modulate these fitness benefits. Moreover, vertically transmitted bacteria might constrain the ability of both the microbiome and host to respond to changing environments. Drosophila melanogaster provides an excellent system to investigate the impacts of interactions between the microbiome and the environment. To address this question, we created field mesocosms of D. melanogaster undergoing seasonal environmental change with and without the vertically transmitted bacteria, Wolbachia pipientis. Sampling temporal patterns in the microbiome revealed that Wolbachia constrained microbial diversity. Furthermore, Wolbachia and a dominant member of the microbiome, Commensalibacter, were associated with differences in two higher-order fitness traits, starvation resistance and lifespan. Our work here suggests that the interplay between the abiotic context and microbe-microbe interactions may shape key host phenotypes that underlie adaptation to changing environments. We conclude by exploring the consequences of complex interactions between Wolbachia and the microbiome for our understanding of eco-evolutionary processes that shape host-microbiome interactions.},
}

@article {pmid39041011,
year = {2024},
author = {Holt, JR and Cavichiolli de Oliveira, N and Medina, RF and Malacrinò, A and Lindsey, ARI},
title = {Insect-microbe interactions and their influence on organisms and ecosystems.},
journal = {Ecology and evolution},
volume = {14},
number = {7},
pages = {e11699},
pmid = {39041011},
issn = {2045-7758},
abstract = {Microorganisms are important associates of insect and arthropod species. Insect-associated microbes, including bacteria, fungi, and viruses, can drastically impact host physiology, ecology, and fitness, while many microbes still have no known role. Over the past decade, we have increased our knowledge of the taxonomic composition and functional roles of insect-associated microbiomes and viromes. There has been a more recent shift toward examining the complexity of microbial communities, including how they vary in response to different factors (e.g., host genome, microbial strain, environment, and time), and the consequences of this variation for the host and the wider ecological community. We provide an overview of insect-microbe interactions, the variety of associated microbial functions, and the evolutionary ecology of these relationships. We explore the influence of the environment and the interactive effects of insects and their microbiomes across trophic levels. Additionally, we discuss the potential for subsequent synergistic and reciprocal impacts on the associated microbiomes, ecological interactions, and communities. Lastly, we discuss some potential avenues for the future of insect-microbe interactions that include the modification of existing microbial symbionts as well as the construction of synthetic microbial communities.},
}

@article {pmid39040930,
year = {2024},
author = {Kumbhare, SV and Pedroso, I and Joshi, B and Muthukumar, KM and Saravanan, SK and Irudayanathan, C and Kochhar, GS and Dulai, PS and Sinha, R and Almonacid, DE},
title = {Longitudinal gut microbial signals are associated with weight loss: insights from a digital therapeutics program.},
journal = {Frontiers in nutrition},
volume = {11},
number = {},
pages = {1363079},
pmid = {39040930},
issn = {2296-861X},
abstract = {INTRODUCTION: The gut microbiome's influence on weight management has gained significant interest for its potential to support better obesity therapeutics. Patient stratification leading to personalized nutritional intervention has shown benefits over one-size-fit-all diets. However, the efficacy and impact on the gut's microbiome of personalizing weight loss diets based on individual factors remains under-investigated.

METHODS: This study assessed the impact of Digbi Health's personalized dietary and lifestyle program on weight loss and the gut microbiome end-points in 103 individuals. Participants' weight loss patterns and gut microbiome profiles were analyzed from baseline to follow-up samples.

RESULTS: Specific microbial genera, functional pathways, and communities associated with BMI changes and the program's effectiveness were identified. 80% of participants achieved weight loss. Analysis of the gut microbiome identified genera and functional pathways associated with a reduction in BMI, including Akkermansia, Christensenella, Oscillospiraceae, Alistipes, and Sutterella, short-chain fatty acid production, and degradation of simple sugars like arabinose, sucrose, and melibiose. Network analysis identified a microbiome community associated with BMI, which includes multiple taxa known for associations with BMI and obesity.

DISCUSSION: The personalized dietary and lifestyle program positively impacted the gut microbiome and demonstrated significant associations between gut microbial changes and weight loss. These findings support the use of the gut microbiome as an endpoint in weight loss interventions, highlighting potential microbiome biomarkers for further research.},
}

@article {pmid39040904,
year = {2024},
author = {Wang, C and Zhang, Y and Wang, S and Lv, X and Xu, J and Zhang, X and Yang, Q and Meng, F and Xu, B},
title = {Differential effects of domesticated and wild Capsicum frutescens L. on microbial community assembly and metabolic functions in rhizosphere soil.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1383526},
pmid = {39040904},
issn = {1664-302X},
abstract = {OBJECTIVE: Rhizosphere microorganisms play crucial roles in the growth and development of plants, disease resistance, and environmental adaptability. As the only wild pepper variety resource in China, domesticated Capsicum frutescens Linn. (Xiaomila) exhibits varying beneficial traits and affects rhizosphere microbial composition compared with its wild counterparts. In this study, we aimed to identify specific rhizosphere microbiome and metabolism patterns established during the domestication process.

METHODS: The rhizosphere microbial diversity and composition of domesticated and wild C. frutescens were detected and analyzed by metagenomics. Non-targeted metabolomics were used to explore the differences of metabolites in rhizosphere soil between wild and domesticated C. frutescens.

RESULTS: We found that the rhizosphere microbial diversity of domesticated variety was significantly different from that of the wild variety, with Massilia being its dominant bacteria. However, the abundance of certain beneficial microbes such as Gemmatimonas, Streptomyces, Rambibacter, and Lysobacter decreased significantly. The main metabolites identified in the wild variety included serylthreonine, deoxyloganic acid, vitamin C, among others. In contrast, those identified in the domesticated group were 4-hydroxy-l-glutamic acid and benzoic acid. Furthermore, the differentially enriched pathways were concentrated in tyrosine and tryptophan biosynthesis, histidine and purine-derived alkaloids biosynthesis, benzoic acid family, two-component system, etc.

CONCLUSION: This study revealed that C. frutescens established specific rhizosphere microbiota and metabolites during domestication, which has important significance for the efficient utilization of beneficial microorganisms in breeding and cultivation practices.},
}

@article {pmid39040901,
year = {2024},
author = {Lin, J and Wang, J and Feng, J and Zhu, R and Guo, Y and Dong, Y and Zhang, H and Jin, X},
title = {Changes in the ocular surface microbiome of patients with coronavirus disease 2019 (COVID-19).},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1389139},
pmid = {39040901},
issn = {1664-302X},
abstract = {PURPOSE: To elucidate the reasons behind the increased incidence of ocular disease in patients with coronavirus disease 2019 (COVID-19), this study delved deeper into the specific effects of COVID-19 on patients' ocular surface microbiome (OSM) and investigated its relationship with the increased incidence of ocular disease.

METHODS: In this study, conjunctival sac swabs were collected from 43 participants for 16S rRNA amplicon sequencing. The participants were categorized into three groups based on their COVID-19 status: the control group (C group) consisted of 15 participants who showed no evidence of COVID-19, the experimental group (E group) included 15 participants who tested positive for COVID-19, and the COVID-19 recovery period group (R group) comprised 13 participants.

RESULTS: In the comparison of alpha diversity, group E had a higher Shannon, Chao1 and Goods coverage index. When comparing beta diversity, groups E and R were more similar to each other. At the phylum level, although the OSM of the three groups was dominated by Proteobacteria, Actinobacteriota, Bacteroidota and Firmicutes, the compositional proportions were significantly different. At the genus level, the dominant species in the three OSM groups were significantly different, with Pseudomonas becoming the dominant genus in groups E and R compared to group C, and the abundance of Ralstonia decreasing significantly.

CONCLUSION: This study provides additional evidence supporting the association between the OSM and COVID-19, which contributes to our understanding of the potential mechanisms underlying ocular symptoms and complications associated with COVID-19 in the future.},
}

@article {pmid39040659,
year = {2024},
author = {van Haaps, AP and Brouns, F and Schreurs, AMF and Keszthelyi, D and Maas, JWM and Mijatovic, V},
title = {A gluten-free diet for endometriosis patients lacks evidence to recommend it.},
journal = {AJOG global reports},
volume = {4},
number = {3},
pages = {100369},
pmid = {39040659},
issn = {2666-5778},
abstract = {Endometriosis is an estrogen-dependent chronic disease characterized by the presence of endometriumlike tissue outside the uterus and is often associated with symptoms, such as dysmenorrhea, dysuria, dyschezia, chronic pelvic pain, and infertility. Moreover, women diagnosed with endometriosis can report gastrointestinal symptoms, including bloating, constipation or diarrhea, and abdominal cramping, which can be associated with irritable bowel syndrome and can result in the misdiagnosis of endometriosis as irritable bowel syndrome at first. Treatment usually involves hormonal therapy, pain management, surgery, and/or assisted reproductive techniques in case of infertility. Nonetheless, these treatment methods can be insufficient for alleviating symptoms or can have unacceptable side effects, leading to noncompliance. Therefore, women often apply self-management strategies, including dietary interventions. One of the diets frequently suggested as a tool to manage endometriosis-related symptoms on social media and patient forums is a gluten-free diet. Although a gluten-free diet has been proven effective in managing nonceliac wheat sensitivity or celiac disease, its effectiveness in endometriosis remains uncertain. The Nurses' Health Study II found it unlikely that gluten intake was a strong factor in endometriosis etiology and symptomatology. To the best of our knowledge, the most frequently cited and sole published intervention study on the efficacy of a gluten-free diet for endometriosis has several important limiting factors, including the absence of a control group. In addition, gluten consumption is highly susceptible to a placebo effect and a nocebo effect, where women might experience symptom relief after eliminating gluten and return of symptoms after they consume gluten again, solely because they believe that gluten is bad for them. Despite the inverse association between body mass index and endometriosis and between a gluten-free diet and increased body mass index, this is an association, and no causality was proven. In addition, other factors should be taken into consideration. Of note, a gluten-free diet is expensive, has limited availability, and has a significant effect on quality of life. Moreover, without proper dietary guidance, it may adversely affect the gastrointestinal microbiome. Therefore, scientifically substantiated advice regarding the use of a gluten-free diet for endometriosis-related symptoms is currently not available, and a gluten-free diet should be discouraged unless there is an additional diagnosis of nonceliac wheat sensitivity or celiac disease.},
}

@article {pmid39040604,
year = {2024},
author = {Hasan, Z and Netherland, M and Hasan, NA and Begum, N and Yasmin, M and Ahmed, S},
title = {An insight into the vaginal microbiome of infertile women in Bangladesh using metagenomic approach.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1390088},
pmid = {39040604},
issn = {2235-2988},
mesh = {Humans ; Female ; *Vagina/microbiology ; *Metagenomics/methods ; *Infertility, Female/microbiology ; Adult ; *Microbiota/genetics ; Bangladesh ; *Bacteria/classification/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Metagenome ; Young Adult ; Lactobacillus/isolation & purification/genetics/classification ; Dysbiosis/microbiology ; Phylogeny ; },
abstract = {INTRODUCTION: The dysbiosis of vaginal microbiota is recognized as a potential underlying factor contributing to infertility in women. This study aimed to compare the vaginal microbiomes of infertile and fertile women to investigate their relationship with infertility.

METHODS: Metagenomic analysis was conducted on samples from 5 infertile and 5 fertile individuals using both amplicon 16S and metagenomics shotgun sequencing methods.

RESULTS AND DISCUSSION: In the infertile group, the bacterial community was primarily represented by three major bacterial genera: Lactobacillus (79.42%), Gardnerella (12.56%) and Prevotella (3.33%), whereas, the fertile group exhibited a more diverse composition with over 8 major bacterial genera, accompanied by significantly reduced abundance of Lactobacillus (48.79%) and Gardnerella (6.98%). At the species level, higher abundances of L. iners, L. gasseri and G. vaginalis were observed in the infertile group. Regarding the microbiome composition, only one fertile and two infertile subjects exhibited the healthiest Community State Types, CST-1, while CST-3 was observed among two infertile and one fertile subject, and CST-4 in three other fertile and one infertile subject. Overall, alpha diversity metrics indicated greater diversity and lower species richness in the control (fertile) group, while the infertile group displayed the opposite trend. However, beta-diversity analysis did not show distinct clustering of samples associated with any specific group; instead, it demonstrated CST-type specific clustering. Shotgun metagenomics further confirmed the dominance of Firmicutes, with a greater abundance of Lactobacillus species in the infertile group. Specifically, L. iners and G. vaginalis were identified as the most dominant and highly abundant in the infertile group. Fungi were only identified in the control group, dominated by Penicillium citrinum (62.5%). Metagenome-assembled genomes (MAGs) corroborated read-based taxonomic profiling, with the taxon L. johnsonii identified exclusively in disease samples. MAG identities shared by both groups include Shamonda orthobunyavirus, L. crispatus, Human endogenous retrovirus K113, L. iners, and G. vaginalis. Interestingly, the healthy microbiomes sequenced in this study contained two clusters, Penicillium and Staphylococcus haemolyticus, not found in the public dataset. In conclusion, this study suggests that lower species diversity with a higher abundance of L. iners, L. gasseri and G. vaginalis, may contribute to female infertility in our study datasets. However, larger sample sizes are necessary to further evaluate such association.},
}

Humans
Female
*Vagina/microbiology
*Metagenomics/methods
*Infertility, Female/microbiology
Adult
*Microbiota/genetics
Bangladesh
*Bacteria/classification/genetics/isolation & purification
RNA, Ribosomal, 16S/genetics
Metagenome
Young Adult
Lactobacillus/isolation & purification/genetics/classification
Dysbiosis/microbiology
Phylogeny

@article {pmid39040376,
year = {2024},
author = {Chen, X and Mei, XY and Ren, ZM and Chen, SS and Tong, YL and Zhang, CP and Chen, J and Dai, GH},
title = {Comprehensive insights into berberine's hypoglycemic mechanisms: A focus on ileocecal microbiome in db/db mice.},
journal = {Heliyon},
volume = {10},
number = {13},
pages = {e33704},
pmid = {39040376},
issn = {2405-8440},
abstract = {The efficacy of berberine in managing diabetes through modulation of gut microbiome has been established through fecal sample analyses. However, relying solely on fecal materials constrains our comprehension of berberine's effects on diverse gastrointestinal locations. This study specifically explores the ileocecal region, a segment characterized by higher microbial diversity than fecal samples. Berberine exhibits a robust hypoglycemic impact by significantly reducing glucose levels in blood and urine. Beyond glycemic control, berberine ameliorates various diabetes-related symptoms in serum, including increased insulin and leptin, but decreased NEFA and MDA. Notably, berberine demonstrates liver-protective functions by alleviating oxidative stress and enhancing hepatic glycogen abundance. These outcomes prompted a high-throughput sequencing analysis of the ileocecal microbiome, revealing an augmentation of beneficial bacterial genera (four genera in the Lachnospiraceae family, Erysipelatoclostridium, and Escherichia-Shigella), along with a reduction in harmful bacterial genera (Romboutsia). Additionally, we predicted the impact of the ileocecal microbiome on clinically relevant factors associated with diabetes. These findings elucidate the multi-pathway mechanisms of berberine in treating T2D, underscoring its potential as a natural anti-diabetic agent or functional food, particularly through the modulation of the gut microbiota.},
}

@article {pmid39040169,
year = {2024},
author = {Carvajal, LP and Rincon, S and Gomez-Villegas, SI and Matiz-González, JM and Ordoñez, K and Santamaria, A and Ospina-Navarro, L and Beltran, J and Guevara, F and Mendez, YR and Salcedo, S and Porras, A and Valencia-Moreno, A and Grennia, H and Deyanov, A and Baptista, R and Tam, VH and Panesso, D and Tran, TT and Miller, WR and Arias, CA and Reyes, J},
title = {Prevalence of the Cefazolin Inoculum Effect (CzIE) in Nasal Colonizing Methicillin-Susceptible Staphylococcus aureus in Patients from Intensive Care Units in Colombia and Use of a Modified Rapid Nitrocefin Test for Detection.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
pmid = {39040169},
abstract = {The cefazolin inoculum effect (CzIE) has been associated with poor clinical outcomes in patients with MSSA infections. We aimed to investigate the point prevalence of the CzIE among nasal colonizing MSSA isolates from ICU patients in a multicenter study in Colombia (2019-2023). Patients underwent nasal swabs to assess for S. aureus colonization on admission to the ICU and some individuals had follow-up swabs. We performed cefazolin MIC by broth-microdilution using standard and high-inoculum and developed a modified nitrocefin-based rapid test to detect the CzIE. Whole genome sequencing was carried out to characterize BlaZ types and allotypes, phylogenomics and Agr-typing. All swabs were subjected to 16S-rRNA metabarcoding sequencing to evaluate microbiome characteristics associated with the CzIE. A total of 352 patients were included; 46/352 (13%) patients were colonized with S. aureus ; 22% (10/46) and 78% (36/46) with MRSA and MSSA, respectively. Among 36 patients that contributed with 43 MSSA colonizing isolates, 21/36 (58%) had MSSA exhibiting the CzIE. BlaZ type A and BlaZ-2 were the predominant type and allotype in 56% and 52%, respectively. MSSA belonging to CC30 were highly associated with the CzIE and SNP analyses supported transmission of MSSA exhibiting the CzIE among some patients of the same unit. The modified nitrocefin rapid test had 100%, 94.4% and 97.7% sensitivity, specificity and accuracy, respectively. We found a high prevalence point prevalence of the CzIE in MSSA colonizing the nares of critically-ill patients in Colombia. A modified rapid test was highly accurate in detecting the CzIE in this patient population.},
}

@article {pmid39040076,
year = {2024},
author = {Onwuka, S and Bravo-Merodio, L and Gkoutos, GV and Acharjee, A},
title = {Explainable AI-prioritized plasma and fecal metabolites in inflammatory bowel disease and their dietary associations.},
journal = {iScience},
volume = {27},
number = {7},
pages = {110298},
pmid = {39040076},
issn = {2589-0042},
abstract = {Fecal metabolites effectively discriminate inflammatory bowel disease (IBD) and show differential associations with diet. Metabolomics and AI-based models, including explainable AI (XAI), play crucial roles in understanding IBD. Using datasets from the UK Biobank and the Human Microbiome Project Phase II IBD Multi'omics Database (HMP2 IBDMDB), this study uses multiple machine learning (ML) classifiers and Shapley additive explanations (SHAP)-based XAI to prioritize plasma and fecal metabolites and analyze their diet correlations. Key findings include the identification of discriminative metabolites like glycoprotein acetyl and albumin in plasma, as well as nicotinic acid metabolites andurobilin in feces. Fecal metabolites provided a more robust disease predictor model (AUC [95%]: 0.93 [0.87-0.99]) compared to plasma metabolites (AUC [95%]: 0.74 [0.69-0.79]), with stronger and more group-differential diet-metabolite associations in feces. The study validates known metabolite associations and highlights the impact of IBD on the interplay between gut microbial metabolites and diet.},
}

@article {pmid39040013,
year = {2024},
author = {Sasidharan Pillai, S and Gagnon, CA and Foster, C and Ashraf, AP},
title = {Exploring the Gut Microbiota: Key Insights into Its Role in Obesity, Metabolic Syndrome, and Type 2 Diabetes.},
journal = {The Journal of clinical endocrinology and metabolism},
volume = {},
number = {},
pages = {},
doi = {10.1210/clinem/dgae499},
pmid = {39040013},
issn = {1945-7197},
abstract = {The gut microbiota (GM), comprising trillions of microorganisms in the gastrointestinal tract, is a key player in the development of obesity and related metabolic disorders, such as type 2 diabetes (T2D), metabolic syndrome (MS), and cardiovascular diseases. This mini-review delves into the intricate roles and mechanisms of the GM in these conditions, offering insights into potential therapeutic strategies targeting the microbiota. The review elucidates the diversity and development of the human GM, highlighting its pivotal functions in host physiology, including nutrient absorption, immune regulation, and energy metabolism. Studies show that GM dysbiosis is linked to increased energy extraction, altered metabolic pathways, and inflammation, contributing to obesity, MS, and T2D. The interplay between dietary habits and GM composition is explored, underscoring the influence of diet on microbial diversity and metabolic functions. Additionally, the review addresses the impact of common medications and therapeutic interventions like fecal microbiota transplantation on GM composition. The evidence so far advocates for further research to delineate the therapeutic potential of GM modulation in mitigating obesity and metabolic diseases, emphasizing the necessity of clinical trials to establish effective and sustainable treatment protocols.},
}

@article {pmid39039570,
year = {2024},
author = {He, M and Zhao, N and Satten, GA},
title = {MIDASim: a fast and simple simulator for realistic microbiome data.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {135},
pmid = {39039570},
issn = {2049-2618},
support = {R01 GM147162/GM/NIGMS NIH HHS/United States ; R01GM147162/NH/NIH HHS/United States ; R01GM141074/NH/NIH HHS/United States ; },
mesh = {Humans ; *Microbiota ; *Computer Simulation ; Gastrointestinal Microbiome ; Software ; Computational Biology/methods ; Bacteria/classification/genetics/isolation & purification ; Female ; },
abstract = {BACKGROUND: Advances in sequencing technology has led to the discovery of associations between the human microbiota and many diseases, conditions, and traits. With the increasing availability of microbiome data, many statistical methods have been developed for studying these associations. The growing number of newly developed methods highlights the need for simple, rapid, and reliable methods to simulate realistic microbiome data, which is essential for validating and evaluating the performance of these methods. However, generating realistic microbiome data is challenging due to the complex nature of microbiome data, which feature correlation between taxa, sparsity, overdispersion, and compositionality. Current methods for simulating microbiome data are deficient in their ability to capture these important features of microbiome data, or can require exorbitant computational time.

METHODS: We develop MIDASim (MIcrobiome DAta Simulator), a fast and simple approach for simulating realistic microbiome data that reproduces the distributional and correlation structure of a template microbiome dataset. MIDASim is a two-step approach. The first step generates correlated binary indicators that represent the presence-absence status of all taxa, and the second step generates relative abundances and counts for the taxa that are considered to be present in step 1, utilizing a Gaussian copula to account for the taxon-taxon correlations. In the second step, MIDASim can operate in both a nonparametric and parametric mode. In the nonparametric mode, the Gaussian copula uses the empirical distribution of relative abundances for the marginal distributions. In the parametric mode, a generalized gamma distribution is used in place of the empirical distribution.

RESULTS: We demonstrate improved performance of MIDASim relative to other existing methods using gut and vaginal data. MIDASim showed superior performance by PERMANOVA and in terms of alpha diversity and beta dispersion in either parametric or nonparametric mode. We also show how MIDASim in parametric mode can be used to assess the performance of methods for finding differentially abundant taxa in a compositional model.

CONCLUSIONS: MIDASim is easy to implement, flexible and suitable for most microbiome data simulation situations. MIDASim has three major advantages. First, MIDASim performs better in reproducing the distributional features of real data compared to other methods, at both the presence-absence level and the relative-abundance level. MIDASim-simulated data are more similar to the template data than competing methods, as quantified using a variety of measures. Second, MIDASim makes few distributional assumptions for the relative abundances, and thus can easily accommodate complex distributional features in real data. Third, MIDASim is computationally efficient and can be used to simulate large microbiome datasets. Video Abstract.},
}

Humans
*Microbiota
*Computer Simulation
Gastrointestinal Microbiome
Software
Computational Biology/methods
Bacteria/classification/genetics/isolation & purification
Female

@article {pmid39039558,
year = {2024},
author = {Dzavakwa, NV and Chisenga, M and McHugh, G and Filteau, S and Gregson, CL and Kasonka, L and Kranzer, K and Mabuda, HB and Mujuru, H and Redzo, N and Rowland-Jones, S and Schaible, UE and Simms, V and Ferrand, RA and , },
title = {Update: Vitamin D3 and calcium carbonate supplementation for adolescents with HIV to reduce musculoskeletal morbidity and immunopathology (VITALITY trial): study protocol for a randomised placebo-controlled trial.},
journal = {Trials},
volume = {25},
number = {1},
pages = {499},
pmid = {39039558},
issn = {1745-6215},
support = {RIA2018CO-2512//European and Developing Countries Clinical Trials Partnership/ ; },
mesh = {Humans ; *Cholecalciferol/administration & dosage ; Adolescent ; *HIV Infections/drug therapy ; *Bone Density/drug effects ; *Dietary Supplements ; Child ; *Calcium Carbonate/administration & dosage/therapeutic use ; Double-Blind Method ; *Randomized Controlled Trials as Topic ; Male ; Female ; Treatment Outcome ; Vitamin D Deficiency/drug therapy ; Young Adult ; Time Factors ; Age Factors ; },
abstract = {BACKGROUND: Of the 2 million children living with HIV globally, 90% live in sub-Saharan Africa. Despite antiretroviral therapy, longstanding HIV infection is associated with several chronic complications in children including growth failure, particularly stunting and delayed puberty. Vitamin D deficiency, which is highly prevalent among children living with HIV in sub-Saharan Africa, has further adverse impact on bone health. This trial aims to establish whether supplementation with vitamin D3 and calcium carbonate improves musculoskeletal health among peripubertal children living with HIV. This paper is an update to an already existing protocol that was previously published in Trials in 2022 and details changes in the trial outcomes.

METHODS/DESIGN: We will conduct an individually randomised, double-blinded, placebo-controlled trial of weekly high-dose vitamin D3 (20,000 IU) plus daily calcium carbonate (500 mg) supplementation for 48 weeks. Eight hundred and forty children living with HIV aged 11-19 years taking ART for ≥ 6 months will be enrolled and followed up for 96 weeks. The primary outcome is DXA-measured total body less-head bone mineral density Z-score (TBLH-BMD) at 48 weeks and is an update to the previous primary outcome total body less-head bone mineral content adjusted for lean mass (TBLH-BMC[LBM]) Z-score. The primary outcome was updated to address the substantial differences in distributions of TBLH-BMC[LBM] Z-score between the two sites as a result of software differences of the DXA machines. Secondary outcomes are DXA-measured TBLH-BMD Z-score adjusted for height at 48 weeks a new secondary outcome, lumbar spine bone mineral apparent density Z-score, number of respiratory infections, lean muscle mass and grip-strength at 48 and 96 weeks, and TBLH-BMD Z-score at 96 weeks. Sub-studies will investigate the effect of the intervention on vitamin D3 pathway metabolites and markers of bone turnover, intestinal microbiota, and innate and acquired immune function.

DISCUSSION: This is the largest trial to date of vitamin D supplementation in children living with HIV. Intervening to address deficits in bone accrual through childhood is critical for optimising adolescent and early adult bone health, and prevention of later adult osteoporotic fractures. Trial results will draw attention to the need to screen for and treat long-term comorbidities in children living with HIV in resource-limited settings.

TRIAL REGISTRATION: Pan African Clinical Trials Registry PACTR20200989766029. Registered on September 3, 2020. URL of trial registry record: https://pactr.samrc.ac.za TRIAL STATUS: Participant follow-up completed; data analysis ongoing.},
}

Humans
*Cholecalciferol/administration & dosage
Adolescent
*HIV Infections/drug therapy
*Bone Density/drug effects
*Dietary Supplements
Child
*Calcium Carbonate/administration & dosage/therapeutic use
Double-Blind Method
*Randomized Controlled Trials as Topic
Male
Female
Treatment Outcome
Vitamin D Deficiency/drug therapy
Young Adult
Time Factors
Age Factors

@article {pmid39039539,
year = {2024},
author = {Song, J and Zhou, D and Cui, L and Wu, C and Jia, L and Wang, M and Li, J and Ya, J and Ji, X and Meng, R},
title = {Advancing stroke therapy: innovative approaches with stem cell-derived extracellular vesicles.},
journal = {Cell communication and signaling : CCS},
volume = {22},
number = {1},
pages = {369},
pmid = {39039539},
issn = {1478-811X},
support = {82101390, 82171297, and 82001258//National Natural Science Foundation of China/ ; 82101390, 82171297, and 82001258//National Natural Science Foundation of China/ ; KM202110025020//the General Science and Technology Programme of Beijing Municipal Education Commission/ ; },
mesh = {*Extracellular Vesicles/metabolism/transplantation ; Humans ; Animals ; *Stem Cells/cytology ; *Stroke/therapy ; Stem Cell Transplantation/methods ; },
abstract = {Stroke is a leading cause of mortality and long-term disability globally, with acute ischemic stroke (AIS) being the most common subtype. Despite significant advances in reperfusion therapies, their limited time window and associated risks underscore the necessity for novel treatment strategies. Stem cell-derived extracellular vesicles (EVs) have emerged as a promising therapeutic approach due to their ability to modulate the post-stroke microenvironment and facilitate neuroprotection and neurorestoration. This review synthesizes current research on the therapeutic potential of stem cell-derived EVs in AIS, focusing on their origin, biogenesis, mechanisms of action, and strategies for enhancing their targeting capacity and therapeutic efficacy. Additionally, we explore innovative combination therapies and discuss both the challenges and prospects of EV-based treatments. Our findings reveal that stem cell-derived EVs exhibit diverse therapeutic effects in AIS, such as promoting neuronal survival, diminishing neuroinflammation, protecting the blood-brain barrier, and enhancing angiogenesis and neurogenesis. Various strategies, including targeting modifications and cargo modifications, have been developed to improve the efficacy of EVs. Combining EVs with other treatments, such as reperfusion therapy, stem cell transplantation, nanomedicine, and gut microbiome modulation, holds great promise for improving stroke outcomes. However, challenges such as the heterogeneity of EVs and the need for standardized protocols for EV production and quality control remain to be addressed. Stem cell-derived EVs represent a novel therapeutic avenue for AIS, offering the potential to address the limitations of current treatments. Further research is needed to optimize EV-based therapies and translate their benefits to clinical practice, with an emphasis on ensuring safety, overcoming regulatory hurdles, and enhancing the specificity and efficacy of EV delivery to target tissues.},
}

*Extracellular Vesicles/metabolism/transplantation
Humans
Animals
*Stem Cells/cytology
*Stroke/therapy
Stem Cell Transplantation/methods

@article {pmid39039501,
year = {2024},
author = {Ma, Y and Peng, X and Zhang, J and Zhu, Y and Huang, R and Li, G and Wu, Y and Zhou, C and You, J and Fang, S and Xiang, S and Qiu, J},
title = {Gut microbiota in preterm infants with late-onset sepsis and pneumonia: a pilot case-control study.},
journal = {BMC microbiology},
volume = {24},
number = {1},
pages = {272},
pmid = {39039501},
issn = {1471-2180},
support = {2023CR03//Clinical Research (Translation) Center of Hunan Children's Hospital, China/ ; 202206034019//Scientific Research Project of Hunan Provincial Health Commission, China/ ; 2020SK1014-3//Science and Technology Department of Hunan Province, China/ ; 2023JJ30319//The Natural Science Foundation of Hunan Province, China/ ; },
mesh = {Humans ; Case-Control Studies ; *Gastrointestinal Microbiome ; Infant, Newborn ; *Infant, Premature ; Male ; Female ; *Bacteria/classification/genetics/isolation & purification ; *RNA, Ribosomal, 16S/genetics ; *Sepsis/microbiology ; Pilot Projects ; *Pneumonia/microbiology ; Feces/microbiology ; },
abstract = {BACKGROUND: Late-onset sepsis (LOS) and pneumonia are common infectious diseases, with high morbidity and mortality in neonates. This study aimed to investigate the differences in the gut microbiota among preterm infants with LOS, or pneumonia, and full-term infants. Furthermore, this study aimed to determine whether there is a correlation between intestinal pathogenic colonization and LOS.

METHODS: In a single-center case‒control study, 16 S rRNA gene sequencing technology was used to compare gut microbiota characteristics and differences among the LOS group, pneumonia group, and control group.

RESULTS: Our study revealed that the gut microbiota in the control group was more diverse than that in the LOS group and pneumonia group (P < 0.05). No significant differences in diversity were detected between the LOS and pneumonia groups (P > 0.05). Compared with the control group, the abundances of Akkermansia, Escherichia/Shigella, and Enterococcus increased, while the abundances of Bacteroides and Stenotrophomonas decreased in the LOS and pneumonia groups. The pathogenic bacteria in infants with LOS were consistent with the distribution of the main bacteria in the intestinal microbiota. An increase in Escherichia/Shigella abundance may predict a high risk of LOS occurrence, with an area under the curve (AUC) of 0.773.

CONCLUSION: Changes in the gut microbiota composition were associated with an increased risk of LOS and pneumonia. The dominant bacteria in the gut microbiota of the LOS group were found to be associated with the causative pathogen of LOS. Moreover, preterm infants exhibiting an elevated abundance of Escherichia/Shigella may be considered potential candidates for predicting the onset of LOS.},
}

Humans
Case-Control Studies
*Gastrointestinal Microbiome
Infant, Newborn
*Infant, Premature
Male
Female
*Bacteria/classification/genetics/isolation & purification
*RNA, Ribosomal, 16S/genetics
*Sepsis/microbiology
Pilot Projects
*Pneumonia/microbiology
Feces/microbiology

@article {pmid39039462,
year = {2024},
author = {Yan, L and Ye, B and Yang, M and Shan, Y and Yan, D and Fang, D and Zhang, K and Yu, Y},
title = {Gut microbiota and metabolic changes in children with idiopathic short stature.},
journal = {BMC pediatrics},
volume = {24},
number = {1},
pages = {468},
pmid = {39039462},
issn = {1471-2431},
mesh = {Humans ; *Gastrointestinal Microbiome ; Child ; Male ; Female ; *Feces/microbiology ; Case-Control Studies ; Adolescent ; Body Height ; Growth Disorders/microbiology/metabolism ; Metabolomics/methods ; Metabolome ; },
abstract = {BACKGROUND: Idiopathic short stature (ISS) is characterized by short stature with unknown causes. Recent studies showed different gut microbiota flora and reduced fecal short-chain fatty acids in ISS children. However, the roles of the microbiome and metabolites in the pathogenesis of ISS remains largely unknown.

METHODS: We recruited 51 Chinese subjects, comprising 26 ISS children and 25 normal-height control individuals. Untargeted metabolomics was performed to explore the fecal metabolic profiles between groups. A shotgun metagenomic sequencing approach was used to investigate the microbiome at the strains level. Mediation analyses were done to reveal correlations between the height standard deviation (SD) value, the gut microbiome and metabolites.

RESULTS: We detected marked differences in the composition of fecal metabolites in the ISS group, particularly a significant increase in erucic acid and a decrease in spermidine, adenosine and L-5-Hydroxytryptophan, when compared to those of controls. We further identified specific groups of bacterial strains to be associated with the different metabolic profile. Through mediation analysis, 50 linkages were established. KEGG pathway analysis of microbiota and metabolites indicated nutritional disturbances. 13 selected features were able to accurately distinguish the ISS children from the controls (AUC = 0.933 [95%CI, 79.9-100%]) by receiver operating characteristic (ROC) analysis.

CONCLUSION: Our study suggests that the microbiome and the microbial-derived metabolites play certain roles in children's growth. These findings provide a new research direction for better understanding the mechanism(s) underlying ISS.},
}

Humans
*Gastrointestinal Microbiome
Child
Male
Female
*Feces/microbiology
Case-Control Studies
Adolescent
Body Height
Growth Disorders/microbiology/metabolism
Metabolomics/methods
Metabolome

@article {pmid39039286,
year = {2024},
author = {Kunath, BJ and De Rudder, C and Laczny, CC and Letellier, E and Wilmes, P},
title = {The oral-gut microbiome axis in health and disease.},
journal = {Nature reviews. Microbiology},
volume = {},
number = {},
pages = {},
pmid = {39039286},
issn = {1740-1534},
abstract = {The human body hosts trillions of microorganisms throughout many diverse habitats with different physico-chemical characteristics. Among them, the oral cavity and the gut harbour some of the most dense and diverse microbial communities. Although these two sites are physiologically distinct, they are directly connected and can influence each other in several ways. For example, oral microorganisms can reach and colonize the gastrointestinal tract, particularly in the context of gut dysbiosis. However, the mechanisms of colonization and the role that the oral microbiome plays in causing or exacerbating diseases in other organs have not yet been fully elucidated. Here, we describe recent advances in our understanding of how the oral and intestinal microbiota interplay in relation to their impact on human health and disease.},
}

@article {pmid39039185,
year = {2024},
author = {Gemmell, MR and Jayawardana, T and Koentgen, S and Brooks, E and Kennedy, N and Berry, S and Lees, C and Hold, GL},
title = {Optimised human stool sample collection for multi-omic microbiota analysis.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {16816},
pmid = {39039185},
issn = {2045-2322},
support = {/WT_/Wellcome Trust/United Kingdom ; Clinical PhD Studentship/WT_/Wellcome Trust/United Kingdom ; },
mesh = {Humans ; *Feces/microbiology ; *Specimen Handling/methods ; *RNA, Ribosomal, 16S/genetics ; *Gastrointestinal Microbiome/genetics ; Fatty Acids, Volatile/analysis/metabolism ; Temperature ; Microbiota/genetics ; Male ; Adult ; Metabolomics/methods ; Female ; Multiomics ; },
abstract = {To accurately define the role of the gut microbiota in health and disease pathogenesis, the preservation of stool sample integrity, in terms of microbial community composition and metabolic function, is critical. This presents a challenge for any studies which rely on participants self-collecting and returning stool samples as this introduces variability and uncertainty of sample storage/handling. Here, we tested the performance of three stool sample collection/preservation buffers when storing human stool samples at different temperatures (room temperature [20 °C], 4 °C and - 80 °C) for up to three days. We compared and quantified differences in 16S rRNA sequencing composition and short-chain fatty acid profiles compared against immediately snap-frozen stool. We found that the choice of preservation buffer had the largest effect on the resulting microbial community and metabolomic profiles. Collectively analysis confirmed that PSP and RNAlater buffered samples most closely recapitulated the microbial diversity profile of the original (immediately - 80 °C frozen) sample and should be prioritised for human stool microbiome studies.},
}

Humans
*Feces/microbiology
*Specimen Handling/methods
*RNA, Ribosomal, 16S/genetics
*Gastrointestinal Microbiome/genetics
Fatty Acids, Volatile/analysis/metabolism
Temperature
Microbiota/genetics
Male
Adult
Metabolomics/methods
Female
Multiomics

@article {pmid39039114,
year = {2024},
author = {Sørensen, J and Cuenca, A and Schmidt, JG and Madsen, SB and Iburg, TM and Madsen, L and Vendramin, N},
title = {A novel high-throughput qPCR chip for solving co-infections in RAS farmed rainbow trout.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {16802},
pmid = {39039114},
issn = {2045-2322},
support = {33111-I-17-054//European Maritime and Fisheries Fund/ ; 34009-19-1510//Grønt Udviklings- og Demonstrations Program/ ; },
mesh = {Animals ; *Oncorhynchus mykiss/virology/microbiology ; *Aquaculture/methods ; *Coinfection/microbiology/veterinary/virology ; *Fish Diseases/virology/microbiology ; Real-Time Polymerase Chain Reaction/methods ; RNA, Ribosomal, 16S/genetics ; Gills/virology/microbiology ; Microbiota/genetics ; },
abstract = {Recirculating aquaculture systems (RAS) have become more attractive due to reduced water consumption and effluent discharge. However, intensification of production increases the risk of introducing pathogens at farming sites. The emergence of uncultivable pathogens and RAS pathobiome diversity shifts the traditional disease paradigm from "one pathogen, one disease" to complex multiple-pathogen disease cases. Piscine orthoreovirus genotype 3 (PRV-3) is an excellent example, as it is capable of inducing anemia and heart pathology resembling heart and skeletal muscle inflammation under experimental conditions, and is associated with increased mortality in association with other pathogens in the field. The aim of this study was to develop a method for detection of multiple pathogens and putative pathogens, as co-infections are common in aquaculture. To do this, in the pilot study, we mapped the pathobiome of RAS-farmed rainbow trout (Oncorhynchus mykiss) (commercial RAS, farm A) using both standard diagnostic methods and metabarcording (16S rRNA) to investigate the gill microbiome. During this study, we observed infections with multiple pathogens, and detected two putative gill pathogens Candidatus Branchiomonas cysticola and Candidatus Piscichlamydia salmonis, both of which have been linked with complex gill disease in Atlantic salmon (Salmo salar). Based on the pilot study, we developed and tested a high throughput qPCR (HT-qPCR) chip targeting 22 viral and bacterial pathogens and putative pathogens, followed by a surveillance of a fish cohort in a commercial RAS farm during production (farm B). Co-infection with PRV-3 and Ca. B. cysticola combined with stress inducing management practices may explain the severe disease outbreak observed (37% mortality). The time course study sets the base for a future screening scheme for disease prediction and addresses limitations of the method when testing environmental DNA/RNA.},
}

Animals
*Oncorhynchus mykiss/virology/microbiology
*Aquaculture/methods
*Coinfection/microbiology/veterinary/virology
*Fish Diseases/virology/microbiology
Real-Time Polymerase Chain Reaction/methods
RNA, Ribosomal, 16S/genetics
Gills/virology/microbiology
Microbiota/genetics

@article {pmid39039075,
year = {2024},
author = {Stothart, MR and McLoughlin, PD and Medill, SA and Greuel, RJ and Wilson, AJ and Poissant, J},
title = {Methanogenic patterns in the gut microbiome are associated with survival in a population of feral horses.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {6012},
pmid = {39039075},
issn = {2041-1723},
support = {2016-06459//Canadian Network for Research and Innovation in Machining Technology, Natural Sciences and Engineering Research Council of Canada (NSERC Canadian Network for Research and Innovation in Machining Technology)/ ; 2019-04388//Canadian Network for Research and Innovation in Machining Technology, Natural Sciences and Engineering Research Council of Canada (NSERC Canadian Network for Research and Innovation in Machining Technology)/ ; 25046//Canada Foundation for Innovation (Fondation canadienne pour l'innovation)/ ; D20EQ-05//Morris Animal Foundation (MAF)/ ; D20EQ-05//Morris Animal Foundation (MAF)/ ; D20EQ-05//Morris Animal Foundation (MAF)/ ; },
mesh = {Animals ; Horses/microbiology ; *Gastrointestinal Microbiome/genetics ; *Feces/microbiology ; *Methane/metabolism ; Animals, Wild/microbiology ; Metagenome ; Fatty Acids, Volatile/metabolism ; Metagenomics/methods ; Male ; Female ; Canada ; },
abstract = {Gut microbiomes are widely hypothesised to influence host fitness and have been experimentally shown to affect host health and phenotypes under laboratory conditions. However, the extent to which they do so in free-living animal populations and the proximate mechanisms involved remain open questions. In this study, using long-term, individual-based life history and shallow shotgun metagenomic sequencing data (2394 fecal samples from 794 individuals collected between 2013-2019), we quantify relationships between gut microbiome variation and survival in a feral population of horses under natural food limitation (Sable Island, Canada), and test metagenome-derived predictions using short-chain fatty acid data. We report detailed evidence that variation in the gut microbiome is associated with a host fitness proxy in nature and outline hypotheses of pathogenesis and methanogenesis as key causal mechanisms which may underlie such patterns in feral horses, and perhaps, wild herbivores more generally.},
}

Animals
Horses/microbiology
*Gastrointestinal Microbiome/genetics
*Feces/microbiology
*Methane/metabolism
Animals, Wild/microbiology
Metagenome
Fatty Acids, Volatile/metabolism
Metagenomics/methods
Male
Female
Canada

@article {pmid39038938,
year = {2024},
author = {Chuang, YF and Fan, KC and Su, YY and Wu, MF and Chiu, YL and Liu, YC and Lin, CC},
title = {Precision probiotics supplement strategy in aging population based on gut microbiome composition.},
journal = {Briefings in bioinformatics},
volume = {25},
number = {4},
pages = {},
pmid = {39038938},
issn = {1477-4054},
support = {//Taiwan National Science and Technology Council/ ; MOST 110-2321-B-418//Ministry of Science and Technology/ ; MOHW111-TDU-B-221-114007//Ministry of Health and Welfare/ ; NYCU-FEMH 112DN11//FEMH-NYCU Joint Research Program/ ; },
mesh = {*Probiotics/therapeutic use/administration & dosage ; Humans ; *Gastrointestinal Microbiome ; Aged ; *Aging ; Female ; Male ; *Dietary Supplements ; Aged, 80 and over ; Middle Aged ; Lactobacillus/genetics ; Metagenomics/methods ; Bifidobacterium ; },
abstract = {With the increasing prevalence of age-related chronic diseases burdening healthcare systems, there is a pressing need for innovative management strategies. Our study focuses on the gut microbiota, essential for metabolic, nutritional, and immune functions, which undergoes significant changes with aging. These changes can impair intestinal function, leading to altered microbial diversity and composition that potentially influence health outcomes and disease progression. Using advanced metagenomic sequencing, we explore the potential of personalized probiotic supplements in 297 older adults by analyzing their gut microbiota. We identified distinctive Lactobacillus and Bifidobacterium signatures in the gut microbiota of older adults, revealing probiotic patterns associated with various population characteristics, microbial compositions, cognitive functions, and neuroimaging results. These insights suggest that tailored probiotic supplements, designed to match individual probiotic profile, could offer an innovative method for addressing age-related diseases and functional declines. Our findings enhance the existing evidence base for probiotic use among older adults, highlighting the opportunity to create more targeted and effective probiotic strategies. However, additional research is required to validate our results and further assess the impact of precision probiotics on aging populations. Future studies should employ longitudinal designs and larger cohorts to conclusively demonstrate the benefits of tailored probiotic treatments.},
}

*Probiotics/therapeutic use/administration & dosage
Humans
*Gastrointestinal Microbiome
Aged
*Aging
Female
Male
*Dietary Supplements
Aged, 80 and over
Middle Aged
Lactobacillus/genetics
Metagenomics/methods
Bifidobacterium

@article {pmid39038910,
year = {2024},
author = {Volkov, M and Kampstra, ASB and van Schie, KAJ and van Mourik, AG and Kwekkeboom, JC and de Ru, A and van Veelen, PA and Huizinga, TWJ and Toes, REM and van der Woude, D},
title = {Acetylated bacterial proteins as potent antigens inducing an anti-modified protein antibody response.},
journal = {RMD open},
volume = {10},
number = {3},
pages = {},
pmid = {39038910},
issn = {2056-5933},
mesh = {Animals ; Mice ; Acetylation ; Humans ; *B-Lymphocytes/immunology/metabolism ; Escherichia coli/immunology ; Bacterial Proteins/immunology ; Cross Reactions/immunology ; Antibody Formation/immunology ; Mice, Inbred C57BL ; Antigens, Bacterial/immunology ; Arthritis, Rheumatoid/immunology ; Receptors, Antigen, B-Cell/metabolism/immunology ; },
abstract = {OBJECTIVE: Gut-residing bacteria, such as Escherichia coli, can acetylate their proteome under conditions of amine starvation. It is postulated that the (gut) microbiome is involved in the breach of immune tolerance to modified self-proteins leading to the anti-modified protein antibodies (AMPAs), hallmarking seropositive rheumatoid arthritis (RA). Our aim was to determine whether acetylated bacterial proteins can induce AMPA responses cross-reactive to modified self-proteins and be recognised by human AMPA (hAMPA).

METHODS: E. coli bacteria were grown under amine starvation to generate endogenously acetylated bacterial proteins. Furthermore, E. coli proteins were acetylated chemically. Recognition of these proteins by hAMPA was analysed by western blotting and ELISA; recognition by B cells carrying a modified protein-reactive B cell receptor (BCR) was analysed by pSyk (Syk phosphorylation) activation assay. C57BL/6 mice were immunised with (modified) bacterial protein fractions, and sera were analysed by ELISA.

RESULTS: Chemically modified bacterial protein fractions contained high levels of acetylated proteins and were readily recognised by hAMPA and able to activate B cells carrying modified protein-reactive BCRs. Likely due to substantially lower levels of acetylation, endogenously acetylated protein fractions were not recognised by hAMPA or hAMPA-expressing B cells. Immunising mice with chemically modified protein fractions induced a strong cross-reactive AMPA response, targeting various modified antigens including citrullinated proteins.

CONCLUSIONS: Acetylated bacterial proteins are recognisable by hAMPA and are capable of inducing cross-reactive AMPA in mice. These observations provide the first conceptual evidence for a novel mechanism involving the (endogenous) acetylation of the bacterial proteome, allowing a breach of tolerance to modified proteins and the formation of cross-reactive AMPA.},
}

Animals
Mice
Acetylation
Humans
*B-Lymphocytes/immunology/metabolism
Escherichia coli/immunology
Bacterial Proteins/immunology
Cross Reactions/immunology
Antibody Formation/immunology
Mice, Inbred C57BL
Antigens, Bacterial/immunology
Arthritis, Rheumatoid/immunology
Receptors, Antigen, B-Cell/metabolism/immunology

@article {pmid39038896,
year = {2024},
author = {Zhan, X and Li, Q and Tian, P and Wang, D},
title = {The attachment factors and attachment receptors of human noroviruses.},
journal = {Food microbiology},
volume = {123},
number = {},
pages = {104591},
doi = {10.1016/j.fm.2024.104591},
pmid = {39038896},
issn = {1095-9998},
mesh = {*Norovirus/genetics/physiology ; Humans ; *Virus Attachment ; *Gastroenteritis/virology/microbiology ; *Caliciviridae Infections/virology ; Receptors, Virus/metabolism/genetics ; Animals ; Blood Group Antigens/metabolism ; Food Microbiology ; },
abstract = {Human noroviruses (HuNoVs) are the leading etiological agent causing the worldwide outbreaks of acute epidemic non-bacterial gastroenteritis. Histo-blood group antigens (HBGAs) are commonly acknowledged as cellular receptors or co-receptors for HuNoVs. However, certain genotypes of HuNoVs cannot bind with any HBGAs, suggesting potential additional co-factors and attachment receptors have not been identified yet. In addition, food items, such as oysters and lettuce, play an important role in the transmission of HuNoVs. In the past decade, a couple of attachment factors other than HBGAs have been identified and analyzed from foods and microbiomes. Attachment factors exhibit potential as inhibitors of viral binding to receptors on host cells. Therefore, it is imperative to further characterize the attachment factors for HuNoVs present in foods to effectively control the spread of HuNoVs within the food chain. This review summarizes the potential attachment factors/receptors of HuNoVs in humans, foods, and microbiome.},
}

*Norovirus/genetics/physiology
Humans
*Virus Attachment
*Gastroenteritis/virology/microbiology
*Caliciviridae Infections/virology
Receptors, Virus/metabolism/genetics
Animals
Blood Group Antigens/metabolism
Food Microbiology

@article {pmid39038855,
year = {2024},
author = {Templeman, I and Parish, E and Rimmer, J and Clarke, G and Troth, T and Goodson, MS and Soares, JW and Harding, SV},
title = {'It takes a village': deciphering the role of the gut microbiome in the health and performance of military personnel.},
journal = {BMJ military health},
volume = {},
number = {},
pages = {},
doi = {10.1136/military-2024-002746},
pmid = {39038855},
issn = {2633-3775},
abstract = {The human gut microbiome can be impacted by a range of environmental and lifestyle factors including diet, antibiotics, physical fitness and acute and chronic stressors. There is also evidence to suggest that specific compositional and/or functional features of the gut microbiome are mediators of aspects of health and performance including disease susceptibility, cognitive and physical states and the immune response. Therefore, understanding microbe-to-microbe and nutrient-to-microbe interactions in the gut and how they interact with host biology (eg, via the gut-brain axis) could enable better design of interventions aimed at modulating the gut microbiome to improve the health and performance of the military. Accordingly, this review summarises a thematic session hosted at the 6th International Conference on Soldier Physical Performance which provided an overview of military-relevant research related to the gut microbiome. It articulates a timely opportunity to leverage this rapidly advancing area to improve personnel health and military performance.},
}

@article {pmid39038849,
year = {2024},
author = {Lee, S and Portlock, T and Le Chatelier, E and Garcia-Guevara, F and Clasen, F and Oñate, FP and Pons, N and Begum, N and Harzandi, A and Proffitt, C and Rosario, D and Vaga, S and Park, J and von Feilitzen, K and Johansson, F and Zhang, C and Edwards, LA and Lombard, V and Gauthier, F and Steves, CJ and Gomez-Cabrero, D and Henrissat, B and Lee, D and Engstrand, L and Shawcross, DL and Proctor, G and Almeida, M and Nielsen, J and Mardinoglu, A and Moyes, DL and Ehrlich, SD and Uhlen, M and Shoaie, S},
title = {Global compositional and functional states of the human gut microbiome in health and disease.},
journal = {Genome research},
volume = {34},
number = {6},
pages = {967-978},
doi = {10.1101/gr.278637.123},
pmid = {39038849},
issn = {1549-5469},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Metagenome ; *Metagenomics/methods ; Machine Learning ; Fusobacterium nucleatum/genetics ; Bacteria/classification/genetics ; },
abstract = {The human gut microbiota is of increasing interest, with metagenomics a key tool for analyzing bacterial diversity and functionality in health and disease. Despite increasing efforts to expand microbial gene catalogs and an increasing number of metagenome-assembled genomes, there have been few pan-metagenomic association studies and in-depth functional analyses across different geographies and diseases. Here, we explored 6014 human gut metagenome samples across 19 countries and 23 diseases by performing compositional, functional cluster, and integrative analyses. Using interpreted machine learning classification models and statistical methods, we identified Fusobacterium nucleatum and Anaerostipes hadrus with the highest frequencies, enriched and depleted, respectively, across different disease cohorts. Distinct functional distributions were observed in the gut microbiomes of both westernized and nonwesternized populations. These compositional and functional analyses are presented in the open-access Human Gut Microbiome Atlas, allowing for the exploration of the richness, disease, and regional signatures of the gut microbiota across different cohorts.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Metagenome
*Metagenomics/methods
Machine Learning
Fusobacterium nucleatum/genetics
Bacteria/classification/genetics

@article {pmid39038635,
year = {2024},
author = {Panduga, S and Vasishta, S and Subramani, R and Vincent, S and Mutalik, S and Joshi, MB},
title = {Epidrugs in the clinical management of atherosclerosis: Mechanisms, challenges and promises.},
journal = {European journal of pharmacology},
volume = {},
number = {},
pages = {176827},
doi = {10.1016/j.ejphar.2024.176827},
pmid = {39038635},
issn = {1879-0712},
abstract = {Atherosclerosis is a complex and multigenic pathology associated with significant epigenetic reprogramming. Traditional factors (age, sex, obesity, hyperglycaemia, dyslipidaemia, hypertension) and nontraditional factors (foetal indices, microbiome alteration, clonal hematopoiesis, air pollution, sleep disorders) induce endothelial dysfunction, resulting in reduced vascular tone and increased vascular permeability, inflammation and shear stress. These factors induce paracrine and autocrine interactions between several cell types, including vascular smooth muscle cells, endothelial cells, monocytes/macrophages, dendritic cells and T cells. Such cellular interactions lead to tissue-specific epigenetic reprogramming regulated by DNA methylation, histone modifications and microRNAs, which manifests in atherosclerosis. Our review outlines epigenetic signatures during atherosclerosis, which are viewed as potential clinical biomarkers that may be adopted as new therapeutic targets. Additionally, we emphasize epigenetic modifiers referred to as 'epidrugs' as potential therapeutic molecules to correct gene expression patterns and restore vascular homeostasis during atherosclerosis. Further, we suggest nanomedicine-based strategies involving the use of epidrugs, which may selectively target cells in the atherosclerotic microenvironment and reduce off-target effects.},
}

@article {pmid39038631,
year = {2024},
author = {Cao, C and Yue, S and Lu, A and Liang, C},
title = {Host-Gut Microbiota Metabolic Interactions and Their Role in Precision Diagnosis and Treatment of Gastrointestinal Cancers.},
journal = {Pharmacological research},
volume = {207},
number = {},
pages = {107321},
doi = {10.1016/j.phrs.2024.107321},
pmid = {39038631},
issn = {1096-1186},
abstract = {The critical role of the gut microbiome in gastrointestinal cancers is becoming increasingly clear. Imbalances in the gut microbial community, referred to as dysbiosis, are linked to increased risks for various forms of gastrointestinal cancers. Pathogens like Fusobacterium and Helicobacter pylori relate to the onset of esophageal and gastric cancers, respectively, while microbes such as Porphyromonas gingivalis and Clostridium species have been associated with a higher risk of pancreatic cancer. In colorectal cancer, bacteria such as Fusobacterium nucleatum are known to stimulate the growth of tumor cells and trigger cancer-promoting pathways. On the other hand, beneficial microbes like Bifidobacteria offer a protective effect, potentially inhibiting the development of gastrointestinal cancers. The potential for therapeutic interventions that manipulate the gut microbiome is substantial, including strategies to engineer anti-tumor metabolites and employ microbiota-based treatments. Despite the progress in understanding the influence of the microbiome on gastrointestinal cancers, significant challenges remain in identifying and understanding the precise contributions of specific microbial species and their metabolic products. This knowledge is essential for leveraging the role of the gut microbiome in the development of precise diagnostics and targeted therapies for gastrointestinal cancers.},
}

@article {pmid39038544,
year = {2024},
author = {Cern, A and Skoczen, SL and Snapp, KS and Hod, A and Zilbersheid, D and Bavli, Y and Alon-Maimon, T and Bachrach, G and Wei, X and Berman, B and Yassour, M and Cedrone, E and Neun, BW and Dobrovolskaia, MA and Clogston, JD and Stern, ST and Barenholz, Y},
title = {Nano-mupirocin as tumor-targeted antibiotic: Physicochemical, immunotoxicological and pharmacokinetic characterization, and effect on gut microbiome.},
journal = {Journal of controlled release : official journal of the Controlled Release Society},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jconrel.2024.07.045},
pmid = {39038544},
issn = {1873-4995},
abstract = {Nano-mupirocin is a PEGylated nano-liposomal formulation of the antibiotic mupirocin, undergoing evaluation for treating infectious diseases and intratumor bacteria. Intratumoral microbiota play an important role in the regulation of tumor progression and therapeutic efficacy. However, antibiotic use to target intratumoral bacteria should be performed in a way that will not affect the gut microbiota, found to enable the efficacy of cancer treatments. Nano-mupirocin may offer such a selective treatment. Herein, we demonstrate the ability of Nano-mupirocin to successfully target tumor-residing Fusobacterium nucleatum without an immediate effect on the gut microbiome. In-depth characterization of this novel formulation was performed, and the main findings include: (i). the pharmacokinetic analysis of mupirocin administered as Nano-mupirocin vs mupirocin lithium (free drug) demonstrated that most of the Nano-mupirocin in plasma is liposome associated; (ii). microbiome analysis of rat feces showed no significant short-term difference between Nano-mupirocin, mupirocin lithium and controls; (iii). Nano-mupirocin was active against intratumoral F. nucleatum, a tumor promoting bacteria that accumulates in tumors of the AT3 mice model of breast cancer. These data suggest the ability of Nano-mupirocin to target tumor residing and promoting bacteria.},
}

@article {pmid39038333,
year = {2024},
author = {Kong, T and Wang, J and Chen, C},
title = {A Promising Candidate in the Treatment of Children with Bronchopneumonia: Erythromycin Plus PIP/TAZ.},
journal = {Alternative therapies in health and medicine},
volume = {},
number = {},
pages = {},
pmid = {39038333},
issn = {1078-6791},
abstract = {OBJECTIVE: To investigate the efficacy of piperacillin-tazobactam (PIP/TAZ) versus PIP/TAZ plus erythromycin in the treatment of children with bronchopneumonia, and to evaluate the influence of these treatments on inflammatory factors and intestinal flora. Assessing the impact on these parameters is crucial to provide a comprehensive understanding of the treatment effects.

METHODS: A total of 120 children with bronchial pneumonia who were treated in Yichang Central People's Hospital from April 2018 to April 2020 were randomized (1:1) either into the control group or the observation group. The control group was given PIP/TAZ treatment. The observation group was additionally treated with erythromycin on the basis of the control group. The clinical efficacy, disappearance time of main symptoms and signs, inflammatory factors, and intestinal flora before and after treatment were compared between the two groups.

RESULTS: The treatment with PIP/TAZ plus erythromycin led to a significantly higher total clinical effective rate versus PIP/TAZ alone (P < .05). PIP/TAZ plus erythromycin resulted in a shorter time taken for the disappearance of fever, cough, and pulmonary rales versus PIP/TAZ alone (P < .05). These findings suggest that the combination regimen was more effective at resolving the key clinical symptoms of bronchopneumonia in children, which is important for improving patient outcomes and reducing the duration of illness. Patients given PIP/TAZ plus erythromycin experienced lower serum levels of the inflammatory markers CRP, TNF-α, and IL-8 as compared with patients given PIP/TAZ alone (P < .05). The reduction in these inflammatory factors indicates that the addition of erythromycin may have provided greater anti-inflammatory benefits beyond the antimicrobial effects of PIP/TAZ alone. Modulating the inflammatory response is clinically significant, as excessive inflammation can contribute to lung damage and disease severity in pneumonia. Conversely, the observation group showed a higher incidence of gastrointestinal disturbances, including increased stool frequency, watery stools, and elevated stool white blood cell counts after treatment (P < .05), suggesting that the erythromycin component may have disrupted the balance of intestinal flora. Maintaining a healthy gut microbiome is important for overall health, immunity, and preventing further complications. The clinical significance of this finding is that the addition of erythromycin to the treatment regimen may have unintended adverse effects on the gut that should be carefully monitored.

CONCLUSION: PIP/TAZ plus erythromycin might be a promising candidate in the treatment of children with bronchopneumonia by significantly improving clinical outcomes, shortening the duration of key symptoms, and regulating the level of inflammatory factors. These findings suggest the combination regimen could provide greater clinical benefits compared to PIP/TAZ alone for managing pediatric bronchopneumonia. However, the addition of erythromycin also appeared to aggravate the imbalance of intestinal flora, as evidenced by the increased incidence of gastrointestinal disturbances. Maintaining a healthy gut microbiome is crucial for overall health and immunity in growing children. Therefore, clinicians must carefully weigh the potential benefits of improved antimicrobial and anti-inflammatory effects against the potential risks of disrupting the delicate gut ecosystem when considering the use of antibiotic combinations for pediatric patients. In conclusion, PIP/TAZ plus erythromycin may be a viable treatment option for children with bronchopneumonia, but clinicians should monitor for any unintended impacts on the gut flora and be prepared to make adjustments to the regimen if necessary. Careful consideration of the balance between therapeutic efficacy and preserving intestinal health is essential when prescribing antibiotic combinations, especially in the pediatric population.},
}

@article {pmid39038258,
year = {2024},
author = {Elkrief, A and Montesion, M and Sivakumar, S and Hale, C and Bowman, AS and Begüm Bektaş, A and Bradic, M and Kang, W and Chan, E and Gogia, P and Manova-Todorova, K and Mata, DA and Egger, JV and Rizvi, H and Socci, ND and Kelly, DW and Rosiek, E and Meng, F and Tam, G and Fan, N and Drilon, A and Yu, HA and Riely, GJ and Rekhtman, N and Quintanal Villalonga, Á and Dogan, S and Bhanot, U and Gönen, M and Loomis, B and Hellmann, MD and Schoenfeld, AJ and Ladanyi, M and Rudin, CM and Vanderbilt, CM},
title = {Intratumoral Escherichia Is Associated With Improved Survival to Single-Agent Immune Checkpoint Inhibition in Patients With Advanced Non-Small-Cell Lung Cancer.},
journal = {Journal of clinical oncology : official journal of the American Society of Clinical Oncology},
volume = {},
number = {},
pages = {JCO2301488},
doi = {10.1200/JCO.23.01488},
pmid = {39038258},
issn = {1527-7755},
abstract = {PURPOSE: The impact of the intratumoral microbiome on immune checkpoint inhibitor (ICI) efficacy in patients with non-small-cell lung cancer (NSCLC) is unknown. Preclinically, intratumoral Escherichia is associated with a proinflammatory tumor microenvironment and decreased metastases. We sought to determine whether intratumoral Escherichia is associated with outcome to ICI in patients with NSCLC.

PATIENTS AND METHODS: We examined the intratumoral microbiome in 958 patients with advanced NSCLC treated with ICI by querying unmapped next-generation sequencing reads against a bacterial genome database. Putative environmental contaminants were filtered using no-template controls (n = 2,378). The impact of intratumoral Escherichia detection on overall survival (OS) was assessed using univariable and multivariable analyses. The findings were further validated in an external independent cohort of 772 patients. Escherichia fluorescence in situ hybridization (FISH) and transcriptomic profiling were performed.

RESULTS: In the discovery cohort, read mapping to intratumoral Escherichia was associated with significantly longer OS (16 v 11 months; hazard ratio, 0.73 [95% CI, 0.59 to 0.92]; P = .0065) in patients treated with single-agent ICI, but not combination chemoimmunotherapy. The association with OS in the single-agent ICI cohort remained statistically significant in multivariable analysis adjusting for prognostic features including PD-L1 expression (P = .023). Analysis of an external validation cohort confirmed the association with improved OS in univariable and multivariable analyses of patients treated with single-agent ICI, and not in patients treated with chemoimmunotherapy. Escherichia localization within tumor cells was supported by coregistration of FISH staining and serial hematoxylin and eosin sections. Transcriptomic analysis correlated Escherichia-positive samples with expression signatures of immune cell infiltration.

CONCLUSION: Read mapping to potential intratumoral Escherichia was associated with survival to single-agent ICI in two independent cohorts of patients with NSCLC.},
}

@article {pmid39037918,
year = {2024},
author = {Kramer, NE and Siracusa, J and Xu, H and Barnett, L and Finnerty, MC and Guo, TL and Wagner, JJ and Leach, FE and Cummings, BS},
title = {The Brominated Flame Retardant Hexabromocyclododecane Causes Systemic Changes in Polyunsaturated Fatty Acid Incorporation in Mouse Lipids.},
journal = {Toxicological sciences : an official journal of the Society of Toxicology},
volume = {},
number = {},
pages = {},
doi = {10.1093/toxsci/kfae094},
pmid = {39037918},
issn = {1096-0929},
abstract = {Brominated flame retardants are used in many household products to reduce flammability, but often leach into the surrounding environment over time. Hexabromocyclododecane (HBCD) is one brominated flame retardant detected in human blood across the world. HBCD exposure can result in neurological problems and altered lipid metabolism, but to date the two remain unlinked. As lipids constitute ∼50% of brain dry weight, lipid metabolism plays a critical role in neuronal function and homeostasis. To determine the effect of HBCD exposure on brain lipid metabolism, young adult male C57BL/6 mice were exposed to 1 mg/kg HBCD every 3 days for 28 days. Major lipid classes were found to change across brain regions, including the membrane glycerolipids phosphatidylcholine and phosphatidylethanolamine, and sphingolipids such as hexosylceramide. In addition, saturated, monounsaturated, and polyunsaturated fatty acids were enriched within brain lipid species. To understand the source of the brain lipidomic alterations, the blood and liver lipidomes and the cecal microbiome were evaluated. The liver and blood demonstrated changes amongst multiple lipid classes, including triacylglycerol suppression, as well as altered esterified fatty acid content. Significant alterations were also detected in the cecal microbiome, with decreases in the Firmicutes to Bacteriodetes ratio, changes in beta diversity, and pathway alterations associated with metabolic pathways and amino acid biosynthesis. These data demonstrate that HBCD can induce lipidomic alterations across brain regions and organs and supports a potential role of the microbiome in these alterations.},
}

@article {pmid39037720,
year = {2024},
author = {Du, S and Bi, L and Lin, D and Zheng, XQ and Neilson, R and Zhu, D},
title = {Viral Communities Suppress the Earthworm Gut Antibiotic Resistome by Lysing Bacteria on a National Scale.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.4c03812},
pmid = {39037720},
issn = {1520-5851},
abstract = {Earthworms are critical in regulating soil processes and act as filters for antibiotic resistance genes (ARGs). Yet, the geographic patterns and main drivers of earthworm gut ARGs remain largely unknown. We collected 52 earthworm and soil samples from arable and forest ecosystems along a 3000 km transect across China, analyzing the diversity and abundance of ARGs using shotgun metagenomics. Earthworm guts harbored a lower diversity and abundance of ARGs compared to soil, resulting in a stronger distance-decay rate of ARGs in the gut. Greater deterministic assembly processes of ARGs were found in the gut than in soil. The earthworm gut had a lower frequency of co-occurrence patterns between ARGs and mobile genetic elements (MGEs) in forest than in arable systems. Viral diversity was higher in the gut compared to soil and was negatively correlated with bacterial diversity. Bacteria such as Streptomyces and Pseudomonas were potential hosts of both viruses and ARGs. Viruses had negative effects on the diversity and abundance of ARGs, likely due to the lysis on ARG-bearing bacteria. These findings provide new insights into the variations of ARGs in the earthworm gut and highlight the vital role of viruses in the regulation of ARGs in the soil ecosystem.},
}

@article {pmid39037634,
year = {2024},
author = {Elmagzoub, WA and Idris, SM and Elnaiem, MHE and Mukhtar, ME and Eltayeb, E and Bakhiet, SM and Okuni, JB and Ojok, L and El Sanousi, SM and El Wahed, AA and Gameel, AA and Eltom, KH},
title = {Faecal microbial diversity in a cattle herd infected by Mycobacterium avium subsp. paratuberculosis: a possible effect of production status.},
journal = {World journal of microbiology & biotechnology},
volume = {40},
number = {9},
pages = {276},
pmid = {39037634},
issn = {1573-0972},
support = {Project number 404935781//Deutsche Forschungsgemeinschaft/ ; },
mesh = {Animals ; Cattle ; *Mycobacterium avium subsp. paratuberculosis/isolation & purification/genetics ; *Feces/microbiology ; *Paratuberculosis/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Cattle Diseases/microbiology ; *Milk/microbiology ; *DNA, Bacterial/genetics ; Gastrointestinal Microbiome ; Female ; Bacteria/classification/genetics/isolation & purification ; Metagenomics/methods ; },
abstract = {Mycobacterium avium subsp. paratuberculosis (MAP) causes Johne's disease, or paratuberculosis (PTB) in ruminants, besides having zoonotic potential. It possibly changes the gut microbiome, but no conclusive data are available yet. This study aimed at investigating the influence of MAP on the faecal microbiome of cattle naturally infected with PTB. In a follow up period of 10 months, PTB status was investigated in a herd of dairy cattle with history of clinical cases. Each animal was tested for MAP infection using serum and milk ELISA for MAP anti-bodies and IS900 real-time PCR and recombinase polymerase amplification assays for MAP DNA in the faeces and milk monthly for 4 successive months, then a last one after 6 months. The faecal samples were subjected to 16S rDNA metagenomic analysis using Oxford Nanopore Sequencing Technology. The microbial content was compared between animal groups based on MAP positivity rate and production status. All animals were MAP positive by one or more tests, but two animals were consistently negative for MAP DNA in the faeces. In all animals, the phyla firmicutes and bacteroidetes were highly enriched with a small contribution of proteobacteria, and increased abundance of the families Oscillospiraceae, Planococcaceae, and Streptococcacaceae was noted. Animals with high MAP positivity rate showed comparable faecal microbial content, although MAP faecal positivity had no significant effect (p > 0.05) on the microbiome. Generally, richness and evenness indices decreased with increasing positivity rate. A significantly different microbial content was found between dry cows and heifers (p < 0.05). Particularly, Oscillospiraceae and Rikenellaceae were enriched in heifers, while Planococcaceae and Streptococcaceae were overrepresented in dry cows. Furthermore, abundance of 72 genera was significantly different between these two groups (p < 0.05). Changes in faecal microbiome composition were notably associated with increasing MAP shedding in the faeces. The present findings suggest a combined influence of the production status and MAP on the cattle faecal microbiome. This possibly correlates with the fate of the infection, the concern in disease control, again remains for further investigations.},
}

Animals
Cattle
*Mycobacterium avium subsp. paratuberculosis/isolation & purification/genetics
*Feces/microbiology
*Paratuberculosis/microbiology
*RNA, Ribosomal, 16S/genetics
*Cattle Diseases/microbiology
*Milk/microbiology
*DNA, Bacterial/genetics
Gastrointestinal Microbiome
Female
Bacteria/classification/genetics/isolation & purification
Metagenomics/methods

@article {pmid39037373,
year = {2024},
author = {D'Afonseca, V and Muñoz, EV and Leal, AL and Soto, PMAS and Parra-Cid, C},
title = {Implications of the microbiome and metabolic intermediaries produced by bacteria in breast cancer.},
journal = {Genetics and molecular biology},
volume = {47Suppl 1},
number = {Suppl 1},
pages = {e20230316},
pmid = {39037373},
issn = {1415-4757},
abstract = {The breast microbiome presents a diverse microbial community that could affects health and disease states, in the context of breast cancer. Sequencing technologies have allowed describing the diversity and abundance of microbial communities among individuals. The complex tumoral microenvironment that includes the microbial composition could influence tumor growth. The imbalance of diversity and abundance inside the microbial community, known as dysbiosis plays a crucial role in this context. One the most prevalent bacterial genera described in breast invasive carcinoma are Bacillus, Pseudomonas, Brevibacillus, Mycobacterium, Thermoviga, Acinetobacter, Corynebacterium, Paenibacillus, Ensifer, and Bacteroides. Paenibacills genus shows a relation with patient survival. When the Paenibacills genus increases its abundance in patients with breast cancer, the survival probability decreases. Within this dysbiotic environment, various bacterial metabolites could play a pivotal role in the progression and modulation of breast cancer. Key bacterial metabolites, such as cadaverine, lipopolysaccharides (LPS), and trimethylamine N-oxide (TMAO), have been found to exhibit potential interactions within breast tissue microenvironments. Understanding the intricate relationships between dysbiosis and these metabolites in breast cancer may open new avenues for diagnostic biomarkers and therapeutic targets. Further research is essential to unravel the specific roles and mechanisms of these microbial metabolites in breast cancer progression.},
}

@article {pmid39037318,
year = {2024},
author = {Kula, A and Stegman, N and Putonti, C},
title = {Draft genome assemblies of one Lactobacillus gasseri strain and two Lactobacillus jensenii strains isolated from voided urine samples.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0061524},
doi = {10.1128/mra.00615-24},
pmid = {39037318},
issn = {2576-098X},
abstract = {We present the draft genome for three Lactobacillus strains isolated from female urine specimens: Lactobacillus gasseri UMB1673, Lactobacillus jensenii UMB1855, and Lactobacillus jensenii UMB5069. Focusing on strains within the female urinary microbiome can provide a more well-rounded understanding of the microbial community and its influence on health and disease.},
}

@article {pmid39037307,
year = {2024},
author = {Taynton, T and Allsup, D and Barlow, G},
title = {How can we optimize antifungal use and stewardship in the treatment of acute leukemia?.},
journal = {Expert review of hematology},
volume = {},
number = {},
pages = {1-13},
doi = {10.1080/17474086.2024.2383401},
pmid = {39037307},
issn = {1747-4094},
abstract = {INTRODUCTION: The global need for antifungal stewardship is driven by spreading antimicrobial and antifungal resistance. Triazoles are the only oral and relatively well-tolerated class of antifungal medications, and usage is associated with acquired resistance and species replacement with intrinsically resistant organisms. On a per-patient basis, hematology patients are the largest inpatient consumers of antifungal drugs, but are also the most vulnerable to invasive fungal disease.

AREAS COVERED: In this review we discuss available and forthcoming antifungal drugs, antifungal prophylaxis and empiric antifungal therapy, and how a screening based and diagnostic-driven approach may be used to reduce antifungal consumption. Finally, we discuss components of an antifungal stewardship program, interventions that can be employed, and how impact can be measured. The search methodology consisted of searching PubMed for journal articles using the term antifungal stewardship plus program, intervention, performance measure or outcome before 1 January 2024.

EXPERT OPINION: Initial focus should be on implementing effective antifungal stewardship programs by developing and implementing local guidelines and using interventions, such as post-prescription review and feedback, which are known to be effective. Technologies such as microbiome analysis and machine learning may allow the development of truly individualized risk-factor-based approaches to antifungal stewardship in the future.},
}

@article {pmid39037193,
year = {2024},
author = {Zhong, HJ and Liu, AQ and Huang, DN and Zhou, ZH and Xu, SP and Wu, L and Yang, XP and Chen, Y and Hong, MF and Zhan, YQ},
title = {Exploring the impact of gut microbiota on liver health in mice and patients with Wilson disease.},
journal = {Liver international : official journal of the International Association for the Study of the Liver},
volume = {},
number = {},
pages = {},
doi = {10.1111/liv.16046},
pmid = {39037193},
issn = {1478-3231},
abstract = {BACKGROUND AND AIMS: Distinctive gut microbial profiles have been observed between patients with Wilson disease (WD) and healthy individuals. Despite this, the exact relationship and influence of gut microbiota on the advancement of WD-related liver damage remain ambiguous. This research seeks to clarify the gut microbiota characteristics in both human patients and mouse models of WD, as well as their impact on liver injury.

METHODS: Gut microbial features in healthy individuals, patients with WD, healthy mice and mice with early- and late-stage WD were analysed using 16S rRNA gene sequencing. Additionally, WD-afflicted mice underwent treatment with either an antibiotic cocktail (with normal saline as a control) or healthy microbiota (using disease microbiota as a control). The study assessed gut microbiota composition, hepatic transcriptome profiles, liver copper concentrations and hepatic pathological injuries.

RESULTS: Patients with hepatic WD and mice with WD-related liver injury displayed altered gut microbiota composition, notably with a significant reduction in Lactobacillus abundance. Additionally, the abundances of several gut genera, including Lactobacillus, Veillonella and Eubacterium coprostanoligenes, showed significant correlations with the severity of liver injury in patients with WD. In WD mice, antibiotic treatment or transplantation of healthy microbiota altered the gut microbial structure, increased Lactobacillus abundance and modified the hepatic transcriptional profile. These interventions resulted in reduced hepatic copper concentration and alleviation of WD-related liver injury.

CONCLUSIONS: Individuals and mice with pronounced WD-related liver injury exhibited shifts in gut microbial composition. Regulating gut microbiota through healthy microbiota transplantation emerges as a promising therapeutic approach for treating WD-related liver injury.},
}

@article {pmid39036494,
year = {2024},
author = {Lu, D and Yao, D and Hu, G and Zhou, J and Shen, X and Qian, L},
title = {Maternal docosahexaenoic acid supplementation during lactation improves exercise performance, enhances intestinal glucose absorption and modulates gut microbiota in weaning offspring mice.},
journal = {Frontiers in nutrition},
volume = {11},
number = {},
pages = {1423576},
pmid = {39036494},
issn = {2296-861X},
abstract = {INTRODUCTION: Intestinal dysfunction induced by weaning stress is common during breastfeeding period. Docosahexaenoic acid (DHA) is well known for promoting visual and brain development, but its effects on early intestinal development remain unknown. This study investigated the impact of maternal DHA supplementation during lactation on intestinal glucose absorption and gut microbiota in weaning offspring mice.

MATERIALS AND METHODS: Dams were supplemented with vehicle (control), 150 mg/(kg body weight · day) DHA (L-DHA), or 450 mg/(kg body weight · day) DHA (H-DHA) throughout lactation by oral administration. After weaning, pups were randomly divided into three groups for athletic analysis, microbial and proteomic analysis, biochemical analysis, 4-deoxy-4-fluoro-D-glucose (4-FDG) absorption test, and gene expression quantitation of glucose transport-associated proteins and mTOR signaling components.

RESULTS: The H-DHA group exhibited enhanced grip strength and prolonged swimming duration compared to the control group. Additionally, there were significant increases in jejunal and ileal villus height, and expanded surface area of jejunal villi in the H-DHA group. Microbial analyses revealed that maternal DHA intake increased the abundance of beneficial gut bacteria and promoted metabolic pathways linked to carbohydrate and energy metabolism. Proteomic studies indicated an increased abundance of nutrient transport proteins and enrichment of pathways involved in absorption and digestion in the H-DHA group. This group also showed higher concentrations of glucose in the jejunum and ileum, as well as elevated glycogen levels in the liver and muscles, in contrast to lower glucose levels in the intestinal contents and feces compared to the control group. The 4-FDG absorption test showed more efficient absorption after oral 4-FDG gavage in the H-DHA group. Moreover, the expressions of glucose transport-associated proteins, GLUT2 and SGLT1, and the activation of mTOR pathway were enhanced in the H-DHA group compared to the control group. The L-DHA group also showed similar but less pronounced improvements in these aspects relative to the H-DHA group.

CONCLUSION: Our findings suggested that maternal DHA supplementation during lactation improves the exercise performance, enhances the intestinal glucose absorption by increasing the expressions of glucose transporters, and beneficially alters the structure of gut microbiome in weaning offspring mice.},
}

@article {pmid39036359,
year = {2024},
author = {Rolli, E and Ghitti, E and Mapelli, F and Borin, S},
title = {Polychlorinated biphenyls modify Arabidopsis root exudation pattern to accommodate degrading bacteria, showing strain and functional trait specificity.},
journal = {Frontiers in plant science},
volume = {15},
number = {},
pages = {1429096},
pmid = {39036359},
issn = {1664-462X},
abstract = {INTRODUCTION: The importance of plant rhizodeposition to sustain microbial growth and induce xenobiotic degradation in polluted environments is increasingly recognized.

METHODS: Here the "cry-for-help" hypothesis, consisting in root chemistry remodeling upon stress, was investigated in the presence of polychlorinated biphenyls (PCBs), highly recalcitrant and phytotoxic compounds, highlighting its role in reshaping the nutritional and signaling features of the root niche to accommodate PCB-degrading microorganisms.

RESULTS: Arabidopsis exposure to 70 µM PCB-18 triggered plant-detrimental effects, stress-related traits, and PCB-responsive gene expression, reproducing PCB phytotoxicity. The root exudates of plantlets exposed for 2 days to the pollutant were collected and characterized through untargeted metabolomics analysis by liquid chromatography-mass spectrometry. Principal component analysis disclosed a different root exudation fingerprint in PCB-18-exposed plants, potentially contributing to the "cry-for-help" event. To investigate this aspect, the five compounds identified in the exudate metabolomic analysis (i.e., scopoletin, N-hydroxyethyl-β-alanine, hypoxanthine, L-arginyl-L-valine, and L-seryl-L-phenylalanine) were assayed for their influence on the physiology and functionality of the PCB-degrading strains Pseudomonas alcaliphila JAB1, Paraburkholderia xenovorans LB400, and Acinetobacter calcoaceticus P320. Scopoletin, whose relative abundance decreased in PCB-18-stressed plant exudates, hampered the growth and proliferation of strains JAB1 and P320, presumably due to its antimicrobial activity, and reduced the beneficial effect of Acinetobacter P320, which showed a higher degree of growth promotion in the scopoletin-depleted mutant f6'h1 compared to Arabidopsis WT plants exposed to PCB. Nevertheless, scopoletin induced the expression of the bph catabolic operon in strains JAB1 and LB400. The primary metabolites hypoxanthine, L-arginyl-L-valine, and L-seryl-L-phenylalanine, which increased in relative abundance upon PCB-18 stress, were preferentially used as nutrients and growth-stimulating factors by the three degrading strains and showed a variable ability to affect rhizocompetence traits like motility and biofilm formation.

DISCUSSION: These findings expand the knowledge on PCB-triggered "cry-for-help" and its role in steering the PCB-degrading microbiome to boost the holobiont fitness in polluted environments.},
}

@article {pmid39036221,
year = {2024},
author = {Saifi, F and Jeoboam, B and Demory Beckler, M and Costin, JM},
title = {The Association Between Lactational Infective Mastitis and the Microbiome: Development, Onset, and Treatments.},
journal = {Cureus},
volume = {16},
number = {6},
pages = {e62717},
pmid = {39036221},
issn = {2168-8184},
abstract = {Lactational infective mastitis (LIM) was previously thought to occur due to trapped milk causing inadequate milk drainage and consequent infection. However, advances in genome sequencing techniques have shown that the abundance of Staphylococcus aureus, Staphylococcus epidermidis, Lactobacilli species, and Bifidobacterium species in the breast milk of lactating women play a key role in the development of LIM. Recent discoveries have revealed that the breast milk microbiome is composed of bacteria and other microorganisms, which are seeded through multiple pathways and are influenced by maternal factors. An imbalance in the microbial abundance in breast milk can lead to LIM. Given that this infection can cause early termination of breastfeeding, it is imperative to discuss prevention and treatment options. The objective of this review is to highlight the pathogens involved in LIM affecting human mothers, routes of bacterial transfer, and contributing factors that may influence changes in the composition of the milk microbiota, as well as propose preventative and curative treatment options.},
}

@article {pmid39036074,
year = {2024},
author = {Montgomery, VA and Wood-Yang, AJ and Styczynski, MP and Prausnitz, MR},
title = {Feasibility of engineered Bacillus subtilis for use as a microbiome-based topical drug delivery platform.},
journal = {Bioengineering & translational medicine},
volume = {9},
number = {4},
pages = {e10645},
pmid = {39036074},
issn = {2380-6761},
abstract = {Non-adherence to medication is a major challenge in healthcare that results in worsened treatment outcomes for patients. Reducing the frequency of required administrations could improve adherence but is challenging for topical drug delivery due to the generally short residence time of topical formulations on the skin. In this study, we sought to determine the feasibility of developing a microbiome-based, long-acting, topical delivery platform using Bacillus subtilis for drug production and delivery on the skin, which was assessed using green fluorescent protein as a model heterologous protein for delivery. We developed a computational model of bacteria population dynamics on the skin and used its qualitative predictions to guide experimental design choices. Using an ex vivo pig skin model and a human skin tissue culture model, we saw persistence of delivered bacteria for multiple days and observed little evidence of cytotoxicity to human keratinocyte cells in vitro. Finally, using an in vivo mouse model, we found that the delivered bacteria persisted on the skin for at least 1 day during every-other-day application and did not appear to present safety concerns. Taken together, our results support the feasibility of using engineered B. subtilis for topical drug delivery.},
}

@article {pmid39035611,
year = {2024},
author = {Tang, J and Huang, M},
title = {Genetic causal association between gut microbiota and sepsis: Evidence from a two-sample bidirectional Mendelian randomization analysis.},
journal = {Journal of intensive medicine},
volume = {4},
number = {3},
pages = {362-367},
pmid = {39035611},
issn = {2667-100X},
abstract = {BACKGROUND: Sepsis is a severe and potentially life-threatening condition characterized by a dysregulated host response and organ dysfunction. The causal relationship between intestinal microbiota and sepsis is unclear.

METHODS: A two-sample Mendelian randomization (MR) study was performed to proxy the causal association between gut microbiota and sepsis. The genome-wide association study (GWAS) data of sepsis and gut microbiome were collected from the Integrative Epidemiology Unit (IEU) OpenGWAS, with summary-level data obtained from the UK Biobank. Five traditional methods were used to estimate the potential causal relationships between gut microbiota and sepsis, including the inverse-variance weighted method, weighted median method, MR-Egger regression, simple mode, and weighted mode. Reverse MR analysis was performed on the bacteria that were found to be causally associated with sepsis in forward MR analysis. Cochran's Q statistic was used to quantify the heterogeneity of instrumental variables.

RESULTS: The inverse-variance weighted estimate suggested that class Lentisphaeria (odds ratio [OR]=0.86, 95% confidence interval [CI]: 0.78 to 0.94, P=0.0017, q=0.1596) and order Victivallales (OR=0.86, 95% CI: 0.78 to 0.94, P=0.0017, q=0.1596) have a protective effect on sepsis. The genus Eubacterium eligens group (OR=1.34, 95% CI: 1.11 to 1.63, P=0.0029, q=0.1881) was positively associated with the risk of sepsis. Sepsis may be a significant risk factor for genus Odoribacter (OR=1.18, 95% CI: 1.10 to 1.39, P=0.0415, q=0.9849) and Phascolarctobacterium (OR=1.21, 95% CI: 1.00 to 1.46, P=0.0471, q=0.9849), but this effect was not statistically significant after false discovery rate correction. There was a suggestive association between sepsis and Faecalibacterium (OR=0.85, 95% CI: 0.73 to 0.98, P=0.0278) and Ruminococcus 1 (OR=0.85, 95% CI: 0.73 to 1.00, P=0.0439), which were not significant after false discovery rate correction (q>0.2).

CONCLUSIONS: This study found that class Lentisphaeria, order Victivallales, and genus Eubacterium eligens group may have a causal relationship with the risk of sepsis.},
}

@article {pmid39035583,
year = {2024},
author = {Nejati, M and Soheili, M and Salami, M and Khedri, M},
title = {The effect of redox bacteria on the programmed cell death-1 cancer immunotherapy.},
journal = {Research in pharmaceutical sciences},
volume = {19},
number = {2},
pages = {228-237},
pmid = {39035583},
issn = {1735-5362},
abstract = {BACKGROUND AND PURPOSE: Extracellular electron transferring (EET) or redox bacteria employ a shuttle of flavins to transfer electrons to the oxygen in the intestinal mucosa. Although clinical studies suggest that the gut microbiome modulates the efficiency of immune checkpoint therapy in patients with cancer, the modulation mechanisms have not been well-characterized yet.

EXPERIMENTAL APPROACH: In the present study, the oral gavage administration of Shewanella oneidensis MR-1 as a prototypic EET bacteria was assayed in a mouse model of lung cancer to determine the effect of EET bacterium on the efficacy of the programmed cell death protein 1 (PD1)-immune checkpoint therapy.

FINDINGS/RESULTS: It was indicated that in vitro EET from S. oneidensis was mediated by riboflavins that were supplied through extrinsic sources. Co-administration of S. oneidensis and anti-PD 1 antibodies represent better tumor remission compared to the single-administration of each one; however, no statistically significant change was observed in the tumor volume.

CONCLUSION AND IMPLICATIONS: More detailed studies are needed to definitively confirm the therapeutic effects of electrogenic bacteria in patients with cancer. Given the findings of the present study, increasing flavin compounds or EET bacteria in the intestine may provide novel strategies for modulating cancer immunotherapy.},
}

@article {pmid39035457,
year = {2024},
author = {Lin, Z and Jiang, T and Chen, M and Ji, X and Wang, Y},
title = {Gut microbiota and sleep: Interaction mechanisms and therapeutic prospects.},
journal = {Open life sciences},
volume = {19},
number = {1},
pages = {20220910},
pmid = {39035457},
issn = {2391-5412},
abstract = {Sleep is crucial for wellness, and emerging research reveals a profound connection to gut microbiota. This review explores the bidirectional relationship between gut microbiota and sleep, exploring the mechanisms involved and the therapeutic opportunities it presents. The gut-brain axis serves as a conduit for the crosstalk between gut microbiota and the central nervous system, with dysbiosis in the microbiota impairing sleep quality and vice versa. Diet, circadian rhythms, and immune modulation all play a part. Specific gut bacteria, like Lactobacillus and Bifidobacterium, enhance sleep through serotonin and gamma-aminobutyric acid production, exemplifying direct microbiome influence. Conversely, sleep deprivation reduces beneficial bacteria, exacerbating dysbiosis. Probiotics, prebiotics, postbiotics, and fecal transplants show therapeutic potential, backed by animal and human research, yet require further study on safety and long-term effects. Unraveling this intricate link paves the way for tailored sleep therapies, utilizing microbiome manipulation to improve sleep and health. Accelerated research is essential to fully tap into this promising field for sleep disorder management.},
}

@article {pmid39035444,
year = {2024},
author = {Jiang, C and Kong, D and Li, Y and Sun, J and Chen, Z and Yang, M and Cao, S and Yu, C and Wang, Z and Jiang, J and Zhu, C and Zhang, N and Sun, G and Zhang, Q},
title = {Degradation and mechanism analysis of protein macromolecules by functional bacteria in tobacco leaves.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1416734},
pmid = {39035444},
issn = {1664-302X},
abstract = {Tobacco, a crop of significant economic importance, was greatly influenced in leaf quality by protein content. However, current processing parameters fail to adequately meet the requirements for protein degradation. Microorganisms possess potential advantages for degrading proteins and enhancing the quality of tobacco leaves, and hold substantial potential in the process of curing. To effectively reduce the protein content in tobacco leaves, thereby improving the quality and safety of the tobacco leaves. In this study, tobacco leaf were used as experimental material. From these, the BSP1 strain capable of effectively degrading proteins was isolated and identified as Bacillus subtilis by 16S rDNA analysis. Furthermore, the mechanisms were analyzed by integrating microbiome, transcriptome, and metabolome. Before curing, BSP1 was applied to the surface of tobacco leaves. The results indicated that BSP1 effectively improves the activity of key enzymes and the content of related substances, thereby enhancing protein degradation. Additionally, protein degradation was achieved by regulating the diversity of the microbial community on the surface of the tobacco leaves and the ubiquitin-proteasome pathway. This study provided new strategies for extracting and utilizing functional strains from tobacco leaves, opening new avenues for enhancing the quality of tobacco leaves.},
}

@article {pmid39035441,
year = {2024},
author = {Guan, Y and Zhao, S and Li, J and Zhang, W and Guo, Z and Luo, Y and Jiang, X and Li, J and Liu, J and Chen, X and Zhao, Z and Zhang, Z},
title = {Insights from metagenomics into gut microbiome associated with acute coronary syndrome therapy.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1369478},
pmid = {39035441},
issn = {1664-302X},
abstract = {Acute coronary syndrome (ACS) is a predominant cause of mortality, and the prompt and precise identification of this condition is crucial to minimize its impact. Recent research indicates that gut microbiota is associated with the onset, progression, and treatment of ACS. To investigate its role, we sequenced the gut microbiota of 38 ACS patients before and after percutaneous coronary intervention and statin therapy at three time points, examining differential species and metabolic pathways. We observed a decrease in the abundance of Parabacteroides, Escherichia, and Blautia in patients after treatment and an increase in the abundance of Gemalla, Klebsiella variicola, Klebsiella pneumoniae, and others. Two pathways related to sugar degradation were more abundant in patients before treatment, possibly correlated with disorders of sugar metabolism and risk factors, such as hyperglycemia, insulin resistance, and insufficient insulin secretion. Additionally, seven pathways related to the biosynthesis of vitamin K2 and its homolog were reduced after treatment, suggesting that ACS patients may gradually recover after therapy. The gut microbiota of patients treated with different statins exhibited notable differences after treatment. Rosuvastatin appeared to promote the growth of anti-inflammatory bacteria while reducing pro-inflammatory bacteria, whereas atorvastatin may have mixed effects on pro-inflammatory and anti-inflammatory bacteria while increasing the abundance of Bacteroides. Our research will provide valuable insights and enhance comprehension of ACS, leading to better patient diagnosis and therapy.},
}

@article {pmid39035357,
year = {2024},
author = {Qadri, H and Shah, AH and Almilaibary, A and Mir, MA},
title = {Microbiota, natural products, and human health: exploring interactions for therapeutic insights.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1371312},
pmid = {39035357},
issn = {2235-2988},
mesh = {Humans ; *Biological Products/pharmacology/metabolism ; *Gastrointestinal Microbiome/physiology ; Bacteria/metabolism/classification ; Animals ; Host Microbial Interactions ; Symbiosis ; },
abstract = {The symbiotic relationship between the human digestive system and its intricate microbiota is a captivating field of study that continues to unfold. Comprising predominantly anaerobic bacteria, this complex microbial ecosystem, teeming with trillions of organisms, plays a crucial role in various physiological processes. Beyond its primary function in breaking down indigestible dietary components, this microbial community significantly influences immune system modulation, central nervous system function, and disease prevention. Despite the strides made in microbiome research, the precise mechanisms underlying how bacterial effector functions impact mammalian and microbiome physiology remain elusive. Unlike the traditional DNA-RNA-protein paradigm, bacteria often communicate through small molecules, underscoring the imperative to identify compounds produced by human-associated bacteria. The gut microbiome emerges as a linchpin in the transformation of natural products, generating metabolites with distinct physiological functions. Unraveling these microbial transformations holds the key to understanding the pharmacological activities and metabolic mechanisms of natural products. Notably, the potential to leverage gut microorganisms for large-scale synthesis of bioactive compounds remains an underexplored frontier with promising implications. This review serves as a synthesis of current knowledge, shedding light on the dynamic interplay between natural products, bacteria, and human health. In doing so, it contributes to our evolving comprehension of microbiome dynamics, opening avenues for innovative applications in medicine and therapeutics. As we delve deeper into this intricate web of interactions, the prospect of harnessing the power of the gut microbiome for transformative medical interventions becomes increasingly tantalizing.},
}

Humans
*Biological Products/pharmacology/metabolism
*Gastrointestinal Microbiome/physiology
Bacteria/metabolism/classification
Animals
Host Microbial Interactions
Symbiosis

@article {pmid39035305,
year = {2024},
author = {Cheng, FC and Wang, LH and Lai, YJ and Chiang, CP},
title = {The utility of microbiome (microbiota) and exosomes in dentistry.},
journal = {Journal of dental sciences},
volume = {19},
number = {3},
pages = {1313-1319},
pmid = {39035305},
issn = {2213-8862},
abstract = {The concept of the oral-systemic link is important in both basic and clinical dentistry. The microbiome (microbiota) and exosomes are two prevalent issues in the modern medical researches. The common advent of oral and general microbiological investigation originated from the initial observations of oral bacteria within the dental plaque known as oral microbiome. In addition to oral diseases related to oral microbiome, the disruption of the oral and intestinal microbiome could result in the onset of systemic diseases. In the past decade, the exosomes have emerged in the field of the medical researches as they play a role in regulating the transport of intracellular vesicles. However, with the rapid advancement of exosomes researches in recent years, oral tissues (such as dental pulp stem cells and salivary gland cells) are used as the research materials to further promote the development of regenerative medicine. This article emphasized the importance of the concept of the oral-systemic link through the examples of microbiome (microbiota) and exosomes. Through the researches related to microbiome (microbiota) and exosomes, many evidences showed that as the basic dentistry developed directly from the assistance of the basic medicine, indirectly the progress of the basic dentistry turns back to promote the development of the basic medicine, indicating the importance of the concept of the oral-systemic link. The understanding of the oral-systemic link is essential for both clinicians and medical researchers, regardless of their dental backgrounds.},
}

@article {pmid39035270,
year = {2024},
author = {Dong, X and Zhao, W and Ma, S and Li, X and Li, G and Zhang, S},
title = {Oral microbial profiles of extrinsic black tooth stain in primary dentition: A literature review.},
journal = {Journal of dental sciences},
volume = {19},
number = {3},
pages = {1369-1379},
pmid = {39035270},
issn = {2213-8862},
abstract = {The extrinsic black tooth stain (EBS) is commonly found in primary dentition. Patients cannot clean the EBS; this can only be done by professional scaling and debridement. It also has a tendency to reform, which significantly compromises children's aesthetics and even affects their quality of life. However, there is no conclusive evidence on the etiology of the EBS. The associations between the EBS and related oral microbial features is one of the research hot topics. No literature review summarized these research progresses in this area. Therefore, we reviewed the literature on the microbiology of the EBS since 1931 and reported as the following 5 aspects: molecular biotechnology, morphological structure and physiochemical characteristics, microbial etiology hypothesis and core microbial characteristics. The EBS is a special dental plaque mainly composed of Gram-positive bacilli and cocci with scattered calcium deposits that acquired salivary pellicle activates. Early studies showed that the Actinomyces was the main pathogenic bacteria. With advances in biological research techniques, the 'core microbiome' was proposed. The potential pathogenic genera were Actinomyces, Prevotella nigrescens, Pseudotropinibacterium, Leptotrichia, Neisseria and Rothia. However, the pathogenic species of the above genera were still unclear. Currently, it is believed that the EBS consists of iron compounds or black substances that oral bacterial metabolism produces or that the bacterial metabolites formed after chemical reactions in the micro-ecological environment.},
}

@article {pmid39035190,
year = {2024},
author = {Kiseleva, YV and Zharikova, TS and Maslennikov, RV and Temirbekov, SM and Olsufieva, AV and Polyakova, OL and Pontes-Silva, A and Zharikov, YO},
title = {Gut Microbiota and Liver Regeneration: A Synthesis of Evidence on Structural Changes and Physiological Mechanisms.},
journal = {Journal of clinical and experimental hepatology},
volume = {14},
number = {6},
pages = {101455},
pmid = {39035190},
issn = {0973-6883},
abstract = {Liver regeneration (LR) is a unique biological process with the ability to restore up to 70% of the organ. This allows for the preservation of liver resections for various liver tumors and for living donor liver transplantation (LDLT). However, in some cases, LR is insufficient and interventions that can improve LR are urgently needed. Gut microbiota (GM) is one of the factors influencing LR, as the liver and intestine are intimately connected through the gut-liver axis. Thus, healthy GM facilitates normal LR, whereas dysbiosis leads to impaired LR due to imbalance of bile acids, inflammatory cytokines, microbial metabolites, signaling pathways, etc. Therefore, GM can be considered as a new possible therapeutic target to improve LR. In this review, we critically observe the current knowledge about the influence of gut microbiota (GM) on liver regeneration (LR) and the possibility to improve this process, which may reduce complication and mortality rates after liver surgery. Although much research has been done on this topic, more clinical trials and systemic reviews are urgently needed to move this type of intervention from the experimental phase to the clinical field.},
}

@article {pmid39034917,
year = {2024},
author = {Verhaar, BJH and Wijdeveld, M and Wortelboer, K and Rampanelli, E and Levels, JHM and Collard, D and Cammenga, M and Nageswaran, V and Haghikia, A and Landmesser, U and Li, XS and DiDonato, JA and Hazen, SL and Garrelds, IM and Danser, AHJ and van den Born, BH and Nieuwdorp, M and Muller, M},
title = {Effects of Oral Butyrate on Blood Pressure in Patients With Hypertension: A Randomized, Placebo-Controlled Trial.},
journal = {Hypertension (Dallas, Tex. : 1979)},
volume = {},
number = {},
pages = {},
doi = {10.1161/HYPERTENSIONAHA.123.22437},
pmid = {39034917},
issn = {1524-4563},
abstract = {BACKGROUND: The microbiota-derived short chain fatty acid butyrate has been shown to lower blood pressure (BP) in rodent studies. Nonetheless, the net effect of butyrate on hypertension in humans remains uncovered. In this study, for the first time, we aimed to determine the effect of oral butyrate on BP in patients with hypertension.

METHODS: We performed a double-blind randomized placebo-controlled trial including 23 patients with hypertension. Antihypertensive medication was discontinued for the duration of the study with a washout period of 4 weeks before starting the intervention. Participants received daily oral capsules containing either sodium butyrate or placebo with an equivalent dosage of sodium chloride for 4 weeks. The primary outcome was daytime 24-hour systolic BP. Differences between groups over time were assessed using linear mixed models (group-by-time interaction).

RESULTS: Study participants (59.0±3.7 years; 56.5% female) had an average baseline office systolic BP of 143.5±14.6 mm Hg and diastolic BP of 93.0±8.3 mm Hg. Daytime 24-hour systolic and diastolic BP significantly increased over the intervention period in the butyrate compared with the placebo group, with an increase of +9.63 (95% CI, 2.02-17.20) mm Hg in daytime 24-hour systolic BP and +5.08 (95% CI, 1.34-8.78) mm Hg in diastolic BP over 4 weeks. Butyrate levels significantly increased in plasma, but not in feces, upon butyrate intake, underscoring its absorption.

CONCLUSIONS: Four-week treatment with oral butyrate increased daytime systolic and diastolic BP in subjects with hypertension. Our findings implicate that butyrate does not have beneficial effects on human hypertension, which warrants caution in future butyrate intervention studies.

REGISTRATION: URL: https://clinicaltrialregister.nl/nl/trial/22936; Unique identifier: NL8924.},
}

@article {pmid39034613,
year = {2024},
author = {Krigul, KL and Feeney, RH and Wongkuna, S and Aasmets, O and Holmberg, SM and Andreson, R and Puértolas-Balint, F and Pantiukh, K and Sootak, L and Org, T and Tenson, T and Org, E and Schroeder, BO},
title = {A history of repeated antibiotic usage leads to microbiota-dependent mucus defects.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2377570},
doi = {10.1080/19490976.2024.2377570},
pmid = {39034613},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; Animals ; *Anti-Bacterial Agents/pharmacology ; Mice ; *Fecal Microbiota Transplantation ; *Mucus/metabolism/microbiology ; *Bacteria/classification/genetics/drug effects/isolation & purification/metabolism ; Intestinal Mucosa/microbiology/metabolism/drug effects ; Male ; Female ; Feces/microbiology ; Adult ; Middle Aged ; Akkermansia ; Mice, Inbred C57BL ; Colon/microbiology ; Bacteroides fragilis/drug effects ; },
abstract = {Recent evidence indicates that repeated antibiotic usage lowers microbial diversity and ultimately changes the gut microbiota community. However, the physiological effects of repeated - but not recent - antibiotic usage on microbiota-mediated mucosal barrier function are largely unknown. By selecting human individuals from the deeply phenotyped Estonian Microbiome Cohort (EstMB), we here utilized human-to-mouse fecal microbiota transplantation to explore long-term impacts of repeated antibiotic use on intestinal mucus function. While a healthy mucus layer protects the intestinal epithelium against infection and inflammation, using ex vivo mucus function analyses of viable colonic tissue explants, we show that microbiota from humans with a history of repeated antibiotic use causes reduced mucus growth rate and increased mucus penetrability compared to healthy controls in the transplanted mice. Moreover, shotgun metagenomic sequencing identified a significantly altered microbiota composition in the antibiotic-shaped microbial community, with known mucus-utilizing bacteria, including Akkermansia muciniphila and Bacteroides fragilis, dominating in the gut. The altered microbiota composition was further characterized by a distinct metabolite profile, which may be caused by differential mucus degradation capacity. Consequently, our proof-of-concept study suggests that long-term antibiotic use in humans can result in an altered microbial community that has reduced capacity to maintain proper mucus function in the gut.},
}

Humans
*Gastrointestinal Microbiome/drug effects
Animals
*Anti-Bacterial Agents/pharmacology
Mice
*Fecal Microbiota Transplantation
*Mucus/metabolism/microbiology
*Bacteria/classification/genetics/drug effects/isolation & purification/metabolism
Intestinal Mucosa/microbiology/metabolism/drug effects
Male
Female
Feces/microbiology
Adult
Middle Aged
Akkermansia
Mice, Inbred C57BL
Colon/microbiology
Bacteroides fragilis/drug effects

@article {pmid39034349,
year = {2024},
author = {Zhuang, Y and Liu, S and Gao, D and Xu, Y and Jiang, W and Chen, T and Xiao, J and Wang, J and Hou, G and Li, S and Zhao, X and Huang, Y and Li, S and Zhang, S and Li, M and Wang, W and Li, S and Cao, Z},
title = {The Bifidobacterium-dominated fecal microbiome in dairy calves shapes the characteristic growth phenotype of host.},
journal = {NPJ biofilms and microbiomes},
volume = {10},
number = {1},
pages = {59},
pmid = {39034349},
issn = {2055-5008},
mesh = {Animals ; *Feces/microbiology ; Cattle ; *RNA, Ribosomal, 16S/genetics ; *Bifidobacterium/genetics/growth & development ; *Gastrointestinal Microbiome ; Mice ; *Fecal Microbiota Transplantation/methods ; Phenotype ; Probiotics/administration & dosage ; Phylogeny ; DNA, Bacterial/genetics ; },
abstract = {The dominant bacteria in the hindgut of calves play an important role in their growth and health, which could even lead to lifelong consequences. However, the identification of core probiotics in the hindgut and its mechanism regulating host growth remain unclear. Here, a total of 1045 fecal samples were analyzed by 16S rRNA gene sequencing from the 408 Holstein dairy calves at the age of 0, 14, 28, 42, 56, and 70 days to characterize the dynamic changes of core taxa. Moreover, the mechanisms of nutrient metabolism of calf growth regulated by core bacteria were investigated using multi-omics analyses. Finally, fecal microbiota transplantation (FMT) in mice were conducted to illustrate the potential beneficial effects of core bacteria. Four calf enterotypes were identified and enterotypes dominated by Bifidobacterium and Oscillospiraceae_UCG-005 were representative. The frequency of enterotype conversion shifted from variable to stable. The close relationship observed between phenotype and enterotype, revealing a potential pro-growth effect of Bifidobacterium, might be implemented by promoting the use of carbohydrate, activating the synthesis of volatile fatty acids, amino acids and vitamin B6, and inhibiting methane production in the hindgut. The FMT results indicated the beneficial effect of Bifidobacterium on host growth and hindgut development. These results support the notion that the Bifidobacterium-dominated fecal microbiome would be an important driving force for promoting the host growth in the early life. Our findings provide new insights into the potential probiotic mining and application strategies to promote the growth of young animals or improve their growth retardation.},
}

Animals
*Feces/microbiology
Cattle
*RNA, Ribosomal, 16S/genetics
*Bifidobacterium/genetics/growth & development
*Gastrointestinal Microbiome
Mice
*Fecal Microbiota Transplantation/methods
Phenotype
Probiotics/administration & dosage
Phylogeny
DNA, Bacterial/genetics

@article {pmid39034003,
year = {2024},
author = {Radziemska, M and Blazejczyk, A and Gusiatin, MZ and Cydzik-Kwiatkowska, A and Majewski, G and Brtnicky, M},
title = {Compost-diatomite-based phytostabilization course under extreme environmental conditions in terms of high pollutant contents and low temperatures.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {174917},
doi = {10.1016/j.scitotenv.2024.174917},
pmid = {39034003},
issn = {1879-1026},
abstract = {The effects of changes in environmental temperatures on the immobilization or removal of cationic potentially toxic elements (PTE) in heavily polluted soils are often poorly understood, although both are widely studied in the context of phytostabilization. To address this issue, a novel compost-diatomite hybrid (CDH) amendment was developed and applied for assisted phytostabilization at two external temperature regimes. (Cd/Ni/Cu/Zn)-extremely contaminated soils (unenriched and CDH-enriched) were cultivated with perennial ryegrass and native soil microbiome under greenhouse conditions and then transferred to freeze-thaw conditions (FTC). The decrease in metal potential toxicity in soils undergoing phytostabilization following both temperature treatments was characterized by a combination of sequential extraction and atomic absorption measurements. The soil microbiome was characterized by high-throughput sequencing. In a relative comparison, the greatest decrease in the content of all different PTEs in CDH-enriched soil (compared to unenriched soil) was highest in FTC. Furthermore, under the influence of FTC, in a relative comparison between two CDH-enriched soils (exposed-, and not-exposed- to FTC) and two unenriched soils (exposed-, and not-exposed- to FTC), the content of all PTEs decreased more sharply in the CDH-enriched series than in the unenriched series. The largest redistribution into four sequentially extracted fractions in CDH-enriched soil was found for Zn. Based on the distribution pattern, Zn immobilization was greater in CDH-enriched soil in FTC. CDH increased species richness in the soil, while FTC stimulated the growth of Bacteroidia, Alphaproteobacteria, Theromomicrobia, and Gammaproteobacteria. Analysis of the functionalities of the microbiome indicated enhanced metal transportation and defense systems in samples exposed to FTC. The current research is crucial for understanding how extreme environmental conditions in the form of high contaminant levels and low temperatures affect the movement and transformation of PTEs in polluted soils during phytostabilization.},
}

@article {pmid39033820,
year = {2024},
author = {Zhang, H and Liang, S and Yin, K and Mo, Y and Li, Y and Lv, Y and Zhan, H and Zhang, Z and Shan, Z and Guo, Z and Yin, S and Yang, W},
title = {Urinary equol and equol-predicting microbial species are favorably associated with body fat measures among Chinese adults.},
journal = {The Journal of nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tjnut.2024.07.024},
pmid = {39033820},
issn = {1541-6100},
abstract = {BACKGROUND: Many studies have investigated the intake of dietary isoflavones in relation to obesity risk, while the association using objective biomarkers of isoflavones, particularly equol (a gut-derived metabolite of daidzein with greater bioavailability than other isoflavones) has been less studied. In addition, the associations between equol and gut microbiota profile at population level remain to be fully characterized.

OBJECTIVE: We aimed to identify equol-predicting microbial species and to investigate the associations of equol-predicting microbial species and urinary excretion of isoflavones including glycitein, genistein, daidzein, and equol with diverse obesity markers in free living-individuals.

METHODS: In this 1-year longitudinal study of 754 community-dwelling adults, urinary isoflavones, fecal microbiota, height, weight, and circumferences of waist and hip were measured at baseline and again after 1-year. Liver fat [indicated by controlled attenuation parameter (CAP)] and other body composition were also measured after 1-year. Linear models and linear mixed-effects models were used to analyze the associations for single measure and repeated measures, respectively.

RESULTS: Among 305 participants (median age: 50 y, IQR: 37-59 y) including 138 men and 167 women, higher urinary excretion of equol was associated with lower CAP (β = -0.013, P < 0.001) and body fat mass (β= -0.014, P = 0.046). No association was found between any other urinary isoflavones and obesity markers (all P>0.05). We identified 21 bacterial genera whose relative abundance were positively associated with urinary equol concentrations (all Pfalsediscovery rate < 0.05), and constructed an equol-predicting microbial score to reflect the overall equol-producing potential of host gut microbiota. This score was inversely associated with CAP (β = -0.040, P = 0.011).

CONCLUSIONS: High urinary equol concentrations and equol-predicting microbial species could be favorably associated with liver fat and other obesity markers.},
}

@article {pmid39033797,
year = {2024},
author = {Xia, L and Zhu, X and Wang, Y and Lu, S},
title = {The gut microbiota improves the efficacy of immune-checkpoint inhibitor immunotherapy against tumors: From association to cause and effect.},
journal = {Cancer letters},
volume = {598},
number = {},
pages = {217123},
doi = {10.1016/j.canlet.2024.217123},
pmid = {39033797},
issn = {1872-7980},
abstract = {Immune-checkpoint inhibitors (ICIs), including anti-PD-1/PD-L1 therapeutic antibodies, have markedly enhanced survival across numerous cancer types. However, the limited number of patients with durable benefits creates an urgent need to identify response biomarkers and to develop novel strategies so as to improve response. It is widely recognized that the gut microbiome is a key mediator in shaping immunity. Additionally, the gut microbiome shows significant potential in predicting the response to and enhancing the efficacy of ICI immunotherapy against cancer. Recent studies encompassing mechanistic analyses and clinical trials of microbiome-based therapy have shown a cause-and-effect relationship between the gut microbiome and the modulation of the ICI immunotherapeutic response, greatly contributing to the establishment of novel strategies that will improve response and overcome resistance to ICI treatment. In this review, we outline the current state of research advances and discuss the future directions of utilizing the gut microbiome to enhance the efficacy of ICI immunotherapy against tumors.},
}

@article {pmid39033501,
year = {2024},
author = {Kulshrestha, S and Narad, P and Singh, B and Pai, SS and Vijayaraghavan, P and Tandon, A and Gupta, P and Modi, D and Sengupta, A},
title = {Biomarker Identification for Preterm Birth Susceptibility: Vaginal Microbiome Meta-Analysis Using Systems Biology and Machine Learning Approaches.},
journal = {American journal of reproductive immunology (New York, N.Y. : 1989)},
volume = {92},
number = {1},
pages = {e13905},
doi = {10.1111/aji.13905},
pmid = {39033501},
issn = {1600-0897},
mesh = {Humans ; Female ; *Vagina/microbiology ; *Premature Birth/microbiology ; *Microbiota/genetics ; *Machine Learning ; Pregnancy ; *RNA, Ribosomal, 16S/genetics ; *Systems Biology ; Biomarkers ; Disease Susceptibility ; Infant, Newborn ; },
abstract = {PROBLEM: The vaginal microbiome has a substantial role in the occurrence of preterm birth (PTB), which contributes substantially to neonatal mortality worldwide. However, current bioinformatics approaches mostly concentrate on the taxonomic classification and functional profiling of the microbiome, limiting their abilities to elucidate the complex factors that contribute to PTB.

METHOD OF STUDY: A total of 3757 vaginal microbiome 16S rRNA samples were obtained from five publicly available datasets. The samples were divided into two categories based on pregnancy outcome: preterm birth (PTB) (N = 966) and term birth (N = 2791). Additionally, the samples were further categorized based on the participants' race and trimester. The 16S rRNA reads were subjected to taxonomic classification and functional profiling using the Parallel-META 3 software in Ubuntu environment. The obtained abundances were analyzed using an integrated systems biology and machine learning approach to determine the key microbes, pathways, and genes that contribute to PTB. The resulting features were further subjected to statistical analysis to identify the top nine features with the greatest effect sizes.

RESULTS: We identified nine significant features, namely Shuttleworthia, Megasphaera, Sneathia, proximal tubule bicarbonate reclamation pathway, systemic lupus erythematosus pathway, transcription machinery pathway, lepA gene, pepX gene, and rpoD gene. Their abundance variations were observed through the trimesters.

CONCLUSIONS: Vaginal infections caused by Shuttleworthia, Megasphaera, and Sneathia and altered small metabolite biosynthesis pathways such as lipopolysaccharide folate and retinal may increase the susceptibility to PTB. The identified organisms, genes, pathways, and their networks may be specifically targeted for the treatment of bacterial infections that increase PTB risk.},
}

Humans
Female
*Vagina/microbiology
*Premature Birth/microbiology
*Microbiota/genetics
*Machine Learning
Pregnancy
*RNA, Ribosomal, 16S/genetics
*Systems Biology
Biomarkers
Disease Susceptibility
Infant, Newborn

@article {pmid39033464,
year = {2024},
author = {Sanford, PA and Woolston, BM},
title = {Development of a Recombineering System for the Acetogen Eubacterium limosum with Cas9 Counterselection for Markerless Genome Engineering.},
journal = {ACS synthetic biology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acssynbio.4c00253},
pmid = {39033464},
issn = {2161-5063},
abstract = {Eubacterium limosum is a Clostridial acetogen that efficiently utilizes a wide range of single-carbon substrates and contributes to metabolism of health-associated compounds in the human gut microbiota. These traits have led to interest in developing it as a platform for sustainable CO2-based biofuel production to combat carbon emissions, and for exploring the importance of the microbiota in human health. However, synthetic biology and metabolic engineering in E. limosum have been hindered by the inability to rapidly make precise genomic modifications. Here, we screened a diverse library of recombinase proteins to develop a highly efficient oligonucleotide-based recombineering system based on the viral recombinase RecT. Following optimization, the system is capable of catalyzing ssDNA recombination at an efficiency of up to 2%. Addition of a Cas9 counterselection system eliminated unrecombined cells, with up to 100% of viable cells encoding the desired mutation, enabling creation of genomic point mutations in a scarless and markerless manner. We deployed this system to create a clean knockout of the extracellular polymeric substance (EPS) gene cluster, generating a strain incapable of biofilm formation. This approach is rapid and simple, not requiring laborious homology arm cloning, and can readily be retargeted to almost any genomic locus. This work overcomes a major bottleneck in E. limosum genetic engineering by enabling precise genomic modifications, and provides both a roadmap and associated recombinase plasmid library for developing similar systems in other Clostridia of interest.},
}

@article {pmid39033279,
year = {2024},
author = {Trinh, P and Teichman, S and Roberts, MC and Rabinowitz, PM and Willis, AD},
title = {A cross-sectional comparison of gut metagenomes between dairy workers and community controls.},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {708},
doi = {10.1186/s12864-024-10562-1},
pmid = {39033279},
issn = {1471-2164},
support = {R35 GM133420/GM/NIGMS NIH HHS/United States ; R35 GM133420/GM/NIGMS NIH HHS/United States ; R35 GM133420/GM/NIGMS NIH HHS/United States ; T32 ES015459/ES/NIEHS NIH HHS/United States ; R21 AI168679/AI/NIAID NIH HHS/United States ; R21 AI168679/AI/NIAID NIH HHS/United States ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Cross-Sectional Studies ; *Metagenome ; Female ; Dairying ; Metagenomics/methods ; Adult ; Animals ; Middle Aged ; Bacteria/genetics/classification ; Farmers ; Male ; Drug Resistance, Bacterial/genetics ; },
abstract = {BACKGROUND: As a nexus of routine antibiotic use and zoonotic pathogen presence, the livestock farming environment is a potential hotspot for the emergence of zoonotic diseases and antibiotic resistant bacteria. Livestock can further facilitate disease transmission by serving as intermediary hosts for pathogens before a spillover event. In light of this, we aimed to characterize the microbiomes and resistomes of dairy workers, whose exposure to the livestock farming environment places them at risk for facilitating community transmission of antibiotic resistant genes and emerging zoonotic diseases.

RESULTS: Using shotgun sequencing, we investigated differences in the taxonomy, diversity and gene presence of 10 dairy farm workers and 6 community controls' gut metagenomes, contextualizing these samples with additional publicly available gut metagenomes. We found no significant differences in the prevalence of resistance genes, virulence factors, or taxonomic composition between the two groups. The lack of statistical significance may be attributed, in part, to the limited sample size of our study or the potential similarities in exposures between the dairy workers and community controls. We did, however, observe patterns warranting further investigation including greater abundance of tetracycline resistance genes and prevalence of cephamycin resistance genes as well as lower average gene diversity (even after accounting for differential sequencing depth) in dairy workers' metagenomes. We also found evidence of commensal organism association with tetracycline resistance genes in both groups (including Faecalibacterium prausnitzii, Ligilactobacillus animalis, and Simiaoa sunii).

CONCLUSIONS: This study highlights the utility of shotgun metagenomics in examining the microbiomes and resistomes of livestock workers, focusing on a cohort of dairy workers in the United States. While our study revealed no statistically significant differences between groups in taxonomy, diversity and gene presence, we observed patterns in antibiotic resistance gene abundance and prevalence that align with findings from previous studies of livestock workers in China and Europe. Our results lay the groundwork for future research involving larger cohorts of dairy and non-dairy workers to better understand the impact of occupational exposure to livestock farming on the microbiomes and resistomes of workers.},
}

Humans
*Gastrointestinal Microbiome/genetics
Cross-Sectional Studies
*Metagenome
Female
Dairying
Metagenomics/methods
Adult
Animals
Middle Aged
Bacteria/genetics/classification
Farmers
Male
Drug Resistance, Bacterial/genetics

@article {pmid39033201,
year = {2024},
author = {Fernández-Rodríguez, D and Cho, J and Chisari, E and Citardi, MJ and Parvizi, J},
title = {Nasal microbiome and the effect of nasal decolonization with a novel povidone-iodine antiseptic solution: a prospective and randomized clinical trial.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {16739},
pmid = {39033201},
issn = {2045-2322},
mesh = {Humans ; *Povidone-Iodine/pharmacology/administration & dosage ; *Anti-Infective Agents, Local/pharmacology/administration & dosage ; *Microbiota/drug effects ; Male ; Female ; Adult ; Prospective Studies ; Middle Aged ; Nose/microbiology ; Young Adult ; Bacteria/drug effects/classification/genetics ; Administration, Intranasal ; Corynebacterium/drug effects ; },
abstract = {The aim of this study was to assess the profile of nasal microbiome and evaluate the effect of a specific nasal decolonization solution on the microbiome. We conducted a randomized, placebo-controlled, and parallel-group clinical study of 50 volunteers aged 18 years and older. The subjects were randomly assigned to receive a nasal antiseptic solution, containing povidone-iodine as the main ingredient, (n = 25) or a control solution (n = 25). Nasal swabs were obtained before application (baseline) and at 3 timepoints after application (5 min, 2 h, 24 h). Nasal swabs were subjected to next generation sequencing analysis and cultured in agar plates. At baseline, there were substantial associations between anaerobic species, Corynebacterium spp., Staphylococcus spp., and Dolosigranulum spp. Then, a high bioburden reduction was observed after the application of povidone-iodine (log10 3.68 ± 0.69 at 5 min; log10 3.57 ± 0.94 at 2 h; log10 1.17 ± 1.40 at 24 h), compared to the control. The top species affected by the treatment were Cutibacterium acnes, Staphylococcus, and Corynebacterium species. None of the subjects experienced any adverse effects, nor increases in mucociliary clearance time. Antiseptic solutions applied to the anterior nares can transiently and markedly reduce the bioburden of the nose. The registration number for this clinical trial is NCT05617729.},
}

Humans
*Povidone-Iodine/pharmacology/administration & dosage
*Anti-Infective Agents, Local/pharmacology/administration & dosage
*Microbiota/drug effects
Male
Female
Adult
Prospective Studies
Middle Aged
Nose/microbiology
Young Adult
Bacteria/drug effects/classification/genetics
Administration, Intranasal
Corynebacterium/drug effects

@article {pmid39033197,
year = {2024},
author = {Visuthranukul, C and Sriswasdi, S and Tepaamorndech, S and Chamni, S and Leelahavanichkul, A and Joyjinda, Y and Aksornkitti, V and Chomtho, S},
title = {Enhancing gut microbiota and microbial function with inulin supplementation in children with obesity.},
journal = {International journal of obesity (2005)},
volume = {},
number = {},
pages = {},
pmid = {39033197},
issn = {1476-5497},
abstract = {BACKGROUND AND OBJECTIVES: Gut dysbiosis that resulted from the alteration between host-microbe interaction might worsen obesity-induced systemic inflammation. Gut microbiota manipulation by supplementation of prebiotic inulin may reverse metabolic abnormalities and improve obesity. This study aimed to determine whether inulin supplementation improved intestinal microbiota and microbial functional pathways in children with obesity.

METHODS: Children with obesity whose BMI above median + 2SDs were recruited to a randomized, double-blinded placebo-controlled study. The participants aged 7-15 years were assigned to inulin supplement extracted from Thai Jerusalem artichoke (intervention), maltodextrin (placebo), and dietary fiber advice groups. All participants received similar monthly conventional advice and follow-up for 6 months. Fecal samples were collected for gut microbiome analysis using 16S rRNA sequencing. Phylogenetic Investigation of Communities by Reconstruction of Unobserved States was performed to infer microbial functional pathways.

RESULTS: One hundred and forty-three children with available taxonomic and functional pathway abundance profiles were evaluated. A significant increase in alpha-diversity was observed in the inulin group. Inulin supplementation substantially enhanced Bifidobacterium, Blautia, Megasphaera, and several butyrate-producing bacteria, including Agathobacter, Eubacterium coprostanoligenes, and Subdoligranulum, compared to the other groups. The inulin group showed a significant difference in functional pathways of proteasome and riboflavin metabolism. These changes correlated with clinical and metabolic outcomes exclusively in the inulin group.

CONCLUSIONS: Inulin supplementation significantly promoted gut bacterial diversity and improved gut microbiota dysbiosis in children with obesity. The modulation of functional pathways by inulin suggests its potential to establish beneficial interactions between the gut microbiota and host physiology. Inulin supplementation could be a strategic treatment to restore the balance of intestinal microbiota and regulate their functions in childhood obesity.},
}

@article {pmid39033123,
year = {2024},
author = {Mercado-Evans, V and Zulk, JJ and Hameed, ZA and Patras, KA},
title = {Gestational diabetes as a risk factor for GBS maternal rectovaginal colonization: a systematic review and meta-analysis.},
journal = {BMC pregnancy and childbirth},
volume = {24},
number = {1},
pages = {488},
pmid = {39033123},
issn = {1471-2393},
support = {AI167547//National Institute of Allergy and Infectious Diseases/ ; AI173448//National Institute of Allergy and Infectious Diseases/ ; DK136201/DK/NIDDK NIH HHS/United States ; DK128053/DK/NIDDK NIH HHS/United States ; GM136554/GM/NIGMS NIH HHS/United States ; NGP10103//Burroughs Wellcome Fund/ ; },
mesh = {Humans ; *Diabetes, Gestational/epidemiology ; Female ; Pregnancy ; Risk Factors ; *Streptococcal Infections/epidemiology ; *Streptococcus agalactiae ; *Vagina/microbiology ; *Pregnancy Complications, Infectious/epidemiology/microbiology ; *Rectum/microbiology ; },
abstract = {BACKGROUND: Maternal rectovaginal colonization by group B Streptococcus (GBS) increases the risk of perinatal GBS disease that can lead to death or long-term neurological impairment. Factors that increase the risk of rectovaginal GBS carriage are incompletely understood resulting in missed opportunities for detecting GBS in risk-based clinical approaches. There is a lacking consensus on whether gestational diabetes mellitus (GDM) is a risk factor for rectovaginal GBS. This systematic review and meta-analysis aims to address current conflicting findings and determine whether GDM should be clinically considered as a risk factor for maternal GBS colonization.

METHODS: Peer-reviewed studies that provided GDM prevalence and documented GBS vaginal and/or rectal colonization in women with and without GDM were included in this analysis. From study inception to October 30, 2023, we identified 6,275 relevant studies from EMBASE and PUBMED of which 19 were eligible for inclusion. Eligible studies were analyzed and thoroughly assessed for risk of bias with a modified Newcastle-Ottawa Scale that interrogated representativeness and comparability of cohorts, quality of reporting for GDM and GBS status, and potential bias from other metabolic diseases. Results were synthesized using STATA 18 and analyzed using random-effects meta-analyses.

RESULTS: Studies encompassed 266,706 women from 10 different countries, with study periods spanning from 1981 to 2020. Meta-analysis revealed that gestational diabetes is associated with a 16% increased risk of rectovaginal GBS carriage (OR 1.16, CI 1.07-1.26, P = 0.003). We also performed subgroup analyses to assess independent effects of pregestational vs. gestational diabetes on risk of maternal GBS carriage. Pregestational diabetes (Type 1 or Type 2 diabetes mellitus) was also associated with an increased risk of 76% (pooled OR 1.76, CI 1.27-2.45, P = 0.0008).

CONCLUSIONS: This study achieved a consensus among previously discrepant observations and demonstrated that gestational diabetes and pregestational diabetes are significant risk factors for maternal rectovaginal carriage of GBS. Recognition of GDM as a risk factor during clinical decisions about GBS screening and intrapartum antibiotic prophylaxis may decrease the global burden of GBS on maternal-perinatal health.},
}

Humans
*Diabetes, Gestational/epidemiology
Female
Pregnancy
Risk Factors
*Streptococcal Infections/epidemiology
*Streptococcus agalactiae
*Vagina/microbiology
*Pregnancy Complications, Infectious/epidemiology/microbiology
*Rectum/microbiology

@article {pmid39032735,
year = {2024},
author = {Yuan, Y and Yang, L and Wan, X and Zhao, Y and Gong, Y and Xing, W and Xue, T and Tao, J},
title = {Microplastics in heavy metal-contaminated soil drives bacterial community and metabolic changes.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {174770},
doi = {10.1016/j.scitotenv.2024.174770},
pmid = {39032735},
issn = {1879-1026},
abstract = {Microplastic (MP) and heavy metal pollution in soil are global issues. When MPs invade the soil, they combine with heavy metals and adversely affect soil organisms. Six common MPs-polyethylene, polypropylene, polystyrene, polyvinyl chloride, polyethylene terephthalate, and polytetrafluoroethylene-were selected for this study to examine the effects of various concentrations and MP types on the physicochemical properties, bacterial community, and soil metabolism of heavy metal-contaminated soil. MP enhanced predation and competition among heavy metal-contaminated soil bacteria. Heavy metal-MPs alter metabolites in lipid metabolism, other pathways, and the bacterial community. MP treatment promotes energy production and oxidative stress of soil bacteria to resist the toxicity of heavy metals and degrade MP pollution. In conclusion, MP treatment changed the metabolism of the microbiome in heavy metal-contaminated soil and increased the abundance of Proteobacteria that responded to MPs and heavy metal pollution by 11.54 % on average. This study explored bacteria for the ecological regeneration and provided ideas for MPs and heavy metal-contaminated soil remediation.},
}

@article {pmid39032655,
year = {2024},
author = {Kandel, SE and Tooker, BC and Lampe, JN},
title = {Drug metabolism of ciprofloxacin, ivacaftor, and raloxifene by Pseudomonas aeruginosa cytochrome P450 CYP107S1.},
journal = {The Journal of biological chemistry},
volume = {},
number = {},
pages = {107594},
doi = {10.1016/j.jbc.2024.107594},
pmid = {39032655},
issn = {1083-351X},
abstract = {Drug metabolism is one of the main processes governing the pharmacokinetics and toxicity of drugs via their chemical biotransformation and elimination. In humans, the liver, enriched with cytochrome P450 (CYP) enzymes, plays a major metabolic and detoxification role. The gut microbiome and its complex community of microorganisms can also contribute to some extent to drug metabolism. However, during an infection when pathogenic microorganisms invade the host, our knowledge of the impact on drug metabolism by this pathobiome remains limited. The intrinsic resistance mechanisms and rapid metabolic adaptation to new environments often allow the human bacterial pathogens to persist, despite the many antibiotic therapies available. Here, we demonstrate that a bacterial CYP enzyme, CYP107S1, from Pseudomonas aeruginosa, a predominant bacterial pathogen in cystic fibrosis (CF) patients, can metabolize multiple drugs from different classes. CYP107S1 demonstrated high substrate promiscuity and allosteric properties much like human hepatic CYP3A4. Our findings demonstrated binding and metabolism by the recombinant CYP107S1 of fluoroquinolone antibiotics (ciprofloxacin and fleroxacin), a CF transmembrane conductance regulator potentiator (ivacaftor), and a SERM antimicrobial adjuvant (raloxifene). Our in vitro metabolism data were further corroborated by molecular docking of each drug to the heme active site using a CYP107S1 homology model. Our findings raise the potential for microbial pathogens modulating drug concentrations locally at the site of infection, if not systemically, via CYP-mediated biotransformation reactions. To our knowledge, this is the first report of a CYP enzyme from a known bacterial pathogen that is capable of metabolizing clinically utilized drugs.},
}