@article {pmid38654401,
year = {2024},
author = {Li, G and Wang, Z and Ren, H and Qi, X and Han, H and Ding, X and Sun, L and Hafeez, R and Wang, Q and Li, B},
title = {Ancient bayberry increased stress resistance by enriching tissue-specific microbiome and metabolites.},
journal = {Physiologia plantarum},
volume = {176},
number = {2},
pages = {e14314},
doi = {10.1111/ppl.14314},
pmid = {38654401},
issn = {1399-3054},
support = {2024SNJF073//"Three Rural and Nine Directions" Science and Technology Collaboration Program/ ; 2021C02009//the Key R & D projects in Zhejiang Province/ ; 2022XTTGGP04//Zhejiang Major Agricultural Technology Collaborative Promotion Plan Project/ ; },
mesh = {*Microbiota ; *Stress, Physiological ; *Rhizosphere ; *Myrica/metabolism/microbiology/genetics ; Plant Roots/microbiology/metabolism ; Plant Leaves/metabolism/microbiology ; Soil Microbiology ; },
abstract = {The ancient bayberry demonstrates superior resistance to both biotic and abiotic stresses compared to cultivated bayberry, yet the underlying mechanisms remain largely unexplored. This study investigates whether long-term bayberry cultivation enhances stress resistance through modulation of tissue-specific microbes and metabolites. Employing microbiome amplicon sequencing alongside untargeted mass spectrometry analysis, we scrutinize the role of endosphere and rhizosphere microbial communities and metabolites in shaping the differential resistance observed between ancient and cultivated bayberry trees. Our findings highlight the presence of core microbiome and metabolites across various bayberry tissues, suggesting that the heightened resistance of ancient bayberry may stem from alterations in rhizosphere and endosphere microbial communities and secondary metabolites. Specifically, enrichment of Bacillus in roots and stems, Pseudomonas in leaves, and Mortierella in rhizosphere soil of ancient bayberry was noted. Furthermore, correlation analysis underscores the significance of enriched microbial species in enhancing ancient bayberry's resistance to stresses, with elevated levels of resistance-associated metabolites such as beta-myrcene, benzothiazole, L-glutamic acid, and gamma-aminobutyric acid identified through GC-MS metabolomics analysis. The beneficial role of these resistance-associated metabolites was further elucidated through assessment of their promotive and allelopathic effects, as well as their phytostatic and antioxidant functions in lettuce plants. Ultimately, our study delves into the intrinsic reasons behind the greater resistance of ancient bayberry to biotic and abiotic stresses by evaluating the impact of long-term planting on the microbial community and metabolites in the bayberry endosphere and rhizosphere, shedding light on the complex dynamics of host-microbial interactions.},
}

*Microbiota
*Stress, Physiological
*Rhizosphere
*Myrica/metabolism/microbiology/genetics
Plant Roots/microbiology/metabolism
Plant Leaves/metabolism/microbiology
Soil Microbiology

@article {pmid38654396,
year = {2024},
author = {Zhang, L and Zhang, X and Leach, JM and Rahman, AF and Yi, N},
title = {Bayesian compositional models for ordinal response.},
journal = {Statistical methods in medical research},
volume = {},
number = {},
pages = {9622802241247730},
doi = {10.1177/09622802241247730},
pmid = {38654396},
issn = {1477-0334},
abstract = {Ordinal response is commonly found in medicine, biology, and other fields. In many situations, the predictors for this ordinal response are compositional, which means that the sum of predictors for each sample is fixed. Examples of compositional data include the relative abundance of species in microbiome data and the relative frequency of nutrition concentrations. Moreover, the predictors that are strongly correlated tend to have similar influence on the response outcome. Conventional cumulative logistic regression models for ordinal responses ignore the fixed-sum constraint on predictors and their associated interrelationships, and thus are not appropriate for analyzing compositional predictors.To solve this problem, we proposed Bayesian Compositional Models for Ordinal Response to analyze the relationship between compositional data and an ordinal response with a structured regularized horseshoe prior for the compositional coefficients and a soft sum-to-zero restriction on coefficients through the prior distribution. The method was implemented with R package rstan using efficient Hamiltonian Monte Carlo algorithm. We performed simulations to compare the proposed approach and existing methods for ordinal responses. Results revealed that our proposed method outperformed the existing methods in terms of parameter estimation and prediction. We also applied the proposed method to a microbiome study HMP2Data, to find microorganisms linked to ordinal inflammatory bowel disease levels. To make this work reproducible, the code and data used in this paper are available at https://github.com/Li-Zhang28/BCO.},
}

@article {pmid38654392,
year = {2024},
author = {Lailheugue, V and Darriaut, R and Tran, J and Morel, M and Marguerit, E and Lauvergeat, V},
title = {Both the scion and rootstock of grafted grapevines influence the rhizosphere and root endophyte microbiomes, but rootstocks have a greater impact.},
journal = {Environmental microbiome},
volume = {19},
number = {1},
pages = {24},
pmid = {38654392},
issn = {2524-6372},
abstract = {BACKGROUND: Soil microorganisms play an extensive role in the biogeochemical cycles providing the nutrients necessary for plant growth. Root-associated bacteria and fungi, originated from soil, are also known to influence host health. In response to environmental stresses, the plant roots exude specific molecules influencing the composition and functioning of the rhizospheric and root microbiomes. This response is host genotype-dependent and is affected by the soil microbiological and chemical properties. It is essential to unravel the influence of grapevine rootstock and scion genotypes on the composition of this microbiome, and to investigate this relationship with plant growth and adaptation to its environment. Here, the composition and the predicted functions of the microbiome of the root system were studied using metabarcoding on ten grapevine scion-rootstock combinations, in addition to plant growth and nutrition measurements.

RESULTS: The rootstock genotype significantly influenced the diversity and the structure of the bacterial and fungal microbiome, as well as its predicted functioning in rhizosphere and root compartments when grafted with the same scion cultivar. Based on β-diversity analyses, 1103P rootstock showed distinct bacterial and fungal communities compared to the five others (RGM, SO4, 41B, 3309 C and Nemadex). The influence of the scion genotype was more variable depending on the community and the investigated compartment. Its contribution was primarily observed on the β-diversity measured for bacteria and fungi in both root system compartments, as well as for the arbuscular mycorrhizal fungi (AMF) in the rhizosphere. Significant correlations were established between microbial variables and the plant phenotype, as well as with the plant mineral status measured in the petioles and the roots.

CONCLUSION: These results shed light on the capacity of grapevine rootstock and scion genotypes to recruit different functional communities of microorganisms, which affect host growth and adaptation to the environment. Selecting rootstocks capable of associating with positive symbiotic microorganisms is an adaptation tool that can facilitate the move towards sustainable viticulture and help cope with environmental constraints.},
}

@article {pmid38654335,
year = {2024},
author = {Quinn-Bohmann, N and Freixas-Coutin, JA and Seo, J and Simmons, R and Diener, C and Gibbons, SM},
title = {Meta-analysis of the human upper respiratory tract microbiome reveals robust taxonomic associations with health and disease.},
journal = {BMC biology},
volume = {22},
number = {1},
pages = {93},
pmid = {38654335},
issn = {1741-7007},
mesh = {Humans ; *Microbiota/genetics ; *RNA, Ribosomal, 16S/genetics ; *Respiratory System/microbiology ; Respiratory Tract Diseases/microbiology ; Case-Control Studies ; Male ; Bacteria/genetics/classification/isolation & purification ; Female ; },
abstract = {BACKGROUND: The human upper respiratory tract (URT) microbiome, like the gut microbiome, varies across individuals and between health and disease states. However, study-to-study heterogeneity in reported case-control results has made the identification of consistent and generalizable URT-disease associations difficult.

RESULTS: In order to address this issue, we assembled 26 independent 16S rRNA gene amplicon sequencing data sets from case-control URT studies, with approximately 2-3 studies per respiratory condition and ten distinct conditions covering common chronic and acute respiratory diseases. We leveraged the healthy control data across studies to investigate URT associations with age, sex, and geographic location, in order to isolate these associations from health and disease states.

CONCLUSIONS: We found several robust genus-level associations, across multiple independent studies, with either health or disease status. We identified disease associations specific to a particular respiratory condition and associations general to all conditions. Ultimately, we reveal robust associations between the URT microbiome, health, and disease, which hold across multiple studies and can help guide follow-up work on potential URT microbiome diagnostics and therapeutics.},
}

Humans
*Microbiota/genetics
*RNA, Ribosomal, 16S/genetics
*Respiratory System/microbiology
Respiratory Tract Diseases/microbiology
Case-Control Studies
Male
Bacteria/genetics/classification/isolation & purification
Female

@article {pmid38654203,
year = {2024},
author = {Tu, J and Wang, Y and Ye, X and Wang, Y and Zou, Y and Jia, L and Yang, S and Yu, R and Liu, W and Huang, P},
title = {Gut microbial features may influence antiviral IgG levels after vaccination against viral respiratory infectious diseases: the evidence from two-sample bidirectional mendelian randomization.},
journal = {BMC infectious diseases},
volume = {24},
number = {1},
pages = {431},
pmid = {38654203},
issn = {1471-2334},
support = {82273741//Natural Science Foundation of China/ ; 82173585//Natural Science Foundation of China/ ; 22KJB330007//Natural Science Foundation of Jiangsu Higher Education Institutions of China/ ; 21KJB330005//Natural Science Foundation of Jiangsu Higher Education Institutions of China/ ; },
mesh = {Humans ; *Immunoglobulin G/blood ; *Mendelian Randomization Analysis ; *Gastrointestinal Microbiome ; *Respiratory Tract Infections/immunology/prevention & control/microbiology ; Genome-Wide Association Study ; Antibodies, Viral/blood/immunology ; Vaccination ; Virus Diseases/immunology/prevention & control ; },
abstract = {BACKGROUND: Vaccination is effective in preventing viral respiratory infectious diseases through protective antibodies and the gut microbiome has been proven to regulate human immunity. This study explores the causal correlations between gut microbial features and serum-specific antiviral immunoglobulin G (IgG) levels.

METHODS: We conduct a two-sample bidirectional Mendelian randomization (MR) analysis using genome-wide association study (GWAS) summary data to explore the causal relationships between 412 gut microbial features and four antiviral IgG (for influenza A, measles, rubella, and mumps) levels. To make the results more reliable, we used four robust methods and performed comprehensive sensitivity analyses.

RESULTS: The MR analyses revealed 26, 13, 20, and 18 causal associations of the gut microbial features influencing four IgG levels separately. ​Interestingly, ten microbial features, like genus Collinsella, species Bifidobacterium longum, and the biosynthesis of L-alanine have shown the capacity to regulate multiple IgG levels with consistent direction (rise or fall). The ​reverse MR analysis suggested several potential causal associations of IgG levels affecting microbial features.

CONCLUSIONS: The human immune response against viral respiratory infectious diseases could be modulated by changing the abundance of gut microbes, which provided new approaches for the intervention of viral respiratory infections.},
}

Humans
*Immunoglobulin G/blood
*Mendelian Randomization Analysis
*Gastrointestinal Microbiome
*Respiratory Tract Infections/immunology/prevention & control/microbiology
Genome-Wide Association Study
Antibodies, Viral/blood/immunology
Vaccination
Virus Diseases/immunology/prevention & control

@article {pmid38654015,
year = {2024},
author = {Lachance, G and Robitaille, K and Laaraj, J and Gevariya, N and Varin, TV and Feldiorean, A and Gaignier, F and Julien, IB and Xu, HW and Hallal, T and Pelletier, JF and Bouslama, S and Boufaied, N and Derome, N and Bergeron, A and Ellis, L and Piccirillo, CA and Raymond, F and Fradet, Y and Labbé, DP and Marette, A and Fradet, V},
title = {The gut microbiome-prostate cancer crosstalk is modulated by dietary polyunsaturated long-chain fatty acids.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {3431},
pmid = {38654015},
issn = {2041-1723},
support = {400345//Canadian Cancer Society Research Institute (Société Canadienne du Cancer)/ ; },
mesh = {Male ; *Gastrointestinal Microbiome ; *Prostatic Neoplasms/metabolism/diet therapy/microbiology ; Animals ; Humans ; Mice ; *Fecal Microbiota Transplantation ; *Feces/microbiology ; Fatty Acids, Omega-3/metabolism/administration & dosage ; Mice, Inbred C57BL ; Fatty Acids, Unsaturated/metabolism ; },
abstract = {The gut microbiota modulates response to hormonal treatments in prostate cancer (PCa) patients, but whether it influences PCa progression remains unknown. Here, we show a reduction in fecal microbiota alpha-diversity correlating with increase tumour burden in two distinct groups of hormonotherapy naïve PCa patients and three murine PCa models. Fecal microbiota transplantation (FMT) from patients with high PCa volume is sufficient to stimulate the growth of mouse PCa revealing the existence of a gut microbiome-cancer crosstalk. Analysis of gut microbial-related pathways in mice with aggressive PCa identifies three enzymes responsible for the metabolism of long-chain fatty acids (LCFA). Supplementation with LCFA omega-3 MAG-EPA is sufficient to reduce PCa growth in mice and cancer up-grading in pre-prostatectomy PCa patients correlating with a reduction of gut Ruminococcaceae in both and fecal butyrate levels in PCa patients. This suggests that the beneficial effect of omega-3 rich diet is mediated in part by modulating the crosstalk between gut microbes and their metabolites in men with PCa.},
}

Male
*Gastrointestinal Microbiome
*Prostatic Neoplasms/metabolism/diet therapy/microbiology
Animals
Humans
Mice
*Fecal Microbiota Transplantation
*Feces/microbiology
Fatty Acids, Omega-3/metabolism/administration & dosage
Mice, Inbred C57BL
Fatty Acids, Unsaturated/metabolism

@article {pmid38653859,
year = {2024},
author = {Kong, FS and Huang, P and Chen, JH and Ma, Y},
title = {The Novel Insight of Gut Microbiota from Mouse Model to Clinical Patients and the Role of NF-κB Pathway in Polycystic Ovary Syndrome.},
journal = {Reproductive sciences (Thousand Oaks, Calif.)},
volume = {},
number = {},
pages = {},
pmid = {38653859},
issn = {1933-7205},
support = {No. F202117//the Maternal and Child Health Research Project of Jiangsu in China/ ; },
abstract = {Polycystic Ovary Syndrome (PCOS) is a metabolic disorder characterized by hyperandrogenism and related symptoms in women of reproductive age. Emerging evidence suggests that chronic low-grade inflammation plays a significant role in the development of PCOS. The gut microbiota, a complex bacterial ecosystem, has been extensively studied for various diseases, including PCOS, while the underlying mechanisms are not fully understood. This review comprehensively summarizes the changes in gut microbiota and metabolites observed in PCOS and their potential association with the condition. Additionally, we discuss the role of abnormal nuclear factor κB signaling in the pathogenesis of PCOS. These findings offer valuable insights into the mechanisms of PCOS and may pave the way for the development of control and therapeutic strategies for this condition in clinical practice. By bridging the gap between mouse models and clinical patients, this review contributes to a better understanding of the interplay between gut microbiota and inflammation in PCOS, thus paving new ways for future investigations and interventions.},
}

@article {pmid38653843,
year = {2024},
author = {Ochieng, TA and Akutse, KS and Ajene, IJ and Kilalo, DC and Muiru, M and Khamis, FM},
title = {Interactions between Bacillus thuringiensis and selected plant extracts for sustainable management of Phthorimaea absoluta.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {9299},
pmid = {38653843},
issn = {2045-2322},
support = {AURG II-2-123-2018//African Union/ ; B2291A- FCDO -BIOPESTICIDE//UK's Foreign, Commonwealth & Development Office (FCDO)/ ; },
mesh = {*Bacillus thuringiensis ; Animals ; *Plant Extracts/pharmacology/chemistry ; *Trigonella/chemistry ; Pest Control, Biological/methods ; Moths/drug effects/microbiology ; Larva/drug effects/microbiology ; Garlic/chemistry ; Gastrointestinal Microbiome/drug effects ; Solanum lycopersicum/microbiology ; },
abstract = {Phthorimaea absoluta is a global constraint to tomato production and can cause up to 100% yield loss. Farmers heavily rely on synthetic pesticides to manage this pest. However, these pesticides are detrimental to human, animal, and environmental health. Therefore, exploring eco-friendly, sustainable Integrated Pest Management approaches, including biopesticides as potential alternatives, is of paramount importance. In this context, the present study (i) evaluated the efficacy of 10 Bacillus thuringiensis isolates, neem, garlic, and fenugreek; (ii) assessed the interactions between the most potent plant extracts and B. thuringiensis isolates, and (iii) evaluated the gut microbial diversity due to the treatments for the development of novel formulations against P. absoluta. Neem recorded the highest mortality of 93.79 ± 3.12% with an LT50 value of 1.21 ± 0.24 days, Bt HD263 induced 91.3 ± 3.68% mortality with LT50 of 2.63 ± 0.11 days, compared to both Bt 43 and fenugreek that caused < 50% mortality. Larval mortality was further enhanced to 99 ± 1.04% when Bt HD263 and neem were combined. Furthermore, the microbiome analyses showed that Klebsiella, Escherichia and Enterobacter had the highest abundance in all treatments with Klebsiella being the most abundant. In addition, a shift in the abundance of the bacterial genera due to the treatments was observed. Our findings showed that neem, garlic, and Bt HD263 could effectively control P. absoluta and be integrated into IPM programs after validation by field efficacy trials.},
}

*Bacillus thuringiensis
Animals
*Plant Extracts/pharmacology/chemistry
*Trigonella/chemistry
Pest Control, Biological/methods
Moths/drug effects/microbiology
Larva/drug effects/microbiology
Garlic/chemistry
Gastrointestinal Microbiome/drug effects
Solanum lycopersicum/microbiology

@article {pmid38653719,
year = {2024},
author = {Williams, A},
title = {Multiomics data integration, limitations, and prospects to reveal the metabolic activity of the coral holobiont.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiae058},
pmid = {38653719},
issn = {1574-6941},
abstract = {Since their radiation in the Middle Triassic period ∼ 240 million years ago, stony corals have survived past climate fluctuations and five mass extinctions. Their long-term survival underscores the inherent resilience of corals, particularly when considering the nutrient-poor marine environments in which they have thrived. However, coral bleaching has emerged as a global threat to coral survival, requiring rapid advancements in coral research to understand holobiont stress responses and allow for interventions before extensive bleaching occurs. This review encompasses the potential, as well as the limits, of multiomics data applications when applied to the coral holobiont. Synopses for how different omics tools have been applied to date and their current restrictions are discussed, in addition to ways these restrictions may be overcome, such as recruiting new technology to studies, utilizing novel bioinformatics approaches, and generally integrating omics data. Lastly, this review presents considerations for the design of holobiont multiomics studies to support lab-to-field advancements of coral stress marker monitoring systems. Although much of the bleaching mechanism has eluded investigation to date, multiomic studies have already produced key findings regarding the holobiont's stress response, and have the potential to advance the field further.},
}

@article {pmid38653672,
year = {2024},
author = {Yang, T and Wu, C and Li, Y and Wang, C and Mao, Z and Huo, W and Li, J and Li, Y and Xing, W and Li, L},
title = {Association of short-chain fatty acids and the gut microbiome with type 2 diabetes: Evidence from the Henan Rural Cohort.},
journal = {Nutrition, metabolism, and cardiovascular diseases : NMCD},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.numecd.2024.03.014},
pmid = {38653672},
issn = {1590-3729},
abstract = {BACKGROUND AND AIMS: Human studies about short-chain fatty acids (SCFAs), the gut microbiome, and Type 2 diabetes (T2DM) are limited. Here we explored the association between SCFAs and T2DM and the effects of gut microbial diversity on glucose status in rural populations.

METHODS AND RESULTS: We performed a cross-sectional study from the Henan Rural Cohort and collected stool samples. Gut microbiota composition and faecal SCFA concentrations were measured by 16S rRNA and GC-MS. The population was divided based on the tertiles of SCFAs, and logistic regression models assessed the relationship between SCFAs and T2DM. Generalized linear models tested the interactions between SCFAs and gut microbial diversity on glucose indicators (glucose, HbAlc and insulin). Compared to the lowest tertile of total SCFA, acetate and butyrate, the highest tertile exhibited lower T2DM prevalence, with ORs and 95% CIs of 0.291 (0.085-0.991), 0.160 (0.044-0.574) and 0.171 (0.047-0.620), respectively. Restricted cubic spline demonstrated an approximately inverse S-shaped association. We also noted interactions of the ACE index with the highest tertile of valerate on glucose levels (P-interaction = 0.022) and the Shannon index with the middle tertile of butyrate on insulin levels (P-interaction = 0.034). Genus Prevotella_9 and Odoribacter were inversely correlated with T2DM, and the genus Blautia was positively associated with T2DM. These bacteria are common SCFA-producing members.

CONCLUSIONS: Inverse S-shaped associations between SCFAs (total SCFA, acetate, and butyrate) and T2DM were observed. Valerate and butyrate modify glucose status with increasing gut microbial diversity.},
}

@article {pmid38653476,
year = {2024},
author = {Salamon, D and Kowalska-Duplaga, K and Krawczyk, A and Duplaga, M and Gurgul, A and Gosiewski, T},
title = {Are there new biomarkers of the gastroduodenal microbiota useful in the diagnosis of coeliac disease in children? A pilot study.},
journal = {Beneficial microbes},
volume = {},
number = {},
pages = {1-13},
doi = {10.1163/18762891-bja00009},
pmid = {38653476},
issn = {1876-2891},
abstract = {The changing of microbiome could precede the development of coeliac disease (CeD). We compared the bacterial profile of microbiota of tissues collected simultaneously from the stomach and duodenum in newly diagnosed patients with CeD. Biopsies were collected from 60 children and adolescents aged 2-18 years: (1) 40 patients with CeD; (2) 20 children as control group. The evaluation of the bacterial microbiota was carried out by sequencing the V3-V4 regions of the 16S rRNA subunit, using next-generation sequencing (NGS). The composition of bacterial microbiota was correlated with clinical and blood parameters. The beta diversity analysis revealed a significant dissimilarity in the gastric samples between the CeD and control group (Bray-Curtis index, P = 0.008, and weighted UniFrac distance, P = 0.024). At L2 (phylum level), Campylobacterota was only present in the stomach of the CeD group. A comparison of the abundance of bacteria between the stomach and duodenum showed significant differences in 10 OTUs (operational taxonomic units) in the control and 9 OTUs in the CeD group at L6 (genus) and in 8 OTUs and in 6 OTUs, respectively, at L7 (species). A significant correlation was observed between the genus Novosphingobium in stomach of CeD group and possession of the DQ2.5 and DQ 8 allele, and in the duodenum - between the DQ 8 allele and the species Blautia wexlerae. Significant differences in selected, little-known genera of bacteria suggest their potential role as new biomarkers in the development of CeD. To fully understand the mechanism of CeD development in genetically predisposed individuals, it is necessary to take into account not only the abundance of a given genus or species of bacteria, but also the anatomical location of its occurrence.},
}

@article {pmid38653334,
year = {2024},
author = {Ortiz, PS and Choudhury, A and Kearney, CM},
title = {Validation of gavage sampling as tool for longitudinal sampling of microbiota of the mouse gastric lumen.},
journal = {Journal of microbiological methods},
volume = {},
number = {},
pages = {106939},
doi = {10.1016/j.mimet.2024.106939},
pmid = {38653334},
issn = {1872-8359},
abstract = {BACKGROUND: Fecal samples are commonly used for longitudinal studies of the gut lumen microbiome to track the course of response to infection or drug treatment, but no comparable method has been evaluated for longitudinal analysis of the gastric lumen microbiome in mice. Herein, a buffer flush of the stomach with a flexible gavage needle was used to collect gastric contents at one or several time points without harming the mouse. These samples were compared to samples collected by sacrifice and dissection of the mouse stomach. Microbiota from these samples were sequenced and evaluated in two ways: the composition of samples as measured by beta diversity and the richness of samples as measured by alpha diversity. Additionally, the effect of multiple sampling every two days on these metrics were studied. DNA was extracted from each of these samples and Illumina 16S rRNA gene sequencing was performed.

RESULTS: First, taxonomic richness of gavage and dissection samples was compared. A greater number of taxa was detected in gavage samples than in dissection samples. Second, taxonomic richness was analyzed over time. No significant difference in taxonomic richness was observed with repeated gavage flushes. Third, a comparison was made of the taxonomic composition of samples collected by gavage versus dissection followed by a comparison of samples collected over multiple samplings. Nonmetric multidimensional scaling analysis revealed no clear differences between collection by gavage flushing or dissection. Using weighted Unifrac and Aitchison taxonomic distances between gavage and dissection samples were not significantly different from distances between gavage samples themselves, and no significant difference was found in the taxonomic composition of mice which were sampled repeatedly. Finally, relative abundances of specific identified taxa were compared, and eleven taxa were found to differ in frequency between collection methods. Using the more stringent Analysis of Composition of Microbiomes (ANCOM), seven was found to differ. Similarly, no significant differences were uncovered using these analyses over multiple samples by gastric flush.

CONCLUSION: In summary, the consistency of the microbiota collected by gastric flushing recommends its use for microbiome analysis of gastric fluid similar to the use of fecal sampling to study the gut lumen microbiome.},
}

@article {pmid38653241,
year = {2024},
author = {Wilde, J and Boyes, R and Robinson, AV and Daisley, BA and Botschner, AJ and Brettingham, DJL and Macpherson, CV and Mallory, E and Allen-Vercoe, E},
title = {Assessing phage-host population dynamics by reintroducing virulent viruses to synthetic microbiomes.},
journal = {Cell host & microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2024.04.001},
pmid = {38653241},
issn = {1934-6069},
abstract = {Microbiomes feature complex interactions between diverse bacteria and bacteriophages. Synthetic microbiomes offer a powerful way to study these interactions; however, a major challenge is obtaining a representative bacteriophage population during the bacterial isolation process. We demonstrate that colony isolation reliably excludes virulent viruses from sample sources with low virion-to-bacteria ratios such as feces, creating "virulent virus-free" controls. When the virulent dsDNA virome is reintroduced to a 73-strain synthetic gut microbiome in a bioreactor model of the human colon, virulent viruses target susceptible strains without significantly altering community structure or metabolism. In addition, we detected signals of prophage induction that associate with virulent predation. Overall, our findings indicate that dilution-based isolation methods generate synthetic gut microbiomes that are heavily depleted, if not devoid, of virulent viruses and that such viruses, if reintroduced, have a targeted effect on community assembly, metabolism, and prophage replication.},
}

@article {pmid38653031,
year = {2024},
author = {Gao, M and Kirk, M and Lash, E and Knight, H and Michalopoulou, M and Guess, N and Browning, M and Weich, S and Burnet, P and Jebb, SA and Stevens, R and Aveyard, P},
title = {Evaluating the efficacy and mechanisms of a ketogenic diet as adjunctive treatment for people with treatment-resistant depression: A protocol for a randomised controlled trial.},
journal = {Journal of psychiatric research},
volume = {174},
number = {},
pages = {230-236},
doi = {10.1016/j.jpsychires.2024.04.023},
pmid = {38653031},
issn = {1879-1379},
abstract = {BACKGROUND: One-third of people with depression do not respond to antidepressants, and, after two adequate courses of antidepressants, are classified as having treatment-resistant depression (TRD). Some case reports suggest that ketogenic diets (KDs) may improve some mental illnesses, and preclinical data indicate that KDs can influence brain reward signalling, anhedonia, cortisol, and gut microbiome which are associated with depression. To date, no trials have examined the clinical effect of a KD on TRD.

METHODS: This is a proof-of-concept randomised controlled trial to investigate the efficacy of a six-week programme of weekly dietitian counselling plus provision of KD meals, compared with an intervention involving similar dietetic contact time and promoting a healthy diet with increased vegetable consumption and reduction in saturated fat, plus food vouchers to purchase healthier items. At 12 weeks we will assess whether participants have continued to follow the assigned diet. The primary outcome is the difference between groups in the change in Patient Health Questionnaire-9 (PHQ-9) score from baseline to 6 weeks. PHQ-9 will be measured at weeks 2, 4, 6 and 12. The secondary outcomes are the differences between groups in the change in remission of depression, change in anxiety score, functioning ability, quality of life, cognitive performance, reward sensitivity, and anhedonia from baseline to 6 and 12 weeks. We will also assess whether changes in reward sensitivity, anhedonia, cortisol awakening response and gut microbiome may explain any changes in depression severity.

DISCUSSION: This study will test whether a ketogenic diet is an effective intervention to reduce the severity of depression, anxiety and improve quality of life and functioning ability for people with treatment-resistant depression.},
}

@article {pmid38652460,
year = {2024},
author = {Blijlevens, NMA and Reijnders, B and Molendijk, E},
title = {Gastrointestinal mucositis: a sign of a (systemic) inflammatory response.},
journal = {Current opinion in supportive and palliative care},
volume = {},
number = {},
pages = {},
doi = {10.1097/SPC.0000000000000701},
pmid = {38652460},
issn = {1751-4266},
abstract = {PURPOSE OF REVIEW: Gastrointestinal mucositis (GIM) is a significant complication of cancer therapy. Whilst inflammation is a central feature of GIM, studies attempting to mitigate mucosal damage via this mechanism are scarce. This review describes the relation between GIM, local and systemic inflammation, and the microbiome and its metabolites, and explores recent research on therapeutics that target this relationship.

RECENT FINDINGS: Recent literature underscores the pivotal role of inflammation in GIM, elucidating its bidirectional relation with disturbance of the gut microbiota composition and intestinal permeability. These events cause a heightened risk of bloodstream infections and lead to systemic inflammation. While studies investigating risk prediction models or therapeutics targeting GIM-related inflammation remain scarce, results have shown promise in finding biomarkers and alleviating GIM and its accompanying clinical symptoms.

SUMMARY: The findings underscore the important role of inflammation and the microbiome in GIM. Understanding the inflammatory pathways driving GIM is crucial for developing effective treatments. Further research is needed using genomics, epigenomics, and microbiomics to explore better risk prediction models or therapeutic strategies aimed at mitigating GIM-related inflammation.},
}

@article {pmid38652457,
year = {2024},
author = {Leonidou, N and Ostyn, L and Coenye, T and Crabbé, A and Dräger, A},
title = {Genome-scale model of Rothia mucilaginosa predicts gene essentialities and reveals metabolic capabilities.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0400623},
doi = {10.1128/spectrum.04006-23},
pmid = {38652457},
issn = {2165-0497},
abstract = {Cystic fibrosis (CF), an inherited genetic disorder caused by mutations in the cystic fibrosis transmembrane conductance regulator gene, results in sticky and thick mucosal fluids. This environment facilitates the colonization of various microorganisms, some of which can cause acute and chronic lung infections, while others may positively impact the disease. Rothia mucilaginosa, an oral commensal, is relatively abundant in the lungs of CF patients. Recent studies have unveiled its anti-inflammatory properties using in vitro three-dimensional lung epithelial cell cultures and in vivo mouse models relevant to chronic lung diseases. Apart from this, R. mucilaginosa has been associated with severe infections. However, its metabolic capabilities and genotype-phenotype relationships remain largely unknown. To gain insights into its cellular metabolism and genetic content, we developed the first manually curated genome-scale metabolic model, iRM23NL. Through growth kinetics and high-throughput phenotypic microarray testings, we defined its complete catabolic phenome. Subsequently, we assessed the model's effectiveness in accurately predicting growth behaviors and utilizing multiple substrates. We used constraint-based modeling techniques to formulate novel hypotheses that could expedite the development of antimicrobial strategies. More specifically, we detected putative essential genes and assessed their effect on metabolism under varying nutritional conditions. These predictions could offer novel potential antimicrobial targets without laborious large-scale screening of knockouts and mutant transposon libraries. Overall, iRM23NL demonstrates a solid capability to predict cellular phenotypes and holds immense potential as a valuable resource for accurate predictions in advancing antimicrobial therapies. Moreover, it can guide metabolic engineering to tailor R. mucilaginosa's metabolism for desired performance.IMPORTANCECystic fibrosis (CF) is a genetic disorder characterized by thick mucosal secretions, leading to chronic lung infections. Rothia mucilaginosa is a common bacterium found in various parts of the human body, acting as a normal part of the flora. In people with weakened immune systems, it can become an opportunistic pathogen, while it is prevalent and active in CF airways. Recent studies have highlighted its anti-inflammatory properties in the lower pulmonary system, indicating the intricate relationship between microbes and human health. Herein, we have developed the first manually curated metabolic model of R. mucilaginosa. Our study examined the previously unknown relationships between the bacterium's genotype and phenotype and identified essential genes that impact the metabolism under various conditions. With this, we opt for paving the way for developing new strategies in antimicrobial therapy and metabolic engineering, leading to enhanced therapeutic outcomes in cystic fibrosis and related conditions.},
}

@article {pmid38651930,
year = {2024},
author = {Reygner, J and Delannoy, J and Barba-Goudiaby, M-T and Gasc, C and Levast, B and Gaschet, E and Ferraris, L and Paul, S and Kapel, N and Waligora-Dupriet, A-J and Barbut, F and Thomas, M and Schwintner, C and Laperrousaz, B and Corvaïa, N},
title = {Reduction of product composition variability using pooled microbiome ecosystem therapy and consequence in two infectious murine models.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0001624},
doi = {10.1128/aem.00016-24},
pmid = {38651930},
issn = {1098-5336},
abstract = {Growing evidence demonstrates the key role of the gut microbiota in human health and disease. The recent success of microbiotherapy products to treat recurrent Clostridioides difficile infection has shed light on its potential in conditions associated with gut dysbiosis, such as acute graft-versus-host disease, intestinal bowel diseases, neurodegenerative diseases, or even cancer. However, the difficulty in defining a "good" donor as well as the intrinsic variability of donor-derived products' taxonomic composition limits the translatability and reproducibility of these studies. Thus, the pooling of donors' feces has been proposed to homogenize product composition and achieve higher taxonomic richness and diversity. In this study, we compared the metagenomic profile of pooled products to corresponding single donor-derived products. We demonstrated that pooled products are more homogeneous, diverse, and enriched in beneficial bacteria known to produce anti-inflammatory short chain fatty acids compared to single donor-derived products. We then evaluated pooled products' efficacy compared to corresponding single donor-derived products in Salmonella and C. difficile infectious mouse models. We were able to demonstrate that pooled products decreased pathogenicity by inducing a structural change in the intestinal microbiota composition. Single donor-derived product efficacy was variable, with some products failing to control disease progression. We further performed in vitro growth inhibition assays of two extremely drug-resistant bacteria, Enterococcus faecium vanA and Klebsiella pneumoniae oxa48, supporting the use of pooled microbiotherapies. Altogether, these results demonstrate that the heterogeneity of donor-derived products is corrected by pooled fecal microbiotherapies in several infectious preclinical models.IMPORTANCEGrowing evidence demonstrates the key role of the gut microbiota in human health and disease. Recent Food and Drug Administration approval of fecal microbiotherapy products to treat recurrent Clostridioides difficile infection has shed light on their potential to treat pathological conditions associated with gut dysbiosis. In this study, we combined metagenomic analysis with in vitro and in vivo studies to compare the efficacy of pooled microbiotherapy products to corresponding single donor-derived products. We demonstrate that pooled products are more homogeneous, diverse, and enriched in beneficial bacteria compared to single donor-derived products. We further reveal that pooled products decreased Salmonella and Clostridioides difficile pathogenicity in mice, while single donor-derived product efficacy was variable, with some products failing to control disease progression. Altogether, these findings support the development of pooled microbiotherapies to overcome donor-dependent treatment efficacy.},
}

@article {pmid38651909,
year = {2024},
author = {Choi, BI and Fontes Noronha, M and Kaindl, J and Wolfe, AJ},
title = {Complete genome sequences of Aerococcus loyolae ATCC TSD-300[T], Aerococcus mictus ATCC TSD-301[T], and Aerococcus tenax ATCC TSD-302[T].},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0015624},
doi = {10.1128/mra.00156-24},
pmid = {38651909},
issn = {2576-098X},
abstract = {Previously identified under the single designation of Aerococcus urinae, three distinct taxonomic species have been distinguished as Aerococcus loyolae, Aerococcus mictus, and Aerococcus tenax. Here, we present the complete genome sequences of the type strains of these species assembled via a combination of short-read and long-read sequencing techniques.Registered at ClinicalTrials.gov (NCT01166438).},
}

@article {pmid38651859,
year = {2024},
author = {Cai, X and Yi, P and Chen, X and Wu, J and Lan, G and Li, S and Luo, S and Huang, F and Huang, J and Shen, P},
title = {Intake of compound probiotics accelerates the construction of immune function and gut microbiome in Holstein calves.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0190923},
doi = {10.1128/spectrum.01909-23},
pmid = {38651859},
issn = {2165-0497},
abstract = {UNLABELLED: Acquired immunity is an important way to construct the intestinal immune barrier in mammals, which is almost dependent on suckling. To develop a new strategy for accelerating the construction of gut microbiome, newborn Holstein calves were continuously fed with 40 mL of compound probiotics (containing Lactobacillus plantarum T-14, Enterococcus faecium T-11, Saccharomyces cerevisiae T-209, and Bacillus licheniformis T-231) per day for 60 days. Through diarrhea rate monitoring, immune index testing, antioxidant capacity detection, and metagenome sequencing, the changes in diarrhea incidence, average daily gain, immune index, and gut microbiome of newborn calves within 60 days were investigated. Results indicated that feeding the compound probiotics reduced the average diarrhea rate of calves by 42.90%, increased the average daily gain by 43.40%, raised the antioxidant indexes of catalase, superoxide dismutase, total antioxidant capacity, and Glutathione peroxidase by 22.81%, 6.49%, 8.33%, and 13.67%, respectively, and increased the immune indexes of IgA, IgG, and IgM by 10.44%, 4.85%, and 6.12%, respectively. Moreover, metagenome sequencing data showed that feeding the compound probiotics increased the abundance of beneficial strains (e.g., Lactococcus lactis and Bacillus massionigeriensis) and decreased the abundance of some harmful strains (e.g., Escherichia sp. MOD1-EC5189 and Mycobacterium brisbane) in the gut microbiome of calves, thus contributing to accelerating the construction of healthy gut microbiome in newborn Holstein calves.

IMPORTANCE: The unstable gut microbiome and incomplete intestinal function of newborn calves are important factors for the high incidence of early diarrhea. This study presents an effective strategy to improve the overall immunity and gut microbiome in calves and provides new insights into the application of compound probiotics in mammals.},
}

@article {pmid38651848,
year = {2023},
author = {Belamarić, M and Miše, J and Bukvić Mokos, Z},
title = {The Association Between Hidradenitis Suppurativa and Diet: An Update.},
journal = {Acta dermatovenerologica Croatica : ADC},
volume = {31},
number = {4},
pages = {213-219},
pmid = {38651848},
issn = {1847-6538},
abstract = {Hidradenitis suppurativa (HS) is a chronic inflammatory skin condition characterized by painful inflammatory lesions, predominantly affecting areas of the skin rich in apocrine glands, such as inguinal, axillary, submammary, and anogenital regions, with an estimated global prevalence between 1%-4%. The treatment of HS is challenging with various treatment modalities employed to control the disease. Since the condition is chronic and life-impairing, many patients have looked for ways to complement their conventional treatment procedures with non-medical interventions, among which dietary interventions have been of particular interest. Researchers have looked for ways to connect the gastrointestinal system with the skin through the ˝skin-gut axis concept˝ introducing a strong association between the microbiome of the gastrointestinal system and the skin. In addition, diet stimulation of insulin and IGF-1 (insulin-like growth factor 1) may impact signaling pathways playing a role in HS pathogenesis. Patients have tried various dietary interventions to alleviate their symptoms of inflammation and suppuration. Among the different dietary approaches that have been described are paleo, autoimmune, Mediterranean, and elimination diet regimes. Dietary supplements have become the mainstay of lifestyle factors aimed at improving the clinical signs and symptoms of HS. This review aims to synthesize and present the current findings on diet as a modifiable factor in HS, helping the patients to navigate through the data and helping them make informed choices on their healthy lifestyles.},
}

@article {pmid38651671,
year = {2024},
author = {Pokrotnieks, J and Sitkin, S},
title = {He who controls Clostridia and Bacteroidia controls the gut microbiome: The concept of targeted probiotics to restore the balance of keystone taxa in irritable bowel syndrome.},
journal = {Neurogastroenterology and motility},
volume = {},
number = {},
pages = {e14805},
doi = {10.1111/nmo.14805},
pmid = {38651671},
issn = {1365-2982},
abstract = {This article describes the concept of probiotics for patients with irritable bowel syndrome to target functionally active bacteria predominantly belonging to the Clostridia and Bacteroidia, which play a key role in maintaining the balance of the gut microbiota.},
}

@article {pmid38651370,
year = {2024},
author = {Mavrogeorgis, E and Valkenburg, S and Siwy, J and Latosinska, A and Glorieux, G and Mischak, H and Jankowski, J},
title = {Integration of Urinary Peptidome and Fecal Microbiome to Explore Patient Clustering in Chronic Kidney Disease.},
journal = {Proteomes},
volume = {12},
number = {2},
pages = {},
pmid = {38651370},
issn = {2227-7382},
support = {Horizon 2020 research and innovation program Marie-Curie ITN "STRATEGY-CKD" (Grant agreement ID: 860329)//European Union/ ; SFB/TRR 219 project-ID: 322900939//Deutsche Forschungsgemeinschaft/ ; SFB 1382 Project-ID 403224013//Deutsche Forschungsgemeinschaft/ ; },
abstract = {Millions of people worldwide currently suffer from chronic kidney disease (CKD), requiring kidney replacement therapy at the end stage. Endeavors to better understand CKD pathophysiology from an omics perspective have revealed major molecular players in several sample sources. Focusing on non-invasive sources, gut microbial communities appear to be disturbed in CKD, while numerous human urinary peptides are also dysregulated. Nevertheless, studies often focus on isolated omics techniques, thus potentially missing the complementary pathophysiological information that multidisciplinary approaches could provide. To this end, human urinary peptidome was analyzed and integrated with clinical and fecal microbiome (16S sequencing) data collected from 110 Non-CKD or CKD individuals (Early, Moderate, or Advanced CKD stage) that were not undergoing dialysis. Participants were visualized in a three-dimensional space using different combinations of clinical and molecular data. The most impactful clinical variables to discriminate patient groups in the reduced dataspace were, among others, serum urea, haemoglobin, total blood protein, urinary albumin, urinary erythrocytes, blood pressure, cholesterol measures, body mass index, Bristol stool score, and smoking; relevant variables were also microbial taxa, including Roseburia, Butyricicoccus, Flavonifractor, Burkholderiales, Holdemania, Synergistaceae, Enterorhabdus, and Senegalimassilia; urinary peptidome fragments were predominantly derived from proteins of collagen origin; among the non-collagen parental proteins were FXYD2, MGP, FGA, APOA1, and CD99. The urinary peptidome appeared to capture substantial variation in the CKD context. Integrating clinical and molecular data contributed to an improved cohort separation compared to clinical data alone, indicating, once again, the added value of this combined information in clinical practice.},
}

@article {pmid38650943,
year = {2024},
author = {Matsutani, T and Akbay, E and Elkord, E},
title = {Editorial: Novel biomarkers in tumor immunity and immunotherapy.},
journal = {Frontiers in immunology},
volume = {15},
number = {},
pages = {1405082},
doi = {10.3389/fimmu.2024.1405082},
pmid = {38650943},
issn = {1664-3224},
}

@article {pmid38650928,
year = {2024},
author = {Chai, Y and Liu, X and Bai, G and Zhou, N and Liu, D and Zhang, X and Li, M and Li, K and Lei, H},
title = {Gut microbiome, T cell subsets, and cytokine analysis identify differential biomarkers in tuberculosis.},
journal = {Frontiers in immunology},
volume = {15},
number = {},
pages = {1323723},
pmid = {38650928},
issn = {1664-3224},
abstract = {INTRODUCTION: The gut microbiota, T cell subsets, and cytokines participate in tuberculosis (TB) pathogenesis. To date, the mechanisms by which these factors interactively promote TB development at different time points remain largely unclear. In the context of this study, We looked into the microorganisms in the digestive tract, T cell types, and cytokines related to tuberculosis.

METHODS: According to QIIME2, we analyzed 16SrDNA sequencing of the gut microbiome on the Illumina MiSeq. Enzyme-linked immunosorbent assay was used to measure the concentrations of cytokines.

RESULTS: We showed the presence of 26 identifiable differential microbiomes in the gut and 44 metabolic pathways between healthy controls and the different time points in the development of TB in patients. Five bacterial genera (Bacteroides, Bifidobacterium, Faecalibacterium, Collinsella, and Clostridium) were most closely associated with CD4/CD8, whereas three bacterial taxa (Faecalibacterium, Collinsella, and Clostridium) were most closely associated with CD4. Three bacterial taxa (Faecalibacterium, Ruminococcus, and Dorea) were most closely associated with IL-4. Ruminococcus was most closely associated with IL-2 and IL-10.

CONCLUSION: Diverse microorganisms, subsets of T cells, and cytokines, exhibiting varying relative abundances and structural compositions, were observed in both healthy controls and patients throughout distinct phases of tuberculosis. Gaining insight into the function of the gut microbiome, T cell subsets, and cytokines may help modulate therapeutic strategies for TB.},
}

@article {pmid38650882,
year = {2024},
author = {Bao, YQ and Zhang, Y and Li, ZN},
title = {Causal associations between gut microbiota and cutaneous melanoma: a Mendelian randomization study.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1339621},
pmid = {38650882},
issn = {1664-302X},
abstract = {BACKGROUND: Cutaneous melanoma (CM) of the skin stands as the leading cause of mortality among skin cancer-related deaths. Despite the successes achieved with novel therapies such as immunotherapy and targeted therapy, their efficacy remains limited, necessitating further exploration of new treatment modalities. The gut microbiota and CM may be linked, as indicated by a growing body of preclinical and observational research. Nevertheless, the exact correlation between the intestinal microbiota and CM remains to be determined. Therefore, this study aims to assess the potential causal relationship between the gut microbiota and CM.

METHODS: The study utilized exposure data obtained from the MiBioGen consortium's microbiome GWAS, which included a total of 18,340 samples gathered from 24 population-based cohorts. Data at the summary level for CM were acquired from the UK Biobank investigation. The main analytical strategy utilized in this research was the inverse variance weighted (IVW) technique, supported by quality assurance measures like the weighted median model, MR-Egger, simple model, and weighted model approaches. The Cochran's Q test was used to evaluate heterogeneity. To ascertain potential pleiotropy, we employed both the MR-Egger regression and the MR-PRESSO test. Sensitivity analysis was conducted using the leave-one-out method.

RESULTS: The study found that the class Bacteroidia (OR = 0.997, 95% CI: 0.995-0.999, p = 0.027), genus Parabacteroides (OR = 0.997, 95% CI: 0.994-0.999, p = 0.037), order Bacteroidales (OR = 0.997, 95% CI: 0.995-0.999, p = 0.027), and genus Veillonella (OR = 0.998, 95% CI: 0.996-0.999, p = 0.046) have protective effects on CM. On the order hand, the genus Blautia (OR = 1.003, 95% CI: 1-1.006, p = 0.001) and phylum Cyanobacteria (OR = 1.002, 95% CI: 1-1.004, p = 0.04) are identified as risk factors for CM.

CONCLUSION: We comprehensively assessed the potential causal relationship between the gut microbiota and CM and identified associations between six gut microbiota and CM. Among these, four gut microbiota were identified as protective factors for CM, while two gut microbiota were identified as risk factors for CM. This study effectively established a causal relationship between the gut microbiota and CM, thereby providing valuable insights into the mechanistic pathways through which the microbiota impacts the progression of CM.},
}

@article {pmid38650709,
year = {2024},
author = {Pan, Z and Ma, T and Steele, M and Guan, LL},
title = {Varied microbial community assembly and specialization patterns driven by early life microbiome perturbation and modulation in young ruminants.},
journal = {ISME communications},
volume = {4},
number = {1},
pages = {ycae044},
pmid = {38650709},
issn = {2730-6151},
abstract = {Perturbations and modulations during early life are vital to affect gut microbiome assembly and establishment. In this study, we assessed how microbial communities shifted during calf diarrhea and with probiotic yeast supplementation (Saccharomyces cerevisiae var. boulardii, SCB) and determined the key bacterial taxa contributing to the microbial assembly shifts using a total of 393 fecal samples collected from 84 preweaned calves during an 8-week trial. Our results revealed that the microbial assembly patterns differed between healthy and diarrheic calves at 6- and 8-week of the trial, with healthy calves being stochastic-driven and diarrheic calves being deterministic-driven. The two-state Markov model revealed that SCB supplementation had a higher possibility to shift microbial assembly from deterministic- to stochastic-driven in diarrheic calves. Furthermore, a total of 23 and 21 genera were specific ecotypes to assembly patterns in SCB-responsive (SCB-fed calves did not exhibit diarrhea) and nonresponsive (SCB-fed calves occurred diarrhea) calves, respectively. Among these ecotypes, the area under a receiver operating characteristic curve revealed that Blautia and Ruminococcaceae UCG 014, two unidentified genera from the Ruminococcaceae family, had the highest predictiveness for microbial assembly patterns in SCB-responsive calves, while Prevotellaceae, Blautia, and Escherichia-Shigella were the most predictive bacterial taxa for microbial assembly patterns in SCB-nonresponsive calves. Our study suggests that microbiome perturbations and probiotic yeast supplementation serving as deterministic factors influenced assembly patterns during early life with critical genera being predictive for assembly patterns, which sheds light on mechanisms of microbial community establishment in the gut of neonatal calves during early life.},
}

@article {pmid38650647,
year = {2024},
author = {Tunsakul, N and Wongsaroj, L and Janchot, K and Pongpirul, K and Somboonna, N},
title = {Non-significant influence between aerobic and anaerobic sample transport materials on gut (fecal) microbiota in healthy and fat-metabolic disorder Thai adults.},
journal = {PeerJ},
volume = {12},
number = {},
pages = {e17270},
pmid = {38650647},
issn = {2167-8359},
mesh = {Humans ; Adult ; *Gastrointestinal Microbiome/physiology/genetics ; *Feces/microbiology ; Thailand ; Male ; *RNA, Ribosomal, 16S/genetics ; Female ; Young Adult ; Specimen Handling/methods ; Anaerobiosis/physiology ; Aerobiosis ; Metagenomics ; Southeast Asian People ; },
abstract = {BACKGROUND: The appropriate sample handling for human fecal microbiota studies is essential to prevent changes in bacterial composition and quantities that could lead to misinterpretation of the data.

METHODS: This study firstly identified the potential effect of aerobic and anaerobic fecal sample collection and transport materials on microbiota and quantitative microbiota in healthy and fat-metabolic disorder Thai adults aged 23-43 years. We employed metagenomics followed by 16S rRNA gene sequencing and 16S rRNA gene qPCR, to analyze taxonomic composition, alpha diversity, beta diversity, bacterial quantification, Pearson's correlation with clinical factors for fat-metabolic disorder, and the microbial community and species potential metabolic functions.

RESULTS: Our study successfully obtained microbiota results in percent and quantitative compositions. Each sample exhibited quality sequences with a >99% Good's coverage index, and a relatively plateau rarefaction curve. Alpha diversity indices showed no statistical difference in percent and quantitative microbiota OTU richness and evenness, between aerobic and anaerobic sample transport materials. Obligate and facultative anaerobic species were analyzed and no statistical difference was observed. Supportively, the beta diversity analysis by non-metric multidimensional scale (NMDS) constructed using various beta diversity coefficients showed resembling microbiota community structures between aerobic and anaerobic sample transport groups (P = 0.86). On the other hand, the beta diversity could distinguish microbiota community structures between healthy and fat-metabolic disorder groups (P = 0.02), along with Pearson's correlated clinical parameters (i.e., age, liver stiffness, GGT, BMI, and TC), the significantly associated bacterial species and their microbial metabolic functions. For example, genera such as Ruminococcus and Bifidobacterium in healthy human gut provide functions in metabolisms of cofactors and vitamins, biosynthesis of secondary metabolites against gut pathogens, energy metabolisms, digestive system, and carbohydrate metabolism. These microbial functional characteristics were also predicted as healthy individual biomarkers by LEfSe scores. In conclusion, this study demonstrated that aerobic sample collection and transport (<48 h) did not statistically affect the microbiota and quantitative microbiota analyses in alpha and beta diversity measurements. The study also showed that the short-term aerobic sample collection and transport still allowed fecal microbiota differentiation between healthy and fat-metabolic disorder subjects, similar to anaerobic sample collection and transport. The core microbiota were analyzed, and the findings were consistent. Moreover, the microbiota-related metabolic potentials and bacterial species biomarkers in healthy and fat-metabolic disorder were suggested with statistical bioinformatics (i.e., Bacteroides plebeius).},
}

Humans
Adult
*Gastrointestinal Microbiome/physiology/genetics
*Feces/microbiology
Thailand
Male
*RNA, Ribosomal, 16S/genetics
Female
Young Adult
Specimen Handling/methods
Anaerobiosis/physiology
Aerobiosis
Metagenomics
Southeast Asian People

@article {pmid38650589,
year = {2024},
author = {Chang, CC and Liu, TC and Lu, CJ and Chiu, HC and Lin, WN},
title = {Explainable machine learning model for identifying key gut microbes and metabolites biomarkers associated with myasthenia gravis.},
journal = {Computational and structural biotechnology journal},
volume = {23},
number = {},
pages = {1572-1583},
pmid = {38650589},
issn = {2001-0370},
abstract = {Diagnostic markers for myasthenia gravis (MG) are limited; thus, innovative approaches are required for supportive diagnosis and personalized care. Gut microbes are associated with MG pathogenesis; however, few studies have adopted machine learning (ML) to identify the associations among MG, gut microbiota, and metabolites. In this study, we developed an explainable ML model to predict biomarkers for MG diagnosis. We enrolled 19 MG patients and 10 non-MG individuals. Stool samples were collected and microbiome assessment was performed using 16S rRNA sequencing. Untargeted metabolic profiling was conducted to identify fecal amplicon significant variants (ASVs) and metabolites. We developed an explainable ML model in which the top ASVs and metabolites are combined to identify the best predictive performance. This model uses the SHapley Additive exPlanations method to generate both global and personalized explanations. Fecal microbe-metabolite composition differed significantly between groups. The key bacterial families were Lachnospiraceae and Ruminococcaceae, and the top three features were Lachnospiraceae, inosine, and methylhistidine. An ML model trained with the top 1 % ASVs and top 15 % metabolites combined outperformed all other models. Personalized explanations revealed different patterns of microbe-metabolite contributions in patients with MG. The integration of the microbiota-metabolite features and the development of an explainable ML framework can accurately identify MG and provide personalized explanations, revealing the associations between gut microbiota, metabolites, and MG. An online calculator employing this algorithm was developed that provides a streamlined interface for MG diagnosis screening and conducting personalized evaluations.},
}

@article {pmid38650068,
year = {2024},
author = {Cerqueira, AES and Lima, HS and Silva, LCF and Veloso, TGR and de Paula, SO and Santana, WC and da Silva, CC},
title = {Melipona stingless bees and honey microbiota reveal the diversity, composition, and modes of symbionts transmission.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiae063},
pmid = {38650068},
issn = {1574-6941},
abstract = {The Melipona gut microbes differ from other social bees, with the absence of crucial corbiculate core gut symbionts and the high occurrence of environmental strains. We studied the microbial diversity and composition of three Melipona species and their honey to understand which strains are obtained by horizontal transmission (HT) from the pollination environment; or represent symbionts co-evolved with Melipona by HT from the hive/food stores or vertical transmission (VT) via social interactions. Bees harbored higher microbial alpha diversity and a different and more species-specific bacterial composition than honey. Otherwise, the fungal communities of bee and honey samples are less dissimilar. As expected, the core symbionts Snodgrassella and Gilliamella were absent in bees that had a prevalence of Lactobacillus Firm-5, environmental Lactobacillaceae, Bifidobacteriaceae and Acetobacteraceae. Also, Pectinatus and Floricoccus have habitat preferences for bees, putatively representing novel symbionts from the environment that co-evolved via VT among generations. Fructilactobacillus found in bees possibly had HT to bees from honey stores. Metschnikowia yeasts, consistent in all bees and honey samples, might have HT to bees from food stores. Similarly, Saccharomycetales might have HT from honey or plants/flowers to bees. This work contributes to the understanding of Melipona symbionts and their modes of transmission.},
}

@article {pmid38650030,
year = {2024},
author = {Brunner, LM and Riebel, M and Wein, S and Koller, M and Zeman, F and Huppertz, G and Emmer, T and Eberhardt, Y and Schwarzbach, J and Rupprecht, R and Nothdurfter, C},
title = {The translocator protein 18kDa ligand etifoxine in the treatment of depressive disorders-a double-blind, randomized, placebo-controlled proof-of-concept study.},
journal = {Trials},
volume = {25},
number = {1},
pages = {274},
pmid = {38650030},
issn = {1745-6215},
support = {422179811//Deutsche Forschungsgemeinschaft/ ; },
abstract = {BACKGROUND: Recent developments suggest that neurosteroids may achieve rapid antidepressant effects. As such, neurosteroidogenesis mediated by the translocator protein 18 kDa (TSPO) might constitute a promising option for the treatment of depression. Therefore, the current clinical trial aims to get the first evidence of whether TPSO ligands promote rapid antidepressant effects. Furthermore, we study which mechanisms of action, e.g., modulation of distinct neuronal networks, neurosteroidogenesis, endocrinological mechanisms, TSPO expression or microbiome composition, contribute to their putative antidepressant effects.

METHODS: This is a randomized, placebo-controlled, double-blind single-center trial of 2-week treatment with the TSPO ligand etifoxine versus placebo in depressive patients. Main eligibility criteria: male or female individuals aged 18 to 65 years with unipolar/bipolar depressive disorder with no other psychiatric main diagnosis or acute neurological/somatic disorder or drug/alcohol dependence during their lifetime. The primary endpoint is the time point at which 50% of the maximal effect has occurred (ET50) estimated by the scores of the Hamilton Depression Scale (HAMD-21). A total of 20 patients per group are needed to detect changes of therapeutic efficacy about 5% and changes of ET50 about 10% with a power of 70%. Assuming a drop-out rate of 10-20%, 50 patients will be randomized in total. The study will be conducted at the Department of Psychiatry and Psychotherapy of the University of Regensburg.

DISCUSSION: This study will provide a first proof-of-concept on the potential of the TSPO ligand etifoxine in the treatment of depressive disorders.

TRIAL REGISTRATION: Clinical Trials Register (EudraCT number: 2021-006773-38 , registration date: 14 September 2022) and German Register of Clinical Studies (DRKS number: DRKS00031099 , registration date: 23 January 2023).},
}

@article {pmid38649625,
year = {2024},
author = {Lee, JJ and Chien, AL},
title = {Rosacea in Older Adults and Pharmacologic Treatments.},
journal = {Drugs & aging},
volume = {},
number = {},
pages = {},
pmid = {38649625},
issn = {1179-1969},
abstract = {Rosacea is a chronic inflammatory skin condition that is often more severe in older patients. The main clinical features are erythema, telangiectasia, and inflammatory lesions of the face. The pathogenesis of this condition is not fully understood but certainly multifaceted. Immune and inflammatory dysregulation, genetics, neurogenic dysregulation, microbiome dysbiosis, and systemic disease have all been implicated in rosacea pathogenesis. As we better understand the various pathways that lead to rosacea, we acknowledge that the different symptoms may have unique underlying triggers and mechanisms. Aging also impacts rosacea diagnosis and treatment. Older adults have more severe rosacea symptoms while also having more sensitive and fragile skin than younger patients; therefore, rosacea treatments for older patients require a balance between delivering adequate potency while also minimizing skin irritation and other adverse effects. Until recently, rosacea diagnoses were based on concrete subtypes that did not necessarily capture each patient's manifestation of rosacea. There is now an emphasis on more personalized phenotype-based diagnoses and treatments, which allows for more emphasis on treating individual symptoms and accounting for the unique characteristics of older patients. Centrofacial erythema is best treated with brimonidine and oxymetazoline, while phymatous change and telangiectasia are best treated with surgery and laser ablation. Treatment for rosacea papules and pustules ranges from topicals, such as azelaic acid, ivermectin, metronidazole, minocycline, and encapsulated benzoyl peroxide, to systemics, such as doxycycline and isotretinoin. It is important to understand these treatments in relation to adverse effects and drug interactions that may specifically arise in older populations to provide optimal care. As we advance in understanding rosacea's pathogenesis and adopt personalized phenotype-based approaches, optimizing care for older patients becomes crucial. Continued research into novel treatments is essential to address their unique needs.},
}

@article {pmid38649387,
year = {2024},
author = {Park, J and Jung, SY and Kim, HY and Lee, KE and Go, YJ and Kim, HS and Yoon, SY and Kwon, CO and Park, YS},
title = {Microbiomic association between the saliva and salivary stone in patients with sialolithiasis.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {9184},
pmid = {38649387},
issn = {2045-2322},
support = {Ewha Womans University Research Grant of 2021//Ewha Womans University/ ; 2020R1C1C1011612, 2020R1A2C1101340//National Research Foundation of Korea/ ; 2020R1C1C1011612, 2020R1A2C1101340//National Research Foundation of Korea/ ; 1415180861//Ministry of Trade, Industry and Energy/ ; 1415180861//Ministry of Trade, Industry and Energy/ ; 1415180861//Ministry of Trade, Industry and Energy/ ; the Research Year of Chungbuk National University in 2023//Chungbuk National University/ ; },
abstract = {Salivary stones, known as sialoliths, form within the salivary ducts due to abnormal salivary composition and cause painful symptoms, for which surgical removal is the primary treatment. This study explored the role of the salivary microbial communities in the formation of sialoliths. We conducted a comparative analysis of microbial communities present in the saliva and salivary stones, and sequenced the 16S rRNA gene in samples obtained from patients with sialoliths and from healthy individuals. Although the diversity in the saliva was high, the essential features of the microbial environment in sialoliths were low diversity and evenness. The association of microbial abundance between stones and saliva revealed a positive correlation between Peptostreptococcus and Porphyromonas, and a negative correlation for Pseudomonas in saliva. The functional potential differences between saliva and stones Bacterial chemotaxis and the citrate cycle were negatively correlated with most genera found in salivary stone samples. However, the functions required for organic compound degradation did not differ between the saliva samples. Although some microbes were shared between the sialoliths and saliva, their compositions differed significantly. Our study presents a novel comparison between salivary stones and salivary microbiomes, suggesting potential preventive strategies against sialolithiasis.},
}

@article {pmid38649365,
year = {2024},
author = {Kwon, D and Zhang, K and Paul, KC and Folle, AD and Del Rosario, I and Jacobs, JP and Keener, AM and Bronstein, JM and Ritz, B},
title = {Diet and the gut microbiome in patients with Parkinson's disease.},
journal = {NPJ Parkinson's disease},
volume = {10},
number = {1},
pages = {89},
pmid = {38649365},
issn = {2373-8057},
abstract = {It has been suggested that gut microbiota influence Parkinson's disease (PD) via the gut-brain axis. Here, we examine associations between diet and gut microbiome composition and its predicted functional pathways in patients with PD. We assessed gut microbiota in fecal samples from 85 PD patients in central California using 16S rRNA gene sequencing. Diet quality was assessed by calculating the Healthy Eating Index 2015 (HEI-2015) based on the Diet History Questionnaire II. We examined associations of diet quality, fiber, and added sugar intake with microbial diversity, composition, taxon abundance, and predicted metagenomic profiles, adjusting for age, sex, race/ethnicity, and sequencing platform. Higher HEI scores and fiber intake were associated with an increase in putative anti-inflammatory butyrate-producing bacteria, such as the genera Butyricicoccus and Coprococcus 1. Conversely, higher added sugar intake was associated with an increase in putative pro-inflammatory bacteria, such as the genera Klebsiella. Predictive metagenomics suggested that bacterial genes involved in the biosynthesis of lipopolysaccharide decreased with higher HEI scores, whereas a simultaneous decrease in genes involved in taurine degradation indicates less neuroinflammation. We found that a healthy diet, fiber, and added sugar intake affect the gut microbiome composition and its predicted metagenomic function in PD patients. This suggests that a healthy diet may support gut microbiome that has a positive influence on PD risk and progression.},
}

@article {pmid38649355,
year = {2024},
author = {Qin, Y and Tong, X and Mei, WJ and Cheng, Y and Zou, Y and Han, K and Yu, J and Jie, Z and Zhang, T and Zhu, S and Jin, X and Wang, J and Yang, H and Xu, X and Zhong, H and Xiao, L and Ding, PR},
title = {Consistent signatures in the human gut microbiome of old- and young-onset colorectal cancer.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {3396},
pmid = {38649355},
issn = {2041-1723},
support = {82073159//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {The incidence of young-onset colorectal cancer (yCRC) has been increasing in recent decades, but little is known about the gut microbiome of these patients. Most studies have focused on old-onset CRC (oCRC), and it remains unclear whether CRC signatures derived from old patients are valid in young patients. To address this, we assembled the largest yCRC gut metagenomes to date from two independent cohorts and found that the CRC microbiome had limited association with age across adulthood. Differential analysis revealed that well-known CRC-associated taxa, such as Clostridium symbiosum, Peptostreptococcus stomatis, Parvimonas micra and Hungatella hathewayi were significantly enriched (false discovery rate <0.05) in both old- and young-onset patients. Similar strain-level patterns of Fusobacterium nucleatum, Bacteroides fragilis and Escherichia coli were observed for oCRC and yCRC. Almost all oCRC-associated metagenomic pathways had directionally concordant changes in young patients. Importantly, CRC-associated virulence factors (fadA, bft) were enriched in both oCRC and yCRC compared to their respective controls. Moreover, the microbiome-based classification model had similar predication accuracy for CRC status in old- and young-onset patients, underscoring the consistency of microbial signatures across different age groups.},
}

@article {pmid38649235,
year = {2024},
author = {Davies, J and Hawkins, S and Winters, A and Farrar, K},
title = {Bacterial endophytic community composition varies by hemp cultivar in commercially sourced seed.},
journal = {Environmental microbiology reports},
volume = {16},
number = {2},
pages = {e13259},
pmid = {38649235},
issn = {1758-2229},
support = {BB/T008776/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
abstract = {The seed-endophytic bacterial community is a potentially beneficial and heritable fraction of the plant microbiome. Its utilization as a sustainable crop improvement strategy could be especially valuable for species such as hemp, where production is being scaled up and new challenges will be faced in managing crop productivity and health. However, little is known about the makeup and variation of the hemp seed microbiome. This study profiled the endophytic bacterial communities harboured by 16 hemp cultivars sourced from commercial suppliers in Europe. A 16S rDNA amplicon sequencing approach identified 917 amplicon sequence variants across samples. Taxonomic classification of sequences revealed 4 phyla and 87 genera to be represented in the dataset. Several genera were widespread while some were specific to one or a few cultivars. Flavobacterium, Pseudomonas, and Pantoea were notable in their high overall abundance and prevalence, but community composition was variable and no one taxon was universally abundant, suggesting a high degree of flexibility in community assembly. Taxonomic composition and alpha diversity differed among cultivars, though further work is required to understand the relative influence of hemp genetic factors on community structure. The taxonomic profiles presented here can be used to inform further work investigating the functional characteristics and potential plant-growth-promoting traits of seed-borne bacteria in hemp.},
}

@article {pmid38649130,
year = {2024},
author = {Chesworth, R and Yim, HC and Watt, G and El-Omar, E and Karl, T},
title = {Cannabidiol (CBD) facilitates cocaine extinction and ameliorates cocaine-induced changes to the gut microbiome in male C57BL/6JArc mice.},
journal = {Progress in neuro-psychopharmacology & biological psychiatry},
volume = {133},
number = {},
pages = {111014},
doi = {10.1016/j.pnpbp.2024.111014},
pmid = {38649130},
issn = {1878-4216},
abstract = {Cocaine use disorder (CUD) is a global health problem with no approved medications. One potential treatment target is the gut microbiome, but it is unknown if cocaine induces long-lasting effects on gut microbes. A novel therapeutic candidate for CUD, cannabidiol (CBD), can improve gut function in rodent models. It is possible that protective effects of CBD against cocaine use are mediated by improving gut health. We examined this question in this experiment. Cocaine conditioned place preference (CPP) was conducted in adult male C57BL/6JArc mice. Mice were treated with vehicle or 20 mg/kg CBD prior to all cocaine CPP sessions (N = 11-13/group). Mice were tested drug free 1, 14 and 28 days after cessation of cocaine and CBD treatment. Fecal samples were collected prior to drug treatment and after each test session. Gut microbiome analyses were conducted using 16 s rRNA sequencing and correlated with behavioural parameters. We found a persistent preference for a cocaine-environment in mice, and long-lasting changes to gut microbe alpha diversity. Cocaine caused persistent changes to beta diversity which lasted for 4 weeks. CBD treatment reduced cocaine-environment preference during abstinence from cocaine and returned gut beta diversity measures to control levels. CBD treatment increased the relative abundance of Firmicutes phyla and Oscillospira genus, but decreased Bacteroidetes phyla and Bacteroides acidifaciens species. Preference score in cocaine-treated mice was positively correlated with abundance of Actinobacteria, whereas in mice treated with CBD and cocaine, the preference score was negatively correlated with Tenericutes abundance. Here we show that CBD facilitates cocaine extinction memory and reverses persistent cocaine-induced changes to gut microbe diversity. Furthermore, CBD increases the abundance of gut microbes which have anti-inflammatory properties. This suggests that CBD may act via the gut to reduce the memory of cocaine reward. Our data suggest that improving gut health and using CBD could limit cocaine abuse.},
}

@article {pmid38649105,
year = {2024},
author = {Xu, L and Wang, S and Wu, L and Cao, H and Fan, Y and Wang, X and Yu, Z and Zhou, M and Gao, R and Wang, J},
title = {Coprococcus eutactus screened from healthy adolescent attenuates chronic restraint stress-induced depression-like changes in adolescent mice: Potential roles in the microbiome and neurotransmitter modulation.},
journal = {Journal of affective disorders},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jad.2024.04.050},
pmid = {38649105},
issn = {1573-2517},
abstract = {The onset of depression commonly occurs in adolescence; therefore, depressive prevention and intervention are pivotal during this period. It is becoming evident that neurotransmitter imbalance and gut microbiota dysbiosis are prominent causes of depression. However, the underlying links and mechanisms remain poorly understood. In this study, with 16S ribosomal RNA gene sequencing, genus Coprococcus markedly differentiated between the healthy and unmedicated depressive adolescents. Based on this, transplantation of Coprococcus eutactus (C.e.) was found to dramatically ameliorate the chronic restraint stress (CRS) induced depression-like changes and prevent synaptic loss and glial-stimulated neuroinflammation in mice. The Ultra-high performance liquid chromatography tandem mass spectrometry analysis (UHPLC-MS/MS) further showed that neurotoxic neurotransmitters in kynurenine pathway (KP) such as 3-hydroxykynurenine (3-HK) and 3-hydroxyanthranilic acid (3-HAA) decreased in mouse brains, mechanistically deciphering the transfer of the tryptophan metabolic pathway to serotonin metabolic signaling in the brain after C.e. treatment, which was also verified in the colon. Molecularly, blockage of KP activities mediated by C.e. was ascribed to the restraint of the limit-step enzymes responsible for kynurenine, 3-HK, and quinolinic acid generation. In the colon, C.e. treatment significantly recovered goblet cells and mucus secretion in CRS mice which may ascribe to the rebalance of the disordered gut microbiota, especially Akkermansia, Roseburia, Rikenella, Blautia, and Alloprevotella. Taken together, the current study reveals for the first time the beneficial effects and potential mechanisms of C.e. in ameliorating CRS-induced depression, unraveling the direct links between C.e. treatment and neurotransmitter rebalance, which may provide efficacious therapeutic avenues for adolescent depressive intervention.},
}

@article {pmid38648770,
year = {2024},
author = {Trubitsina, NP and Matiiv, AB and Rogoza, TM and Zudilova, AA and Bezgina, MD and Zhouravleva, GA and Bondarev, SA},
title = {Role of the Gut Microbiome and Bacterial Amyloids in the Development of Synucleinopathies.},
journal = {Biochemistry. Biokhimiia},
volume = {89},
number = {3},
pages = {523-542},
doi = {10.1134/S0006297924030118},
pmid = {38648770},
issn = {1608-3040},
abstract = {Less than ten years ago, evidence began to accumulate about association between the changes in the composition of gut microbiota and development of human synucleinopathies, in particular sporadic form of Parkinson's disease. We collected data from more than one hundred and thirty experimental studies that reported similar results and summarized the frequencies of detection of different groups of bacteria in these studies. It is important to note that it is extremely rare that a unidirectional change in the population of one or another group of microorganisms (only an elevation or only a reduction) was detected in the patients with Parkinson's disease. However, we were able to identify several groups of bacteria that were overrepresented in the patients with Parkinson's disease in the analyzed studies. There are various hypotheses about the molecular mechanisms that explain such relationships. Usually, α-synuclein aggregation is associated with the development of inflammatory processes that occur in response to the changes in the microbiome. However, experimental evidence is accumulating on the influence of bacterial proteins, including amyloids (curli), as well as various metabolites, on the α-synuclein aggregation. In the review, we provided up-to-date information about such examples.},
}

@article {pmid38648751,
year = {2024},
author = {Lim, JJ and Goedken, M and Jin, Y and Gu, H and Cui, JY},
title = {Single cell transcriptomics unveiled that early life BDE-99 exposure reprogrammed the gut-liver axis to promote a pro-inflammatory metabolic signature in male mice at late adulthood.},
journal = {Toxicological sciences : an official journal of the Society of Toxicology},
volume = {},
number = {},
pages = {},
doi = {10.1093/toxsci/kfae047},
pmid = {38648751},
issn = {1096-0929},
abstract = {Polybrominated diphenyl ethers (PBDEs) are legacy flame retardants that bioaccumulate in the environment. The gut microbiome is an important regulator of liver functions including xenobiotic biotransformation and immune regulation. We recently showed that neonatal exposure to polybrominated diphenyl ether-99 (BDE-99), a human breast milk-enriched PBDE congener, up-regulated pro-inflammation- and down-regulated drug metabolism-related genes predominantly in males in young adulthood. However, the persistence of dysregulation into late adulthood, differential impact of hepatic cell types, and the involvement of the gut microbiome from neonatal BDE-99 exposure remains unknown. To address these knowledge gaps, male C57BL/6 mouse pups were orally exposed to corn oil (10 ml/kg) or BDE-99 (57 mg/kg) once daily from postnatal days 2-4. At 15 months of age, neonatal BDE-99 exposure down-regulated xenobiotic and lipid metabolizing enzymes and up-regulated genes involved in microbial influx in hepatocytes. Neonatal BDE-99 exposure also increased the hepatic proportion of neutrophils and led to a predicted increase of macrophage migration inhibitory factor signaling. This was associated with decreased intestinal tight junction protein (Tjp) transcripts, altered gut environment, and dysregulation of inflammation-related metabolites. ScRNA-seq using germ-free (GF) mice demonstrated the necessity of a normal gut microbiome in maintaining hepatic immune tolerance. Microbiota transplant to GF mice using large intestinal microbiome from adults neonatally exposed to BDE-99 down-regulated Tjp transcripts and up-regulated several cytokines in the large intestine. In conclusion, neonatal BDE-99 exposure reprogrammed cell type-specific gene expression and communication in liver towards pro-inflammation, and BDE-99-mediated pro-inflammatory signatures may be partly due to the dysregulated gut environment.},
}

@article {pmid38648726,
year = {2024},
author = {Wang, Y and Zhang, Y and Yang, Z and Fei, J and Zhou, X and Rong, X and Peng, J and Luo, G},
title = {Intercropping improves maize yield and nitrogen uptake by regulating nitrogen transformation and functional microbial abundance in rhizosphere soil.},
journal = {Journal of environmental management},
volume = {358},
number = {},
pages = {120886},
doi = {10.1016/j.jenvman.2024.120886},
pmid = {38648726},
issn = {1095-8630},
abstract = {Intercropping-driven changes in nitrogen (N)-acquiring microbial genomes and functional expression regulate soil N availability and plant N uptake. However, present data seem to be limited to a specific community, obscuring the viewpoint of entire N-acquiring microbiomes and functions. Taking maize intercropped with legumes (peanut and soybean) and non-legumes (gingelly and sweet potato) as models, we studied the effects of intercropping on N transformations and N-acquiring microbiomes in rhizosphere soil across four maize growth stages. Meanwhile, we compiled promising strategies such as random forest analysis and structural equation model for the exploitation of the associations between microbe-driven N dynamics and soil-plant N trade-offs and maize productivity. Compared with monoculture, maize intercropping significantly increased the denitrification rate of rhizosphere soils across four maize growth stages, net N mineralization in the elongation and flowering stages, and the nitrification rate in the seedling and mature stages. The abundance of most N-acquiring microbial populations was influenced significantly by intercropping patterns and maize growth stages. Soil available N components (NH4[+]-N, NO3[-]-N, and dissolved organic N content) showed a highly direct effect on plant N uptake, which mainly mediated by N transformations (denitrification rate) and N-acquiring populations (amoB, nirK3, and hzsB genes). Overall, the adaptation of N-acquiring microbiomes to changing rhizosphere micro-environments caused by intercropping patterns and maize development could promote soil N transformations and dynamics to meet demand of maize for N nutrient. This would offer another unique perspective to manage the benefits of the highly N-effective and production-effective intercropping ecosystems.},
}

@article {pmid38648518,
year = {2024},
author = {Morowitz, MJ},
title = {From Tofu to T-Bones: How Vegan and Ketogenic Diets Shape Our Immune Defenses.},
journal = {Journal of leukocyte biology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jleuko/qiae097},
pmid = {38648518},
issn = {1938-3673},
abstract = {Link et al. conducted a controlled study comparing the impacts of ketogenic and vegan diets on energy intake and immune function in humans. Deep -omics analyses revealed distinct effects of each diet on the immune system, including changes in cell populations and blood transcriptomes indicative of diet-induced shifts between adaptive and innate immunity. The study highlights the potentially significant, rapid impact of diet on immune function and health.},
}

@article {pmid38648292,
year = {2024},
author = {Zhang, Z and Zhao, H and Chen, X and Tian, G and Liu, G and Cai, J and Jia, G},
title = {Enhancing pig growth and gut health with fermented Jatropha curcas cake: Impacts on microbiota, metabolites, and neurotransmitters.},
journal = {Journal of animal physiology and animal nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1111/jpn.13960},
pmid = {38648292},
issn = {1439-0396},
support = {2021ZDZX0009//Sichuan Science and Technology Program/ ; 2023KJZD086//Meishan Science and Technology Program/ ; },
abstract = {Given the escalating global crisis in feed protein availability, Jatropha curcas L. cake has attracted significant interest as a viable alternative protein source in animal feed. This experiment was conducted to investigate the effects of fermented Jatropha curcas L. cake (FJCC) as a protein feed in the diet of pigs. A total of 96 growing pigs with an average weight of 27.60 ± 1.59 kg were divided into three dietary groups with varying FJCC inclusion levels (0, 2.5, and 5%) for a 28 d trial. Results showed that the diet with 5% FJCC (FJCC5) demonstrated significant improvements in average daily gain (p = 0.009), feed-to-gain ratio (p = 0.036), nutrient digestibility, and intestinal morphology. Furthermore, the FJCC5 diet resulted in a decrease in pH values in different gut sections (jejunum p = 0.045, cecum p = 0.001, colon p = 0.012), and favorably altered the profile of short-chain fatty acids (SCFAs) with increased butyric acid content (p = 0.005) and total SCFAs (p = 0.019). Additionally, this diet notably decreased IL-6 levels in the jejunum (p = 0.008) and colon (=0.047), significantly reduced IL-1 levels in the hypothalamus (p < 0.001), and lowered IL-1, IL-6, and IL-10 levels in plasma (p < 0.05). Microbiota and metabolite profile analysis revealed an elevated abundance of beneficial microbes (p < 0.05) and key metabolites such as 4-aminobutyric acid (GABA) (p = 0.003) and serotonin (5-HT) (p = 0.022), linked to neuroactive ligand-receptor interaction. Moreover, FJCC5 significantly boosted circulating neurotransmitter levels of 5-HT (p = 0.006) and GABA (p = 0.002) in plasma and hypothalamus, with corresponding increases in precursor amino acids (p < 0.05). These findings suggest that FJCC, particularly at a 5% inclusion rate, can be an effective substitute for traditional protein sources like soybean meal, offering benefits beyond growth enhancement to gut health and potentially impacting the gut-brain axis. This research underscores FJCC's potential as a valuable component in sustainable animal nutrition strategies.},
}

@article {pmid38648288,
year = {2024},
author = {Alvarez-Aponte, ZI and Govindaraju, AM and Hallberg, ZF and Nicolas, AM and Green, MA and Mok, KC and Fonseca-Garcia, C and Coleman-Derr, D and Brodie, EL and Carlson, HK and Taga, ME},
title = {Phylogenetic distribution and experimental characterization of corrinoid production and dependence in soil bacterial isolates.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrae068},
pmid = {38648288},
issn = {1751-7370},
abstract = {Soil microbial communities impact carbon sequestration and release, biogeochemical cycling, and agricultural yields. These global effects rely on metabolic interactions that modulate community composition and function. However, the physicochemical and taxonomic complexity of soil and the scarcity of available isolates for phenotypic testing are significant barriers to studying soil microbial interactions. Corrinoids-the vitamin B12 family of cofactors-are critical for microbial metabolism, yet they are synthesized by only a subset of microbiome members. Here, we evaluated corrinoid production and dependence in soil bacteria as a model to investigate the ecological roles of microorganisms involved in metabolic interactions. We isolated and characterized a taxonomically diverse collection of 161 soil bacteria from a single study site. Most corrinoid-dependent bacteria in the collection prefer B12 over other corrinoids, while all tested producers synthesize B12, indicating metabolic compatibility between producers and dependents in the collection. Furthermore, a subset of producers release B12 at levels sufficient to support dependent isolates in laboratory culture at estimated ratios of up to 1000 dependents per producer. Within our isolate collection, we did not find strong phylogenetic patterns in corrinoid production or dependence. Upon investigating trends in the phylogenetic dispersion of corrinoid metabolism categories across sequenced bacteria from various environments, we found that these traits are conserved in 47 out of 85 genera. Together, these phenotypic and genomic results provide evidence for corrinoid-based metabolic interactions among bacteria and provide a framework for the study of nutrient-sharing ecological interactions in microbial communities.},
}

@article {pmid38648089,
year = {2024},
author = {Maglione, R and Ciotola, M and Cadieux, M and Toussaint, V and Laforest, M and Kembel, SW},
title = {Winter rye cover crops shelter competent squash phyllosphere bacteria to reduce Pseudomonas syringae pv. lachrymans growth and angular leaf spot symptoms.},
journal = {Phytopathology},
volume = {},
number = {},
pages = {},
doi = {10.1094/PHYTO-08-22-0291-R},
pmid = {38648089},
issn = {0031-949X},
abstract = {Cover crops, a soil conservation practice, can contribute to reducing disease pressure caused by Pseudomonas syringae, considered one of the most important bacterial plant pathogens. We recently demonstrated that phyllosphere (leaf surface) bacterial community structure changed when squash (Cucurbita pepo) was grown with a rye (Secale cereale) cover crop treatment, followed by a decrease of angular leaf spot (ALS) disease symptoms on squash caused by P. syringae pv. lachrymans. Application of biocontrol agents is a known agricultural practice to mitigate crop losses due to microbial disease. In this study, we tested the hypothesis that some phyllosphere bacteria promoted when squash are grown on cover crops could be isolated and used as a biocontrol agent to decrease ALS symptoms. We grew squash during a two-year field experiment using four agricultural practices: bare soil, cover crops, chemically terminated cover crops, and plastic cover. We sampled squash leaves at 3 different dates each year and constructed a collection of cultivable bacterial strains isolated from squash leaves and rye cover crop material. Each isolated strain was identified by 16S rRNA gene sequencing and used in in vitro (Petri dish) pathogen growth and in vivo (greenhouse) symptom control assays. Four bacterial isolates belonging to the genera Pseudarthrobacter, Pseudomonas, Delftia and Rhizobium were shown to inhibit P. syringae pv. lachrymans growth and ALS symptom development. Strikingly, the symptom control efficacy of all strains was stronger on older leaves. This study sheds light on the importance of bacterial isolation from cover crops sources to promote disease control.},
}

@article {pmid38507780,
year = {2024},
author = {Kosmopoulos, JC and Batstone-Doyle, RT and Heath, KD},
title = {Co-inoculation with novel nodule-inhabiting bacteria reduces the benefits of legume-rhizobium symbiosis.},
journal = {Canadian journal of microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1139/cjm-2023-0209},
pmid = {38507780},
issn = {1480-3275},
abstract = {The ecologically and economically vital symbiosis between nitrogen-fixing rhizobia and leguminous plants is often thought of as a bi-partite interaction, yet studies increasingly show the prevalence of non-rhizobial endophytes (NREs) that occupy nodules alongside rhizobia. Yet, what impact these NREs have on plant or rhizobium fitness remains unclear. Here, we investigated four NRE strains found to naturally co-occupy nodules of the legume Medicago truncatula alongside Sinorhizobium meliloti in native soils. Our objectives were to (1) examine the direct and indirect effects of NREs on M. truncatula and S. meliloti fitness, and (2) determine whether NREs can re-colonize root and nodule tissues upon reinoculation. We identified one NRE strain (522) as a novel Paenibacillus species, another strain (717A) as a novel Bacillus species, and the other two (702A and 733B) as novel Pseudomonas species. Additionally, we found that two NREs (Bacillus 717A and Pseudomonas 733B) reduced the fitness benefits obtained from symbiosis for both partners, while the other two (522, 702A) had little effect. Lastly, we found that NREs were able to co-infect host tissues alongside S. meliloti. This study demonstrates that variation of NREs present in natural populations must be considered to better understand legume-rhizobium dynamics in soil communities.},
}

@article {pmid38647645,
year = {2024},
author = {Zhang, M and Guo, D and Wang, H and Wu, G and Ding, N and Shi, Y and Zhou, J and Zhao, E and Li, X},
title = {Integrated characterization of filler tobacco leaves: HS-SPME-GC-MS, E-nose, and microbiome analysis across different origins.},
journal = {Bioresources and bioprocessing},
volume = {11},
number = {1},
pages = {11},
pmid = {38647645},
issn = {2197-4365},
support = {W2023JSKF0083//State-Owned Enterprises Cooperative External Program/ ; },
abstract = {This study delves into the aroma characteristics and microbial composition of filler tobacco leaves (FTLs) sourced from six distinct cigar-growing regions within Yunnan, China, following standardized fermentation. An integrated approach using gas chromatography-mass spectrometry (GC-MS), electronic nose (E-nose), and microbiome analysis was employed for comprehensive profiling. Results derived from Linear Discriminant Analysis (LDA) using E-nose data confirmed the presence of notable variability in flavor substance profiles among the FTLs from six regions. Additionally, GC-MS was used to discern disparities in volatile organic compound (VOC) distribution across FTLs from these regions, identifying 92, 81, 79, 58, 69, and 92 VOCs within each respective sample set. Significantly, 24 VOCs emerged as pivotal determinants contributing to the heterogeneity of flavor profiles among FTLs from diverse origins, as indicated by Variable Importance for the Projection (VIP) analysis. Furthermore, distinctions in free amino acid content and chemical constituents were observed across FTLs. Of noteworthy significance, solanone, isophorone, durene, (-)-alpha-terpineol, and 2,3'-bipyridine exhibited the strongest correlations with microbiome data, with fungal microorganisms exerting a more pronounced influence on metabolites, as elucidated through two-way orthogonal partial least-squares (O2PLS) modeling. These findings provide a theoretical and technical basis for accurately evaluating the synchronization of FTLs in aromas and fermentation processes, and they will enhance the quality of fermented FTLs and foster the growth of the domestic cigar tobacco industry ultimately.},
}

@article {pmid38647957,
year = {2024},
author = {Singh, V and Mahra, K and Jung, D and Shin, JH},
title = {Gut Microbes in Polycystic Ovary Syndrome and Associated Comorbidities; Type 2 Diabetes, Non-Alcoholic Fatty Liver Disease (NAFLD), Cardiovascular Disease (CVD), and the Potential of Microbial Therapeutics.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {38647957},
issn = {1867-1314},
support = {2021R1A6C101A416//Korea Basic Science Institute/ ; },
abstract = {Polycystic ovary syndrome (PCOS) is one of the most common endocrine anomalies among females of reproductive age, highlighted by hyperandrogenism. PCOS is multifactorial as it can be associated with obesity, insulin resistance, low-grade chronic inflammation, and dyslipidemia. PCOS also leads to dysbiosis by lowering microbial diversity and beneficial microbes, such as Faecalibacterium, Roseburia, Akkermenisa, and Bifidobacterium, and by causing a higher load of opportunistic pathogens, such as Escherichia/Shigella, Fusobacterium, Bilophila, and Sutterella. Wherein, butyrate producers and Akkermansia participate in the glucose uptake by inducing glucagon-like peptide-1 (GLP-1) and glucose metabolism, respectively. The abovementioned gut microbes also maintain the gut barrier function and glucose homeostasis by releasing metabolites such as short-chain fatty acids (SCFAs) and Amuc_1100 protein. In addition, PCOS-associated gut is found to be higher in gut-microbial enzyme β-glucuronidase, causing the de-glucuronidation of conjugated androgen, making it susceptible to reabsorption by entero-hepatic circulation, leading to a higher level of androgen in the circulatory system. Overall, in PCOS, such dysbiosis increases the gut permeability and LPS in the systemic circulation, trimethylamine N-oxide (TMAO) in the circulatory system, chronic inflammation in the adipose tissue and liver, and oxidative stress and lipid accumulation in the liver. Thus, in women with PCOS, dysbiosis can promote the progression and severity of type 2 diabetes, non-alcoholic fatty liver disease (NAFLD), and cardiovascular diseases (CVD). To alleviate such PCOS-associated complications, microbial therapeutics (probiotics and fecal microbiome transplantation) can be used without any side effects, unlike in the case of hormonal therapy. Therefore, this study sought to understand the mechanistic significance of gut microbes in PCOS and associated comorbidities, along with the role of microbial therapeutics that can ease the life of PCOS-affected women.},
}

@article {pmid38647290,
year = {2024},
author = {Jensen, O and Trujillo, E and Hanson, L and Ost, KS},
title = {Controlling Candida: immune regulation of commensal fungi in the gut.},
journal = {Infection and immunity},
volume = {},
number = {},
pages = {e0051623},
doi = {10.1128/iai.00516-23},
pmid = {38647290},
issn = {1098-5522},
abstract = {The intestinal microbiome harbors fungi that pose a significant risk to human health as opportunistic pathogens and drivers of inflammation. Inflammatory and autoimmune diseases are associated with dysbiotic fungal communities and the expansion of potentially pathogenic fungi. The gut is also the main reservoir for disseminated fungal infections. Immune interactions are critical for preventing commensal fungi from becoming pathogenic. Significant strides have been made in defining innate and adaptive immune pathways that regulate intestinal fungi, and these discoveries have coincided with advancements in our understanding of the fungal molecular pathways and effectors involved in both commensal colonization and pathogenesis within the gut. In this review, we will discuss immune interactions important for regulating commensal fungi, with a focus on how specific cell types and effectors interact with fungi to limit their colonization or pathogenic potential. This will include how innate and adaptive immune pathways target fungi and orchestrate antifungal immune responses, in addition to how secreted immune effectors, such as mucus and antimicrobial peptides, regulate fungal colonization and inhibit pathogenic potential. These immune interactions will be framed around our current understanding of the fungal effectors and pathways regulating colonization and pathogenesis within this niche. Finally, we highlight important unexplored mechanisms by which the immune system regulates commensal fungi in the gut.},
}

@article {pmid38647288,
year = {2024},
author = {Waegenaar, F and García-Timermans, C and Van Landuyt, J and De Gusseme, B and Boon, N},
title = {Impact of operational conditions on drinking water biofilm dynamics and coliform invasion potential.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0004224},
doi = {10.1128/aem.00042-24},
pmid = {38647288},
issn = {1098-5336},
abstract = {UNLABELLED: Biofilms within drinking water distribution systems serve as a habitat for drinking water microorganisms. However, biofilms can negatively impact drinking water quality by causing water discoloration and deterioration and can be a reservoir for unwanted microorganisms. In this study, we investigated whether indicator organisms for drinking water quality, such as coliforms, can settle in mature drinking water biofilms. Therefore, a biofilm monitor consisting of glass rings was used to grow and sample drinking water biofilms. Two mature drinking water biofilms were characterized by flow cytometry, ATP measurements, confocal laser scanning microscopy, and 16S rRNA sequencing. Biofilms developed under treated chlorinated surface water supply exhibited lower cell densities in comparison with biofilms resulting from treated groundwater. Overall, the phenotypic as well as the genotypic characteristics were significantly different between both biofilms. In addition, the response of the biofilm microbiome and possible biofilm detachment after minor water quality changes were investigated. Limited changes in pH and free chlorine addition, to simulate operational changes that are relevant for practice, were evaluated. It was shown that both biofilms remained resilient. Finally, mature biofilms were prone to invasion of the coliform, Serratia fonticola. After spiking low concentrations (i.e., ±100 cells/100 mL) of the coliform to the corresponding bulk water samples, the coliforms were able to attach and get established within the mature biofilms. These outcomes emphasize the need for continued research on biofilm detachment and its implications for water contamination in distribution networks.

IMPORTANCE: The revelation that even low concentrations of coliforms can infiltrate into mature drinking water biofilms highlights a potential public health concern. Nowadays, the measurement of coliform bacteria is used as an indicator for fecal contamination and to control the effectiveness of disinfection processes and the cleanliness and integrity of distribution systems. In Flanders (Belgium), 533 out of 18,840 measurements exceeded the established norm for the coliform indicator parameter in 2021; however, the source of microbial contamination is mostly unknown. Here, we showed that mature biofilms, are susceptible to invasion of Serratia fonticola. These findings emphasize the importance of understanding and managing biofilms in drinking water distribution systems, not only for their potential to influence water quality, but also for their role in harboring and potentially disseminating pathogens. Further research into biofilm detachment, long-term responses to operational changes, and pathogen persistence within biofilms is crucial to inform strategies for safeguarding drinking water quality.},
}

@article {pmid38647231,
year = {2024},
author = {Landeen, KC and DeSisto, NG and Jordan, MK and Colaianni, CA and Phillips, J},
title = {Recurrent Peritonsillar Abscess Caused by Vaginal Flora: A Common Problem From a Unique Source.},
journal = {Ear, nose, & throat journal},
volume = {},
number = {},
pages = {1455613241246486},
doi = {10.1177/01455613241246486},
pmid = {38647231},
issn = {1942-7522},
abstract = {Peritonsillar abscesses (PTAs) are typically caused by group A Streptococcus or mixed oral flora. Gardnerella vaginalis is a part of the normal vaginal microbiome, and overgrowth can cause bacterial vaginosis. We present a case of recurrent PTA with G. vaginalis superinfection, which occurred after the patient performed oral sex on a female after incision and drainage of her initial PTA. The patient continued to have recurrent PTAs until G. vaginalis was identified, and antibiotic coverage was broadened to cover both group A Streptococcus and G. vaginalis. This case highlights the importance of culturing PTA aspirate for directed antibiosis in persistent or recurrent infections. The rare superinfection also raises the question of advising abstinence from oral-genital contact after oral procedures to minimize risk of superinfection.},
}

@article {pmid38647010,
year = {2024},
author = {Sun, T and Chen, G and Jiang, W and Xu, W and You, L and Jiang, C and Chen, S and Wang, D and Zheng, X and Yuan, Y},
title = {Distinguishing bipolar depression, bipolar mania, and major depressive disorder by gut microbial characteristics.},
journal = {Bipolar disorders},
volume = {},
number = {},
pages = {},
doi = {10.1111/bdi.13439},
pmid = {38647010},
issn = {1399-5618},
support = {//Postgraduate Research & Practice Innovation Program of Jiangsu Province/ ; //National Natural Science Foundation of China/ ; //"Double-first" Discipline funding of China Pharmaceutical University under the grant/ ; },
abstract = {BACKGROUND: Gut microbial disturbance has been widely confirmed in mood disorders. However, little is known about whether gut microbial characteristics can distinguish major depressive disorder (MDD), bipolar depression (BP-D), and bipolar mania (BP-M).

METHODS: This was a prospective case-control study. The composition of gut microbiota was profiled using 16S ribosomal RNA (rRNA) gene sequencing of fecal samples and compared between healthy controls (HC; n = 46), MDD (n = 51), BP-D (n = 44), and patients with BP-M (n = 45).

RESULTS: Gut microbial compositions were remarkably changed in the patients with MDD, BP-D, and BP-M. Compared to HC, distinct gut microbiome signatures were found in MDD, BP-D, and BP-M, and some gut microbial changes were overlapping between the three mood disorders. Furthermore, we identified a signature of 7 operational taxonomic units (OUT; Prevotellaceae-related OUT22, Prevotellaceae-related OUT31, Prevotellaceae-related OTU770, Ruminococcaceae-related OUT70, Bacteroidaceae-related OTU1536, Propionibacteriaceae-related OTU97, Acidaminococcaceae-related OTU34) that can distinguish patients with MDD from those with BP-D, BP-M, or HC, with area under the curve (AUC) values ranging from 0.910 to 0.996.

CONCLUSION: Our results provide the clinical rationale for the discriminative diagnosis of MDD, BP-D, and BP-M by characteristic gut microbial features.},
}

@article {pmid38646847,
year = {2024},
author = {Fontana, F and Longhi, G and Carli, E and Alessandri, G and Mancabelli, L and Lugli, GA and Tarracchini, C and Viappiani, A and Anzalone, R and Turroni, F and Milani, C and Ventura, M},
title = {Revealing the genetic traits of the foodborne microbial genus hafnia: Implications for the human gut microbiome.},
journal = {Environmental microbiology},
volume = {26},
number = {4},
pages = {e16626},
doi = {10.1111/1462-2920.16626},
pmid = {38646847},
issn = {1462-2920},
support = {//Cariparma/ ; //GenProbio Srl/ ; CUP D93C22000890001//Concession Decree No.1550 of 11 October 2022, Italian Ministry of University and Research/ ; PE00000003//Mission 4 Component 2 Investment 1.3 - Call for tender No. 341 of 15 March 2022, Italian Ministry of University and Research funded by the European Union-NextGenerationEU/ ; //the National Recovery and Resilience Plan (NRRP)/ ; //ON Foods - Research and innovation network on food and nutrition Sustainability, Safety and Security -Working ON Foods/ ; },
mesh = {*Gastrointestinal Microbiome/genetics ; Humans ; Animals ; Bees/microbiology ; Fatty Acids, Volatile/metabolism ; Genome, Bacterial ; Food Microbiology ; Metagenomics ; Vitamins/metabolism ; Phylogeny ; },
abstract = {The bacterial genus Hafnia has recently attracted attention due to its complex metabolic features and host-interaction capabilities, which are associated with health benefits, primarily weight loss. However, significant gaps remain in our understanding of the genomic characteristics of this emerging microbial group. In this study, we utilized all available high-quality genomes of Hafnia alvei and Hafnia paralvei to uncover the broad distribution of Hafnia in human and honeybee guts, as well as in dairy products, by analysing 1068 metagenomic datasets. We then investigated the genetic traits related to Hafnia's production of vitamins and short-chain fatty acids (SCFAs) through a comparative genomics analysis that included all dominant bacterial species in the three environments under study. Our findings underscore the extensive metabolic capabilities of Hafnia, particularly in the production of vitamins such as thiamine (B1), nicotinate (B3), pyridoxine (B6), biotin (B7), folate (B9), cobalamin (B12), and menaquinone (K2). Additionally, Hafnia demonstrated a conserved genetic makeup associated with SCFA production, including acetate, propanoate, and butanoate. These metabolic traits were further confirmed using RNAseq analyses of a newly isolated H. paralvei strain T10. Overall, our study illuminates the ecological distribution and genetic attributes of this bacterial genus, which is of increasing scientific and industrial relevance.},
}

*Gastrointestinal Microbiome/genetics
Humans
Animals
Bees/microbiology
Fatty Acids, Volatile/metabolism
Genome, Bacterial
Food Microbiology
Metagenomics
Vitamins/metabolism
Phylogeny

@article {pmid38646773,
year = {2024},
author = {Weng, LY and Luan, DD and Zhou, DP and Guo, QG and Wang, GZ and Zhang, JL},
title = {Improving crop health by synthetic microbial communities: Progress and prospects.},
journal = {Ying yong sheng tai xue bao = The journal of applied ecology},
volume = {35},
number = {3},
pages = {847-857},
doi = {10.13287/j.1001-9332.202403.028},
pmid = {38646773},
issn = {1001-9332},
mesh = {*Crops, Agricultural/growth & development/microbiology ; *Microbiota ; *Rhizosphere ; Soil Microbiology ; Synthetic Biology/methods ; Agriculture/methods ; },
abstract = {Crop health directly affects yields and food security. At present, agrochemicals such as fertilizers and pesticides are mainly used in agricultural production to promote crop health. However, long-term excessive utilization of agrochemicals will damage the ecological environment of farmlands and increase the safety risk of agricultural products. It is urgent to explore efficient and environment-friendly agricultural products. Rhizosphere microbiome are considered as the second genome of plants, which are closely related to crop health. Understanding the key functional microbes, microbe-microbe interactions, and plant-microbe interactions are fundamental for exploring the potential of beneficial microbes in promoting crop health. However, due to the heterogeneity and complexity of the natural environment, stimulating the function of indigenous microorganisms remains uncertain. Synthetic microbial community (SynCom) is an artificial combination of two or more different strain isolates of microorganisms, with different taxonomic, genetic, or functional characteristic. Because of the advantages of maintaining species diversity and community stability, SynCom has been widely applied in the fields of human health, environmental governance and industrial production, and may also have great potential in promoting crop health. We summarized the concept and research status of SynCom, expounded the principles and methods of constructing SynCom, and analyzed the research on the promotion of crop health by exploring the mechanism of plant-microbe interactions, promoting plant growth and development, and improving stress resistance. Finally, we envisaged the future prospects to guide the using SynCom to improve crop health.},
}

*Crops, Agricultural/growth & development/microbiology
*Microbiota
*Rhizosphere
Soil Microbiology
Synthetic Biology/methods
Agriculture/methods

@article {pmid38646630,
year = {2024},
author = {Zheng, SJ and Hu, H and Li, Y and Chen, J and Li, X and Bai, T},
title = {Editorial: Microbial interaction with banana: mechanisms, symbiosis, and integrated diseases control.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1390969},
pmid = {38646630},
issn = {1664-302X},
}

@article {pmid38646629,
year = {2024},
author = {Nivetha, N and Shukla, PS and Nori, SS and Kumar, S and Suryanarayan, S},
title = {A red seaweed Kappaphycus alvarezii-based biostimulant (AgroGain[®]) improves the growth of Zea mays and impacts agricultural sustainability by beneficially priming rhizosphere soil microbial community.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1330237},
pmid = {38646629},
issn = {1664-302X},
abstract = {The overuse of chemical-based agricultural inputs has led to the degradation of soil with associated adverse effects on soil attributes and microbial population. This scenario leads to poor soil health and is reportedly on the rise globally. Additionally, chemical fertilizers pose serious risks to the ecosystem and human health. In this study, foliar sprays of biostimulant (AgroGain/LBS6) prepared from the cultivated, tropical red seaweed Kappaphycus alvarezii increased the phenotypic growth of Zea mays in terms of greater leaf area, total plant height, and shoot fresh and dry weights. In addition, LBS6 improved the accumulation of chlorophyll a and b, total carotenoids, total soluble sugars, amino acids, flavonoids, and phenolics in the treated plants. LBS6 applications also improved the total bacterial and fungal count in rhizospheric soil. The V3-V4 region of 16S rRNA gene from the soil metagenome was analyzed to study the abundance of bacterial communities which were increased in the rhizosphere of LBS6-treated plants. Treatments were found to enrich beneficial soil bacteria, i.e., Proteobacteria, especially the classes Alphaproteobacteria, Cyanobacteria, Firmicutes, Actinobacteriota, Verrucomicrobiota, Chloroflexi, and Acidobacteriota and several other phyla related to plant growth promotion. A metagenomic study of those soil samples from LBS6-sprayed plants was correlated with functional potential of soil microbiota. Enrichment of metabolisms such as nitrogen, sulfur, phosphorous, plant defense, amino acid, co-factors, and vitamins was observed in soils grown with LBS6-sprayed plants. These results were further confirmed by a significant increase in the activity of soil enzymes such as urease, acid phosphatase, FDAse, dehydrogenase, catalase, and biological index of fertility in the rhizosphere of LBS6-treated corn plant. These findings conclude that the foliar application of LBS6 on Z. mays improves and recruits beneficial microbes and alters soil ecology in a sustainable manner.},
}

@article {pmid38646625,
year = {2024},
author = {Luangphiphat, W and Prombutara, P and Muangsillapasart, V and Sukitpunyaroj, D and Eeckhout, E and Taweechotipatr, M},
title = {Exploring of gut microbiota features in dyslipidemia and chronic coronary syndrome patients undergoing coronary angiography.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1384146},
pmid = {38646625},
issn = {1664-302X},
abstract = {Chronic coronary syndrome (CCS) has a high mortality rate, and dyslipidemia is a major risk factor. Atherosclerosis, a cause of CCS, is influenced by gut microbiota dysbiosis and its metabolites. The objective of this study was to study the diversity and composition of gut microbiota and related clinical parameters among CCS patients undergoing coronary angiography and dyslipidemia patients in comparison to healthy volunteers in Thailand. CCS patients had more risk factors and higher inflammatory markers, high-sensitivity C-reactive protein (hs-CRP) than others. The alpha diversity was lower in dyslipidemia and CCS patients than in the healthy group. A significant difference in the composition of gut microbiota was observed among the three groups. The relative abundance of Proteobacteria, Fusobacteria, Enterobacteriaceae, Prevotella, and Streptococcus was significantly increased while Roseburia, Ruminococcus, and Faecalibacterium were lower in CCS patients. In CCS patients, Lachnospiraceae, Peptostreptococcaceae, and Pediococcus were positively correlated with hs-CRP. In dyslipidemia patients, Megasphaera was strongly positively correlated with triglyceride (TG) level and negatively correlated with high-density lipoprotein cholesterol (HDL-C). The modification of gut microbiota was associated with changes in clinical parameters involved in the development of coronary artery disease (CAD) in CCS patients.},
}

@article {pmid38646576,
year = {2024},
author = {Yu, Z and Yan, M and Somasundaram, S},
title = {Rumen protozoa and viruses: The predators within and their functions-A mini-review.},
journal = {JDS communications},
volume = {5},
number = {3},
pages = {236-240},
pmid = {38646576},
issn = {2666-9102},
abstract = {The rumen microbiome digests plant feedstuff that would be otherwise indigestible and provides most of the metabolizable energy and protein the host animals need. Until recently, research efforts have primarily been directed to bacteria and archaea, leaving the protozoa, fungi, and viruses much less understood. Protozoa contribute to feed digestion and fermentation, but as predators, they affect the microbiome and its function by regulating the abundance and activities of other rumen microbes both in a top-down (by directly killing the prey) and bottom-up (by affecting the metabolism of other microbes) manner. Rumen viruses (or phages, used interchangeably below) are diverse and abundant but the least understood. They are also predators (intracellular "predators") because of their lytic lifecycle, although they can co-exist peacefully with their hosts and reprogram host metabolism, buttressing host ecological fitness. In doing so, rumen viruses also affect the rumen microbiome in both a top-down and a bottom-up manner. Here we review the recent advancement in understanding both types of predators, focusing on their potential impact on the rumen microbiome and functions.},
}

@article {pmid38646566,
year = {2024},
author = {Botlagunta, N and Babu, S},
title = {Growth enhancement and changes in bacterial microbiome of cucumber plants exhibited by biopriming with some native bacteria.},
journal = {Saudi journal of biological sciences},
volume = {31},
number = {6},
pages = {103997},
pmid = {38646566},
issn = {1319-562X},
abstract = {This study investigated the impact of a mixture of six endophytic bacterial strains isolated from cucumber plants on the growth and microbiome diversity of six cucumber traditional varieties and hybrids. Six bacterial species were isolated and identified by 16 s rRNA sequencing. All the bacteria showed plant growth promoting traits. Bacillus tequilensis showed 80 % inhibition of the mycelia growth of Fusarium oxysporum f.sp. cucumarinum (Foc). Mixed culture of all the bacteria was prepared and applied back to the varieties and hybrids of cucumber plants through seed soaking. Plant growth characteristics indicated that the treated plants showed increased plant growth in terms of plant height, number of leaves, vine length, male:female flower ratio, number of fruits and fruit length. Bacteria treated plants of hybrid HiVeg Chitra recorded 19 cm increase in vine length compared to control plants. The matataxonomic analysis of leaf samples by Illumina sequencing highlighted a diverse bacterial community shift in treated plants, with significant increases in genera like Bacillus and Staphylococcus. The core microbiome analysis identified key genera such as Bacillus, Staphylococcus, Sphingomonas, Methylobacterium, etc that could be pivotal in plant growth promotion. Bacillus and Staphylococcus showed increased abundance in treated varieties, correlating with the observed in plant growth parameters thus indicating their role in growth promotion of cucumber plants. Endophytic bacterial species identified from cucumber plants when re-applied by seed soaking, they promote the plant growth by modulating the microbiome. The bacterial species identified in the study could be potential candidates as microbial bioinputs for cucumber cultivation.},
}

@article {pmid38646524,
year = {2024},
author = {Dey, S and Vieyra-Garcia, PA and Joshi, AA and Trajanoski, S and Wolf, P},
title = {Modulation of the skin microbiome in cutaneous T-cell lymphoma delays tumour growth and increases survival in the murine EL4 model.},
journal = {Frontiers in immunology},
volume = {15},
number = {},
pages = {1255859},
pmid = {38646524},
issn = {1664-3224},
mesh = {Animals ; *Microbiota/drug effects ; Mice ; *Skin/microbiology/pathology/immunology/drug effects ; *Skin Neoplasms/microbiology/immunology/pathology ; *Lymphoma, T-Cell, Cutaneous/microbiology/pathology/drug therapy/therapy ; *Mice, Inbred C57BL ; Disease Models, Animal ; Anti-Bacterial Agents/therapeutic use/pharmacology/administration & dosage ; Cell Line, Tumor ; Female ; Humans ; },
abstract = {Cutaneous T-cell lymphomas (CTCL) are a group of lymphoproliferative disorders of skin-homing T cells causing chronic inflammation. These disorders cause impairment of the immune environment, which leads to severe infections and/or sepsis due to dysbiosis. In this study, we elucidated the host-microbial interaction in CTCL that occurs during the phototherapeutic treatment regime and determined whether modulation of the skin microbiota could beneficially affect the course of CTCL. EL4 T-cell lymphoma cells were intradermally grafted on the back of C57BL/6 mice. Animals were treated with conventional therapeutics such as psoralen + UVA (PUVA) or UVB in the presence or absence of topical antibiotic treatment (neomycin, bacitracin, and polymyxin B sulphate) as an adjuvant. Microbial colonisation of the skin was assessed to correlate with disease severity and tumour growth. Triple antibiotic treatment significantly delayed tumour occurrence (p = 0.026), which prolonged the survival of the mice (p = 0.033). Allocation to phototherapeutic agents PUVA, UVB, or none of these, along with antibiotic intervention, reduced the tumour growth significantly (p = 0.0327, p ≤ 0.0001, p ≤ 0.0001 respectively). The beta diversity indices calculated using the Bray-Curtis model showed that the microbial population significantly differed after antibiotic treatment (p = 0.001). Upon modulating the skin microbiome by antibiotic treatment, we saw an increase in commensal Clostridium species, e.g., Lachnospiraceae sp. (p = 0.0008), Ruminococcaceae sp. (p = 0.0001)., Blautia sp. (p = 0.007) and a significant reduction in facultative pathogens Corynebacterium sp. (p = 0.0009), Pelomonas sp. (p = 0.0306), Streptococcus sp. (p ≥ 0.0001), Pseudomonas sp. (p = 0.0358), and Cutibacterium sp. (p = 0.0237). Intriguingly, we observed a significant decrease in Staphylococcus aureus frequency (p = 0.0001) but an increase in the overall detection frequency of the Staphylococcus genus, indicating that antibiotic treatment helped regain the microbial balance and increased the number of non-pathogenic Staphylococcus populations. These study findings show that modulating microbiota by topical antibiotic treatment helps to restore microbial balance by diminishing the numbers of pathogenic microbes, which, in turn, reduces chronic inflammation, delays tumour growth, and increases survival rates in our CTCL model. These findings support the rationale to modulate the microbial milieu during the disease course of CTCL and indicate its therapeutic potential.},
}

Animals
*Microbiota/drug effects
Mice
*Skin/microbiology/pathology/immunology/drug effects
*Skin Neoplasms/microbiology/immunology/pathology
*Lymphoma, T-Cell, Cutaneous/microbiology/pathology/drug therapy/therapy
*Mice, Inbred C57BL
Disease Models, Animal
Anti-Bacterial Agents/therapeutic use/pharmacology/administration & dosage
Cell Line, Tumor
Female
Humans

@article {pmid38646477,
year = {2024},
author = {Xia, Y and Feng, J and Zhang, H and Xiong, D and Kong, L and Seviour, R and Kong, Y},
title = {Effects of soil pH on the growth, soil nutrient composition, and rhizosphere microbiome of Ageratina adenophora.},
journal = {PeerJ},
volume = {12},
number = {},
pages = {e17231},
pmid = {38646477},
issn = {2167-8359},
mesh = {Hydrogen-Ion Concentration ; *Rhizosphere ; *Microbiota/physiology ; *Soil/chemistry ; *Ageratina/chemistry ; *Soil Microbiology ; Plant Leaves/microbiology/chemistry ; Plant Weeds/chemistry/growth & development ; Plant Roots/microbiology ; Antioxidants/metabolism/analysis ; },
abstract = {Ageratina adenophora is an invasive weed species found in many countries. Methods to control the spread of this weed have been largely unsuccessful. Soil pH is the most important soil factor affecting the availability of nutrients for plant and impacting its growth. Understanding the mechanisms of the influence of soil pH on the growth of A. adenophora may help to develop effective control measures. In this study, we artificially changed the soil pH in pot experiments for A. adenophora. We studied the effects of acidic (pH 5.5), weakly acidic (pH 6.5), neutral (pH 7.2), and alkaline (pH 9.0) soils on the growth, availability of soil nutrients, activity of antioxidant enzymes, levels of redox markers in the leaves, and the structure and diversity of the rhizosphere microbiome. Soil with a pH 7.2 had a higher (47.8%) below-ground height versus soils of pH 5.5 at day 10; plant had a higher (11.3%) above-ground height in pH 7.2 soils than pH 9.0 soils at day 90; no differences in the fresh and dry weights of its above- and belowground parts, plant heights, and root lengths were observed in plants growing in acid, alkaline, or neutral pH soil were observed at day 180. Correspondingly, the antioxidant enzymes SOD (superoxide dismutase), POD (peroxidase), CAT (catalase) and redox markers GSH (glutathione) and MDA (malondialdehyde) were measured in the leaves. Significant differences existed in the activities of CAT and the levels of GSH between those growing in acidic and alkaline soils and those in neutral pH soil at day 90; however, only lower (36.8%) CAT activities in those grown at pH 5.5 than those grown at pH 7.2 were found at day 180. Similarly, significant differences in available P (16.89 vs 3.04 mg Kg[-1]) and total K (3.67 vs 0.96 mg Kg[-1]), total P (0.37 vs 0.25 g Kg[-1]) and total N (0.45 vs 1.09 g Kg[-1]) concentrations were found between the rhizosphere soils of A. adenophora grown at pH 9.0 and 7.2 at day 90; no such differences were seen at day 180. High throughput analyses of the 16S rRNA and ITS fragments showed that the rhizosphere microbiome diversity and composition under different soil pH conditions changed over 180 days. The rhizosphere microbiomes differed in diversity, phylum, and generic composition and population interactions under acid and alkaline conditions versus those grown in neutral soils. Soil pH had a greater impact on the diversity and composition of the prokaryotic rhizosphere communities than those of the fungal communities. A. adenophora responded successfully to pH stress by changing the diversity and composition of the rhizosphere microbiome to maintain a balanced nutrient supply to support its normal growth. The unusual pH tolerance of A. adenophora may be one crucial reason for its successful invasion. Our results suggest that attempts use soil pH to control its invasion by changing the soil pH (for example, using lime) will fail.},
}

Hydrogen-Ion Concentration
*Rhizosphere
*Microbiota/physiology
*Soil/chemistry
*Ageratina/chemistry
*Soil Microbiology
Plant Leaves/microbiology/chemistry
Plant Weeds/chemistry/growth & development
Plant Roots/microbiology
Antioxidants/metabolism/analysis

@article {pmid38646363,
year = {2024},
author = {Farahbod, K and Slouha, E and Gerts, A and Rezazadah, A and Clunes, LA and Kollias, TF},
title = {The Effects of Diet Intervention on the Gut Microbiota in Type 2 Diabetes Mellitus: A Systematic Review.},
journal = {Cureus},
volume = {16},
number = {3},
pages = {e56737},
pmid = {38646363},
issn = {2168-8184},
abstract = {The GI tract hosts a dynamic community known as the gut microbiota, which encompasses thriving bacteria that actively contribute to the physiological functions of the human body. The intricacies of its composition are profoundly influenced by dietary preferences, where the quality, quantity, and frequency of food consumption play a pivotal role in either fostering or impeding specific bacterial strains. Type 2 diabetes mellitus (T2DM) is a prevalent and deleterious condition that originates from excessive hyperglycemia. Do lifestyle interventions targeting dietary adjustments, nutritional supplements, physical activity, and weight management programs exhibit a significant relationship in altering the composition of the gut microbiome and managing T2DM? This paper aims to evaluate the effects of lifestyle interventions on patients with T2DM and the implications of these changes on disease outcomes and progression. Lifestyle interventions can significantly impact the management of T2DM, especially those targeting dietary adjustments, nutritional supplements, physical activity, and weight management programs. The adoption of a high-fiber diet and increased fruit consumption have shown positive impacts on both insulin sensitivity and the composition of the gut microbiota. Additionally, promising outcomes emerge from supplementing with Omega-3 fatty acids, Vitamin K2 (MK-7), and transglucosidase, which influence insulin levels, glycemic control, and gut microbiota composition. Personalized diet interventions and the transformative effects of the Mediterranean diet present positive outcomes in metabolic control. The intensity of exercise plays a pivotal role in shaping the composition of the gut microbiota, with moderate-intensity continuous exercise displaying positive effects on anti-inflammatory microbes. Chronic exercise showcases favorable impacts on glycemic control and systemic inflammation. Emphasizing the intricate relationship between dietary habits, gut microbiota, and the risk of T2DM underscores the potential of the gut microbiota as a universal biomarker for assessing diabetes risk. Nutritional supplements and exercise interventions provide potential avenues for the management of T2DM, emphasizing the necessity for tailored strategies. Further research is encouraged to delve into the long-term effects and intricate interplay between lifestyle factors and the gut microbiome, enhancing our understanding of T2DM pathophysiology for targeted therapeutic approaches.},
}

@article {pmid38645704,
year = {2024},
author = {Han, H and Lee, HJ and Kim, KS and Chung, J and Na, HS},
title = {Comparison of the performance of MiSeq and NovaSeq in oral microbiome study.},
journal = {Journal of oral microbiology},
volume = {16},
number = {1},
pages = {2344293},
pmid = {38645704},
issn = {2000-2297},
abstract = {OBJECTIVE: Next generation sequencing is commonly used to characterize the microbiome structure. MiSeq is most commonly used to analyze the microbiome due to its relatively long read length. Illumina also introduced the 250 × 2 chip for NovaSeq. The purpose of this study was to compare the performance of MiSeq and NovaSeq in the context of oral microbiome study.

METHODS: Total read count, read quality score, relative bacterial abundance, community diversity, and correlation between two platforms were analyzed. Phylogenetic trees were analyzed for Streptococcus and periodontopathogens.

RESULTS: NovaSeq produced significantly more read counts and assigned more operational taxonomic units (OTUs) compared to MiSeq. Community diversity was similar between MiSeq and NovaSeq. NovaSeq were able to detect more unique OTUs compared to MiSeq. When phylogenetic trees were constructed for Streptococcus and periodontopathogens, both platforms detected OTUs for most of the clades.

CONCLUSION: Taken together, while both MiSeq and NovaSeq platforms effectively characterize the oral microbiome, NovaSeq outperformed MiSeq in terms of read counts and detection of unique OTUs, highlighting its potential as a valuable tool for large scale oral microbiome studies.},
}

@article {pmid38645683,
year = {2024},
author = {Chen, L and Bian, L and Ma, Q and Li, Y and Wang, X and Liu, Y},
title = {Defensive alteration of root exudate composition by grafting Prunus sp. onto resistant rootstock contributes to reducing crown gall disease.},
journal = {Horticulture research},
volume = {11},
number = {4},
pages = {uhae049},
pmid = {38645683},
issn = {2662-6810},
abstract = {Grafting is a traditional and significant strategy to suppress soil-borne diseases, such as the crown gall disease caused by tumorigenic Agrobacterium and Rhizobium. Root exudates and the rhizosphere microbiome play critical roles in controlling crown gall disease, but their roles in suppressing crown gall disease in grafted plants remain unclear. Here, disease-susceptible cherry rootstock 'Gisela 6' and disease-resistant cherry rootstock 'Haiying 1' were grafted onto each other or self-grafted. The effect of their root exudates on the soil microbiome composition and the abundance of pathogenic Agrobacterium were studied. Grafting onto the disease-resistant rootstock helped to reduce the abundance of pathogenic Agrobacterium, accompanied by altering root exudation, enriching potential beneficial bacteria, and changing soil function. Then, the composition of the root exudates from grafted plants was analyzed and the potential compounds responsible for decreasing pathogenic Agrobacterium abundance were identified. Based on quantitative measurement of the concentrations of the compounds and testing the impacts of supplied pure chemicals on abundance and chemotaxis of pathogenic Agrobacterium and potential beneficial bacteria, the decreased valine in root exudates of the plant grafted onto resistant rootstock was found to contribute to decreasing Agrobacterium abundance, enriching some potential beneficial bacteria and suppressing crown gall disease. This study provides insights into the mechanism whereby grafted plants suppress soil-borne disease.},
}

@article {pmid38645395,
year = {2024},
author = {Maitra, P and Hrynkiewicz, K and Szuba, A and Jagodziński, AM and Al-Rashid, J and Mandal, D and Mucha, J},
title = {Metabolic niches in the rhizosphere microbiome: dependence on soil horizons, root traits and climate variables in forest ecosystems.},
journal = {Frontiers in plant science},
volume = {15},
number = {},
pages = {1344205},
pmid = {38645395},
issn = {1664-462X},
abstract = {Understanding belowground plant-microbial interactions is important for biodiversity maintenance, community assembly and ecosystem functioning of forest ecosystems. Consequently, a large number of studies were conducted on root and microbial interactions, especially in the context of precipitation and temperature gradients under global climate change scenarios. Forests ecosystems have high biodiversity of plants and associated microbes, and contribute to major primary productivity of terrestrial ecosystems. However, the impact of root metabolites/exudates and root traits on soil microbial functional groups along these climate gradients is poorly described in these forest ecosystems. The plant root system exhibits differentiated exudation profiles and considerable trait plasticity in terms of root morphological/phenotypic traits, which can cause shifts in microbial abundance and diversity. The root metabolites composed of primary and secondary metabolites and volatile organic compounds that have diverse roles in appealing to and preventing distinct microbial strains, thus benefit plant fitness and growth, and tolerance to abiotic stresses such as drought. Climatic factors significantly alter the quantity and quality of metabolites that forest trees secrete into the soil. Thus, the heterogeneities in the rhizosphere due to different climate drivers generate ecological niches for various microbial assemblages to foster beneficial rhizospheric interactions in the forest ecosystems. However, the root exudations and microbial diversity in forest trees vary across different soil layers due to alterations in root system architecture, soil moisture, temperature, and nutrient stoichiometry. Changes in root system architecture or traits, e.g. root tissue density (RTD), specific root length (SRL), and specific root area (SRA), impact the root exudation profile and amount released into the soil and thus influence the abundance and diversity of different functional guilds of microbes. Here, we review the current knowledge about root morphological and functional (root exudation) trait changes that affect microbial interactions along drought and temperature gradients. This review aims to clarify how forest trees adapt to challenging environments by leveraging their root traits to interact beneficially with microbes. Understanding these strategies is vital for comprehending plant adaptation under global climate change, with significant implications for future research in plant biodiversity conservation, particularly within forest ecosystems.},
}

@article {pmid38645272,
year = {2024},
author = {Xu, H and Pudlo, NA and Cantu-Jungles, TM and Tuncil, YE and Nie, X and Kaur, A and Reuhs, BL and Martens, EC and Hamaker, BR},
title = {When simplicity triumphs: niche specialization of gut bacteria exists even for simple fiber structures.},
journal = {ISME communications},
volume = {4},
number = {1},
pages = {ycae037},
pmid = {38645272},
issn = {2730-6151},
abstract = {Structurally complex corn bran arabinoxylan (CAX) was used as a model glycan to investigate gut bacteria growth and competition on different AX-based fine structures. Nine hydrolyzate segments of the CAX polymer varying in chemical structure (sugars and linkages), CAX, five less complex non-corn arabinoxylans, and xylose and glucose were ranked from structurally complex to simple. The substrate panel promoted different overall growth and rates of growth of eight Bacteroides xylan-degrading strains. For example, Bacteroides cellulosilyticus DSM 14838 (Bacteroides cellulosilyticus) grew well on an array of complex and simple structures, while Bacteroides ovatus 3-1-23 grew well only on the simple structures. In a competition experiment, B. cellulosilyticus growth was favored over B. ovatus on the complex AX-based structure. On the other hand, on the simple structure, B. ovatus strongly outcompeted B. cellulosilyticus, which was eliminated from the competitive environment by Day 11. This adaptation to fine structure and resulting competition dynamics indicate that dietary fiber chemical structures, whether complex or simple, favor certain gut bacteria. Overall, this work supports a concept that fiber degraders diversify their competitive abilities to access substrates across the spectrum of heterogeneity of fine structural features of dietary fibers.},
}

@article {pmid38645218,
year = {2024},
author = {Moodley, S and Kroon, E and Naidoo, CC and Nyawo, GR and Wu, BG and Naidoo, S and Chiyaka, TL and Tshivhula, H and Singh, S and Li, Y and Warren, RM and Hoal, EG and Schurr, E and Clemente, J and Segal, LN and Möller, M and Theron, G},
title = {Latent tuberculosis infection is associated with an enrichment of short chain fatty acid producing bacteria in the stool of women living with HIV.},
journal = {Research square},
volume = {},
number = {},
pages = {},
pmid = {38645218},
abstract = {Background: Latent tuberculosis infection (LTBI) is common in people living with HIV (PLHIV) in high TB burden settings. Active TB is associated with specific stool taxa; however, little is known about the stool microbiota and LTBI, including in PLHIV. Method : Within a parent study that recruited adult females with HIV from Cape Town, South Africa into predefined age categories (18-25, 35-60 years), we characterised the stool microbiota of those with [interferon- γ release assay (IGRA)- and tuberculin skin test (TST)-positive] or without (IGRA- and TST-negative) LTBI (n=25 per group). 16S rRNA DNA sequences were analysed using QIIME2, Dirichlet Multinomial Mixtures, DESeq2 and PICRUSt2. Results: No α- or β-diversity differences occurred by LTBI status; however, LTBI-positives were Faecalibacterium-, Blautia-, Gemmiger-, Bacteroides- enriched and Moryella-, Atopobium-, Corynebacterium-, Streptococcus -depleted. Inferred metagenome data showed LTBI-negative-enriched pathways included several involved in methylglyoxal degradation, L-arginine, putrescine, 4-aminobutanoate degradation and L-arginine and ornithine degradation. Stool from LTBI-positives demonstrated differential taxa abundance based on a quantitative response to antigen stimulation (Acidaminococcus- enrichment and Megamonas -, Alistipes -, and Paraprevotella -depletion associated with higher IGRA or TST responses, respectively). In LTBI-positives, older people had different β-diversities than younger people whereas, in LTBI-negatives, no differences occurred across age groups. Conclusion: Amongst female PLHIV, those with LTBI had, vs. those without LTBI, Faecalibacterium , Blautia , Gemmiger, Bacteriodes -enriched, which are producers of short chain fatty acids. Taxonomic differences amongst people with LTBI occurred according to quantitative response to antigen stimulation and age. These data enhance our understanding of the microbiome's potential role in LTBI.},
}

@article {pmid38645092,
year = {2024},
author = {Petrone, BL and Bartlett, A and Jiang, S and Korenek, A and Vintila, S and Tenekjian, C and Yancy, WS and David, LA and Kleiner, M},
title = {Metaproteomics and DNA metabarcoding as tools to assess dietary intake in humans.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {38645092},
abstract = {Objective biomarkers of food intake are a sought-after goal in nutrition research. Most biomarker development to date has focused on metabolites detected in blood, urine, skin or hair, but detection of consumed foods in stool has also been shown to be possible via DNA sequencing. An additional food macromolecule in stool that harbors sequence information is protein. However, the use of protein as an intake biomarker has only been explored to a very limited extent. Here, we evaluate and compare measurement of residual food-derived DNA and protein in stool as potential biomarkers of intake. We performed a pilot study of DNA sequencing-based metabarcoding (FoodSeq) and mass spectrometry-based metaproteomics in five individuals' stool sampled in short, longitudinal bursts accompanied by detailed diet records (n=27 total samples). Dietary data provided by stool DNA, stool protein, and written diet record independently identified a strong within-person dietary signature, identified similar food taxa, and had significantly similar global structure in two of the three pairwise comparisons between measurement techniques (DNA-to-protein and DNA-to-diet record). Metaproteomics identified proteins including myosin, ovalbumin, and beta-lactoglobulin that differentiated food tissue types like beef from dairy and chicken from egg, distinctions that were not possible by DNA alone. Overall, our results lay the groundwork for development of targeted metaproteomic assays for dietary assessment and demonstrate that diverse molecular components of food can be leveraged to study food intake using stool samples.},
}

@article {pmid38647897,
year = {2022},
author = {Mon, ML and Marrero Díaz de Villegas, R and Campos, E and Soria, MA and Talia, PM},
title = {Characterization of a novel GH10 alkali-thermostable xylanase from a termite microbiome.},
journal = {Bioresources and bioprocessing},
volume = {9},
number = {1},
pages = {84},
pmid = {38647897},
issn = {2197-4365},
support = {PI 102//Instituto Nacional de Tecnología Agropecuaria/ ; 106//Instituto Nacional de Tecnología Agropecuaria/ ; 116//Instituto Nacional de Tecnología Agropecuaria/ ; 149//Instituto Nacional de Tecnología Agropecuaria/ ; 159//Instituto Nacional de Tecnología Agropecuaria/ ; (PICT) 2018-#4149//Agencia Nacional de Promoción Científica y Tecnológica/ ; 2020-#3570//Agencia Nacional de Promoción Científica y Tecnológica/ ; PIP-2021-2561//Consejo Nacional de Investigaciones Científicas y Técnicas/ ; },
abstract = {The aim of the present study was to assess the biochemical and molecular structural characteristics of a novel alkali-thermostable GH10 xylanase (Xyl10B) identified in a termite gut microbiome by a shotgun metagenomic approach. This endoxylanase candidate was amplified, cloned, heterologously expressed in Escherichia coli and purified. The recombinant enzyme was active at a broad range of temperatures (37-60 ºC) and pH values (4-10), with optimal activity at 50 ºC and pH 9. Moreover, its activity remained at more than 80% of its maximum at 50 °C for 8 h. In addition, Xyl10B was found to be stable in the presence of salt and several ions and chemical reagents frequently used in the industry. These characteristics make this enzyme an interesting candidate for pulp and paper bleaching industries, since this process requires enzymes without cellulase activity and resistant to high temperatures and alkaline pH (thermo-alkaliphilic enzymes). The products of xylan hydrolysis by Xyl10B (short xylooligosaccharides, xylose and xylobiose) could be suitable for application as prebiotics and in the production of bioethanol.},
}

@article {pmid38647867,
year = {2022},
author = {Dzulkarnain, ELN and Audu, JO and Wan Dagang, WRZ and Abdul-Wahab, MF},
title = {Microbiomes of biohydrogen production from dark fermentation of industrial wastes: current trends, advanced tools and future outlook.},
journal = {Bioresources and bioprocessing},
volume = {9},
number = {1},
pages = {16},
pmid = {38647867},
issn = {2197-4365},
support = {MyBrainSC scholarship//Ministry of Higher Education, Malaysia/ ; 05G24//Universiti Teknologi Malaysia/ ; 09G86//Universiti Teknologi Malaysia/ ; },
abstract = {Biohydrogen production through dark fermentation is very attractive as a solution to help mitigate the effects of climate change, via cleaner bioenergy production. Dark fermentation is a process where organic substrates are converted into bioenergy, driven by a complex community of microorganisms of different functional guilds. Understanding of the microbiomes underpinning the fermentation of organic matter and conversion to hydrogen, and the interactions among various distinct trophic groups during the process, is critical in order to assist in the process optimisations. Research in biohydrogen production via dark fermentation is currently advancing rapidly, and various microbiology and molecular biology tools have been used to investigate the microbiomes. We reviewed here the different systems used and the production capacity, together with the diversity of the microbiomes used in the dark fermentation of industrial wastes, with a special emphasis on palm oil mill effluent (POME). The current challenges associated with biohydrogen production were also included. Then, we summarised and discussed the different molecular biology tools employed to investigate the intricacy of the microbial ecology associated with biohydrogen production. Finally, we included a section on the future outlook of how microbiome-based technologies and knowledge can be used effectively in biohydrogen production systems, in order to maximise the production output.},
}

@article {pmid38645157,
year = {2024},
author = {Goh, CE and Bohn, B and Genkinger, JM and Molinsky, R and Roy, S and Paster, BJ and Chen, CY and Yuzefpolskaya, M and Colombo, PC and Rosenbaum, M and Knight, R and Desvarieux, M and Papapanou, PN and Jacobs, DR and Demmer, RT},
title = {Dietary nitrate intake and net nitrite-generating capacity of the oral microbiome interact to enhance cardiometabolic health: Results from the Oral Infections Glucose Intolerance and Insulin Resistance Study (ORIGINS).},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.04.10.24305636},
pmid = {38645157},
abstract = {BACKGROUND: We investigated the association between dietary nitrate intake and early clinical cardiometabolic risk biomarkers, and explored whether the oral microbiome modifies the association between dietary nitrate intake and cardiometabolic biomarkers.

METHODS: Cross-sectional data from 668 (mean [SD] age 31 [9] years, 73% women) participants was analyzed. Dietary nitrate intakes and alternative healthy eating index (AHEI) scores were calculated from food frequency questionnaire responses and a validated US food database. Subgingival 16S rRNA microbial genes (Illumina, MiSeq) were sequenced, and PICRUSt2 estimated metagenomic content. The Microbiome Induced Nitric oxide Enrichment Score (MINES) was calculated as a microbial gene abundance ratio representing enhanced net capacity for NO generation. Cardiometabolic risk biomarkers included systolic and diastolic blood pressure, HbA1c, glucose, insulin, and insulin resistance (HOMA-IR), and were regressed on nitrate intake tertiles in adjusted multivariable linear models.

RESULTS: Mean nitrate intake was 190[171] mg/day. Higher nitrate intake was associated with lower insulin, and HOMA-IR but particularly among participants with low abundance of oral nitrite enriching bacteria. For example, among participants with a low MINES, mean insulin[95%CI] levels in high vs. low dietary nitrate consumers were 5.8[5.3,6.5] vs. 6.8[6.2,7.5] (p=0.004) while respective insulin levels were 6.0[5.4,6.6] vs. 5.9[5.3,6.5] (p=0.76) among partcipants with high MINES (interaction p=0.02).

CONCLUSION: Higher dietary nitrate intake was only associated with lower insulin and insulin resistance among individuals with reduced capacity for oral microbe-induced nitrite enrichment. These findings have implications for future precision medicine-oriented approaches that might consider assessing the oral microbiome prior to enrollment into dietary interventions or making dietary recommendations.

CLINICAL PERSPECTIVE: What is new?: In this population-based study we identified an interaction between dietary nitrate intake and oral nitrite enriching bacteria on cardiometabolic outcomes. Higher dietary nitrate intake was associated with lower insulin and insulin resistance only among participants with low abundance of oral nitrite enriching bacteria. This study suggests that cardiometabolic benefits of nitrate consumption might depend on the host microbiome's capacity to metabolize nitrates.What are the clinical implications?: Among people with low microbiome capacity for nitrate metabolism, higher levels of nitrate might be necessary to realize cardiometabolic benefits.Lack of microbiome assessments in prior studies could partially explain inconsistent findings from previous nitrate supplementation trials and observational studies.Future precision-medicine oriented trials studying the effects of dietary nitrate recommendations on cardiometabolic health, should consider assessing the oral microbiome.},
}

@article {pmid38645133,
year = {2024},
author = {Zelasko, S and Swaney, MH and Sandstrom, S and Davenport, TC and Seroogy, CM and Gern, JE and Kalan, LR and Currie, CR},
title = {Upper respiratory microbial communities of healthy populations are shaped by niche and age.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.04.14.589416},
pmid = {38645133},
abstract = {BACKGROUND: Alterations in upper respiratory microbiomes have been implicated in shaping host health trajectories, including by limiting mucosal pathogen colonization. However, limited comparative studies of respiratory microbiome development and functioning across age groups have been performed. Herein, we perform shotgun metagenomic sequencing paired with pathogen inhibition assays to elucidate differences in nasal and oral microbiome composition and functioning across healthy 24-month-old infant (n=229) and adult (n=100) populations.

RESULTS: We find that beta diversity of nasal and oral microbiomes varies with age, with nasal microbiomes showing greater population-level variation compared to oral microbiomes. Infant microbiome alpha diversity was significantly lower across nasal samples and higher in oral samples, relative to adults. Accordingly, we demonstrate significant differences in genus- and species-level composition of microbiomes between sites and age groups. Antimicrobial resistome patterns likewise varied across body sites, with oral microbiomes showing higher resistance gene abundance compared to nasal microbiomes. Biosynthetic gene clusters encoding specialized metabolite production were found in higher abundance across infant oral microbiomes, relative to adults. Investigation of pathogen inhibition revealed greater inhibition of gram-negative and gram-positive bacteria by oral commensals, while nasal isolates had higher antifungal activity.

CONCLUSIONS: In summary, we identify significant differences in the microbial communities inhabiting nasal and oral cavities of healthy infants relative to adults. These findings inform our understanding of the interactions impacting respiratory microbiome composition and functioning, with important implications for host health across the lifespan.},
}

@article {pmid38645126,
year = {2024},
author = {Schmidt, N and Ham, KVD and Bower, L and Li, S and Lorenzi, H and Doumbo, S and Doumtabe, D and Kayentao, K and Ongoiba, A and Traore, B and Crompton, P},
title = {Susceptibility to febrile malaria is associated with an inflammatory gut microbiome.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-3974068/v1},
pmid = {38645126},
abstract = {Malaria is a major public health problem, but many of the factors underlying the pathogenesis of this disease are not well understood. Here, we demonstrate in Malian children that susceptibility to febrile malaria following infection with Plasmodium falciparum is associated with the composition of the gut microbiome prior to the malaria season. Gnotobiotic mice colonized with the fecal samples of malaria-susceptible children had a significantly higher parasite burden following Plasmodium infection compared to gnotobiotic mice colonized with the fecal samples of malaria-resistant children. The fecal microbiome of the susceptible children was enriched for bacteria associated with inflammation, mucin degradation, gut permeability and inflammatory bowel disorders (e.g., Ruminococcus gauvreauii , Ruminococcus torques , Dorea formicigenerans , Dorea longicatena , Lachnoclostridium phocaeense and Lachnoclostridium sp. YL32). However, the susceptible children also had a greater abundance of bacteria known to produce anti-inflammatory short-chain fatty acids and those associated with favorable prognosis and remission following dysbiotic intestinal events (e.g., Anaerobutyricum hallii , Blautia producta and Sellimonas intestinalis). Metabolomics analysis of the human fecal samples corroborated the existence of inflammatory and recovery-associated features within the gut microbiome of the susceptible children. There was an enrichment of nitric oxide-derived DNA adducts (deoxyinosine and deoxyuridine) and long-chain fatty acids, the absorption of which has been shown to be inhibited by inflamed intestinal epithelial cells, and a decrease in the abundance of mucus phospholipids. Nevertheless, there were also increased levels of pseudouridine and hypoxanthine, which have been shown to be regulated in response to cellular stress and to promote recovery following injury or hypoxia. Overall, these results indicate that the gut microbiome may contribute malaria pathogenesis and suggest that therapies targeting intestinal inflammation could decrease malaria susceptibility.},
}

@article {pmid38645104,
year = {2024},
author = {Holcomb, M and Marshall, A and Flinn, H and Lozano, M and Soriano, S and Gomez-Pinilla, F and Treangen, TJ and Villapol, S},
title = {Probiotic treatment causes sex-specific neuroprotection after traumatic brain injury in mice.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-4196801/v1},
pmid = {38645104},
abstract = {Background Recent studies have shed light on the potential role of gut dysbiosis in shaping traumatic brain injury (TBI) outcomes. Changes in the levels and types of Lactobacillus bacteria present might impact the immune system disturbances, neuroinflammatory responses, anxiety and depressive-like behaviors, and compromised neuroprotection mechanisms triggered by TBI. Objective This study aimed to investigate the effects of a daily pan-probiotic (PP) mixture in drinking water containing strains of Lactobacillus plantarum, L. reuteri, L. helveticus, L. fermentum, L. rhamnosus, L. gasseri , and L. casei , administered for either two or seven weeks before inducing TBI on both male and female mice. Methods Mice were subjected to controlled cortical impact (CCI) injury. Short-chain fatty acids (SCFAs) analysis was performed for metabolite measurements. The taxonomic profiles of murine fecal samples were evaluated using 16S rRNA V1-V3 sequencing analysis. Histological analyses were used to assess neuroinflammation and gut changes post-TBI, while behavioral tests were conducted to evaluate sensorimotor and cognitive functions. Results Our findings suggest that PP administration modulates the diversity and composition of the microbiome and increases the levels of SCFAs in a sex-dependent manner. We also observed a reduction of lesion volume, cell death, and microglial and macrophage activation after PP treatment following TBI in male mice. Furthermore, PP-treated mice show motor function improvements and decreases in anxiety and depressive-like behaviors. Conclusion Our findings suggest that PP administration can mitigate neuroinflammation and ameliorate motor and anxiety and depressive-like behavior deficits following TBI. These results underscore the potential of probiotic interventions as a viable therapeutic strategy to address TBI-induced impairments, emphasizing the need for gender-specific treatment approaches.},
}

@article {pmid38645042,
year = {2024},
author = {Scheible, K and Beblavy, R and Sohn, MB and Qui, X and Gill, AL and Narvaez-Miranda, J and Brunner, J and Miller, RK and Barrett, ES and O'Connor, TG and Gill, SR},
title = {Affective Symptoms in Pregnancy are Associated with the Vaginal Microbiome.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.04.12.589254},
pmid = {38645042},
abstract = {UNLABELLED: Composition of the vaginal microbiome in pregnancy is associated with adverse maternal, obstetric, and child health outcomes. Identifying the sources of individual differences in the vaginal microbiome is therefore of considerable clinical and public health interest. The current study tested the hypothesis that vaginal microbiome composition during pregnancy is associated with an individual's experience of affective symptoms and stress exposure. Data were based on a prospective longitudinal study of a diverse and medically healthy community sample of 275 mother-infant pairs. Affective symptoms and stress exposure and select measures of associated biomarkers (diurnal salivary cortisol, serum measures of sex hormones) were collected at each trimester; self-report, clinical, and medical records were used to collect detailed data on socio-demographic factors and health behavior, including diet and sleep. Vaginal microbiome samples were collected in the third trimester (34-40 weeks) and characterized by 16S rRNA sequencing. Identified taxa were clustered into three community state types (CST1-3) based on dissimilarity of vaginal microbiota composition. Results indicate that depressive symptoms during pregnancy were reliably associated with individual taxa and CST3 in the third trimester. Prediction of functional potential from 16S taxonomy revealed a differential abundance of metabolic pathways in CST1-3 and individual taxa, including biosynthetic pathways for the neuroactive metabolites, serotonin and dopamine. With the exception of bioavailable testosterone, no significant associations were found between symptoms- and stress-related biomarkers and CSTs. Our results provide further evidence of how prenatal psychological distress during pregnancy alters the maternal-fetal microbiome ecosystem that may be important for understanding maternal and child health outcomes.

IMPORTANCE: Prenatal affective symptoms and stress are associated with maternal, obstetric, and child health outcomes, but the mechanisms underlying these links and their application to intervention remain unclear. The findings from this investigation extend prior microbiome-oriented research by demonstrating that the maternal vaginal microbiome composition has a biologically plausible mechanistic link with affective symptoms that also suggest additional clinical applications for assessment and intervention.},
}

@article {pmid38644496,
year = {2024},
author = {Gaston, JM and Alm, EJ and Zhang, AN},
title = {Fast and accurate variant identification tool for sequencing-based studies.},
journal = {BMC biology},
volume = {22},
number = {1},
pages = {90},
pmid = {38644496},
issn = {1741-7007},
support = {6934500//Massachusetts Institute of Technology/ ; },
mesh = {*SARS-CoV-2/genetics ; *INDEL Mutation ; Computational Biology/methods ; Humans ; Software ; COVID-19/virology ; High-Throughput Nucleotide Sequencing/methods ; Point Mutation ; Genetic Variation ; Sequence Analysis, DNA/methods ; },
abstract = {BACKGROUND: Accurate identification of genetic variants, such as point mutations and insertions/deletions (indels), is crucial for various genetic studies into epidemic tracking, population genetics, and disease diagnosis. Genetic studies into microbiomes often require processing numerous sequencing datasets, necessitating variant identifiers with high speed, accuracy, and robustness.

RESULTS: We present QuickVariants, a bioinformatics tool that effectively summarizes variant information from read alignments and identifies variants. When tested on diverse bacterial sequencing data, QuickVariants demonstrates a ninefold higher median speed than bcftools, a widely used variant identifier, with higher accuracy in identifying both point mutations and indels. This accuracy extends to variant identification in virus samples, including SARS-CoV-2, particularly with significantly fewer false negative indels than bcftools. The high accuracy of QuickVariants is further demonstrated by its detection of a greater number of Omicron-specific indels (5 versus 0) and point mutations (61 versus 48-54) than bcftools in sewage metagenomes predominated by Omicron variants. Much of the reduced accuracy of bcftools was attributable to its misinterpretation of indels, often producing false negative indels and false positive point mutations at the same locations.

CONCLUSIONS: We introduce QuickVariants, a fast, accurate, and robust bioinformatics tool designed for identifying genetic variants for microbial studies. QuickVariants is available at https://github.com/caozhichongchong/QuickVariants .},
}

*SARS-CoV-2/genetics
*INDEL Mutation
Computational Biology/methods
Humans
Software
COVID-19/virology
High-Throughput Nucleotide Sequencing/methods
Point Mutation
Genetic Variation
Sequence Analysis, DNA/methods

@article {pmid38644373,
year = {2024},
author = {Niccolai, E and Pedone, M and Martinelli, I and Nannini, G and Baldi, S and Simonini, C and Di Gloria, L and Zucchi, E and Ramazzotti, M and Spezia, PG and Maggi, F and Quaranta, G and Masucci, L and Bartolucci, G and Stingo, FC and Mandrioli, J and Amedei, A},
title = {Amyotrophic lateral sclerosis stratification: unveiling patterns with virome, inflammation, and metabolism molecules.},
journal = {Journal of neurology},
volume = {},
number = {},
pages = {},
pmid = {38644373},
issn = {1432-1459},
support = {Grant-No. RF-2016-02361616//Ministero della Salute/ ; Grant no. B008-P00634//University of Florence/ ; },
abstract = {Amyotrophic lateral sclerosis (ALS) is an untreatable and clinically heterogeneous condition primarily affecting motor neurons. The ongoing quest for reliable biomarkers that mirror the disease status and progression has led to investigations that extend beyond motor neurons' pathology, encompassing broader systemic factors such as metabolism, immunity, and the microbiome. Our study contributes to this effort by examining the potential role of microbiome-related components, including viral elements, such as torque tenovirus (TTV), and various inflammatory factors, in ALS. In our analysis of serum samples from 100 ALS patients and 34 healthy controls (HC), we evaluated 14 cytokines, TTV DNA load, and 18 free fatty acids (FFA). We found that the evaluated variables are effective in differentiating ALS patients from healthy controls. In addition, our research identifies four unique patient clusters, each characterized by distinct biological profiles. Intriguingly, no correlations were found with site of onset, sex, progression rate, phenotype, or C9ORF72 expansion. A remarkable aspect of our findings is the discovery of a gender-specific relationship between levels of 2-ethylhexanoic acid and patient survival. In addition to contributing to the growing body of evidence suggesting altered peripheral immune responses in ALS, our exploratory research underscores metabolic diversity challenging conventional clinical classifications. If our exploratory findings are validated by further research, they could significantly impact disease understanding and patient care customization. Identifying groups based on biological profiles might aid in clustering patients with varying responses to treatments.},
}

@article {pmid38644360,
year = {2024},
author = {Oh, EJ and Jang, HH and Park, S and Lim, HP and Yun, KD and Jang, W and Kim, OS and Park, C and Won, EJ},
title = {Fretibacterium Species to Fusobacterium periodonticum Ratio as a Potential Biomarker of Periodontitis Based on Salivary Microbiome Profiling.},
journal = {Annals of laboratory medicine},
volume = {},
number = {},
pages = {},
doi = {10.3343/alm.2024.0043},
pmid = {38644360},
issn = {2234-3814},
}

@article {pmid38644048,
year = {2024},
author = {Wielkopolan, B and Szabelska-Beręsewicz, A and Gawor, J and Obrępalska-Stęplowska, A},
title = {Cereal leaf beetle-associated bacteria enhance the survival of their host upon insecticide treatments and respond differently to insecticides with different modes of action.},
journal = {Environmental microbiology reports},
volume = {16},
number = {2},
pages = {e13247},
pmid = {38644048},
issn = {1758-2229},
support = {UMO-2020/37/N/NZ9/02577//Polish National Science Centre/ ; },
mesh = {Animals ; *Insecticides/pharmacology ; *Bacteria/genetics/classification/drug effects/isolation & purification ; *Larva/microbiology/drug effects ; *Coleoptera/microbiology/drug effects ; RNA, Ribosomal, 16S/genetics ; Microbiota/drug effects ; Metagenomics ; Pyrethrins/pharmacology ; Chlorpyrifos ; Pantoea/genetics/drug effects ; },
abstract = {The cereal leaf beetle (CLB, Oulema melanopus) is one of the major cereal pests. The effect of insecticides belonging to different chemical classes, with different mechanisms of action and the active substances' concentrations on the CLB bacterial microbiome, was investigated. Targeted metagenomic analysis of the V3-V4 regions of the 16S ribosomal gene was used to determine the composition of the CLB bacterial microbiome. Each of the insecticides caused a decrease in the abundance of bacteria of the genus Pantoea, and an increase in the abundance of bacteria of the genus Stenotrophomonas, Acinetobacter, compared to untreated insects. After cypermethrin application, a decrease in the relative abundance of bacteria of the genus Pseudomonas was noted. The dominant bacterial genera in cypermethrin-treated larvae were Lactococcus, Pantoea, while in insects exposed to chlorpyrifos or flonicamid it was Pseudomonas. Insecticide-treated larvae were characterized, on average, by higher biodiversity and richness of bacterial genera, compared to untreated insects. The depletion of CLB-associated bacteria resulted in a decrease in larval survival, especially after cypermethrin and chlorpyrifos treatments. The use of a metagenome-based functional prediction approach revealed a higher predicted function of bacterial acetyl-CoA C-acetyltransferase in flonicamid and chlorpyrifos-treated larvae and tRNA dimethyltransferase in cypermethrin-treated insects than in untreated insects.},
}

Animals
*Insecticides/pharmacology
*Bacteria/genetics/classification/drug effects/isolation & purification
*Larva/microbiology/drug effects
*Coleoptera/microbiology/drug effects
RNA, Ribosomal, 16S/genetics
Microbiota/drug effects
Metagenomics
Pyrethrins/pharmacology
Chlorpyrifos
Pantoea/genetics/drug effects

@article {pmid38643860,
year = {2024},
author = {Xian, M and Ma, Z and Zhan, S and Shen, L and Li, T and Lin, H and Huang, M and Cai, J and Hu, T and Liang, J and Liang, S and Wang, S},
title = {Network analysis of microbiome and metabolome to explore the mechanism of raw rhubarb in the protection against ischemic stroke via microbiota-gut-brain axis.},
journal = {Fitoterapia},
volume = {},
number = {},
pages = {105969},
doi = {10.1016/j.fitote.2024.105969},
pmid = {38643860},
issn = {1873-6971},
abstract = {Ischemic stroke (IS) has attracted worldwide attention due to the high mortality and disability rate. Raw rhubarb (RR) is a traditional medicinal plant and whole-food that has been used in China for its various pharmacological activities, such as antioxidant and anti-inflammatory properties. Recent pharmacological research has shown the role of RR against IS, but its mechanism of action remains unclear, particularly in the context of the brain-gut axis. To address this gap in knowledge, the present study was conducted in the middle cerebral artery occlusion/reperfusion (MCAO/R) model with the aim of investigating the effects of RR on regulating the intestinal microbiota barrier and metabolism and thereby reducing inflammatory response so as to improve the IS. The results showed that pre-treatment of RR attenuated cerebral infarct area and inflammation response in MCAO rats. Furthermore, RR also improved intestinal barrier function, including the integrity and permeability of the intestinal barrier. Additionally, RR intervention significantly attenuated gut microbiota dysbiosis caused by ischemic stroke, especially the increased Firmicutes. Notably, the pseudo-germ-free (PGF) rats further demonstrated that the anti-stroke effect of RR might rely on intestinal microbiota. In addition, the UPLC/Q-Orbitrap-MS-Based metabolomics revealed the disrupted metabolic profiles caused by MCAO/R, and a total of 11 differential metabolites were modulated by RR administration, especially bile acids. Further correlation analysis and network pharmacology analysis also demonstrated a strong association between specific bacteria, such as Firmicutes and bile acids. In conclusion, our work demonstrated that RR could effectively ameliorate ischemic stroke by modulating the microbiota and metabolic disorders.},
}

@article {pmid38643839,
year = {2024},
author = {Chen, Z and Huang, L},
title = {Fusobacterium nucleatum carcinogenesis and drug delivery interventions.},
journal = {Advanced drug delivery reviews},
volume = {},
number = {},
pages = {115319},
doi = {10.1016/j.addr.2024.115319},
pmid = {38643839},
issn = {1872-8294},
abstract = {The microbiome has emerged as a significant biomarker and modulator in cancer development and treatment response. Recent research highlights the notable role of Fusobacterium nucleatum (F. nucleatum) in various tumor types, including breast, colorectal, esophageal, gastric, pancreatic, and lung cancers. Accumulating evidence suggests that the local microbial community forms an integral component of the tumor microenvironment, with bacterial communities within tumors displaying specificity to tumor types. Mechanistic investigations indicate that tumor-associated microbiota can directly influence tumor initiation, progression, and responses to chemotherapy or immunotherapy. This article presents a comprehensive review of microbial communities especially F. nucleatum in tumor tissue, exploring their roles and underlying mechanisms in tumor development, treatment, and prevention. When the tumor-associated F. nucleatum is killed, the host immune response is activated to recognize tumor cells. Bacteria epitopes restricted by the host antigens, can be identified for future anti-bacteria/tumor vaccine development.},
}

@article {pmid38643622,
year = {2024},
author = {Hwang, O and Emmett, B and Andersen, D and Howe, A and Ro, K and Trabue, S},
title = {Effects of swine manure dilution with lagoon effluent on microbial communities and odor formation in pit recharge systems.},
journal = {Journal of environmental management},
volume = {358},
number = {},
pages = {120884},
doi = {10.1016/j.jenvman.2024.120884},
pmid = {38643622},
issn = {1095-8630},
abstract = {Pit recharge systems (PRS) control odor by managing organic solids in swine manure. However, there needs to be more understanding of PRS's effect on the microbiome composition and its impact on odor formation. A study was conducted to understand how recharge intervals used in PRS impact manure microbiome and odor formation. Bioreactors dynamically loaded simulated recharge intervals of 14, 10, and 4 days by diluting swine manure with lagoon effluent at varying ratios. Treatment ratios tested included 10:0 (control), 7:3 (typical Korean PRS), 5:5 (enhanced PRS #1), and 2:8 (enhanced PRS #2). Manure microbial membership, chemical concentrations, and odorant concentrations were used to identify the interactions between microbiota, manure, and odor. The initial microbial community structure was controlled by dilution ratio and manure barn source material. Firmicutes and Proteobacteria were the dominant microbial phyla in manure and lagoon effluent, respectively, and significantly decreased or increased with dilution. Key microbial species were Clostridium saudiense in manure and Pseudomonas caeni in lagoon effluent. Percentages of these species declined by 8.9% or increased by 17.6%, respectively, with each unit dilution. Microbial community composition was controlled by both treatment (i.e., manure dilution ratio and barn source material) and environmental factors (i.e., solids and pH). Microbiome composition was correlated with manure odor formation profiles, but this effect was inseparable from environmental factors, which explained over 75% of the variance in odor profiles. Consequently, monitoring solids and pH in recharge waters will significantly impact odor control in PRS.},
}

@article {pmid38643472,
year = {2024},
author = {Kerekes, IK and Nagy, Á and Ősz, Á and Zalka, P},
title = {[Examination possibilities of microbial nucleic acid samples derived from the environment].},
journal = {Orvosi hetilap},
volume = {165},
number = {16},
pages = {613-619},
doi = {10.1556/650.2024.33025},
pmid = {38643472},
issn = {1788-6120},
mesh = {Humans ; *Nucleic Acids/analysis ; Environmental Microbiology ; },
}

Humans
*Nucleic Acids/analysis
Environmental Microbiology

@article {pmid38643372,
year = {2024},
author = {Hu, J and Bi, R and Luo, Y and Wu, K and Jin, S and Liu, Z and Jia, Y and Mao, CX},
title = {The gut microbiome promotes locomotion of Drosophila larvae via octopamine signaling.},
journal = {Insect science},
volume = {},
number = {},
pages = {},
doi = {10.1111/1744-7917.13370},
pmid = {38643372},
issn = {1744-7917},
support = {31500839//National Natural Science Foundation of China/ ; 81871121//National Natural Science Foundation of China/ ; },
abstract = {The gut microbiome is a key partner of animals, influencing various aspects of their physiology and behaviors. Among the diverse behaviors regulated by the gut microbiome, locomotion is vital for survival and reproduction, although the underlying mechanisms remain unclear. Here, we reveal that the gut microbiome modulates the locomotor behavior of Drosophila larvae via a specific neuronal type in the brain. The crawling speed of germ-free (GF) larvae was significantly reduced compared to the conventionally reared larvae, while feeding and excretion behaviors were unaffected. Recolonization with Acetobacter and Lactobacillus can fully and partially rescue the locomotor defects in GF larvae, respectively, probably due to the highest abundance of Acetobacter as a symbiotic bacterium in the larval gut, followed by Lactobacillus. Moreover, the gut microbiome promoted larval locomotion, not by nutrition, but rather by enhancing the brain levels of tyrosine decarboxylase 2 (Tdc2), which is an enzyme that synthesizes octopamine (OA). Overexpression of Tdc2 rescued locomotion ability in GF larvae. These findings together demonstrate that the gut microbiome specifically modulates larval locomotor behavior through the OA signaling pathway, revealing a new mechanism underlying larval locomotion regulated by the gut microbiome.},
}

@article {pmid38643366,
year = {2024},
author = {Lei, C and Xu, Y and Zhang, S and Huang, C and Qin, J},
title = {The role of microbiota in gastric cancer: A comprehensive review.},
journal = {Helicobacter},
volume = {29},
number = {2},
pages = {e13071},
doi = {10.1111/hel.13071},
pmid = {38643366},
issn = {1523-5378},
mesh = {Humans ; *Stomach Neoplasms ; *Helicobacter pylori ; *Helicobacter Infections ; *Microbiota ; Risk Factors ; },
abstract = {BACKGROUND: Gastric cancer (GC) continues to pose a significant global threat in terms of cancer-related fatalities. Despite notable advancements in medical research and therapies, further investigation is warranted to elucidate its underlying etiology and risk factors. Recent times have witnessed an escalated emphasis on comprehending the role of the microbiota in cancer development.

METHODS: This review briefly delves into recent developments in microbiome-related research pertaining to gastric cancer.

RESULTS: According to studies, the microbiota can influence GC growth by inciting inflammation, disrupting immunological processes, and generating harmful microbial metabolites. Furthermore, there is ongoing research into how the microbiome can impact a patient's response to chemotherapy and immunotherapy.

CONCLUSION: The utilization of the microbiome for detecting, preventing, and managing stomach cancer remains an active area of exploration.},
}

Humans
*Stomach Neoplasms
*Helicobacter pylori
*Helicobacter Infections
*Microbiota
Risk Factors

@article {pmid38643272,
year = {2024},
author = {Hauptfeld, E and Pappas, N and van Iwaarden, S and Snoek, BL and Aldas-Vargas, A and Dutilh, BE and von Meijenfeldt, FAB},
title = {Integrating taxonomic signals from MAGs and contigs improves read annotation and taxonomic profiling of metagenomes.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {3373},
pmid = {38643272},
issn = {2041-1723},
mesh = {*Metagenome/genetics ; Software ; Algorithms ; *Microbiota/genetics ; Metagenomics ; },
abstract = {Metagenomic analysis typically includes read-based taxonomic profiling, assembly, and binning of metagenome-assembled genomes (MAGs). Here we integrate these steps in Read Annotation Tool (RAT), which uses robust taxonomic signals from MAGs and contigs to enhance read annotation. RAT reconstructs taxonomic profiles with high precision and sensitivity, outperforming other state-of-the-art tools. In high-diversity groundwater samples, RAT annotates a large fraction of the metagenomic reads, calling novel taxa at the appropriate, sometimes high taxonomic ranks. Thus, RAT integrative profiling provides an accurate and comprehensive view of the microbiome from shotgun metagenomics data. The package of Contig Annotation Tool (CAT), Bin Annotation Tool (BAT), and RAT is available at https://github.com/MGXlab/CAT_pack (from CAT pack v6.0). The CAT pack now also supports Genome Taxonomy Database (GTDB) annotations.},
}

*Metagenome/genetics
Software
Algorithms
*Microbiota/genetics
Metagenomics

@article {pmid38643212,
year = {2024},
author = {Ren, M and Pan, H and Zhou, X and Yu, M and Ji, F},
title = {Alterations of the duodenal mucosal microbiome in patients with metabolic dysfunction-associated steatotic liver disease.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {9124},
pmid = {38643212},
issn = {2045-2322},
support = {2019C03031//Key Research and Development Program of Zhejiang Province/ ; 82370571//National Natural Science Foundation of China/ ; },
mesh = {Humans ; RNA, Ribosomal, 16S/genetics ; *Metabolic Diseases ; Duodenum ; *Microbiota ; *Non-alcoholic Fatty Liver Disease ; },
abstract = {Metabolic dysfunction-associated steatotic liver disease (MASLD), formerly known as nonalcoholic fatty liver disease (NAFLD), is associated with altered gut microbiota; however, there has been a focus on fecal samples, which are not representative of the entire digestive tract. Mucosal biopsies of the descending duodenum were collected. Five regions of the 16S rRNA gene were amplified and sequenced. Other assessments conducted on the study subjects included body mass index, transient elastography, liver enzymes, and lipid profile. Fifty-one subjects (36 with MASLD and 15 controls) were evaluated. There was no significant difference between the two groups regarding alpha- or beta-diversity of the duodenal mucosal microbiota. Linear discriminant analysis effect size (LEfSe) analysis showed that the genera Serratia and Aggregatibacter were more abundant in the duodenal mucosa of patients with MASLD, whereas the duodenal mucosal microbiota of the healthy controls was enriched with the genus Petrobacter. PICRUSt2 analysis revealed that genes associated with amino acid degradation and carboxylate degradation were significantly enriched in the duodenal mucosal microbiota of patients with MASLD. Our findings reveal the duodenal mucosal microbiota in patients with MASLD, which could contribute to future studies investigating the causal relationship between duodenal microbiota and MASLD.},
}

Humans
RNA, Ribosomal, 16S/genetics
*Metabolic Diseases
Duodenum
*Microbiota
*Non-alcoholic Fatty Liver Disease

@article {pmid38643180,
year = {2024},
author = {Ramaboli, MC and Ocvirk, S and Khan Mirzaei, M and Eberhart, BL and Valdivia-Garcia, M and Metwaly, A and Neuhaus, K and Barker, G and Ru, J and Nesengani, LT and Mahdi-Joest, D and Wilson, AS and Joni, SK and Layman, DC and Zheng, J and Mandal, R and Chen, Q and Perez, MR and Fortuin, S and Gaunt, B and Wishart, D and Methé, B and Haller, D and Li, JV and Deng, L and Swart, R and O'Keefe, SJD},
title = {Diet changes due to urbanization in South Africa are linked to microbiome and metabolome signatures of Westernization and colorectal cancer.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {3379},
pmid = {38643180},
issn = {2041-1723},
support = {R01 CA204403/CA/NCI NIH HHS/United States ; },
mesh = {Animals ; Humans ; Urbanization ; South Africa/epidemiology ; Cross-Sectional Studies ; Diet ; Metabolome ; *Gastrointestinal Microbiome ; Diet, Western ; *Colorectal Neoplasms/epidemiology/microbiology ; Feces/microbiology ; *Southern African People ; },
abstract = {Transition from traditional high-fiber to Western diets in urbanizing communities of Sub-Saharan Africa is associated with increased risk of non-communicable diseases (NCD), exemplified by colorectal cancer (CRC) risk. To investigate how urbanization gives rise to microbial patterns that may be amenable by dietary intervention, we analyzed diet intake, fecal 16 S bacteriome, virome, and metabolome in a cross-sectional study in healthy rural and urban Xhosa people (South Africa). Urban Xhosa individuals had higher intakes of energy (urban: 3,578 ± 455; rural: 2,185 ± 179 kcal/d), fat and animal protein. This was associated with lower fecal bacteriome diversity and a shift from genera favoring degradation of complex carbohydrates (e.g., Prevotella) to taxa previously shown to be associated with bile acid metabolism and CRC. Urban Xhosa individuals had higher fecal levels of deoxycholic acid, shown to be associated with higher CRC risk, but similar short-chain fatty acid concentrations compared with rural individuals. Fecal virome composition was associated with distinct gut bacterial communities across urbanization, characterized by different dominant host bacteria (urban: Bacteriodota; rural: unassigned taxa) and variable correlation with fecal metabolites and dietary nutrients. Food and skin microbiota samples showed compositional differences along the urbanization gradient. Rural-urban dietary transition in South Africa is linked to major changes in the gut microbiome and metabolome. Further studies are needed to prove cause and identify whether restoration of specific components of the traditional diet will arrest the accelerating rise in NCDs in Sub-Saharan Africa.},
}

Animals
Humans
Urbanization
South Africa/epidemiology
Cross-Sectional Studies
Diet
Metabolome
*Gastrointestinal Microbiome
Diet, Western
*Colorectal Neoplasms/epidemiology/microbiology
Feces/microbiology
*Southern African People

@article {pmid38643126,
year = {2024},
author = {Xiao, W and Chen, YL and Du, LY and Wu, J and Wang, Z and Mao, B and Wen, FQ and Gibson, PG and McDonald, VM and Yu, H and Fu, JJ},
title = {Bacterial interactome disturbance in chronic obstructive pulmonary disease clinical stability and exacerbations.},
journal = {Respiratory research},
volume = {25},
number = {1},
pages = {173},
pmid = {38643126},
issn = {1465-993X},
support = {No.82100046//National Natural Science Foundation of China/ ; No.81870014//National Natural Science Foundation of China/ ; 2023NSFSC1460//Sichuan Science and Technology Program of China/ ; 2020YFS0145//Sichuan Science and Technology Program of China/ ; },
mesh = {Humans ; *Dysbiosis ; *Pulmonary Disease, Chronic Obstructive/drug therapy ; Lung ; Haemophilus ; Sputum/microbiology ; Disease Progression ; },
abstract = {RATIONALE: Our understanding of airway dysbiosis in chronic obstructive pulmonary disease (COPD) remains incomplete, which may be improved by unraveling the complexity in microbial interactome.

OBJECTIVES: To characterize reproducible features of airway bacterial interactome in COPD at clinical stability and during exacerbation, and evaluate their associations with disease phenotypes.

METHODS: We performed weighted ensemble-based co-occurrence network analysis of 1742 sputum microbiomes from published and new microbiome datasets, comprising two case-control studies of stable COPD versus healthy control, two studies of COPD stability versus exacerbation, and one study with exacerbation-recovery time series data.

RESULTS: Patients with COPD had reproducibly lower degree of negative bacterial interactions, i.e. total number of negative interactions as a proportion of total interactions, in their airway microbiome compared with healthy controls. Evaluation of the Haemophilus interactome showed that the antagonistic interaction networks of this established pathogen rather than its abundance consistently changed in COPD. Interactome dynamic analysis revealed reproducibly reduced antagonistic interactions but not diversity loss during COPD exacerbation, which recovered after treatment. In phenotypic analysis, unsupervised network clustering showed that loss of antagonistic interactions was associated with worse clinical symptoms (dyspnea), poorer lung function, exaggerated neutrophilic inflammation, and higher exacerbation risk. Furthermore, the frequent exacerbators (≥ 2 exacerbations per year) had significantly reduced antagonistic bacterial interactions while exhibiting subtle compositional changes in their airway microbiota.

CONCLUSIONS: Bacterial interactome disturbance characterized by reduced antagonistic interactions, rather than change in pathogen abundance or diversity, is a reproducible feature of airway dysbiosis in COPD clinical stability and exacerbations, which suggests that we may target interactome rather than pathogen alone for disease treatment.},
}

Humans
*Dysbiosis
*Pulmonary Disease, Chronic Obstructive/drug therapy
Lung
Haemophilus
Sputum/microbiology
Disease Progression

@article {pmid38643115,
year = {2024},
author = {Ren, Y and Ma, Q and Zeng, X and Huang, C and Tan, S and Fu, X and Zheng, C and You, F and Li, X},
title = {Saliva‑microbiome‑derived signatures: expected to become a potential biomarker for pulmonary nodules (MCEPN-1).},
journal = {BMC microbiology},
volume = {24},
number = {1},
pages = {132},
pmid = {38643115},
issn = {1471-2180},
mesh = {Humans ; Saliva/microbiology ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Biomarkers ; *Lung Neoplasms/diagnosis/genetics ; Oxidoreductases ; },
abstract = {BACKGROUND: Oral microbiota imbalance is associated with the progression of various lung diseases, including lung cancer. Pulmonary nodules (PNs) are often considered a critical stage for the early detection of lung cancer; however, the relationship between oral microbiota and PNs remains unknown.

METHODS: We conducted a 'Microbiome with pulmonary nodule series study 1' (MCEPN-1) where we compared PN patients and healthy controls (HCs), aiming to identify differences in oral microbiota characteristics and discover potential microbiota biomarkers for non-invasive, radiation-free PNs diagnosis and warning in the future. We performed 16 S rRNA amplicon sequencing on saliva samples from 173 PN patients and 40 HCs to compare the characteristics and functional changes in oral microbiota between the two groups. The random forest algorithm was used to identify PN salivary microbial markers. Biological functions and potential mechanisms of differential genes in saliva samples were preliminarily explored using the Kyoto Encyclopedia of Genes and Genomes (KEGG) and Cluster of Orthologous Groups (COG) analyses.

RESULTS: The diversity of salivary microorganisms was higher in the PN group than in the HC group. Significant differences were noted in community composition and abundance of oral microorganisms between the two groups. Neisseria, Prevotella, Haemophilus and Actinomyces, Porphyromonas, Fusobacterium, 7M7x, Granulicatella and Selenomonas were the main differential genera between the PN and HC groups. Fusobacterium, Porphyromonas, Parvimonas, Peptostreptococcus and Haemophilus constituted the optimal marker sets (area under curve, AUC = 0.80), which can distinguish between patients with PNs and HCs. Further, the salivary microbiota composition was significantly correlated with age, sex, and smoking history (P < 0.001), but not with personal history of cancer (P > 0.05). Bioinformatics analysis of differential genes showed that patients with PN showed significant enrichment in protein/molecular functions related to immune deficiency and energy metabolisms, such as the cytoskeleton protein RodZ, nicotinamide adenine dinucleotide phosphate dehydrogenase (NADPH) dehydrogenase, major facilitator superfamily transporters and AraC family transcription regulators.

CONCLUSIONS: Our study provides the first evidence that the salivary microbiota can serve as potential biomarkers for identifying PN. We observed a significant association between changes in the oral microbiota and PNs, indicating the potential of salivary microbiota as a new non-invasive biomarker for PNs.

TRIAL REGISTRATION: Clinical trial registration number: ChiCTR2200062140; Date of registration: 07/25/2022.},
}

Humans
Saliva/microbiology
RNA, Ribosomal, 16S/genetics
*Microbiota/genetics
Biomarkers
*Lung Neoplasms/diagnosis/genetics
Oxidoreductases

@article {pmid38643067,
year = {2024},
author = {Zhu, Q and Li, MX and Yu, MC and Ma, QW and Huang, MJ and Lu, CW and Chen, CB and Chung, WH and Chang, CJ},
title = {Altered microbiome of serum exosomes in patients with acute and chronic cholecystitis.},
journal = {BMC microbiology},
volume = {24},
number = {1},
pages = {133},
pmid = {38643067},
issn = {1471-2180},
support = {CMRPG1E0908 and CMRPG1E0907, CMRPG1E0905//Scientific Research Project of Xiamen Chang Gung Hospital/ ; 3502Z20224ZD1135, 3502Z20224ZD113, 3502Z20224ZD1132//Xiamen Science and Technology Project Fund/ ; CMRPG1E0886, CGMH-XMCG-2022-002//CGMH-XMCG Joint Research Program/ ; GMRPG1E0221, 2020D021//Fujian Provincial Department of Science and Technology/ ; },
mesh = {Humans ; RNA, Ribosomal, 16S/genetics ; *Exosomes ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology ; *Microbiota/genetics ; *Cholecystitis ; *Cholecystitis, Acute ; },
abstract = {BACKGROUND: This study aimed to investigate the differences in the microbiota composition of serum exosomes from patients with acute and chronic cholecystitis.

METHOD: Exosomes were isolated from the serum of cholecystitis patients through centrifugation and identified and characterized using transmission electron microscopy and nano-flow cytometry. Microbiota analysis was performed using 16S rRNA sequencing.

RESULTS: Compared to patients with chronic cholecystitis, those with acute cholecystitis exhibited lower richness and diversity. Beta diversity analysis revealed significant differences in the microbiota composition between patients with acute and chronic cholecystitis. The relative abundance of Proteobacteria was significantly higher in exosomes from patients with acute cholecystitis, whereas Actinobacteria, Bacteroidetes, and Firmicutes were significantly more abundant in exosomes from patients with chronic cholecystitis. Furthermore, functional predictions of microbial communities using Tax4Fun analysis revealed significant differences in metabolic pathways such as amino acid metabolism, carbohydrate metabolism, and membrane transport between the two patient groups.

CONCLUSIONS: This study confirmed the differences in the microbiota composition within serum exosomes of patients with acute and chronic cholecystitis. Serum exosomes could serve as diagnostic indicators for distinguishing acute and chronic cholecystitis.},
}

Humans
RNA, Ribosomal, 16S/genetics
*Exosomes
*Gastrointestinal Microbiome/genetics
Feces/microbiology
*Microbiota/genetics
*Cholecystitis
*Cholecystitis, Acute

@article {pmid38642914,
year = {2024},
author = {Todor, LA and Hill, DM},
title = {Retrospective analysis of pathogens for guided creation of an EMPIRic antibiotic prEscribing pathway (EMPIRE).},
journal = {Journal of burn care & research : official publication of the American Burn Association},
volume = {},
number = {},
pages = {},
doi = {10.1093/jbcr/irae069},
pmid = {38642914},
issn = {1559-0488},
abstract = {The objective of this study was to evaluate the susceptibilities of pathogens isolated from cultures within the first 7 days of admission to the burn center and in the absence of healthcare-associated infection risk factors (HAIRF) to determine if current empiric antibiotics can be narrowed for refinement of an empiric antibiotic prescribing pathway according to suspected source. A 3-year sample of patients and cultures was utilized in hopes of obtaining at least 30 isolates of the most common pathogens and their respective susceptibilities. Two-hundred and sixty-eight clinically-relevant (e.g., deemed infectious, versus colonization) pathogens were included in the final sample with sources including wounds, respiratory, blood, urine, and bone. Of the 268 pathogens included, 45% were Gram-negative and 69% of all pathogens were isolated from wound cultures. The existing empiric pathway, vancomycin plus cefepime, covered 98% and 84% of all Gram-positive and Gram-negative pathogens, respectively. In patients without HAIRF, coverage rose to 98% and 90%, respectively. Initial use of vancomycin and cefepime remains adequate for pathogens isolated within one week of admission in patients without HAIRF. For pneumonias, a narrower spectrum beta-lactam would not sufficiently cover respiratory pathogens isolated within the first week of admission. Regarding early wound infections, difficult-to-treat pathogens remain as a rare isolate of wound cultures within one week of admission.},
}

@article {pmid38642761,
year = {2024},
author = {Wu, WF and Li, XY and Chen, SC and Jin, BJ and Wu, CY and Li, G and Sun, CL and Zhu, YG and Lin, XY},
title = {Nitrogen fertilization modulates rice phyllosphere functional genes and pathogens through fungal communities.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {172622},
doi = {10.1016/j.scitotenv.2024.172622},
pmid = {38642761},
issn = {1879-1026},
abstract = {The phyllosphere is a vital yet often neglected habitat hosting diverse microorganisms with various functions. However, studies regarding how the composition and functions of the phyllosphere microbiome respond to agricultural practices, like nitrogen fertilization, are limited. This study investigated the effects of long-term nitrogen fertilization with different levels (CK, N90, N210, N330) on the functional genes and pathogens of the rice phyllosphere microbiome. Results showed that the relative abundance of many microbial functional genes in the rice phyllosphere was significantly affected by nitrogen fertilization, especially those involved in C fixation and denitrification genes. Different nitrogen fertilization levels have greater effects on fungal communities than bacteria communities in the rice phyllosphere, and network analysis and structural equation models further elucidate that fungal communities not only changed bacterial-fungal inter-kingdom interactions in the phyllosphere but also contributed to the variation of biogeochemical cycle potential. Besides, the moderate nitrogen fertilization level (N210) was associated with an enrichment of beneficial microbes in the phyllosphere, while also resulting in the lowest abundance of pathogenic fungi (1.14 %). In contrast, the highest abundance of pathogenic fungi (1.64 %) was observed in the highest nitrogen fertilization level (N330). This enrichment of pathogen due to high nitrogen level was also regulated by the fungal communities, as revealed through SEM analysis. Together, we demonstrated that the phyllosphere fungal communities were more sensitive to the nitrogen fertilization levels and played a crucial role in influencing phyllosphere functional profiles including element cycling potential and pathogen abundance. This study expands our knowledge regarding the role of phyllosphere fungal communities in modulating the element cycling and plant health in sustainable agriculture.},
}

@article {pmid38642533,
year = {2024},
author = {Xiong, S and Xu, X and Du, T and Liu, Q and Huang, T and Ren, H and Xiong, T and Xie, M},
title = {Organic acids drove the microbiota succession and consequently altered the flavor quality of Laotan Suancai across fermentation rounds: Insights from the microbiome and metabolome.},
journal = {Food chemistry},
volume = {450},
number = {},
pages = {139335},
doi = {10.1016/j.foodchem.2024.139335},
pmid = {38642533},
issn = {1873-7072},
abstract = {Laotan Suancai, a popular traditional Chinese fermented vegetable, is manufactured in the industry via four fermentation rounds. However, the differences in flavor quality of Laotan Suancai from the four fermentation rounds and the causes of this variation remain unclear. Metabolome analysis indicated that the different content of five taste compounds and 31 aroma compounds caused the differences in flavor quality among the variated fermentation rounds of Laotan Suancai. Amplicon sequencing indicated that the microbial succession exhibited a certain pattern during four fermentation rounds and further analysis unveiled that organic acids drove the microbiota shift to more acid-resistant populations. Spearman correlation analysis highlighted that seven core microbes may be involved in the formation of differential flavor and the corresponding metabolic pathways were reconstructed by function prediction. Our findings offer a novel perspective on comprehending the deterioration of flavor quality across the fermentation rounds of Laotan Suancai.},
}

@article {pmid38642506,
year = {2024},
author = {Hao, Y and Lu, C and Xiang, Q and Sun, A and Su, JQ and Chen, QL},
title = {Unveiling the overlooked microbial niches thriving on building exteriors.},
journal = {Environment international},
volume = {187},
number = {},
pages = {108649},
doi = {10.1016/j.envint.2024.108649},
pmid = {38642506},
issn = {1873-6750},
abstract = {Rapid urbanization in the Asia-Pacific region is expected to place two-thirds of its population in concrete-dominated urban landscapes by 2050. While diverse architectural facades define the unique appearance of these urban systems. There remains a significant gap in our understanding of the composition, assembly, and ecological potential of microbial communities on building exteriors. Here, we examined bacterial and protistan communities on building surfaces along an urbanization gradient (urban, suburban and rural regions), investigating their spatial patterns and the driving factors behind their presence. A total of 55 bacterial and protist phyla were identified. The bacterial community was predominantly composed of Proteobacteria (33.7% to 67.5%). The protistan community exhibited a prevalence of Opisthokonta and Archaeplastida (17.5% to 82.1% and 1.8% to 61.2%, respectively). The composition and functionality of bacterial communities exhibited spatial patterns correlated with urbanization. In urban buildings, factors such as facade type, light exposure, and building height had comparatively less impact on bacterial composition compared to suburban and rural areas. The highest bacterial diversity and lowest Weighted Average Community Identity (WACI) were observed on suburban buildings, followed by rural buildings. In contrast, protists did not show spatial distribution characteristics related to facade type, light exposure, building height and urbanization level. The distinct spatial patterns of protists were primarily shaped by community diffusion and the bottom-up regulation exerted by bacterial communities. Together, our findings suggest that building exteriors serve as attachment points for local microbial metacommunities, offering unique habitats where bacteria and protists exhibit independent adaptive strategies closely tied to the overall ecological potential of the community.},
}

@article {pmid38642272,
year = {2024},
author = {Chen, LA and Boyle, K},
title = {The Role of the Gut Microbiome in Health and Disease in the Elderly.},
journal = {Current gastroenterology reports},
volume = {},
number = {},
pages = {},
pmid = {38642272},
issn = {1534-312X},
abstract = {PURPOSE OF REVIEW: Growing evidence supports the contribution of age in the composition and function of the gut microbiome, with specific findings associated with health in old age and longevity.

RECENT FINDINGS: Current studies have associated certain microbiota, such as Butyricimonas, Akkermansia, and Odoribacter, with healthy aging and the ability to survive into extreme old age. Furthermore, emerging clinical and pre-clinical research have shown promising mechanisms for restoring a healthy microbiome in elderly populations through various interventions such as fecal microbiota transplant (FMT), dietary interventions, and exercise programs. Despite several conceptually exciting interventional studies, the field of microbiome research in the elderly remains limited. Specifically, large longitudinal studies are needed to better understand causative relationships between the microbiome and healthy aging. Additionally, individualized approaches to microbiome interventions based on patients' co-morbidities and the underlying functional capacity of their microbiomes are needed to achieve optimal results.},
}

@article {pmid38642195,
year = {2024},
author = {Tampanna, N and Chansuwan, W and Wichienchot, S},
title = {Effect of Plant-Based Mung Bean Products on Digestibility and Gut Microbiome Profiling Using In Vitro Fecal Fermentation.},
journal = {Plant foods for human nutrition (Dordrecht, Netherlands)},
volume = {},
number = {},
pages = {},
pmid = {38642195},
issn = {1573-9104},
support = {AGR6505031M//the National Science, Research and Innovation Fund (NSRF) and the Prince of Songkla University/ ; },
abstract = {The concept of plant-based protein consumption has been increasing recently because of the growing health consciousness among people. Mung bean is one of the most consumed legumes with a dense nutrient profile. Hence, current research is aimed to study the effect of mung bean protein-based products including mung bean snack (MBS) and textured vegetable protein (TVP) for treatment groups against the control groups, commercial ingredients group consisting of mung bean powder (MBP) and pea powder (PP) and commercial products group include commercial pea texture (cPT) and commercial textured vegetable protein (cTVP) for their proximate composition, digestibility, gut microbial profile and fatty acid metabolite profiling. The MBS and TVP samples had significantly higher digestibility of 74.43% and 73.24% than the commercial products. The protein content of TVP was 0.8 times higher than its commercial control. Gut microbiome profiling showed that all the samples shared around 162 similar genera. Post-fermentation analysis provided promising results by reflecting the growth of beneficial bacteria (Parabacteroides, Bifidobacterium and Lactobacillus) and the suppression of pathogens (Escherichia-Shigella, Dorea and Klebsiella). The dual relationship between gut microbiota and nutrient interaction proved the production of abundant short- and branched-chain fatty acids. The MBS sample was able to produce SCFAs (41.27 mM) significantly and BCFAs (2.02 mM) than the TVP sample (27.58 mM and 2.14 mM, respectively). Hence, our research outcomes proved that the mung bean protein-based products might infer numerous health benefits to the host due to enriched probiotics in the gut and the production of their corresponding metabolites.},
}

@article {pmid38642188,
year = {2024},
author = {Liu, Y and Lin, H and Zhong, W and Zeng, Y and Zhou, G and Chen, Z and Huang, S and Zhang, L and Liu, X},
title = {Multi-omics analysis of immune-related microbiome and prognostic model in head and neck squamous cell carcinoma.},
journal = {Clinical oral investigations},
volume = {28},
number = {5},
pages = {263},
pmid = {38642188},
issn = {1436-3771},
support = {8217102092//National Natural Science Foundation of China/ ; },
mesh = {Humans ; Prognosis ; Squamous Cell Carcinoma of Head and Neck ; Multiomics ; *Microbiota ; *Head and Neck Neoplasms ; },
abstract = {OBJECTIVES: The aim of our study is to explore the transcriptional and microbial characteristics of head and neck cancer's immune phenotypes using a multi-omics approach.

MATERIALS AND METHODS: Employing TCGA data, we analyzed head and neck squamous cell carcinoma (HNSCC) immune cells with CIBERSORT and identified differentially expressed genes using DESeq2. Microbial profiles, obtained from the TCMA database, were analyzed using LEfSe algorithm to identify differential microbes in immune cell infiltration (ICI) subgroups. Random Forest algorithm and deep neural network (DNN) were employed to select microbial features and developed a prognosis model.

RESULTS: We categorized HNSCC into three immune subtypes, finding ICI-2 with the worst prognosis and distinct microbial diversity. Our immune-related microbiome (IRM) model outperformed the TNM staging model in predicting survival, linking higher IRM model scores with poorer prognosis, and demonstrating clinical utility over TNM staging. Patients categorized as low-risk by the IRM model showed higher sensitivity to cisplatin and sorafenib treatments.

CONCLUSIONS: This study offers a comprehensive exploration of the ICI landscape in HNSCC. We provide a detailed scenario of immune regulation in HNSCC and report a correlation between differing ICI patterns, intratumor microbiome, and prognosis. This research aids in identifying prime candidates for optimizing treatment strategies in HNSCC.

CLINICAL RELEVANCE: This study revealed the microbial signatures associated with immunophenotyping of HNSCC and further found the microbial signatures associated with prognosis. The prognostic model based on IRM microbes is helpful for early prediction of patient prognosis and assisting clinical decision-making.},
}

Humans
Prognosis
Squamous Cell Carcinoma of Head and Neck
Multiomics
*Microbiota
*Head and Neck Neoplasms

@article {pmid38642171,
year = {2024},
author = {Araujo, TT and Dionizio, A and Carvalho, TS and Boas Feitosa, CMV and Vertuan, M and Câmara, JVF and Henrique-Silva, F and Marchetto, R and Chiaratti, MR and Santos, AC and Alves, LO and Ferro, M and Buzalaf, MAR},
title = {Acquired enamel pellicle and biofilm engineering with a combination of acid-resistant proteins (CaneCPI-5, StN15, and Hemoglobin) for enhanced protection against dental caries - in vivo and in vitro investigations.},
journal = {Clinical oral investigations},
volume = {28},
number = {5},
pages = {261},
pmid = {38642171},
issn = {1436-3771},
support = {2019/08032-5//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2019/26070-1//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 302371/2018-4 ; 304554/2023-5//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; },
mesh = {Humans ; Dental Pellicle/chemistry/microbiology ; *Dental Caries/prevention & control ; Proteomics ; Biofilms ; Hemoglobins/analysis ; *Tooth Demineralization/prevention & control ; },
abstract = {OBJECTIVE: This study was designed in two-legs. In the in vivo, we explored the potential of a rinse solution containing a combination (Comb) of 0.1 mg/mL CaneCPI-5 (sugarcane-derive cystatin), 1.88 × 10[- 5]M StN15 (statherin-derived peptide) and 1.0 mg/mL hemoglobin (Hb) to change the protein profile of the acquired enamel pellicle(AEP) and the microbiome of the enamel biofilm. The in vitro, was designed to reveal the effects of Comb on the viability and bacterial composition of the microcosm biofilm, as well as on enamel demineralization.

MATERIALS AND METHODS: In vivo study, 10 participants rinsed (10mL,1 min) with either deionized water (H2O-control) or Comb. AEP and biofilm were collected after 2 and 3 h, respectively, after rinsing. AEP samples underwent proteomics analysis, while biofilm microbiome was assessed via 16 S-rRNA Next Generation Sequencing(NGS). In vitro study, a microcosm biofilm protocol was employed. Ninety-six enamel specimens were treated with: 1)Phosphate-Buffered Solution-PBS(negative-control), 2)0.12%Chlorhexidine, 3)500ppmNaF and 4)Comb. Resazurin, colony-forming-units(CFU) and Transversal Microradiography(TMR) were performed.

RESULTS: The proteomic results revealed higher quantity of proteins in the Comb compared to control associated with immune system response and oral microbial adhesion. Microbiome showed a significant increase in bacteria linked to a healthy microbiota, in the Comb group. In the in vitro study, Comb group was only efficient in reducing mineral-loss and lesion-depth compared to the PBS.

CONCLUSIONS: The AEP modification altered the subsequent layers, affecting the initial process of bacterial adhesion of pathogenic and commensal bacteria, as well as enamel demineralization.

CLINICAL RELEVANCE: Comb group shows promise in shaping oral health by potentially introducing innovative approaches to prevent enamel demineralization and deter tooth decay.},
}

Humans
Dental Pellicle/chemistry/microbiology
*Dental Caries/prevention & control
Proteomics
Biofilms
Hemoglobins/analysis
*Tooth Demineralization/prevention & control

@article {pmid38641855,
year = {2024},
author = {Coskun, M and Babayeva, A and Barlas, T and Yalcin, MM and Akturk, M and Toruner, F and Karakoc, MA and Karakan, T and Cindoruk, M and Yetkin, İ and Altinova, A},
title = {EXPRESS: Relationship between Gut Microbiome and Bone Deficits in Primary Hyperparathyroidism: A Proof of Concept Pilot Study.},
journal = {Journal of investigative medicine : the official publication of the American Federation for Clinical Research},
volume = {},
number = {},
pages = {10815589241251695},
doi = {10.1177/10815589241251695},
pmid = {38641855},
issn = {1708-8267},
abstract = {Parathyroid hormone (PTH) interacts with components of the gut microbiota to exert its bone-regulating effects. This study aimed to investigate the gut microbial composition in patients with primary hyperparathyroidism (PHPT). Nine patients with PHPT and nine age-sex and body mass index-matched healthy controls were included. Gut microbial composition was assessed using 16S rRNA gene amplicon sequencing in both groups at baseline and one month after parathyroidectomy in the PHPT group. Data were imported into QIIME-2 and both QIIME-2 and R packages were used for microbiome analysis. Alpha and beta diversity were similar between the groups and remained unchanged after parathyroidectomy. The relative abundance of Subdoligranulum was significantly higher, whereas Ruminococcus, Alloprevotella, Phascolarctobacterium and Clostridium sensu stricto_1 were significantly lower in PHPT than in controls (p<0.001). After parathyroidectomy, the relative abundance of Subdoligranulum decreased, Ruminococcus and Alloprevotella increased (p<0.001). The PHPT group had lower total femoral and lumbar bone mineral density (BMD) than the controls (p<0.05). At baseline, Alloprevotella abundance was positively correlated with serum phosphorus and Subdoligranulum was positively correlated with total lumbar BMD. Clostridium sensu stricto_1 was negatively correlated with serum calcium and positively correlated with femoral neck BMD. Postoperatively, Alloprevotella was positively correlated with baseline serum phosphorus, and Phascolarctobacterium was positively correlated with distal radius BMD. This study demonstrated that the diversity of the gut microbiome was altered, possibly in response to electrolyte changes in PHPT, both before and after parathyroidectomy.},
}

@article {pmid38641815,
year = {2024},
author = {Liu, Z and Zhang, D and Chen, S},
title = {Unveiling the gastric microbiota: implications for gastric carcinogenesis, immune responses, and clinical prospects.},
journal = {Journal of experimental & clinical cancer research : CR},
volume = {43},
number = {1},
pages = {118},
pmid = {38641815},
issn = {1756-9966},
support = {82074074//National Natural Science Foundation of China/ ; 82104447//National Natural Science Foundation of China/ ; 81874353//National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Microbiota ; *Stomach Neoplasms/pathology ; Carcinogenesis ; *Helicobacter pylori ; Immunity ; },
abstract = {High-throughput sequencing has ushered in a paradigm shift in gastric microbiota, breaking the stereotype that the stomach is hostile to microorganisms beyond H. pylori. Recent attention directed toward the composition and functionality of this 'community' has shed light on its potential relevance in cancer. The microbial composition in the stomach of health displays host specificity which changes throughout a person's lifespan and is subject to both external and internal factors. Distinctive alterations in gastric microbiome signature are discernible at different stages of gastric precancerous lesions and malignancy. The robust microbes that dominate in gastric malignant tissue are intricately implicated in gastric cancer susceptibility, carcinogenesis, and the modulation of immunosurveillance and immune escape. These revelations offer fresh avenues for utilizing gastric microbiota as predictive biomarkers in clinical settings. Furthermore, inter-individual microbiota variations partially account for differential responses to cancer immunotherapy. In this review, we summarize current literature on the influence of the gastric microbiota on gastric carcinogenesis, anti-tumor immunity and immunotherapy, providing insights into potential clinical applications.},
}

Humans
*Microbiota
*Stomach Neoplasms/pathology
Carcinogenesis
*Helicobacter pylori
Immunity