@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

@article {pmid38641475,
year = {2024},
author = {Addison, SL and Rúa, MA and Smaill, SJ and Singh, BK and Wakelin, SA},
title = {Partner or perish: tree microbiomes and climate change.},
journal = {Trends in plant science},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tplants.2024.03.008},
pmid = {38641475},
issn = {1878-4372},
abstract = {Understanding the complex relationships between plants, their microbiomes, and environmental changes is crucial for improving growth and survival, especially for long-lived tree species. Trees, like other plants, maintain close associations with a multitude of microorganisms on and within their tissues, forming a 'holobiont'. However, a comprehensive framework for detailed tree-microbiome dynamics, and the implications for climate adaptation, is currently lacking. This review identifies gaps in the existing literature, emphasizing the need for more research to explore the coevolution of the holobiont and the full extent of climate change impact on tree growth and survival. Advancing our knowledge of plant-microbial interactions presents opportunities to enhance tree adaptability and mitigate adverse impacts of climate changes on trees.},
}

@article {pmid38641252,
year = {2024},
author = {Liu, B and Mashimo, C and Nambu, T and Maruyama, H and Okinaga, T},
title = {Transposon insertion in Rothia dentocariosa.},
journal = {Journal of oral biosciences},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.job.2024.04.006},
pmid = {38641252},
issn = {1880-3865},
abstract = {OBJECTIVES: Rothia spp. are emerging as significant bacteria associated with oral health, with Rothia dentocariosa being one of the most prevalent species. However, there is a lack of studies examining these properties at the genetic level. This study aimed to establish a genetic modification platform for R. dentocariosa.

METHODS: Rothia spp. were isolated from saliva samples collected from healthy volunteers. Subsequently, R. dentocariosa strains were identified through colony morphology, species-specific polymerase chain reaction (PCR), and 16S ribosomal RNA gene sequencing. The identified strains were then transformed with plasmid pJRD215, and the most efficient strain was selected. Transposon insertion mutagenesis was performed to investigate the possibility of genetic modifications.

RESULTS: A strain demonstrating high transforming ability, designated as R. dentocariosa LX16, was identified. This strain underwent transposon insertion mutagenesis and was screened for 5-fluoroorotic acid-resistant transposants. The insertion sites were confirmed using arbitrary primed PCR, gene-specific PCR, and Sanger sequencing.

CONCLUSION: This study marks the first successful genetic modification of R. dentocariosa. Investigating R. dentocariosa at the genetic level can provide insights into its role within the oral microbiome.},
}

@article {pmid38641145,
year = {2024},
author = {Saeid, AB and De Rubis, G and Williams, KA and Yeung, S and Chellappan, DK and Singh, SK and Gupta, G and Hansbro, PM and Shahbazi, MA and Gulati, M and Kaur, IP and Santos, HA and Paudel, KR and Dua, K},
title = {Revolutionising Lung Health: Exploring the Latest Breakthroughs and Future Prospects of Synbiotic Nanostructures in Lung Diseases.},
journal = {Chemico-biological interactions},
volume = {},
number = {},
pages = {111009},
doi = {10.1016/j.cbi.2024.111009},
pmid = {38641145},
issn = {1872-7786},
abstract = {The escalating prevalence of lung diseases underscores the need for innovative therapies. Dysbiosis in human body microbiome has emerged as a significant factor in these diseases, indicating a potential role for synbiotics in restoring microbial equilibrium. However, effective delivery of synbiotics to the target site remains challenging. Here, we aim to explore suitable nanoparticles for encapsulating synbiotics tailored for applications in lung diseases. Nanoencapsulation has emerged as a prominent strategy to address the delivery challenges of synbiotics in this context. Through a comprehensive review, we assess the potential of nanoparticles in facilitating synbiotic delivery and their structural adaptability for this purpose. Our review reveals that nanoparticles such as nanocellulose, starch, and chitosan exhibit high potential for synbiotic encapsulation. These offer flexibility in structure design and synthesis, making them promising candidates for addressing delivery challenges in lung diseases. Furthermore, our analysis highlights that synbiotics, when compared to probiotics alone, demonstrate superior anti-inflammatory, antioxidant, antibacterial and anticancer activities. This review underscores the promising role of nanoparticle-encapsulated synbiotics as a targeted and effective therapeutic approach for lung diseases, contributing valuable insights into the potential of nanomedicine in revolutionizing treatment strategies for respiratory conditions, ultimately paving the way for future advancements in this field.},
}

@article {pmid38641112,
year = {2024},
author = {Meng, J and Xu, F and Yang, H and Li, X and Zhao, P},
title = {Exploring microbiome and plankton responses and interactions in the mangrove ecosystem through eDNA and network analysis.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {172581},
doi = {10.1016/j.scitotenv.2024.172581},
pmid = {38641112},
issn = {1879-1026},
abstract = {The comprehensive analysis of multiple biological communities is essential for assessing diversities within mangrove ecosystems, yet such studies are infrequent. Environmental DNA (eDNA) facilitates the simultaneous exploration of organisms across various levels within a single ecosystem. In this investigation, 16S rRNA, cytochrome C oxidase I (COI), and Mito-fish primers were employed to characterize the microbiome, eukaryotic plankton, and fish communities, along with their intricate interactions, across 24 samples from three Chinese mangrove reservoirs. The resulting dataset encompasses 3779 taxonomic groups (genus level), spanning from the microbiome to vertebrates. Diversity analysis unveiled a higher level of stability in the microbiome community compared to plankton, underscoring the superior site-specificity of plankton. The association analysis revealed that biodiversity was primarily affected by temperature, turbidity, and fluorescent dissolved organic matter (fDOM). Notably, the physicochemical factors, turbidity, and fDOM had a more pronounced impact on the microbiome than on plankton, explaining their distinct sensitivities to site-specific conditions. Network analysis constructed 15 biological interaction subnetworks representing various community connections. The most connected genera in each subnetwork, highly responsive to different environmental factors, could serve as potential indicators of distinct ecosystem states. In summary, our findings represent the first comparison of the response sensitivities of different communities and the construction of their interaction networks in mangrove environments. These results contribute valuable insights into marine ecosystem dynamics and the role of environmental factors in shaping biodiversity.},
}

@article {pmid38641088,
year = {2024},
author = {Jain, N},
title = {The molecular interplay between human and bacterial amyloids: Implications in neurodegenerative diseases.},
journal = {Biochimica et biophysica acta. Proteins and proteomics},
volume = {1872},
number = {4},
pages = {141018},
doi = {10.1016/j.bbapap.2024.141018},
pmid = {38641088},
issn = {1878-1454},
abstract = {Neurodegenerative disorders such as Parkinson's (PD) and Alzheimer's diseases (AD) are linked with the assembly and accumulation of proteins into structured scaffold called amyloids. These diseases pose significant challenges due to their complex and multifaceted nature. While the primary focus has been on endogenous amyloids, recent evidence suggests that bacterial amyloids may contribute to the development and exacerbation of such disorders. The gut-brain axis is emerging as a communication pathway between bacterial and human amyloids. This review delves into the novel role and potential mechanism of bacterial amyloids in modulating human amyloid formation and the progression of AD and PD.},
}

@article {pmid38641025,
year = {2024},
author = {Chakraborty, P and Gamage, HKAH and Laird, AS},
title = {Butyrate as a potential therapeutic agent for neurodegenerative disorders.},
journal = {Neurochemistry international},
volume = {},
number = {},
pages = {105745},
doi = {10.1016/j.neuint.2024.105745},
pmid = {38641025},
issn = {1872-9754},
abstract = {Maintaining an optimum microbial community within the gastrointestinal tract is intricately linked to human metabolic, immune and brain health. Disturbance to these microbial populations perturbs the production of vital bioactive compounds synthesised by the gut microbiome, such as short-chain fatty acids (SCFAs). Of the SCFAs, butyrate is known to be a major source of energy for colonocytes and has valuable effects on the maintenance of intestinal epithelium and blood brain barrier integrity, gut motility and transit, anti-inflammatory effects, and autophagy induction. Inducing endogenous butyrate production is likely to be beneficial for gut-brain homeostasis and for optimal neuronal function. For these reasons, butyrate has gained interest as a potential therapy for not only metabolic and immunological disorders, but also conditions related to the brain, including neurodegenerative diseases. While direct and indirect sources of butyrate, including prebiotics, probiotics, butyrate pro-drugs and glucosidase inhibitors, offer a promising therapeutic avenue, their efficacy and dosage in neurodegenerative conditions remain largely unknown. Here, we review current literature on effects of butyrate relevant to neuronal function, the impact of butyrate in a range of neurodegenerative diseases and related treatments that may have potential for the treatment of neurodegenerative diseases.},
}

@article {pmid38640799,
year = {2024},
author = {Jin, X and Pan, J and Zhang, C and Cao, X and Wang, C and Yue, L and Li, X and Liu, Y and Wang, Z},
title = {Toxic mechanism in Daphnia magna due to phthalic acid esters and CuO nanoparticles co-exposure: The insight of physiological, microbiomic and metabolomic profiles.},
journal = {Ecotoxicology and environmental safety},
volume = {277},
number = {},
pages = {116338},
doi = {10.1016/j.ecoenv.2024.116338},
pmid = {38640799},
issn = {1090-2414},
abstract = {Various phthalic acid esters (PAEs) such as dibutyl phthalate (DBP) and butyl benzyl phthalate (BBP) co-exist with nanopollutants in aquatic environment. In this study, Daphnia magna was exposed to nano-CuO and DBP or BBP at environmental relevant concentrations for 21-days to investigate these combined toxic effects. Acute EC50 values (48 h) of nano-CuO, DBP, and BBP were 12.572 mg/L, 8.978 mg/L, and 4.785 mg/L, respectively. Results showed that co-exposure with nano-CuO (500 μg/L) for 21 days significantly enhanced the toxicity of DBP (100 μg/L) and BBP (100 μg/L) to Daphnia magna by 18.37% and 18.11%, respectively. The activities of superoxide dismutase, catalase, and glutathione S-transferase were enhanced by 10.95% and 14.07%, 25.63% and 25.91%, and 39.93% and 35.01% in nano-CuO+DBP and nano-CuO+BBP treatments as compared to the individual exposure groups, verifying that antioxidative defense responses were activated. Furthermore, the co-exposure of nano-CuO and PAEs decreased the population richness and diversity microbiota, and changed the microbial community composition in Daphnia magna. Metabolomic analysis elucidated that nano-CuO + PAEs exposure induced stronger disturbance on metabolic network and molecular function, including amino acid, nucleotides, and lipid metabolism-related metabolic pathways, as comparison to PAEs single exposure treatments. In summary, the integration of physiological, microflora, and untargeted metabolomics analysis offers a fresh perspective into the potential ecological risk associated with nanopollutants and phthalate pollution in aquatic ecosystems.},
}

@article {pmid38640559,
year = {2024},
author = {Muttaleb Asfoor, H and Saied Hamied, A},
title = {Immune response to colonization of Candida albicans in mice treated with Cefoperazone.},
journal = {Cytokine},
volume = {179},
number = {},
pages = {156611},
doi = {10.1016/j.cyto.2024.156611},
pmid = {38640559},
issn = {1096-0023},
abstract = {Candida species are a normal human flora in humans' digestive and reproductive systems, oral cavity, skin, and mucosal surfaces. This study aimed to detect the immunological role of Candida infection by using some immunological markers. The results of levels in serum showed high concentrations of IgA (56.20 ± 12 pg/ml,29.55 ± 4.5 pg/ml respectively) and IgG (12.05 ± 3.218 pg/ml, 3.836 ± 1.23 pg/ml respectively) in mice infected with C. albicans and mice treated with Cefoperazone and infected with Candida with significant differences (P value < 0.05). The results showed high serum levels of IL-17(191.5 ± 42.81 pg/ml) and TLR2(7.651 ± 1.5 pg/ml) in group mice infected with C. albicans compared with negative control and group mice treated with Cefoperazone. Also, high levels of IL-17 (91.33 ± 4.816 pg/ml) and TLR2 (2.630 ± 0.5 pg/ml) in group mice treated with Cefoperazone and infected with Candida compared with negative control and group mice treated with Cefoperazone (P value < 0.05). The results of antibodies and immunological markers in the intestine showed high levels of IgA and IgG in mice infected with C.albicans (55.7 ± 4.9 pg/ml, 18.19 ± 0.63 pg/ml respectively).Also,IgA and IgG in mice treated with Cefoperazone and infected with Candida were high level (43.04 ± 2.1 pg/ml, 2.927 ± 0.2 pg/ml respectively) in mice infected with C. albicans with significant differences (P value < 0.05). The results levels of IL-17 and TLR2 were increased in mice infected with C. albicans (191.5 ± 42.81 pg/ml, 7.651 ± 1.5 pg/ml respectively) and mice treated with Cefoperazone and infected with Candida (91.33 ± 4.816 pg/ml,2.630 ± 0.5 pg/ml respectively) with significant differences (P < 0.05). In conclusion, this study demonstrated that cefoperazone treatment and infection by Candida albicans changed the microbiome components in the gut and finally can change host immune responses. It was observed that elevated levels of the antibodies production (IgA and IgG) and immunological markers (IL-17, and TLR2) in serum and the gut.},
}

@article {pmid38640440,
year = {2024},
author = {Bosch, J and Dobbler, PT and Větrovský, T and Tláskal, V and Baldrian, P and Brabcová, V},
title = {Decomposition of Fomes fomentatius fruiting bodies - transition of healthy living fungus into a decayed bacteria-rich habitat is primarily driven by Arthropoda.},
journal = {FEMS microbiology ecology},
volume = {100},
number = {5},
pages = {},
pmid = {38640440},
issn = {1574-6941},
support = {21-09334 J//Czech Science Foundation/ ; },
mesh = {Animals ; *Arthropods ; *Coriolaceae ; *Microbiota/genetics ; *Ascomycota ; Fruiting Bodies, Fungal ; Bacteria/genetics ; },
abstract = {Fomes fomentarius is a widespread, wood-rotting fungus of temperate, broadleaved forests. Although the fruiting bodies of F. fomentarius persist for multiple years, little is known about its associated microbiome or how these recalcitrant structures are ultimately decomposed. Here we used metagenomics and metatranscriptomics to analyse the microbial community associated with healthy living and decomposing F. fomentarius fruiting bodies to assess the functional potential of the fruiting body-associated microbiome and to determine the main players involved in fruiting body decomposition. F. fomentarius sequences in the metagenomes were replaced by bacterial sequences as the fruiting body decomposed. Most CAZymes expressed in decomposing fruiting bodies targeted components of the fungal cell wall with almost all chitin-targeting sequences, plus a high proportion of beta-glucan-targeting sequences, belonging to Arthropoda. We suggest that decomposing fruiting bodies of F. fomentarius represent a habitat rich in bacteria, while its decomposition is primarily driven by Arthropoda. Decomposing fruiting bodies thus represent a specific habitat supporting both microorganisms and microfauna.},
}

Animals
*Arthropods
*Coriolaceae
*Microbiota/genetics
*Ascomycota
Fruiting Bodies, Fungal
Bacteria/genetics

@article {pmid38640403,
year = {2024},
author = {Ekpruke, CD and Alford, R and Parker, E and Silveyra, P},
title = {Gonadal sex and chromosome complement influence the gut microbiome in a mouse model of allergic airway inflammation.},
journal = {Physiological genomics},
volume = {},
number = {},
pages = {},
doi = {10.1152/physiolgenomics.00003.2024},
pmid = {38640403},
issn = {1531-2267},
support = {R01HL159764//HHS | NIH | National Heart, Lung, and Blood Institute (NHLBI)/ ; R03HL141618//HHS | NIH | National Heart, Lung, and Blood Institute (NHLBI)/ ; },
abstract = {Evidence abounds that gut microbiome components are associated with sex disparities in the immune system. However, it remains unclear whether the observed sex disparity in asthma incidence is associated with sex-dependent differences in immune-modulating gut microbiota, and/or its influence on allergic airway inflammatory processes. Using a mouse model of house dust mite (HDM)-induced allergic inflammation and the four core genotypes (FCG) model, we have previously reported sex differences in lung inflammatory phenotypes. Here, we investigated associations of gut microbiomes to these phenotypes by challenging FCG mice (XXM, XXF, XYM, XYF, n=7/group) withHDM (25 μg) or PBS intranasally for 5 weeks and collecting fecal samples. We extracted fecal DNA and analyzed the 16S microbiome via Targeted Metagenomic Sequencing. We compared alpha and beta diversity across genotypes and assessed the Firmicutes/Bacteroidetes ratio (F/B). When comparing baseline and after exposure for the FCG, we found that the gut F/B was only increased in the XXM genotype. We also found that alpha diversity was significantly increased in all FCG mice upon HDM challenge, with the highest increase in the XXF, and the lowest in the XXM genotypes. Similarly, beta diversity of the microbial community was also affected by challenge in a gonad- and chromosome-dependent manner. In summary, our results indicated that HDM treatment, gonads, and sex chromosomes significantly influence the gut microbial community composition. We concluded that allergic lung inflammation may be affected by the gut microbiome in a sex-dependent manner involving both hormonal and genetic influences.},
}

@article {pmid38639049,
year = {2024},
author = {Peng, Z and Zhang, J and Zhang, M and Yin, L and Zhou, Z and Lv, C and Wang, Z and Tang, J},
title = {Tryptophan metabolites relieve intestinal Candida albicans infection by altering the gut microbiota to reduce IL-22 release from group 3 innate lymphoid cells of the colon lamina propria.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d4fo00432a},
pmid = {38639049},
issn = {2042-650X},
abstract = {Invasive candidiasis may be caused by Candida albicans (C. albicans) colonization of the intestinal tract. Preventing intestinal damage caused by Candida albicans infection and protecting intestinal barrier function have become a critical issue. Integrated analyses of the microbiome with metabolome revealed a remarkable shift of the gut microbiota and tryptophan metabolites, kynurenic acid (KynA), and indolacrylic acid (IA) in mice infected with C. albicans. The transcriptome sequencing indicated that differentially expressed genes were significantly associated with innate immune responses and inflammatory responses. The results of this study suggest that KynA and IA (KI) can alleviate intestinal damage caused by Candida albicans infection in mice by reducing intestinal permeability, increasing intestinal firmness, alleviating intestinal inflammation, and reducing the secretion of interleukin-22 (IL-22) in the 3 groups of colon innate lymphoid cells (ILC3). We performed a fecal microbiota transplantation (FMT) experiment and found that the intestinal barrier function, inflammation, and IL-22 secretion of ILC3 in the colon lamina propria of the recipient mice subjected to C. albicans infection and KI treatment were consistent with the trends of the donor mice. Our results suggest that tryptophan metabolites may directly regulate colon lamina ILC3 to promote intestinal resistance to C. albicans invasion, or indirectly regulate the ILC3 secretion of IL-22 to play a protective role in the intestinal barrier by affecting intestinal microorganisms, which may become a potential target for alleviating intestine borne C. albicans infection.},
}

@article {pmid38638911,
year = {2024},
author = {Wan, S and You, P and Shi, Q and Hu, H and Zhang, L and Chen, L and Wu, Z and Lin, S and Song, X and Luo, Y and Wang, Y and Ju, F and Jin, D and Chen, Y},
title = {Gut microbiome changes in mouse, Mongolian gerbil, and hamster models following Clostridioides difficile challenge.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1368194},
pmid = {38638911},
issn = {1664-302X},
abstract = {INTRODUCTION: Clostridioides difficile infection (CDI), as well as its etiology and pathogenesis, have been extensively investigated. However, the absence of suitable CDI animal models that reflect CDI symptoms and the associated gut microbiome changes in humans has limited research progress in this field. Thus, we aimed to investigate whether Mongolian gerbils, which present a range of human pathological conditions, can been used in studies on CDI. Methods: In this study, we infected Mongolian gerbils and two existing CDI model animals, mice and hamsters, with the hypervirulent ribotype 027 C. difficile strain, and comparatively analyzed changes in their gut microbiome composition via 16S rRNA gene sequencing.

METHODS: In this study, we infected Mongolian gerbils and two existing CDI model animals, mice and hamsters, with the hypervirulent ribotype 027 C. difficile strain, and comparatively analyzed changes in their gut microbiome composition via 16S rRNA gene sequencing.

RESULTS: The results obtained showed that C. difficile colonized the gastrointestinal tracts of the three rodents, and after the C. difficile challenge, C57BL/6J mice did not manifest CDI symptoms and their intestines showed no significant pathological changes. However, the hamsters showed explosive intestinal bleeding and inflammation and the Mongolian gerbils presented diarrhea as well as increased infiltration of inflammatory cells, mucus secretion, and epithelial cell shedding in their intestinal tissue. Further, intestinal microbiome analysis revealed significant differences with respect to intestinal flora abundance and diversity. Specifically, after C. difficile challenge, the Firmicutes/Bacteroidetes ratio decreased for C57BL/6J mice, but increased significantly for Mongolian gerbils and hamsters. Furthermore, the abundance of Proteobacteria increased in all three models, especially in hamsters, while that of Verrucomicrobia only increased significantly in C57BL/6J mice and Mongolian gerbils. Our results also indicated that differences in the relative abundances of Lactobacillaceae and Akkermansia were primarily responsible for the observed differences in response to C. difficile challenge.

CONCLUSION: Based on the observed responses to C. difficile challenge, we concluded for the first time that the Mongolian gerbil could be used as an animal model for CDI. Additionally, the taxa identified in this study may be used as biomarkers for further studies on CDI and to improve understanding regarding changes in gut microbiome in CDI-related diseases.},
}

@article {pmid38638909,
year = {2024},
author = {Santangelo, BE and Apgar, M and Colorado, ASB and Martin, CG and Sterrett, J and Wall, E and Joachimiak, MP and Hunter, LE and Lozupone, CA},
title = {Integrating biological knowledge for mechanistic inference in the host-associated microbiome.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1351678},
pmid = {38638909},
issn = {1664-302X},
abstract = {Advances in high-throughput technologies have enhanced our ability to describe microbial communities as they relate to human health and disease. Alongside the growth in sequencing data has come an influx of resources that synthesize knowledge surrounding microbial traits, functions, and metabolic potential with knowledge of how they may impact host pathways to influence disease phenotypes. These knowledge bases can enable the development of mechanistic explanations that may underlie correlations detected between microbial communities and disease. In this review, we survey existing resources and methodologies for the computational integration of broad classes of microbial and host knowledge. We evaluate these knowledge bases in their access methods, content, and source characteristics. We discuss challenges of the creation and utilization of knowledge bases including inconsistency of nomenclature assignment of taxa and metabolites across sources, whether the biological entities represented are rooted in ontologies or taxonomies, and how the structure and accessibility limit the diversity of applications and user types. We make this information available in a code and data repository at: https://github.com/lozuponelab/knowledge-source-mappings. Addressing these challenges will allow for the development of more effective tools for drawing from abundant knowledge to find new insights into microbial mechanisms in disease by fostering a systematic and unbiased exploration of existing information.},
}

@article {pmid38638907,
year = {2024},
author = {Huang, F and Lyu, B and Xie, F and Li, F and Xing, Y and Han, Z and Lai, J and Ma, J and Zou, Y and Zeng, H and Xu, Z and Gao, P and Luo, Y and Bolund, L and Tong, G and Fengping, X},
title = {From gut to liver: unveiling the differences of intestinal microbiota in NAFL and NASH patients.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1366744},
pmid = {38638907},
issn = {1664-302X},
abstract = {Non-alcoholic fatty liver disease (NAFLD) is increasingly recognized for its global prevalence and potential progression to more severe liver diseases such as non-alcoholic steatohepatitis (NASH). The gut microbiota plays a pivotal role in the pathogenesis of NAFLD, yet the detailed characteristics and ecological alterations of gut microbial communities during the progression from non-alcoholic fatty liver (NAFL) to NASH remain poorly understood. Methods: In this study, we conducted a comparative analysis of gut microbiota composition in individuals with NAFL and NASH to elucidate differences and characteristics. We utilized 16S rRNA sequencing to compare the intestinal gut microbiota among a healthy control group (65 cases), NAFL group (64 cases), and NASH group (53 cases). Random forest machine learning and database validation methods were employed to analyze the data. Results: Our findings indicate a significant decrease in the diversity of intestinal flora during the progression of NAFLD (p < 0.05). At the phylum level, high abundances of Bacteroidetes and Fusobacteria were observed in both NAFL and NASH patients, whereas Firmicutes were less abundant. At the genus level, a significant decrease in Prevotella expression was seen in the NAFL group (AUC 0.738), whereas an increase in the combination of Megamonas and Fusobacterium was noted in the NASH group (AUC 0.769). Furthermore, KEGG pathway analysis highlighted significant disturbances in various types of glucose metabolism pathways in the NASH group compared to the NAFL group, as well as notably compromised flavonoid and flavonol biosynthesis functions. The study uncovers distinct microbiota characteristics and microecological changes within the gut during the transition from NAFL to NASH, providing insights that could facilitate the discovery of novel biomarkers and therapeutic targets for NAFLD.},
}

@article {pmid38638900,
year = {2024},
author = {Yang, W and Li, X and Yan, H and Sun, Y and Wu, D and Du, Y and Luo, Y},
title = {Recruitment of beneficial cucumber rhizosphere microbes mediated by amino acid secretion induced by biocontrol Bacillus subtilis isolate 1JN2.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1379566},
pmid = {38638900},
issn = {1664-302X},
abstract = {INTRODUCTION: At present, the use of beneficial microorganisms to control cucumber Fusarium wilt is a widely used method, and the rhizosphere microecological reset is one of the mechanisms involved. However, how biocontrol strains reshape cucumber rhizosphere microecology remains to be further studied.

METHODS: The composition changes of cucumber root exudates induced by biocontrol strain 1JN2, the microbial ecology of cucumber rhizosphere and the colonization ability of biocontrol strain 1JN2 in cucumber rhizosphere were analyzed through UHPLC-MS/MS analysis, Illumina high-throughput sequencing and SEM, respectively.

RESULTS: First, cucumber plants treated with biocontrol Bacillus 1JN2 reduced the disease severity of Fusarium wilt by 60%. Significant changes in cucumber root exudates were found after 1JN2 inoculation and the contents of four amino acids including glutamine, tryptophan, glycine and glutamic acid were significantly increased. Second, It was found that the bacterial diversity in the rhizosphere of cucumber was significantly increased in both the strain treatment group and the amino acid mixture treatment group, The number of Bacillus was the largest in all dominant populations, exceeded 20% in all treatment groups. The bacteria of Hydrogenispora and Vicinamibacteria were significantly increased after treatment.

DISCUSSION: Overall, the results demonstrated that amino acid substances in cucumber root exudates induced by biocontrol strain 1JN2 can shift the cucumber root microenvironment and prevent the occurrence of Fusarium wilt disease.},
}

@article {pmid38638898,
year = {2024},
author = {Hua, H and Yongtong, W and Xufeng, D and Fang, L and Jing, G and Fumao, Z and Jie, J and Lijiang, J},
title = {Hemp seeds attenuate loperamide-induced constipation in mice.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1353015},
pmid = {38638898},
issn = {1664-302X},
abstract = {Constipation is a common gastrointestinal disease that seriously affects human physical and mental health. Studies have reported that hemp seeds can improve constipation, however the specific mechanism is still unclear. This study investigates that hemp seed (HS) and its water-ethanol extract (HSE) attenuates loperamide-induced constipation in mice. The research results show that: the fecal water content and small intestinal transit rate of mice in the hemp seed group and hemp seed hydroalcoholic extract group were significantly increased compared with MC group, and the first red feces defecation time was significantly shortened; HS and HSE significantly influence serum levels of Gastrin (Gas), motilin (MTL), substance P (SP), and endothelin (ET), potentially mediating their effects on gastrointestinal motility. HS and HSE can improve colon inflammation in constipated mice with H&E staining. Compared with the model of constipation group, the content of short-chain fatty acids in the HS group and HSE group increased significantly. Gut microbiome studies have shown that the structure and abundance of intestinal flora are altered. HS and HSE changed the abundance of Odoribacter, Bacteroide, Lactobacillus and Prevotella. Together, these results suggest that HS have the potential to stimulate the proliferation of beneficial gut microbes and promote intestinal motility, thereby improving gut health and relieving symptoms of constipation.},
}

@article {pmid38638832,
year = {2024},
author = {Filardo, S and Di Pietro, M and Sessa, R},
title = {Current progresses and challenges for microbiome research in human health: a perspective.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1377012},
pmid = {38638832},
issn = {2235-2988},
mesh = {Humans ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Metagenome ; Metagenomics ; },
abstract = {It is becoming increasingly clear that the human microbiota, also known as "the hidden organ", possesses a pivotal role in numerous processes involved in maintaining the physiological functions of the host, such as nutrient extraction, biosynthesis of bioactive molecules, interplay with the immune, endocrine, and nervous systems, as well as resistance to the colonization of potential invading pathogens. In the last decade, the development of metagenomic approaches based on the sequencing of the bacterial 16s rRNA gene via Next Generation Sequencing, followed by whole genome sequencing via third generation sequencing technologies, has been one of the great advances in molecular biology, allowing a better profiling of the human microbiota composition and, hence, a deeper understanding of the importance of microbiota in the etiopathogenesis of different pathologies. In this scenario, it is of the utmost importance to comprehensively characterize the human microbiota in relation to disease pathogenesis, in order to develop novel potential treatment or preventive strategies by manipulating the microbiota. Therefore, this perspective will focus on the progress, challenges, and promises of the current and future technological approaches for microbiome profiling and analysis.},
}

Humans
RNA, Ribosomal, 16S/genetics
*Microbiota/genetics
Metagenome
Metagenomics

@article {pmid38638830,
year = {2024},
author = {Narrowe, AB and Lemons, JMS and Mahalak, KK and Firrman, J and den Abbeele, PV and Baudot, A and Deyaert, S and Li, Y and Yu, LL and Liu, L},
title = {Targeted remodeling of the human gut microbiome using Juemingzi (Senna seed extracts).},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1296619},
pmid = {38638830},
issn = {2235-2988},
mesh = {Humans ; *Gastrointestinal Microbiome ; Senna Extract/analysis/pharmacology ; *Microbiota ; Bacteria ; Feces/microbiology ; Seeds ; Sennosides/analysis/pharmacology ; *Anti-Infective Agents/pharmacology ; *Drugs, Chinese Herbal ; },
abstract = {The genus Senna contains globally distributed plant species of which the leaves, roots, and seeds have multiple traditional medicinal and nutritional uses. Notable chemical compounds derived from Senna spp. include sennosides and emodin which have been tested for antimicrobial effects in addition to their known laxative functions. However, studies of the effects of the combined chemical components on intact human gut microbiome communities are lacking. This study evaluated the effects of Juemingzi (Senna sp.) extract on the human gut microbiome using SIFR[®] (Systemic Intestinal Fermentation Research) technology. After a 48-hour human fecal incubation, we measured total bacterial cell density and fermentation products including pH, gas production and concentrations of short chain fatty acids (SCFAs). The initial and post-incubation microbial community structure and functional potential were characterized using shotgun metagenomic sequencing. Juemingzi (Senna seed) extracts displayed strong, taxon-specific anti-microbial effects as indicated by significant reductions in cell density (40%) and intra-sample community diversity. Members of the Bacteroidota were nearly eliminated over the 48-hour incubation. While generally part of a healthy gut microbiome, specific species of Bacteroides can be pathogenic. The active persistence of the members of the Enterobacteriaceae and selected Actinomycetota despite the reduction in overall cell numbers was demonstrated by increased fermentative outputs including high concentrations of gas and acetate with correspondingly reduced pH. These large-scale shifts in microbial community structure indicate the need for further evaluation of dosages and potential administration with prebiotic or synbiotic supplements. Overall, the very specific effects of these extracts may offer the potential for targeted antimicrobial uses or as a tool in the targeted remodeling of the gut microbiome.},
}

Humans
*Gastrointestinal Microbiome
Senna Extract/analysis/pharmacology
*Microbiota
Bacteria
Feces/microbiology
Seeds
Sennosides/analysis/pharmacology
*Anti-Infective Agents/pharmacology
*Drugs, Chinese Herbal

@article {pmid38638561,
year = {2024},
author = {Ma, X and Lazarowski, L and Zhang, Y and Krichbaum, S and Smith, JG and Zheng, J and Cao, W and Haney, PS and Wilborn, RR and Price, SB and Singletary, M and Waggoner, P and Wang, X},
title = {Associations between memory performance and Bifidobacterium pseudolongum abundance in the canine gut microbiome.},
journal = {iScience},
volume = {27},
number = {5},
pages = {109611},
pmid = {38638561},
issn = {2589-0042},
abstract = {Memory has been identified as the least heritable cognitive trait in canines, suggesting a significant influence of non-genetic factors. We observed a trend that overall memory scores (OMS) improve with age in a cohort of 27 young dogs, but considerable plasticity exists. Employing linear discriminant analysis of gut microbiome data from dogs exhibiting low and high OMS, a single bacterial species, Bifidobacterium pseudolongum, was identified and confirmed to be correlated with elevated OMS. Subsequent analysis using a random forest regression model revealed that sex, litter, and breed identity had minimal predictive importance. Age had some predictive value but failed to achieve statistical significance in this dataset. In sharp contrast, the abundance of 17 bacterial taxa in the microbiome showed a stronger predictive capacity for memory performance. Our findings provide insights into microbiome underpinnings of mammalian cognitive functions and suggest avenues for developing psychobiotics to enhance canine memory and learning.},
}

@article {pmid38638560,
year = {2024},
author = {Yan, Y and Zheng, X and Liu, G and Shi, G and Li, C and Chen, H and He, X and Lin, K and Deng, Z and Zhang, H and Li, WG and Chen, H and Tong, X and Zhu, Z},
title = {Gut microbiota-derived cholic acid mediates neonatal brain immaturity and white matter injury under chronic hypoxia.},
journal = {iScience},
volume = {27},
number = {5},
pages = {109633},
pmid = {38638560},
issn = {2589-0042},
abstract = {Chronic hypoxia, common in neonates, disrupts gut microbiota balance, which is crucial for brain development. This study utilized cyanotic congenital heart disease (CCHD) patients and a neonatal hypoxic rat model to explore the association. Both hypoxic rats and CCHD infants exhibited brain immaturity, white matter injury (WMI), brain inflammation, and motor/learning deficits. Through 16s rRNA sequencing and metabolomic analysis, a reduction in B. thetaiotaomicron and P. distasonis was identified, leading to cholic acid accumulation. This accumulation triggered M1 microglial activation and inflammation-induced WMI. Administration of these bacteria rescued cholic acid-induced WMI in hypoxic rats. These findings suggest that gut microbiota-derived cholic acid mediates neonatal WMI and brain inflammation, contributing to brain immaturity under chronic hypoxia. Therapeutic targeting of these bacteria provides a non-invasive intervention for chronic hypoxia patients.},
}

@article {pmid38638559,
year = {2024},
author = {Paraschiv, AC and Vacaras, V and Nistor, C and Vacaras, C and Strilciuc, S and Muresanu, DF},
title = {The effect of multiple sclerosis therapy on gut microbiota dysbiosis: a longitudinal prospective study.},
journal = {Microbial cell (Graz, Austria)},
volume = {11},
number = {},
pages = {106-115},
pmid = {38638559},
issn = {2311-2638},
abstract = {Gut microbiota has complex immune functions, related to different pathologies, including multiple sclerosis (MS).This study evaluated the influence of treatments on gut microbiota in people with MS (PwMS). The research comprised 60 participants, including 39 PwMS and 21 healthy controls (HC). Among the PwMS, 20 were prescribed a disease-modifying therapy (DMT), either interferon beta1a or teriflunomide, while 19 received a combination of classical DMT and an immunoglobulin Y (IgY) supplement. For each participant, two sets of gut samples were collected: one at the study's outset and another after two months. Alpha and beta diversity analyses revealed no significant differences between groups. In comparison to the HC, the MS group exhibited an increase in Prevotella stercorea and a decrease in Faecalibacterium prausnitzii. Following treatment, individuals with MS showed enrichment in Lachnospiraceae and Streptococcus. The second sample, compared to the first one, demonstrated an increase in Bifidobacterium angulatum and a decrease in Oscillospira for individuals with MS. Gut microbiota diversity in PwMS is not significantly different to HC.However, specific taxonomic changes indicate the presence of a dysbiosis state. The use of DMTs and immunoglobulin Y supplements may contribute to alterations in microbial composition, potentially leading to the restoration of a healthier microbiome.},
}

@article {pmid38638485,
year = {2024},
author = {Atchade, AM and Williams, JL and Mermelstein, L and Nemesure, B},
title = {Unraveling the complexities of early-onset colorectal cancer: a perspective on dietary and microbial influences.},
journal = {Frontiers in public health},
volume = {12},
number = {},
pages = {1370108},
pmid = {38638485},
issn = {2296-2565},
mesh = {Adult ; Humans ; *Colorectal Neoplasms/epidemiology/diagnosis/pathology ; Diet ; Obesity/epidemiology ; *Gastrointestinal Microbiome ; Anti-Bacterial Agents ; },
abstract = {While advances in screening have resulted in declining rates of colorectal cancer (CRC) among adults ≥50 years of age since the mid-2000s, the incidence of early-onset CRC (EOCRC) has steadily increased over the last decade. This increase is not fully accounted for by hereditary factors, and the hypothesis that a sedentary lifestyle and obesity are the primary culprits is not fully supported by recent reports indicating that many affected individuals lead active lifestyles, maintain normal weight, and are otherwise healthy. Attention has shifted toward dietary patterns, notably the consumption of processed and ultra-processed foods found in Western diets, which are suspected of disrupting the gut microbiome balance that potentially leads to EOCRC. The impact of antibiotic use on the gut microbiome is also posited as a contributing factor, given its rising prevalence in medical and agricultural practices. We propose that a paradigm shift is necessary for EOCRC research, moving beyond metabolic factors to a broader exploration of dietary and microbial influences. Future research must prioritize understanding the relationship between dietary habits, particularly processed food intake, antibiotic exposure, and gut microbiome dynamics, to unravel the complex etiology of EOCRC. This will be crucial in developing comprehensive preventive strategies to address the increasing incidence of this malignancy in younger populations.},
}

Adult
Humans
*Colorectal Neoplasms/epidemiology/diagnosis/pathology
Diet
Obesity/epidemiology
*Gastrointestinal Microbiome
Anti-Bacterial Agents

@article {pmid38638378,
year = {2024},
author = {Yang, K and Zeng, J and Wu, H and Liu, H and Ding, Z and Liang, W and Wu, L and Lin, Z and Huang, W and Xu, J and Dong, F},
title = {Nonalcoholic Fatty Liver Disease: Changes in Gut Microbiota and Blood Lipids.},
journal = {Journal of clinical and translational hepatology},
volume = {12},
number = {4},
pages = {333-345},
pmid = {38638378},
issn = {2310-8819},
abstract = {BACKGROUND AND AIMS: The global prevalence of nonalcoholic fatty liver disease (NAFLD) is 25%. This study aimed to explore differences in the gut microbial community and blood lipids between normal livers and those affected by NAFLD using 16S ribosomal deoxyribonucleic acid sequencing.

METHODS: Gut microbiome profiles of 40 NAFLD and 20 non-NAFLD controls were analyzed. Information about four blood lipids and 13 other clinical features was collected. Patients were divided into three groups by ultrasound and FibroScan, those with a normal liver, mild FL (FL1), and moderate-to-severe FL (FL2). FL1 and FL2 patients were divided into two groups, those with either hyperlipidemia or non-hyperlipidemia based on their blood lipids. Potential keystone species within the groups were identified using univariate analysis and a specificity-occupancy plot. Significant difference in biochemical parameters ion NAFLD patients and healthy individuals were identified by detrended correspondence analysis and canonical correspondence analysis.

RESULTS: Decreased gut bacterial diversity was found in patients with NAFLD. Firmicutes/Bacteroidetes decreased as NAFLD progressed. Faecalibacterium and Ruminococcus 2 were the most representative fatty-related bacteria. Glutamate pyruvic transaminase, aspartate aminotransferase, and white blood cell count were selected as the most significant biochemical indexes. Calculation of areas under the curve identified two microbiomes combined with the three biochemical indexes that identified normal liver and FL2 very well but performed poorly in diagnosing FL1.

CONCLUSIONS: Faecalibacterium and Ruminococcus 2, combined with glutamate pyruvic transaminase, aspartate aminotransferase, and white blood cell count distinguished NAFLD. We speculate that regulating the health of gut microbiota may release NAFLD, in addition to providing new targets for clinicians to treat NAFLD.},
}

@article {pmid38638154,
year = {2024},
author = {Huang, F and Lei, M and Li, W},
title = {The rhizosphere and root selections intensify fungi-bacteria interaction in abiotic stress-resistant plants.},
journal = {PeerJ},
volume = {12},
number = {},
pages = {e17225},
pmid = {38638154},
issn = {2167-8359},
mesh = {*Fungi/genetics ; *Rhizosphere ; Plant Roots/microbiology ; Soil Microbiology ; Soil ; Plants ; Bacteria ; Stress, Physiological ; },
abstract = {The microbial communities, inhabiting around and in plant roots, are largely influenced by the compartment effect, and in turn, promote the growth and stress resistance of the plant. However, how soil microbes are selected to the rhizosphere, and further into the roots is still not well understood. Here, we profiled the fungal, bacterial communities and their interactions in the bulk soils, rhizosphere soils and roots of eleven stress-resistant plant species after six months of growth. The results showed that the root selection (from the rhizosphere soils to the roots) was stronger than the rhizosphere selection (from the bulk soils to the rhizosphere soils) in: (1) filtering stricter on the fungal (28.5% to 40.1%) and bacterial (48.9% to 68.1%) amplicon sequence variants (ASVs), (2) depleting more shared fungal (290 to 56) and bacterial (691 to 2) ASVs measured by relative abundance, and (3) increasing the significant fungi-bacteria crosskingdom correlations (142 to 110). In addition, the root selection, but not the rhizosphere selection, significantly increased the fungi to bacteria ratios (f:b) of the observed species and shannon diversity index, indicating unbalanced effects to the fungal and bacteria communities exerted by the root selection. Based on the results of network analysis, the unbalanced root selection effects were associated with increased numbers of negative interaction (140 to 99) and crosskingdom interaction (123 to 92), suggesting the root selection intensifies the negative fungi-bacteria interactions in the roots. Our findings provide insights into the complexity of crosskingdom interactions and improve the understanding of microbiome assembly in the rhizosphere and roots.},
}

*Fungi/genetics
*Rhizosphere
Plant Roots/microbiology
Soil Microbiology
Soil
Plants
Bacteria
Stress, Physiological

@article {pmid38638142,
year = {2024},
author = {Megow, A and Bouras, G and Alsuliman, Y and Cooksley, C and Vyskocil, E and Murphy, W and Vreugde, S and Wormald, PJ},
title = {Chitogel with deferiprone following endoscopic sinus surgery: improved wound healing and microbiome.},
journal = {Frontiers in surgery},
volume = {11},
number = {},
pages = {1338209},
pmid = {38638142},
issn = {2296-875X},
abstract = {BACKGROUND: Adhesion formation, sinus ostial narrowing, and presence of pathogenic bacteria are associated with poor outcomes following endoscopic sinus surgery (ESS) for chronic rhinosinusitis. Chitogel has been shown to improve wound healing, restore a healthier microbiome, and reduce post-operative infections post ESS. Deferiprone has antibacterial properties and has been shown to reduce adhesion formation. The aim of the study was to assess whether the addition of low concentration deferiprone to Chitogel further improves surgical outcomes following ESS compared with Chitogel alone.

METHODS: In this double-blinded trial, 45 patients undergoing ESS were prospectively recruited. At the end of the surgery, patients were randomised to receive Chitogel alone, Chitogel with 1 mM of deferiprone, or Chitogel with 5 mM of deferiprone to one side of the sinuses (allowing the other side to serve as control). Patients underwent routine follow-ups with symptom questionnaires and nasoendoscopies performed at 2, 6, and 12 weeks post-operatively. Sinus ostial measurements, microbiology, and microbiome swabs from bilateral middle meatuses were collected intraoperatively and at 12 weeks post-operatively.

RESULTS: A significant improvement in the endoscopic appearance of the sinuses and frontal ostial patency was noted at 12 weeks post-operatively (p < 0.05) in all three treatment groups compared with the control. There was no significant difference noted between patients who received Chitogel alone and those who received Chitogel with 1 or 5 mM deferiprone.

CONCLUSION: Chitogel alone, Chitogel with 1 mM deferiprone, and Chitogel with 5 mM deferiprone used following ESS led to a significant improvement in endoscopic appearance of the sinuses and frontal ostial preservation at 12 weeks post-operatively. No significant difference was found with the addition of deferiprone to Chitogel.},
}

@article {pmid38638127,
year = {2023},
author = {Zeng, Z and Jiang, M and Li, X and Yuan, J and Zhang, H},
title = {Precision medicine in inflammatory bowel disease.},
journal = {Precision clinical medicine},
volume = {6},
number = {4},
pages = {pbad033},
pmid = {38638127},
issn = {2516-1571},
abstract = {Inflammatory bowel disease (IBD) is an incurable disease characterized by remission-relapse cycles throughout its course. Both Crohn's disease (CD) and ulcerative colitis (UC), the two main forms of IBD, exhibit tendency to develop complications and substantial heterogeneity in terms of frequency and severity of relapse, thus posing great challenges to the clinical management for IBD. Current treatment strategies are effective in different ways in induction and maintenance therapies for IBD. Recent advances in studies of genetics, pharmacogenetics, proteomics and microbiome provide a strong driving force for identifying molecular markers of prognosis and treatment response, which should help clinicians manage IBD patients more effectively, and then, improve clinical outcomes and reduce treatment costs of patients. In this review, we summarize and discuss precision medicine in IBD, focusing on predictive markers of disease course and treatment response, and monitoring indices during therapeutic drug monitoring.},
}

@article {pmid38637894,
year = {2024},
author = {Wainwright, BJ and Leon, J and Vilela, E and Hickman, KJE and Caldwell, J and Aimone, B and Bischoff, P and Ohran, M and Morelli, MW and Arlyza, IS and Marwayana, ON and Zahn, G},
title = {Wallace's line structures seagrass microbiota and is a potential barrier to the dispersal of marine bacteria.},
journal = {Environmental microbiome},
volume = {19},
number = {1},
pages = {23},
pmid = {38637894},
issn = {2524-6372},
abstract = {BACKGROUND: The processes that shape microbial biogeography are not well understood, and concepts that apply to macroorganisms, like dispersal barriers, may not affect microorganisms in the same predictable ways. To better understand how known macro-scale biogeographic processes can be applied at micro-scales, we examined seagrass associated microbiota on either side of Wallace's line to determine the influence of this cryptic dispersal boundary on the community structure of microorganisms. Communities were examined from twelve locations throughout Indonesia on either side of this theoretical line.

RESULTS: We found significant differences in microbial community structure on either side of this boundary (R[2] = 0.09; P = 0.001), and identified seven microbial genera as differentially abundant on either side of the line, six of these were more abundant in the West, with the other more strongly associated with the East. Genera found to be differentially abundant had significantly smaller minimum cell dimensions (GLM: t923 = 59.50, P < 0.001) than the overall community.

CONCLUSION: Despite the assumed excellent dispersal ability of microbes, we were able to detect significant differences in community structure on either side of this cryptic biogeographic boundary. Samples from the two closest islands on opposite sides of the line, Bali and Komodo, were more different from each other than either was to its most distant island on the same side. We suggest that limited dispersal across this barrier coupled with habitat differences are primarily responsible for the patterns observed. The cryptic processes that drive macroorganism community divergence across this region may also play a role in the bigeographic patterns of microbiota.},
}

@article {pmid38637854,
year = {2024},
author = {Arponen, H and Vakkilainen, S and Tomnikov, N and Kallonen, T and Silling, S and Mäkitie, O and Rautava, J},
title = {Altered oral microbiome, but normal human papilloma virus prevalence in cartilage-hair hypoplasia patients.},
journal = {Orphanet journal of rare diseases},
volume = {19},
number = {1},
pages = {169},
pmid = {38637854},
issn = {1750-1172},
mesh = {Humans ; Human Papillomavirus Viruses ; *Papillomavirus Infections/epidemiology ; Prevalence ; Cross-Sectional Studies ; *Osteochondrodysplasias/genetics/*congenital ; *Microbiota ; *Primary Immunodeficiency Diseases ; Hair/*abnormalities ; *Hirschsprung Disease ; },
abstract = {BACKGROUND: Cartilage-hair hypoplasia (CHH) is a rare syndromic immunodeficiency with metaphyseal chondrodysplasia and increased risk of malignancy. In this cross-sectional observational study, we examined HPV status and oral microbiome in individuals with CHH. Oral brush samples were collected from 20 individuals with CHH (aged 5-59 years) and 41 controls (1-69 years). Alpha HPVs (43 types) were tested by nested PCR followed by bead-based probe hybridization. Separately, beta-, gamma-, mu- and nu- HPV types were investigated, and a genome-based bacterial microbiome sequencing was performed.

RESULTS: We found a similar alpha HPV prevalence in individuals with CHH (45%) and controls (36%). The HPV types of individuals with CHH were HPV-16 (25%), 27, 28, and 78, and of controls HPV-3, 16 (21%), 27, and 61. Beta HPV positivity and combined beta/gamma/mu/nu prevalence was detected in 11% and 11% of individuals with CHH and in 5% and 3% of the controls, respectively. Individuals with CHH differed from the controls in bacterial microbiota diversity, richness, and in microbial composition. Individuals with CHH had lower abundance of species Mitsuokella sp000469545, Parascardovia denticolens, Propionibacterium acidifaciens, UMGS1907 sp004151455, Salinicola halophilus, Haemophilus_A paraphrohaemolyticus, Fusobacterium massiliense, and Veillonella parvula, and higher abundance of Slackia exigua.

CONCLUSIONS: Individuals with CHH exhibit similar prevalence of HPV DNA but different bacterial microbiota on their oral mucosa compared to healthy controls. This may partly explain the previously observed high prevalence of oral diseases in CHH, and regular oral examination is warranted.},
}

Humans
Human Papillomavirus Viruses
*Papillomavirus Infections/epidemiology
Prevalence
Cross-Sectional Studies
*Osteochondrodysplasias/genetics/*congenital
*Microbiota
*Primary Immunodeficiency Diseases
Hair/*abnormalities
*Hirschsprung Disease

@article {pmid38637580,
year = {2024},
author = {Wan, S and Wang, K and Huang, P and Guo, X and Liu, W and Li, Y and Zhang, J and Li, Z and Song, J and Yang, W and Zhang, X and Ding, X and Leong, DT and Wang, L},
title = {Mechanoelectronic stimulation of autologous extracellular vesicle biosynthesis implant for gut microbiota modulation.},
journal = {Nature communications},
volume = {15},
number = {1},
pages = {3343},
pmid = {38637580},
issn = {2041-1723},
support = {52203170, 22207056 and 62288102//National Natural Science Foundation of China (National Science Foundation of China)/ ; BK20220384 and BK20210580//Natural Science Foundation of Jiangsu Province (Jiangsu Provincial Natural Science Foundation)/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Microbiota ; *Colitis ; *Extracellular Vesicles ; Hydrogels/pharmacology ; Dysbiosis ; },
abstract = {Pathogenic gut microbiota is responsible for a few debilitating gastrointestinal diseases. While the host immune cells do produce extracellular vesicles to counteract some deleterious effects of the microbiota, the extracellular vesicles are of insufficient doses and at unreliable exposure times. Here we use mechanical stimulation of hydrogel-embedded macrophage in a bioelectronic controller that on demand boost production of up to 20 times of therapeutic extracellular vesicles to ameliorate the microbes' deleterious effects in vivo. Our miniaturized wireless bioelectronic system termed inducible mechanical activation for in-situ and sustainable generating extracellular vesicles (iMASSAGE), leverages on wireless electronics and responsive hydrogel to impose mechanical forces on macrophages to produce extracellular vesicles that rectify gut microbiome dysbiosis and ameliorate colitis. This in vivo controllable extracellular vesicles-produced system holds promise as platform to treat various other diseases.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Microbiota
*Colitis
*Extracellular Vesicles
Hydrogels/pharmacology
Dysbiosis

@article {pmid38637223,
year = {2024},
author = {Wortelboer, K and Herrema, H},
title = {Opportunities and challenges in phage therapy for cardiometabolic diseases.},
journal = {Trends in endocrinology and metabolism: TEM},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tem.2024.03.007},
pmid = {38637223},
issn = {1879-3061},
abstract = {The worldwide prevalence of cardiometabolic diseases (CMD) is increasing, and emerging evidence implicates the gut microbiota in this multifactorial disease development. Bacteriophages (phages) are viruses that selectively target a bacterial host; thus, phage therapy offers a precise means of modulating the gut microbiota, limiting collateral damage on the ecosystem. Several studies demonstrate the potential of phages in human disease, including alcoholic and steatotic liver disease. In this opinion article we discuss the potential of phage therapy as a predefined medicinal product for CMD and discuss its current challenges, including the generation of effective phage combinations, product formulation, and strict manufacturing requirements.},
}

@article {pmid38637108,
year = {2024},
author = {Tarracchini, C and Milani, C and Lugli, GA and Mancabelli, L and Turroni, F and van Sinderen, D and Ventura, M},
title = {The infant gut microbiota as the cornerstone for future gastrointestinal health.},
journal = {Advances in applied microbiology},
volume = {126},
number = {},
pages = {93-119},
doi = {10.1016/bs.aambs.2024.02.001},
pmid = {38637108},
issn = {0065-2164},
mesh = {Infant ; Female ; Humans ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/microbiology ; *Microbiota ; Mothers ; Diet ; },
abstract = {The early postnatal period represents a critical window of time for the establishment and maturation of the human gut microbiota. The gut microbiota undergoes dramatic developmental changes during the first year of life, being influenced by a variety of external factors, with diet being a major player. Indeed, the introduction of complementary feeding provides novel nutritive substrates and triggers a shift from milk-adapted gut microbiota toward an adult-like bacterial composition, which is characterized by an enhancement in diversity and proportions of fiber-degrading bacterial genera like Ruminococcus, Prevotella, Eubacterium, and Bacteroides genera. Inadequate gut microbiota development in early life is frequently associated with concomitant and future adverse health conditions. Thus, understanding the processes that govern initial colonization and establishment of microbes in the gastrointestinal tract is of great importance. This review summarizes the actual understanding of the assembly and development of the microbial community associated with the infant gut, emphasizing the importance of mother-to-infant vertical transmission events as a fundamental arrival route for the first colonizers.},
}

Infant
Female
Humans
*Gastrointestinal Microbiome
Gastrointestinal Tract/microbiology
*Microbiota
Mothers
Diet

@article {pmid38637082,
year = {2024},
author = {Sonets, IV and Solovyev, MA and Ivanova, VA and Vasiluev, PA and Kachalkin, AV and Ochkalova, SD and Korobeynikov, AI and Razin, SV and Ulianov, SV and Tyakht, AV},
title = {Hi-C metagenomics facilitate comparative genome analysis of bacteria and yeast from spontaneous beer and cider.},
journal = {Food microbiology},
volume = {121},
number = {},
pages = {104520},
doi = {10.1016/j.fm.2024.104520},
pmid = {38637082},
issn = {1095-9998},
mesh = {*Saccharomyces cerevisiae/genetics ; Beer/microbiology ; Bacteria/genetics ; Plasmids ; *Saccharomyces/genetics ; Metagenome ; Metagenomics ; Enterobacteriaceae/genetics ; },
abstract = {Sequence-based analysis of fermented foods and beverages' microbiomes offers insights into their impact on taste and consumer health. High-throughput metagenomics provide detailed taxonomic and functional community profiling, but bacterial and yeast genome reconstruction and mobile genetic elements tracking are to be improved. We established a pipeline for exploring fermented foods microbiomes using metagenomics coupled with chromosome conformation capture (Hi-C metagenomics). The approach was applied to analyze a collection of spontaneously fermented beers and ciders (n = 12). The Hi-C reads were used to reconstruct the metagenome-assembled genomes (MAGs) of bacteria and yeasts facilitating subsequent comparative genomic analysis, assembly scaffolding and exploration of "plasmid-bacteria" links. For a subset of beverages, yeasts were isolated and characterized phenotypically. The reconstructed Hi-C MAGs primarily belonged to the Lactobacillaceae family in beers, along with Acetobacteraceae and Enterobacteriaceae in ciders, exhibiting improved quality compared to conventional metagenomic MAGs. Comparative genomic analysis of Lactobacillaceae Hi-C MAGs revealed clustering by niche and suggested genetic determinants of survival and probiotic potential. For Pediococcus damnosus, Hi-C-based networks of contigs enabled linking bacteria with plasmids. Analyzing phylogeny and accessory genes in the context of known reference genomes offered insights into the niche specialization of beer lactobacilli. The subspecies-level diversity of cider Tatumella spp. was disentangled using a Hi-C-based graph. We obtained highly complete yeast Hi-C MAGs primarily represented by Brettanomyces and Saccharomyces, with Hi-C-facilitated chromosome-level genome assembly for the former. Utilizing Hi-C metagenomics to unravel the genomic content of individual species can provide a deeper understanding of the ecological interactions within the food microbiome, aid in bioprospecting beneficial microorganisms, improving quality control and improving innovative fermented products.},
}

*Saccharomyces cerevisiae/genetics
Beer/microbiology
Bacteria/genetics
Plasmids
*Saccharomyces/genetics
Metagenome
Metagenomics
Enterobacteriaceae/genetics

@article {pmid38637066,
year = {2024},
author = {Lee, AW and Ng, IC and Wong, EY and Wong, IT and Sze, RP and Chan, KY and So, TY and Zhang, Z and Ka-Yee Fung, S and Choi-Ying Wong, S and Tam, WY and Lao, HY and Lee, LK and Leung, JS and Chan, CT and Ng, TT and Zhang, J and Chow, FW and Leung, PH and Siu, GK},
title = {Comprehensive identification of pathogenic microbes and antimicrobial resistance genes in food products using nanopore sequencing-based metagenomics.},
journal = {Food microbiology},
volume = {121},
number = {},
pages = {104493},
doi = {10.1016/j.fm.2024.104493},
pmid = {38637066},
issn = {1095-9998},
mesh = {Food Microbiology ; Anti-Bacterial Agents/pharmacology ; *Nanopore Sequencing ; Drug Resistance, Bacterial/genetics ; *Anti-Infective Agents ; Bacteria/genetics ; Metagenomics ; },
abstract = {Foodborne pathogens, particularly antimicrobial-resistant (AMR) bacteria, remain a significant threat to global health. Given the limitations of conventional culture-based approaches, which are limited in scope and time-consuming, metagenomic sequencing of food products emerges as a promising solution. This method provides a fast and comprehensive way to detect the presence of pathogenic microbes and antimicrobial resistance genes (ARGs). Notably, nanopore long-read sequencing provides more accurate bacterial taxonomic classification in comparison to short-read sequencing. Here, we revealed the impact of food types and attributes (origin, retail place, and food processing methods) on microbial communities and the AMR profile using nanopore metagenomic sequencing. We analyzed a total of 260 food products, including raw meat, sashimi, and ready-to-eat (RTE) vegetables. Clostridium botulinum, Acinetobacter baumannii, and Vibrio parahaemolyticus were identified as the top three foodborne pathogens in raw meat and sashimi. Importantly, even with low pathogen abundance, higher percentages of samples containing carbapenem and cephalosporin resistance genes were identified in chicken and RTE vegetables, respectively. In parallel, our results demonstrated that fresh, peeled, and minced foods exhibited higher levels of pathogenic bacteria. In conclusion, this comprehensive study offers invaluable data that can contribute to food safety assessments and serve as a basis for quality indicators.},
}

Food Microbiology
Anti-Bacterial Agents/pharmacology
*Nanopore Sequencing
Drug Resistance, Bacterial/genetics
*Anti-Infective Agents
Bacteria/genetics
Metagenomics

@article {pmid38636860,
year = {2024},
author = {Zhou, ZZ and Zhu, J and Yin, Y and Ding, LJ},
title = {Seasonal variations of profiles of antibiotic resistance genes and virulence factor genes in household dust from Beijing, China revealed by the metagenomics.},
journal = {The Science of the total environment},
volume = {928},
number = {},
pages = {172542},
doi = {10.1016/j.scitotenv.2024.172542},
pmid = {38636860},
issn = {1879-1026},
abstract = {Household-related microbiome is closely related with human health. However, the knowledge about profiles of antibiotic resistance genes (ARGs) and virulence factor genes (VFGs) which are carried by microbes inside homes and their temporal dynamics are rather limited. Here we monitored the seasonal changes of bacterial community (especially pathogenic bacteria), ARGs, and VFGs in household dust samples during two years. Based on metagenomic sequencing, the dust-related bacterial pathogenic community, ARGs, and VFGs all harbored the lowest richness in spring among four seasons. Their structure (except that of VFGs) also exhibited remarkable differences among the seasons. The structural variations of ARGs and VFGs were almost explained by mobile genetic elements (MGEs), bacterial pathogens, and particulate matter-related factors, with MGEs explaining the most. Moreover, the total normalized abundance of ARGs or VFGs showed no significant change across the seasons. Results of metagenomic binning and microbial network both showed that several pathogenic taxa (e.g., Ralstonia pickettii) were strongly linked with numerous ARGs (mainly resistant to multidrug) and VFGs (mainly encoding motility) simultaneously. Overall, these findings underline the significance of MGEs in structuring ARGs and VFGs inside homes along with seasonal variations, suggesting that household dust is a neglected reservoir for ARGs and VFGs.},
}

@article {pmid38636822,
year = {2024},
author = {Nannini, G and Di Gloria, L and Russo, E and Sterrantino, G and Kiros, ST and Coppi, M and Niccolai, E and Baldi, S and Ramazzotti, M and Di Pilato, V and Lagi, F and Bartolucci, G and Rossolini, GM and Bartoloni, A and Amedei, A},
title = {Oral microbiota signatures associated with viremia and CD4 recovery in treatment-naïve HIV-1-infected patients.},
journal = {Microbes and infection},
volume = {},
number = {},
pages = {105339},
doi = {10.1016/j.micinf.2024.105339},
pmid = {38636822},
issn = {1769-714X},
abstract = {PURPOSE: Few reports focused on the role of oral microbiome diversity in HIV infection. We characterized the microbiota-immunity axis in a cohort of treatment-naïve HIV-1-infected patients undergoing antiretroviral therapy (ART) focusing on the oral microbiome (OM) and immunological responsivity.

METHODS: The sequencing of 16S rRNA V3-V4 hypervariable region was performed on salivary samples of 15 healthy control (HC) and 12 HIV+ patients before starting ART and after reaching virological suppression. Then, we correlated the OM composition with serum cytokines and the Short Chain Fatty acids (SCFAs).

RESULTS: The comparison between HIV patients and HC oral microbiota showed differences in the bacterial α-diversity and richness. We documented a negative correlation between oral Prevotella and intestinal valeric acid at before starting ART and a positive correlation between oral Veillonella and gut acetic acid after reaching virological suppression. Finally, an increase in the phylum Proteobacteria was observed comparing saliva samples of immunological responders (IRs) patients against immunological non-responders (INRs).

CONCLUSIONS: For the first time, we described an increase in the oral pro-inflammatory Proteobacteria phylum in INRs compared to IRs. We provided more evidence that saliva could be a non-invasive and less expensive approach for research involving the oral cavity microbiome in HIV patients.},
}

@article {pmid38636749,
year = {2024},
author = {Xu, Y and Niu, C and Liang, S and Guo, J and Li, K and Zhang, J and Li, J and Jin, Y and Bai, J and Dai, J and Lu, C},
title = {An inulin-based glycovesicle for pathogen-targeted drug delivery to ameliorate salmonellosis.},
journal = {International journal of biological macromolecules},
volume = {267},
number = {Pt 2},
pages = {131656},
doi = {10.1016/j.ijbiomac.2024.131656},
pmid = {38636749},
issn = {1879-0003},
abstract = {The gut microbiota plays a significant role in the pathogenesis and remission of inflammatory bowel disease. However, conventional antibiotic therapies may alter microbial ecology and lead to dysbiosis of the gut microbiome, which greatly limits therapeutic efficacy. To address this challenge, novel nanomicelles that couple inulin with levofloxacin via disulfide bonds for the treatment of salmonellosis were developed in this study. Owing to their H2S-responsiveness, the nanomicelles can target the inflamed colon and rapidly release levofloxacin to selectively fight against enteric pathogens. Moreover, the embedded inulin can serve as prebiotic fiber to increase the amount of Bifidobacteria and Lactobacilli in mice with salmonellosis, thus maintaining the intestinal mechanical barrier and regulating the balance of the intestinal flora. Therefore, multifunctional nanomicelles had a better curative effect than pure levofloxacin on ameliorating inflammation in vivo. The pathogen-targeted glycovesicle represents a promising drug delivery platform to maximize the efficacy of antibacterial drugs for the treatment of inflammatory bowel disease.},
}

@article {pmid38636612,
year = {2024},
author = {Biessy, L and Pearman, JK and Mertens, KN and Réveillon, D and Savar, V and Hess, P and Hampton, H and Thompson, L and Lebrun, L and Terre-Terrillon, A and Smith, KF},
title = {Sudden peak in tetrodotoxin in French oysters during the summer of 2021: Source investigation using microscopy, metabarcoding and droplet digital PCR.},
journal = {Toxicon : official journal of the International Society on Toxinology},
volume = {243},
number = {},
pages = {107721},
doi = {10.1016/j.toxicon.2024.107721},
pmid = {38636612},
issn = {1879-3150},
abstract = {Tetrodotoxin (TTX) is a potent neurotoxin causing human intoxications from contaminated seafood worldwide and is of emerging concern in Europe. Shellfish have been shown to contain varying TTX concentrations globally, with concentrations typically higher in Pacific oysters Crassostrea gigas in Europe. Despite many decades of research, the source of TTX remains unknown, with bacterial or algal origins having been suggested. The aim of this study was to identify potential source organisms causing TTX contamination in Pacific oysters in French coastal waters, using three different techniques. Oysters were deployed in cages from April to September 2021 in an estuary where TTX was previously detected. Microscopic analyses of water samples were used to investigate potential microalgal blooms present prior or during the peak in TTX. Differences in the bacterial communities from oyster digestive glands (DG) and remaining flesh were explored using metabarcoding, and lastly, droplet digital PCR assays were developed to investigate the presence of Cephalothrix sp., one European TTX-bearing species in the DG of toxic C. gigas. Oysters analysed by liquid chromatography-tandem mass spectrometry contained quantifiable levels of TTX over a three-week period (24 June-15 July 2021), with concentrations decreasing in the DG from 424 μg/kg for the first detection to 101 μg/kg (equivalent to 74 to 17 μg/kg of total flesh), and trace levels being detected until August 13, 2021. These concentrations are the first report of the European TTX guidance levels being exceeded in French shellfish. Microscopy revealed that some microalgae bloomed during the TTX peak, (e.g., Chaetoceros spp., reaching 40,000 cells/L). Prokaryotic metabarcoding showed increases in abundance of Rubritaleaceae (genus Persicirhabdus) and Neolyngbya, before and during the TTX peak. Both phyla have previously been described as possible TTX-producers and should be investigated further. Droplet digital PCR analyses were negative for the targeted TTX-bearing genus Cephalothrix.},
}

@article {pmid38636461,
year = {2024},
author = {Zafar, H and Saier, MH},
title = {An insider's perspective about the pathogenic relevance of gut bacterial transportomes.},
journal = {Microbial physiology},
volume = {},
number = {},
pages = {},
doi = {10.1159/000538779},
pmid = {38636461},
issn = {2673-1673},
abstract = {BACKGROUND: The gut microbiome is integral to host health, hosting complex interactions between the host and numerous microbial species in the gastrointestinal tract. Key among the molecular mechanisms employed by gut bacteria are transportomes, consisting of diverse transport proteins crucial for bacterial adaptation to the dynamic, nutrient-rich environment of the mammalian gut. These transportomes facilitate the movement of a wide array of molecules, impacting both the host and the microbial community.

SUMMARY: This communication explores the significance of transportomes in gut bacteria, focusing on their role in nutrient acquisition, competitive interactions among microbes, and potential pathogenicity. It delves into the transportomes of key gut bacterial species like E. coli, Salmonella, Bacteroides, Lactobacillus, Clostridia, and Bifidobacterium, examining the functions of predicted transport proteins. The overview synthesizes recent research efforts, highlighting how these transportomes influence host-microbe interactions and contribute to the microbial ecology of the gut.

KEY MESSAGES: Transportomes are vital for the survival and adaptation of bacteria in the gut, enabling the import and export of various nutrients and molecules. The complex interplay of transport proteins not only supports bacterial growth and competition but also has implications for host health, potentially contributing to pathogenic processes. Understanding the pathogenic potential of transportomes in major gut bacterial species provides insights into gut health and disease, offering avenues for future research and therapeutic strategies.},
}

@article {pmid38636269,
year = {2024},
author = {Chen, H and Xu, Z and Zhou, Y and Jiang, YH and Chen, J and Xiong, Y and Zhou, M and Wu, X and Hong, D},
title = {Rituximab-induced gut microbiota changes in Chinese neuromyelitis optica spectrum disorders.},
journal = {Multiple sclerosis and related disorders},
volume = {86},
number = {},
pages = {105606},
doi = {10.1016/j.msard.2024.105606},
pmid = {38636269},
issn = {2211-0356},
abstract = {BACKGROUND: Recent evidence shows that immunosuppressive agents can affect the gut microbiota in autoimmune diseases. However, the relationship between the gut microbiome and B-cell depletion immunotherapy in neuromyelitis optica spectrum disorder (NMOSD) remains poorly understood.

OBJECTIVES: To evaluate the distinct intestinal microbial patterns and serum cytokine levels after short-term rituximab treatment (three months) in patients with NMOSD.

METHODS: Firstly, we conducted a cross-sectional study involving 46 treatment-naïve NMOSD patients and 48 matched healthy controls. We collected fecal specimens, which were then analyzed using next-generation sequencing, and quantified serum cytokines. Subsequently, fecal and serum samples were re-collected and re-evaluated in 31 of the 46 treatment-naïve NMOSD patients after RTX treatment.

RESULTS: Comparing the gut microbiome of treatment-naïve NMOSD patients to that of healthy controls revealed low α-diversity and distinct microbial compositions in the former. The microbial composition in NMOSD patients underwent changes following three months of RTX treatment. Specifically, the levels of IL-17F and IL-6 decreased, while those of IL-10 and TNFα increased after RTX treatment. LEfSe analysis identified 27 KEGG categories with significantly differential abundances between NMOSD patients and RTX treatment group.

CONCLUSIONS: Our study provides a comprehensive understanding of the gut microbiota landscape in the context of B-cell depletion immunotherapy. We observed dysbiosis in the gut microbiome of NMOSD patients, which was partially alleviated by three months of RTX treatment. This suggests that B-cell depletion may play a crucial role in driving changes in the gastrointestinal environment.},
}

@article {pmid38636203,
year = {2024},
author = {Chang, Y and Guo, R and Gu, T and Zong, Y and Sun, H and Xu, W and Chen, L and Tian, Y and Li, G and Lu, L and Zeng, T},
title = {Integrated transcriptome and microbiome analyses of residual feed intake in ducks during high production period.},
journal = {Poultry science},
volume = {103},
number = {6},
pages = {103726},
pmid = {38636203},
issn = {1525-3171},
abstract = {Residual feed intake (RFI) is a crucial parameter for assessing the feeding efficiency of poultry. Minimizing RFI can enhance feed utilization and reduce costs. In this study, 315 healthy female ducks were individually housed in cages. Growth performance was monitored during the high laying period, from 290 to 325 d of age. The cecal transcriptome and microbiome of 12 ducks with high RFI and 12 with low residual feed intake (LRFI) were analyzed. Regarding growth performance, the LRFI group exhibited significantly lower RFI, feed conversion ratio (FCR), and feed intake (Fi) compared to the HRFI group (p < 0.01). However, there were no significant differences observed in body weight (BW), body weight gain (BWG), and egg mass (EML) between the groups (p > 0.05). Microbiome analysis demonstrated that RFI impacted gut microbial abundance, particularly affecting metabolism and disease-related microorganisms such as Romboutsia, Enterococcus, and Megamonas funiformis. Transcriptome analysis revealed that varying RFI changed the expression of genes related to glucose metabolism and lipid metabolism, including APOA1, G6PC1, PCK1, and PLIN1. The integrated analysis indicated that host genes were closely linked to the microbiota and primarily function in lipid metabolism, which may enhance feeding efficiency by influencing metabolism and maintaining gut homeostasis.},
}

@article {pmid38636083,
year = {2024},
author = {Nakao, T and Shimada, M and Yoshikawa, K and Tokunaga, T and Nishi, M and Kashihara, H and Takasu, C and Wada, Y and Yoshimoto, T},
title = {Number of Healthy Teeth Can Predict the Response of Rectal Cancer to Chemoradiotherapy: A Retrospective Study.},
journal = {The American surgeon},
volume = {},
number = {},
pages = {31348241244628},
doi = {10.1177/00031348241244628},
pmid = {38636083},
issn = {1555-9823},
abstract = {BACKGROUND: It has been reported that the oral and gut microbiomes are associated with the prognosis in patients who undergo surgery, chemotherapy, and radiation for colorectal cancer. This study is the first to identify a correlation between the number of healthy teeth, which is an oral health indicator, and the efficacy of preoperative chemotherapy for rectal cancer.

METHODS: This retrospective single-center study included 30 patients who underwent radical surgery after preoperative chemoradiotherapy (CRT) between December 2013 and June 2021. The relationship between number of teeth before CRT and the efficacy of CRT, CRT-related adverse events, postoperative complications, and long-term postoperative outcomes was examined.

RESULTS: The number of healthy teeth was significantly greater in patients with downstaging of their disease than in those without downstaging (P = .027) and in patients with a complete response according to the Response Evaluation Criteria in Solid Tumors than in those who did not have a complete response (P = .014). Patients were divided into two groups according to whether they had ≥15 teeth or ≤14 teeth. There was no significant between-group difference in CRT-related adverse events. The incidence of all postoperative complications and grade II postoperative complications tended to be higher in patients with ≥15 teeth (P = .071 and P = .092, respectively), as did the 5-year overall survival rate (P = .083) and the 5-year disease-free rate (P = .007).

DISCUSSION: The number of healthy teeth predicted the response to preoperative CRT, postoperative complications, and the outcome of subsequent surgery in patients with rectal cancer.},
}

@article {pmid38635882,
year = {2024},
author = {Al Radi, ZMA and Prins, FM and Collij, V and Vich Vila, A and Festen, EAM and Dijkstra, G and Weersma, RK and Klaassen, MAY and Gacesa, R},
title = {Exploring the Predictive Value of Gut Microbiome Signatures for Therapy Intensification in Patients With Inflammatory Bowel Disease: A 10-Year Follow-up Study.},
journal = {Inflammatory bowel diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/ibd/izae064},
pmid = {38635882},
issn = {1536-4844},
support = {//Netherlands Organization for Scientific Research/ ; MLDS D16-14//Dutch Digestive Foundation/ ; },
abstract = {BACKGROUND: Inflammatory bowel diseases (IBDs) pose a significant challenge due to their diverse, often debilitating, and unpredictable clinical manifestations. The absence of prognostic tools to anticipate the future complications that require therapy intensification presents a substantial burden to patient private life and health. We aimed to explore whether the gut microbiome is a potential biomarker for future therapy intensification in a cohort of 90 IBD patients.

METHODS: We conducted whole-genome metagenomics sequencing on fecal samples from these patients, allowing us to profile the taxonomic and functional composition of their gut microbiomes. Additionally, we conducted a retrospective analysis of patients' electronic records over a period of 10 years following the sample collection and classified patients into (1) those requiring and (2) not requiring therapy intensification. Therapy intensification included medication escalation, intestinal resections, or a loss of response to a biological treatment. We applied gut microbiome diversity analysis, dissimilarity assessment, differential abundance analysis, and random forest modeling to establish associations between baseline microbiome profiles and future therapy intensification.

RESULTS: We identified 12 microbial species (eg, Roseburia hominis and Dialister invisus) and 16 functional pathways (eg, biosynthesis of L-citrulline and L-threonine) with significant correlations to future therapy intensifications. Random forest models using microbial species and pathways achieved areas under the curve of 0.75 and 0.72 for predicting therapy intensification.

CONCLUSIONS: The gut microbiome is a potential biomarker for therapy intensification in IBD patients and personalized management strategies. Further research should validate our findings in other cohorts to enhance the generalizability of these results.},
}

@article {pmid38635872,
year = {2024},
author = {Zhong, Z and Zhang, Y and Wei, Y and Li, X and Ren, L and Li, Y and Zhang, X and Chen, C and Yin, X and Liu, R and Wang, Q},
title = {Fucoidan Improves Early Stage Diabetic Nephropathy via the Gut Microbiota-Mitochondria Axis in High-Fat Diet-Induced Diabetic Mice.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.3c08503},
pmid = {38635872},
issn = {1520-5118},
abstract = {Diabetic nephropathy (DN) is a common microvascular complication of diabetes. Fucoidan, a polysaccharide containing fucose and sulfate group, ameliorates DN. However, the underlying mechanism has not been fully understood. This study aimed to explore the effects and mechanism of fucoidan on DN in high-fat diet-induced diabetic mice. A total of 90 C57BL/6J mice were randomly assigned to six groups (n = 15) as follows: normal control (NC), diabetes mellitus (DM), metformin (MTF), low-dose fucoidan (LFC), medium-dose fucoidan (MFC), and high-dose fucoidan (HFC). A technique based on fluorescein isothiocyanate (FITC-sinistin) elimination kinetics measured percutaneously was applied to determine the glomerular filtration rate (GFR). After 24 weeks, the mice were sacrificed and an early stage DN model was confirmed by GFR hyperfiltration, elevated urinary creatinine, normal urinary albumin, tubulointerstitial fibrosis, and glomerular hypertrophy. Fucoidan significantly improved the GFR hyperfiltration and renal fibrosis. An enriched SCFAs-producing bacteria and increased acetic concentration in cecum contents were found in fucoidan groups, as well as increased renal ATP levels and improved mitochondrial dysfunction. The renal inflammation and fibrosis were ameliorated through inhibiting the MAPKs pathway. In conclusion, fucoidan improved early stage DN targeting the microbiota-mitochondria axis by ameliorating mitochondrial oxidative stress and inhibiting the MAPKs pathway.},
}

@article {pmid38635629,
year = {2024},
author = {Wang, T and Weiss, A and You, L},
title = {A generic approach to infer community-level fitness of microbial genes.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {121},
number = {17},
pages = {e2318380121},
doi = {10.1073/pnas.2318380121},
pmid = {38635629},
issn = {1091-6490},
support = {R01AI125604//HHS | National Institutes of Health (NIH)/ ; R01GM098642//HHS | National Institutes of Health (NIH)/ ; R01EB031869//HHS | National Institutes of Health (NIH)/ ; MCB-1937259//National Science Foundation (NSF)/ ; },
abstract = {The gene content in a metagenomic pool defines the function potential of a microbial community. Natural selection, operating on the level of genomes or genes, shapes the evolution of community functions by enriching some genes while depriving the others. Despite the importance of microbiomes in the environment and health, a general metric to evaluate the community-wide fitness of microbial genes remains lacking. In this work, we adapt the classic neutral model of species and use it to predict how the abundances of different genes will be shaped by selection, regardless of at which level the selection acts. We establish a simple metric that quantitatively infers the average survival capability of each gene in a microbiome. We then experimentally validate the predictions using synthetic communities of barcoded Escherichia coli strains undergoing neutral assembly and competition. We further show that this approach can be applied to publicly available metagenomic datasets to gain insights into the environment-function interplay of natural microbiomes.},
}

@article {pmid38635587,
year = {2024},
author = {Ohdera, AH and Mansbridge, M and Wang, M and Naydenkov, P and Kamel, B and Goentoro, L},
title = {The microbiome of a Pacific moon jellyfish Aurelia coerulea.},
journal = {PloS one},
volume = {19},
number = {4},
pages = {e0298002},
pmid = {38635587},
issn = {1932-6203},
abstract = {The impact of microbiome in animal physiology is well appreciated, but characterization of animal-microbe symbiosis in marine environments remains a growing need. This study characterizes the microbial communities associated with the moon jellyfish Aurelia coerulea, first isolated from the East Pacific Ocean and has since been utilized as an experimental system. We find that the microbiome of this Pacific Aurelia culture is dominated by two taxa, a Mollicutes and Rickettsiales. The microbiome is stable across life stages, although composition varies. Mining the host sequencing data, we assembled the bacterial metagenome-assembled genomes (MAGs). The bacterial MAGs are highly reduced, and predict a high metabolic dependence on the host. Analysis using multiple metrics suggest that both bacteria are likely new species. We therefore propose the names Ca. Mariplasma lunae (Mollicutes) and Ca. Marinirickettsia aquamalans (Rickettsiales). Finally, comparison with studies of Aurelia from other geographical populations suggests the association with Ca. Mariplasma lunae occurs in Aurelia from multiple geographical locations. The low-diversity microbiome of Aurelia provides a relatively simple system to study host-microbe interactions.},
}

@article {pmid38635321,
year = {2024},
author = {Wang, M and Lkhagva, E and Kim, S and Zhai, C and Islam, MM and Kim, HJ and Hong, ST},
title = {The gut microbe pair of Oribacterium sp. GMB0313 and Ruminococcus sp. GMB0270 confers complete protection against SARS-CoV-2 infection by activating CD8+ T cell-mediated immunity.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2342497},
pmid = {38635321},
issn = {1949-0984},
mesh = {Animals ; Cricetinae ; Ruminococcus ; *Gastrointestinal Microbiome ; *COVID-19 ; SARS-CoV-2 ; Clostridiales ; CD8-Positive T-Lymphocytes ; Immunity, Cellular ; },
abstract = {Despite the potential protective role of the gut microbiome against COVID-19, specific microbes conferring resistance to COVID-19 have not yet been identified. In this work, we aimed to identify and validate gut microbes at the species level that provide protection against SARS-CoV-2 infection. To identify gut microbes conferring protection against COVID-19, we conducted a fecal microbiota transplantation (FMT) from an individual with no history of COVID-19 infection or immunization into a lethal COVID-19 hamster model. FMT from this COVID-19-resistant donor resulted in significant phenotypic changes related to COVID-19 sensitivity in the hamsters. Metagenomic analysis revealed distinct differences in the gut microbiome composition among the hamster groups, leading to the identification of two previously unknown bacterial species: Oribacterium sp. GMB0313 and Ruminococcus sp. GMB0270, both associated with COVID-19 resistance. Subsequently, we conducted a proof-of-concept confirmation animal experiment adhering to Koch's postulates. Oral administration of this gut microbe pair, Oribacterium sp. GMB0313 and Ruminococcus sp. GMB0270, to the hamsters provided complete protection against SARS-CoV-2 infection through the activation of CD8+ T cell mediated immunity. The prophylactic efficacy of the gut microbe pair against SARS-CoV-2 infection was comparable to, or even superior to, current mRNA vaccines. This strong prophylactic efficacy suggests that the gut microbe pair could be developed as a host-directed universal vaccine for all betacoronaviruses, including potential future emerging viruses.},
}

Animals
Cricetinae
Ruminococcus
*Gastrointestinal Microbiome
*COVID-19
SARS-CoV-2
Clostridiales
CD8-Positive T-Lymphocytes
Immunity, Cellular

@article {pmid38635106,
year = {2024},
author = {Jang, YJ and Choi, HS and Oh, I and Chung, JH and Moon, JS},
title = {Effects of Limosilactobacillus reuteri ID-D01 Probiotic Supplementation on Exercise Performance and Gut Microbiota in Sprague-Dawley Rats.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {38635106},
issn = {1867-1314},
support = {Ministry of Education (MOE)(2021RIS-001) (no.1345370811)//National Research Foundation of Korea (NRF)/ ; },
abstract = {The gut microbiota composition in animals and humans has recently been found to be influenced by exercise. Although Limosilactobacillus reuteri strains have notable probiotic properties that promote human health, understanding of its effects in combination with exercise and physical activity is limited. Therefore, this study examined the effects of L. reuteri ID-D01, a human-derived probiotic, on exercise performance and fatigue in Sprague-Dawley rats. Organ weight, maximal running distance, serum biochemistry, muscle performance, microbial community composition, and short-chain fatty acid (SCFA) levels were assessed. Results indicated that ID-D01 supplementation significantly improved endurance performance. Rats in the probiotic group demonstrated a significant increase in maximal running distance compared with that in the control group (p < 0.05). Additionally, levels of fatigue markers, such as lactate and creatine phosphokinase, were significantly reduced in the ID-D01-administered groups, suggesting its potential to alleviate exercise-induced fatigue. Microbiome analysis revealed a distinct shift in gut microbiota composition in response to ID-D01 administration. The group that received ID-D01 probiotics exhibited a significant increase in the abundance of SCFA-producing bacteria, particularly Akkermansia spp., compared with that in the control groups. Furthermore, they showed elevated production of SCFAs, such as acetate and butyrate. In conclusion, this study demonstrated that ID-D01 can enhance exercise performance and reduce fatigue. Herein, we highlighted that human-derived probiotics could improve physical performance, as observed by changes in gut microbiota composition and SCFA production.},
}

@article {pmid38635003,
year = {2024},
author = {Lee, SH and Lee, JH and Lee, SW},
title = {Application of Microbiome-Based Therapies in Chronic Respiratory Diseases.},
journal = {Journal of microbiology (Seoul, Korea)},
volume = {},
number = {},
pages = {},
pmid = {38635003},
issn = {1976-3794},
support = {2020R1A2C1008431//National Research Foundation of Korea/ ; 2023R1A2C2006688//National Research Foundation of Korea/ ; RS-2023-00222687//National Research Foundation of Korea/ ; 2022M3A9G8017220//National Research Foundation of Korea/ ; },
abstract = {The application of microbiome-based therapies in various areas of human disease has recently increased. In chronic respiratory disease, microbiome-based clinical applications are considered compelling options due to the limitations of current treatments. The lung microbiome is ecologically dynamic and affected by various conditions, and dysbiosis is associated with disease severity, exacerbation, and phenotype as well as with chronic respiratory disease endotype. However, it is not easy to directly modulate the lung microbiome. Additionally, studies have shown that chronic respiratory diseases can be improved by modulating gut microbiome and administrating metabolites. Although the composition, diversity, and abundance of the microbiome between the gut and lung are considerably different, modulation of the gut microbiome could improve lung dysbiosis. The gut microbiome influences that of the lung via bacterial-derived components and metabolic degradation products, including short-chain fatty acids. This phenomenon might be associated with the cross-talk between the gut microbiome and lung, called gut-lung axis. There are multiple alternatives to modulate the gut microbiome, such as prebiotics, probiotics, and postbiotics ingestion and fecal material transplantation. Several studies have shown that high-fiber diets, for example, present beneficial effects through the production of short-chain fatty acids. Additionally, genetically modified probiotics to secrete some beneficial molecules might also be utilized to treat chronic respiratory diseases. Further studies on microbial modulation to regulate immunity and potentiate conventional pharmacotherapy will improve microbiome modulation techniques, which will develop as a new therapeutic area in chronic respiratory diseases.},
}

@article {pmid38634795,
year = {2024},
author = {Siqueira, JF and Silva, WO and Romeiro, K and Gominho, LF and Alves, FRF and Rôças, IN},
title = {Apical root canal microbiome associated with primary and posttreatment apical periodontitis: A systematic review.},
journal = {International endodontic journal},
volume = {},
number = {},
pages = {},
doi = {10.1111/iej.14071},
pmid = {38634795},
issn = {1365-2591},
support = {//CNPq/ ; //FAPERJ/ ; },
abstract = {BACKGROUND: Microorganisms colonizing the apical root canal system are conceivably the ones directly involved with the causation and maintenance of apical periodontitis.

OBJECTIVES: This article systematically reviews the reports on the microbiome occurring exclusively at the apical root canal of teeth with primary and posttreatment apical periodontitis.

METHODS: The electronic databases PubMed, Embase, Web of Science, Science Direct, and Proquest were searched up to August 2023. Clinical studies using culture and molecular microbiology methods to identify the microbial taxa present exclusively in the apical root canal segment of infected teeth with apical periodontitis were included. Studies were critically assessed using the Joanna Briggs Institute Critical Prevalence Assessment Checklist.

RESULTS: From 2277 articles initially detected, 52 were selected for full reading and 21 were eventually included in this review. Of these, molecular methods were used in 19 and culture in 2 studies. Ten studies evaluated primary infections, 8 evaluated posttreatment infections, and 3 included both. Cryopulverization of the apical root specimens was conducted in 11 studies. All studies evaluated the prevalence and diversity of bacteria, and only one also reported on fungi. Overall, the most frequent/abundant bacterial taxa found in the apical canal of primary infections were Pseudoramibacter alactolyticus, Olsenella uli, Fusobacterium species, Streptococcus species, Porphyromonas endodontalis, Prevotella species, Actinomyces species, Parvimonas micra, Treponema denticola, Synergistetes species, and an as-yet uncharacterized taxon. In posttreatment infections, the most prevalent/abundant bacterial taxa included species of Streptococcus, Enterococcus, Fusobacterium, Actinomyces, Pseudoramibacter, Pseudomonas, and Propionibacterium. At the phylum level, Firmicutes was the most represented. The average apical bacterial load ranged from 10[5] to 10[6] in primary infections and from 10[3] to 10[4] in posttreatment infections.

DISCUSSION: Microbial diversity in the apical part of the root canal system was examined encompassing data from both primary and posttreatment infections. Heterogeneity amongst the studies, especially in sample collection and microbial identification methods, is an important limitation that prevented a meta-analysis.

CONCLUSIONS: There is a pronounced bacterial diversity in the infected apical canal, with a high interindividual variability. Different microbiome compositions at the species/genus level are observed according to the infection type.

REGISTRATION: PROSPERO CRD42021275886.},
}

@article {pmid38634770,
year = {2024},
author = {Lee, I and Jo, JW and Woo, HJ and Suk, KT and Lee, SS and Kim, BS},
title = {Proton pump inhibitors increase the risk of carbapenem-resistant Enterobacteriaceae colonization by facilitating the transfer of antibiotic resistance genes among bacteria in the gut microbiome.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2341635},
pmid = {38634770},
issn = {1949-0984},
mesh = {Humans ; Proton Pump Inhibitors ; *Gastrointestinal Microbiome ; *Carbapenem-Resistant Enterobacteriaceae ; Case-Control Studies ; Bacteria ; Anti-Bacterial Agents ; Drug Resistance, Microbial ; },
abstract = {Carbapenem-resistant Enterobacteriaceae (CRE) pose a global health threat; however, there is still limited understanding of the risk factors and underlying mechanisms of CRE colonization in the gut microbiome. We conducted a matched case-control study involving 282 intensive care unit patients to analyze influencing covariates on CRE colonization. Subsequently, their effects on the gut microbiome were analyzed in a subset of 98 patients (47 CRE carriers and 51 non-CRE carriers) using whole metagenome sequences. The concomitant use of proton pump inhibitors (PPIs) and antibiotics was a significant risk factor for CRE colonization. The gut microbiome differed according to PPI administration, even within the CRE and non-CRE groups. Moreover, the transfer of mobile genetic elements (MGEs) harboring carbapenem resistance genes (CRGs) between bacteria was higher in the PPI-treated group than in the PPI-not-treated group among CRE carriers. The concomitant use of PPIs and antibiotics significantly alters the gut microbiome and increases the risk of CRE colonization by facilitating the transfer of CRGs among bacteria of the gut microbiome. Based on these findings, improved stewardship of PPIs as well as antibiotics can provide strategies to reduce the risk of CRE colonization, thereby potentially improving patient prognosis.},
}

Humans
Proton Pump Inhibitors
*Gastrointestinal Microbiome
*Carbapenem-Resistant Enterobacteriaceae
Case-Control Studies
Bacteria
Anti-Bacterial Agents
Drug Resistance, Microbial

@article {pmid38634692,
year = {2024},
author = {Zimmermann, J and Piecyk, A and Sieber, M and Petersen, C and Johnke, J and Moitinho-Silva, L and Künzel, S and Bluhm, L and Traulsen, A and Kaleta, C and Schulenburg, H},
title = {Gut-associated functions are favored during microbiome assembly across a major part of C. elegans life.},
journal = {mBio},
volume = {},
number = {},
pages = {e0001224},
doi = {10.1128/mbio.00012-24},
pmid = {38634692},
issn = {2150-7511},
abstract = {UNLABELLED: The microbiome expresses a variety of functions that influence host biology. The range of functions depends on the microbiome's composition, which can change during the host's lifetime due to neutral assembly processes, host-mediated selection, and environmental conditions. To date, the exact dynamics of microbiome assembly, the underlying determinants, and the effects on host-associated functions remain poorly understood. Here, we used the nematode Caenorhabditis elegans and a defined community of fully sequenced, naturally associated bacteria to study microbiome dynamics and functions across a major part of the worm's lifetime of hosts under controlled experimental conditions. Bacterial community composition initially shows strongly declining levels of stochasticity, which increases during later time points, suggesting selective effects in younger animals as opposed to more random processes in older animals. The adult microbiome is enriched in genera Ochrobactrum and Enterobacter compared to the direct substrate and a host-free control environment. Using pathway analysis, metabolic, and ecological modeling, we further find that the lifetime assembly dynamics increase competitive strategies and gut-associated functions in the host-associated microbiome, indicating that the colonizing bacteria benefit the worm. Overall, our study introduces a framework for studying microbiome assembly dynamics based on stochastic, ecological, and metabolic models, yielding new insights into the processes that determine host-associated microbiome composition and function.

IMPORTANCE: The microbiome plays a crucial role in host biology. Its functions depend on the microbiome composition that can change during a host's lifetime. To date, the dynamics of microbiome assembly and the resulting functions still need to be better understood. This study introduces a new approach to characterize the functional consequences of microbiome assembly by modeling both the relevance of stochastic processes and metabolic characteristics of microbial community changes. The approach was applied to experimental time-series data obtained for the microbiome of the nematode Caenorhabditis elegans across the major part of its lifetime. Stochastic processes played a minor role, whereas beneficial bacteria as well as gut-associated functions enriched in hosts. This indicates that the host might actively shape the composition of its microbiome. Overall, this study provides a framework for studying microbiome assembly dynamics and yields new insights into C. elegans microbiome functions.},
}

@article {pmid38634357,
year = {2024},
author = {Xu, YJ and He, Y and Chen, C and Shi, J and He, M and Liu, Y and Zhang, Y and Liu, Y and Zhang, Y},
title = {Multiomics Analysis Revealed Colorectal Cancer Pathogenesis.},
journal = {Journal of proteome research},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jproteome.3c00894},
pmid = {38634357},
issn = {1535-3907},
abstract = {Gut microbiota-derived microbial compounds may link to the pathogenesis of colorectal cancer (CRC). However, the role of the host-microbiome in the incidence and progression of CRC remains elusive. We performed 16S rRNA sequencing, metabolomics, and proteomic studies on samples from 85 CRC patients who underwent colonoscopy examination and found two distinct changed patterns of microbiome in CRC patients. The relative abundances of Catabacter and Mogibacterium continuously increased from intramucosal carcinoma to advanced stages, whereas Clostridium, Anaerostipes, Vibrio, Flavonifractor, Holdemanella, and Hungatella were significantly altered only in intermediate lesions. Fecal metabolomics analysis exhibited consistent increases in bile acids, indoles, and urobilin as well as a decrease in heme. Serum metabolomics uncovered the highest levels of bilin, glycerides, and nucleosides together with the lowest levels of bile acids and amino acids in the stage of intermediate lesions. Three fecal and one serum dipeptides were elevated in the intermediate lesions. Proteomics analysis of colorectal tissues showed that oxidation and autophagy through the PI3K/Akt-mTOR signaling pathway contribute to the development of CRC. Diagnostic analysis showed multiomics features have good predictive capability, with AUC greater than 0.85. Our overall findings revealed new candidate biomarkers for CRC, with potentially significant diagnostic and prognostic capabilities.},
}

@article {pmid38634147,
year = {2024},
author = {Qian, J and Zhao, X and Yuan, S and Su, S and Chen, C and Gao, J and Tang, X and Men, S and Wen, B},
title = {Metabolome-microbiome insights into therapeutic impact of 8-O-acetylharpagide against breast cancer in a murine model.},
journal = {Biomedical chromatography : BMC},
volume = {},
number = {},
pages = {e5880},
doi = {10.1002/bmc.5880},
pmid = {38634147},
issn = {1099-0801},
support = {JJ-2020-39//Beijing Science and Technology Development Fund Project of Traditional Chinese Medicine/ ; },
abstract = {Iridoid glycosides extract, which is the main active extract of Ajuga decumbens Thunb, has been proved to have anti-breast cancer activity in previous studies. However, it is still unknown whether 8-O-acetylharpagide, a main active compound in the extract, has anti-breast cancer activity. In this study, 4 T1 breast cancer mice model was first successfully established. Then the anti-breast cancer effect of 8-O-acetylharpagide was systematically investigated. Feces were collected for metabolomics and 16S rRNA analysis to assess the potential mechanism. The results showed that 8-O-acetylharpagide was effective in reducing 4 T1 mouse tumor volume and weight compared with the model group. Metabolome analysis revealed 12 potential metabolite biomarkers in feces, mainly involved in primary bile acid biosynthesis and arachidonic acid metabolism. The 16S rRNA sequencing results demonstrated that 8-O-acetylharpagide modulated the abundance of the intestinal flora in 4 T1 mice. Spearman correlation analysis showed that calcitriol and prostaglandin G2 strongly correlated with Akkermansia, Firmicutes and Muribaculum. Overall, the active compound 8-O-acetylharpagide could inhibit significantly breast cancer growth in 4 T1 breast cancer model mice. The mechanism of the anti-breast cancer effect of 8-O-acetylharpagide may be related to the regulation of primary bile acid biosynthesis and arachidonic acid metabolism and modulation of the abundance of Akkermansia and Firmicutes.},
}

@article {pmid38634136,
year = {2024},
author = {Moore, BN and Medcalf, AD and Muir, RQ and Xu, C and Marques, FZ and Pluznick, JL},
title = {Commensal Microbiota Regulate Aldosterone.},
journal = {American journal of physiology. Renal physiology},
volume = {},
number = {},
pages = {},
doi = {10.1152/ajprenal.00051.2024},
pmid = {38634136},
issn = {1522-1466},
support = {R01DK137762/NH/NIH HHS/United States ; },
abstract = {The gut microbiome regulates many important host physiological processes associated with cardiovascular health and disease; however, the impact of the gut microbiome on aldosterone is unclear. Investigating whether gut microbiota regulate aldosterone can offer novel insights into how the microbiome affects blood pressure. In this study, we aimed to determine whether gut microbiota regulate host aldosterone. We employed enzyme-linked immunosorbent assays (ELISAs) to assess plasma aldosterone and plasma renin activity (PRA) in female and male mice in which gut microbiota are intact, suppressed, or absent. In addition, we examined urinary aldosterone. Our findings demonstrated that when the gut microbiota is suppressed following antibiotic treatment, there is an increase in plasma and urinary aldosterone in both female and male mice. In contrast, an increase in PRA is seen only in males. We also found that when gut microbiota are absent (germ-free mice), plasma aldosterone is significantly increased compared to conventional animals (in both females and males), but PRA is not. Understanding how gut microbiota influence aldosterone levels could provide valuable insights into the development and treatment of hypertension and/or primary aldosteronism. This knowledge may open new avenues for therapeutic interventions, such as probiotics or dietary modifications to help regulate blood pressure via microbiota-based changes to aldosterone.},
}

@article {pmid38634007,
year = {2024},
author = {Wen, C and Chen, D and Zhong, R and Peng, X},
title = {Animal models of inflammatory bowel disease: category and evaluation indexes.},
journal = {Gastroenterology report},
volume = {12},
number = {},
pages = {goae021},
pmid = {38634007},
issn = {2052-0034},
abstract = {Inflammatory bowel disease (IBD) research often relies on animal models to study the etiology, pathophysiology, and management of IBD. Among these models, rats and mice are frequently employed due to their practicality and genetic manipulability. However, for studies aiming to closely mimic human pathology, non-human primates such as monkeys and dogs offer valuable physiological parallels. Guinea pigs, while less commonly used, present unique advantages for investigating the intricate interplay between neurological and immunological factors in IBD. Additionally, New Zealand rabbits excel in endoscopic biopsy techniques, providing insights into mucosal inflammation and healing processes. Pigs, with their physiological similarities to humans, serve as ideal models for exploring the complex relationships between nutrition, metabolism, and immunity in IBD. Beyond mammals, non-mammalian organisms including zebrafish, Drosophila melanogaster, and nematodes offer specialized insights into specific aspects of IBD pathology, highlighting the diverse array of model systems available for advancing our understanding of this multifaceted disease. In this review, we conduct a thorough analysis of various animal models employed in IBD research, detailing their applications and essential experimental parameters. These include clinical observation, Disease Activity Index score, pathological assessment, intestinal barrier integrity, fibrosis, inflammatory markers, intestinal microbiome, and other critical parameters that are crucial for evaluating modeling success and drug efficacy in experimental mammalian studies. Overall, this review will serve as a valuable resource for researchers in the field of IBD, offering insights into the diverse array of animal models available and their respective applications in studying IBD.},
}

@article {pmid38633890,
year = {2024},
author = {Amponsah, AS and Ankar-Brewoo, GM and Lutterodt, HE and Ofosu, IW},
title = {Assessing the microbial diversity and proximate composition of smoked-fermented bushmeat from four different bushmeat samples.},
journal = {Biotechnologia},
volume = {105},
number = {1},
pages = {5-17},
pmid = {38633890},
issn = {2353-9461},
abstract = {The ever-increasing demand for wildlife-derived raw or processed meat commonly known as bushmeat, has been identified as one of the critical factors driving the emergence of infectious diseases. This study focused on examining the bacterial community composition of smoked and fermented bushmeats, specifically grasscutter, rat, rabbit, and mona monkey. The analysis involved exploring 16Sr RNA amplicon sequences isolated from bushmeat using QIIME2. Microbiome profiles and their correlation with proximate components (PLS regression) were computed in STAMP and XLSTAT, respectively. Results indicate the predominance of Firmicutes (70.9%), Actinobacteria (18.58%), and Proteobacteria (9.12%) in bushmeat samples at the phylum level. Staphylococcus, Arthrobacter, Macrococcus, and Proteus constituted the core microbiomes in bushmeat samples, ranked in descending order. Notably, significant differences were observed between the bacterial communities of bushmeat obtained from omnivores and herbivores (rat and mona monkey, and grasscutter and mona monkey), as well as those with similar feeding habits (rat and monkey, and grasscutter and rabbit) at the family and genus levels. Each type of bushmeat possessed unique microbial diversity, with some proximate components such as fat in rat samples correlating with Staphylococcus, while proteins in Mona monkey correlated with Arthrobacter and Brevibacterium, respectively. The study underscores public health concerns and highlights probiotic benefits, as bushmeat samples contained both pathogenic and beneficial bacteria. Therefore, future research efforts could focus on improving bushmeat quality.},
}

@article {pmid38633809,
year = {2024},
author = {Dedon, LR and Yuan, H and Chi, J and Gu, H and Arias, AJ and Covault, JM and Zhou, Y},
title = {Baseline gut microbiome and metabolites are correlated with alcohol consumption in a zonisamide clinical trial of heavy drinking alcoholic civilians.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.04.02.24305199},
pmid = {38633809},
abstract = {Development and severity of alcohol use disorder (AUD) has been linked to variations in gut microbiota and their associated metabolites in both animal and human studies. However, the involvement of the gut microbiome in alcohol consumption of individuals with AUD undergoing treatment remains unclear. To address this, stool samples (n=48) were collected at screening (baseline) and trial completion from a single site of a multi-site double-blind, placebo-controlled trial of Zonisamide in individuals with AUD. Alcohol consumption, gamma-glutamyl transferase (GGT), and phosphatidylethanol (PEth)levels were measured both at baseline and endpoint of 16-week trial period. Fecal microbiome was analyzed via 16S rRNA sequencing and metabolome via untargeted LC-MS. Both sex (p = 0.003) and psychotropic medication usage (p = 0.025) are associated with baseline microbiome composition. The relative abundance of 12 genera at baseline was correlated with percent drinking reduction, baseline and endpoint alcohol consumption, and changes in GGT and PeTH over the course of treatment (p.adj < 0.05). Overall microbiome community structure at baseline differed between high and low responders (67-100% and 0-33% drinking reduction, respectively; p = 0.03). A positive relationship between baseline fecal GABA levels and percent drinking reduction (R=0.43, p < 0.05) was identified by microbiome function prediction and confirmed by ELISA and metabolomics. Predicted microbiome function and metabolomics analysis have found that tryptophan metabolic pathways are over-represented in low responders. These findings highlight importance of baseline microbiome and metabolites in alcohol consumption in AUD patients undergoing zonisamide treatment.},
}

@article {pmid38633744,
year = {2024},
author = {Shao, Z and Gao, H and Wang, B and Zhang, S},
title = {Exploring the impact of pathogenic microbiome in orthopedic diseases: machine learning and deep learning approaches.},
journal = {Frontiers in cellular and infection microbiology},
volume = {14},
number = {},
pages = {1380136},
pmid = {38633744},
issn = {2235-2988},
mesh = {Humans ; *Deep Learning ; Quality of Life ; *Musculoskeletal Diseases ; Machine Learning ; *Microbiota ; },
abstract = {Osteoporosis, arthritis, and fractures are examples of orthopedic illnesses that not only significantly impair patients' quality of life but also complicate and raise the expense of therapy. It has been discovered in recent years that the pathophysiology of orthopedic disorders is significantly influenced by the microbiota. By employing machine learning and deep learning techniques to conduct a thorough analysis of the disease-causing microbiome, we can enhance our comprehension of the pathophysiology of many illnesses and expedite the creation of novel treatment approaches. Today's science is undergoing a revolution because to the introduction of machine learning and deep learning technologies, and the field of biomedical research is no exception. The genesis, course, and management of orthopedic disorders are significantly influenced by pathogenic microbes. Orthopedic infection diagnosis and treatment are made more difficult by the lengthy and imprecise nature of traditional microbial detection and characterization techniques. These cutting-edge analytical techniques are offering previously unheard-of insights into the intricate relationships between orthopedic health and pathogenic microbes, opening up previously unimaginable possibilities for illness diagnosis, treatment, and prevention. The goal of biomedical research has always been to improve diagnostic and treatment methods while also gaining a deeper knowledge of the processes behind the onset and development of disease. Although traditional biomedical research methodologies have demonstrated certain limits throughout time, they nevertheless rely heavily on experimental data and expertise. This is the area in which deep learning and machine learning approaches excel. The advancements in machine learning (ML) and deep learning (DL) methodologies have enabled us to examine vast quantities of data and unveil intricate connections between microorganisms and orthopedic disorders. The importance of ML and DL in detecting, categorizing, and forecasting harmful microorganisms in orthopedic infectious illnesses is reviewed in this work.},
}

Humans
*Deep Learning
Quality of Life
*Musculoskeletal Diseases
Machine Learning
*Microbiota

@article {pmid38633690,
year = {2024},
author = {Zhao, M and Zhang, Y and Li, Y and Liu, K and Bao, K and Li, G},
title = {Impact of Pediococcus acidilactici GLP06 supplementation on gut microbes and metabolites in adult beagles: a comparative analysis.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1369402},
pmid = {38633690},
issn = {1664-302X},
abstract = {There is growing interest in the potential health benefits of probiotics for both humans and animals. The study aimed to investigate the effects of feeding the canine-derived probiotic Pediococcus acidilactici GLP06 to adult beagles by analysing the microbiome and metabolome. Twenty-four healthy adult beagles were randomly assigned to four groups. The CK group received a standard diet, while the three probiotic groups, the LG group (2 × 10[8] CFU/day/dog), MG group (2 × 10[9] CFU/day/dog), and HG group (2 × 10[10] CFU/day/dog), received the standard diet supplemented with varying amounts of probiotics. The results show that, compared to the CK group, total antioxidant capacity was significantly increased in the MG and HG groups (p < 0.05), and superoxide dismutase and catalase were significantly increased in the HG group (p < 0.05). Compared to the CK group, malondialdehyde and blood urea nitrogen content were significantly decreased in the MG and HG groups (p < 0.05). Additionally, secretory immunoglobulin A activity was significantly increased in the HG group compared to the CK and LG groups (p < 0.05), and immunoglobulin G activity was significantly increased in the HG group compared to the CK, LG, and MG groups (p < 0.05). In addition, compared with the CK group, the abundance of Faecalitalea and Collinsella increased in the LG group, and the relative abundance of Tyzzerella and Parasutterella increased in the MG group. The α diversity and the relative abundances of beneficial bacteria (Faecalibacterium, Lachnospiraceae_NK4A1316, and Ruminococcaceae_UCG-005) were higher in the HG group than in the CK group. Furthermore, acetic acid content was significantly increased in the HG group compared to the CK, LG, and MG groups (p < 0.05). Butyric acid, isobutyric acid, and the total SCFA content were significantly increased in the HG group compared to the CK group (p < 0.05). Moreover, metabolome analysis revealed 111 upregulated and 171 downregulated metabolites in the HG group. In conclusion, this study presents evidence that supplementing with P. acidilactici GLP06 can have a positive impact on antioxidant activity, immunoproteins, SCFAs, and gut microbiota in adult beagles. These findings highlight the potential of probiotics as a dietary intervention to enhance gut health and overall wellbeing in companion animals.},
}

@article {pmid38633603,
year = {2024},
author = {Bacha, AA and Suhail, M and Awwad, FA and Ismail, EAA and Ahmad, H},
title = {Role of dietary fiber and lifestyle modification in gut health and sleep quality.},
journal = {Frontiers in nutrition},
volume = {11},
number = {},
pages = {1324793},
pmid = {38633603},
issn = {2296-861X},
abstract = {Dietary fiber has an immense role in the gut microbiome by modulating juvenile growth, immune system maturation, glucose, and lipid metabolism. Lifestyle changes might disrupt gut microbiota symbiosis, leading to various chronic diseases with underlying inflammatory conditions, obesity, and its associated pathologies. An interventional study of 16 weeks examined the impact of psyllium husk fiber with and without lifestyle modification on gut health and sleep quality in people with central obesity (men = 60 and women = 60), those aged from 40 to 60 years, those having WC ≥ 90 cm (men) and WC ≥ 80 cm (women), and no history of any chronic disease or regular medication. The participants were subgrouped into three intervention groups, namely, the psyllium husk fiber (PSH) group, the lifestyle modification (LSM) group, and the LSM&PSH group and control group with equal gender bifurcation (men = 15 and women = 15). A 24-h dietary recall, gastrointestinal tract (GIT) symptoms, and sleep quality analysis data were collected on validated questionnaires. The analyses of variance and covariance were used for baseline and post-intervention, respectively. Student's t-test was applied for pre- and post-intervention changes on the variable of interest. The intervention effect on GIT health was highly significant (P < 0.001). The mean GIT scores of the LSM, PSH, and LSM&PSH groups were 2.99 ± 0.14, 2.49 ± 0.14, and 2.71 ± 0.14, respectively, compared to the mean GIT scores of the control group. No significant (P = 0.205) effect of either intervention was observed on sleep quality. The study concluded that psyllium husk fiber significantly improved the GIT symptoms, while no significant effect of the intervention was observed on sleep quality analysis.},
}

@article {pmid38633411,
year = {2024},
author = {Han, M and Wang, N and Han, W and Liu, X and Sun, T and Xu, J},
title = {Highly specific vaginal microbiome signature for gynecological cancers.},
journal = {Open life sciences},
volume = {19},
number = {1},
pages = {20220850},
doi = {10.1515/biol-2022-0850},
pmid = {38633411},
issn = {2391-5412},
abstract = {To investigate the vaginal microbiota signature of patients with gynecologic cancer and evaluate its diagnostic biomarker potential. We incorporated vaginal 16S rRNA-seq data from 529 women and utilized VSEARCH to analyze the raw data. α-Diversity was evaluated utilizing the Chao1, Shannon, and Simpson indices, and β-diversity was evaluated through principal component analysis using Bray-Curtis distances. Linear discriminant analysis effect size (LEfSe) was utilized to determine species differences between groups. A bacterial co-abundance network was constructed utilizing Spearman correlation analysis. A random forest model of gynecologic tumor risk based on genus was constructed and validated to test its diagnostic efficacy. In gynecologic cancer patients, vaginal α-diversity was significantly greater than in controls, and vaginal β-diversity was significantly separated from that of controls; there was no correlation between these characteristics and menopause status among the subject women. Women diagnosed with gynecological cancer exhibited a reduction in the abundance of vaginal Firmicutes and Lactobacillus, while an increase was observed in the proportions of Bacteroidetes, Proteobacteria, Prevotella, Streptococcus, and Anaerococcus. A random forest model constructed based on 56 genus achieved high accuracy (area under the curve = 84.96%) in gynecological cancer risk prediction. Furthermore, there were discrepancies observed in the community complexity of co-abundance networks between gynecologic cancer patients and the control group. Our study provides evidence that women with gynecologic cancer have a unique vaginal flora structure and microorganisms may be involved in the gynecologic carcinogenesis process. A gynecological cancer risk prediction model based on characteristic genera has good diagnostic value.},
}

@article {pmid38633385,
year = {2024},
author = {Rooney, J and Rivera-de-Torre, E and Li, R and Mclean, K and Price, DRG and Nisbet, AJ and Laustsen, AH and Jenkins, TP and Hofmann, A and Bakshi, S and Zarkan, A and Cantacessi, C},
title = {Structural and functional analyses of nematode-derived antimicrobial peptides support the occurrence of direct mechanisms of worm-microbiota interactions.},
journal = {Computational and structural biotechnology journal},
volume = {23},
number = {},
pages = {1522-1533},
pmid = {38633385},
issn = {2001-0370},
abstract = {The complex relationships between gastrointestinal (GI) nematodes and the host gut microbiota have been implicated in key aspects of helminth disease and infection outcomes. Nevertheless, the direct and indirect mechanisms governing these interactions are, thus far, largely unknown. In this proof-of-concept study, we demonstrate that the excretory-secretory products (ESPs) and extracellular vesicles (EVs) of key GI nematodes contain peptides that, when recombinantly expressed, exert antimicrobial activity in vitro against Bacillus subtilis. In particular, using time-lapse microfluidics microscopy, we demonstrate that exposure of B. subtilis to a recombinant saposin-domain containing peptide from the 'brown stomach worm', Teladorsagia circumcincta, and a metridin-like ShK toxin from the 'barber's pole worm', Haemonchus contortus, results in cell lysis and significantly reduced growth rates. Data from this study support the hypothesis that GI nematodes may modulate the composition of the vertebrate gut microbiota directly via the secretion of antimicrobial peptides, and pave the way for future investigations aimed at deciphering the impact of such changes on the pathophysiology of GI helminth infection and disease.},
}

@article {pmid38633306,
year = {2024},
author = {Zhang, L and Liu, X and Fan, B and Chen, J and Chen, J and Li, Q and Wu, X},
title = {Microbiome features in bronchoalveolar lavage fluid of patients with idiopathic inflammatory myopathy-related interstitial lung disease.},
journal = {Frontiers in medicine},
volume = {11},
number = {},
pages = {1338947},
pmid = {38633306},
issn = {2296-858X},
abstract = {BACKGROUND: Interstitial lung disease (ILD) is a common complication of idiopathic inflammatory myopathy (IIM), which is one of the connective tissue diseases (CTD). It can lead to poor prognosis and increased mortality. However, the distribution and role of the lower respiratory tract (LRT) microbiome in patients with IIM-ILD remains unclear. This study aimed to investigate the microbial diversity and community differences in bronchoalveolar lavage fluid (BALF) in patients with IIM-ILD.

METHODS: From 28 June 2021 to 26 December 2023, 51 individual BALF samples were enrolled, consisting of 20 patients with IIM-ILD, 16 patients with other CTD-ILD (including 8 patients with SLE and 8 with RA) and 15 patients with CAP. The structure and function of microbiota in BALF were identified by metagenomic next-generation sequencing (mNGS).

RESULTS: The community evenness of LRT microbiota within the IIM-ILD group was marginally lower compared to the other CTD-ILD and CAP groups. Nonetheless, there were no noticeable differences. The species community structure was similar among the three groups, based on the Bray-Curtis distance between the samples. At the level of genus, the IIM-ILD group displayed a considerably higher abundance of Pseudomonas and Corynebacterium in comparison to the CAP group (p < 0.01, p < 0.05). At the species level, we found that the relative abundance of Pseudomonas aeruginosa increased significantly in the IIM-ILD group compared to the CAP group (p < 0.05). Additionally, the relative abundance of Prevotella pallens was significantly higher in other CTD-ILD groups compared to that in the IIM-ILD group (p < 0.05). Of all the clinical indicators examined in the correlation analysis, ferritin level demonstrated the strongest association with LRT flora, followed by Serum interleukin-6 level (p < 0.05).

CONCLUSION: Our research has identified particular LRT microorganisms that were found to be altered in the IIM-ILD group and were significantly associated with immune function and inflammatory markers in patients. The lower respiratory tract microbiota has potential in the diagnosis and treatment of IIM-ILD.},
}

@article {pmid38632606,
year = {2024},
author = {Liu, X and Zeng, X and Li, X and Xin, S and Zhang, F and Liu, F and Zeng, Y and Wu, J and Zou, Y and Xiong, X},
title = {Landscapes of gut bacterial and fecal metabolic signatures and their relationship in severe preeclampsia.},
journal = {Journal of translational medicine},
volume = {22},
number = {1},
pages = {360},
pmid = {38632606},
issn = {1479-5876},
support = {82160298//National Natural Science Foundation of China/ ; },
mesh = {Female ; Pregnancy ; Humans ; *Gastrointestinal Microbiome/genetics ; *Pre-Eclampsia ; *Agmatine ; Reproducibility of Results ; Feces/microbiology ; Metabolome ; Inflammation ; *Pregnancy Complications ; Bacteria ; *Hypertension ; RNA, Ribosomal, 16S ; },
abstract = {BACKGROUND: Preeclampsia is a pregnancy-specific disease leading to maternal and perinatal morbidity. Hypertension and inflammation are the main characteristics of preeclampsia. Many factors can lead to hypertension and inflammation, including gut microbiota which plays an important role in hypertension and inflammation in humans. However, alterations to the gut microbiome and fecal metabolome, and their relationships in severe preeclampsia are not well known. This study aims to identify biomarkers significantly associated with severe preeclampsia and provide a knowledge base for treatments regulating the gut microbiome.

METHODS: In this study, fecal samples were collected from individuals with severe preeclampsia and healthy controls for shotgun metagenomic sequencing to evaluate changes in gut microbiota composition. Quantitative polymerase chain reaction analysis was used to validate the reliability of our shotgun metagenomic sequencing results. Additionally, untargeted metabolomics analysis was performed to measure fecal metabolome concentrations.

RESULTS: We identified several Lactobacillaceae that were significantly enriched in the gut of healthy controls, including Limosilactobacillus fermentum, the key biomarker distinguishing severe preeclampsia from healthy controls. Limosilactobacillus fermentum was significantly associated with shifts in KEGG Orthology (KO) genes and KEGG pathways of the gut microbiome in severe preeclampsia, such as flagellar assembly. Untargeted fecal metabolome analysis found that severe preeclampsia had higher concentrations of Phenylpropanoate and Agmatine. Increased concentrations of Phenylpropanoate and Agmatine were associated with the abundance of Limosilactobacillus fermentum. Furthermore, all metabolites with higher abundances in healthy controls were enriched in the arginine and proline metabolism pathway.

CONCLUSION: Our research indicates that changes in metabolites, possibly due to the gut microbe Limosilactobacillus fermentum, can contribute to the development of severe preeclampsia. This study provides insights into the interaction between gut microbiome and fecal metabolites and offers a basis for improving severe preeclampsia by modulating the gut microbiome.},
}

Female
Pregnancy
Humans
*Gastrointestinal Microbiome/genetics
*Pre-Eclampsia
*Agmatine
Reproducibility of Results
Feces/microbiology
Metabolome
Inflammation
*Pregnancy Complications
Bacteria
*Hypertension
RNA, Ribosomal, 16S

@article {pmid38632579,
year = {2024},
author = {Yin, X and Duan, C and Zhang, L and Zhu, Y and Qiu, Y and Shi, K and Wang, S and Zhang, X and Zhang, H and Hao, Y and Yuan, F and Tian, Y},
title = {Microbiota-derived acetate attenuates neuroinflammation in rostral ventrolateral medulla of spontaneously hypertensive rats.},
journal = {Journal of neuroinflammation},
volume = {21},
number = {1},
pages = {101},
pmid = {38632579},
issn = {1742-2094},
support = {QN2021103//Science and Technology Project of Higher Education of Hebei Province/ ; H2021206203//Natural Science Foundation of Hebei Province for Innovative Research Group Project/ ; 82000401//National Natural Science Foundation of China/ ; },
mesh = {Humans ; Rats ; Animals ; Rats, Inbred SHR ; Neuroinflammatory Diseases ; *Hypertension/metabolism ; Blood Pressure ; Medulla Oblongata/metabolism ; *Microbiota ; Acetates/pharmacology ; },
abstract = {BACKGROUND: Increased neuroinflammation in brain regions regulating sympathetic nerves is associated with hypertension. Emerging evidence from both human and animal studies suggests a link between hypertension and gut microbiota, as well as microbiota-derived metabolites short-chain fatty acids (SCFAs). However, the precise mechanisms underlying this gut-brain axis remain unclear.

METHODS: The levels of microbiota-derived SCFAs in spontaneously hypertensive rats (SHRs) were determined by gas chromatography-mass spectrometry. To observe the effect of acetate on arterial blood pressure (ABP) in rats, sodium acetate was supplemented via drinking water for continuous 7 days. ABP was recorded by radio telemetry. The inflammatory factors, morphology of microglia and astrocytes in rostral ventrolateral medulla (RVLM) were detected. In addition, blood-brain barrier (BBB) permeability, composition and metabolomics of the gut microbiome, and intestinal pathological manifestations were also measured.

RESULTS: The serum acetate levels in SHRs are lower than in normotensive control rats. Supplementation with acetate reduces ABP, inhibits sympathetic nerve activity in SHRs. Furthermore, acetate suppresses RVLM neuroinflammation in SHRs, increases microglia and astrocyte morphologic complexity, decreases BBB permeability, modulates intestinal flora, increases fecal flora metabolites, and inhibits intestinal fibrosis.

CONCLUSIONS: Microbiota-derived acetate exerts antihypertensive effects by modulating microglia and astrocytes and inhibiting neuroinflammation and sympathetic output.},
}

Humans
Rats
Animals
Rats, Inbred SHR
Neuroinflammatory Diseases
*Hypertension/metabolism
Blood Pressure
Medulla Oblongata/metabolism
*Microbiota
Acetates/pharmacology

@article {pmid38632506,
year = {2024},
author = {Alkathiry, HA and Alghamdi, SQ and Sinha, A and Margos, G and Stekolnikov, AA and Alagaili, AN and Darby, AC and Makepeace, BL and Khoo, JJ},
title = {Microbiome and mitogenomics of the chigger mite Pentidionis agamae: potential role as an Orientia vector and associations with divergent clades of Wolbachia and Borrelia.},
journal = {BMC genomics},
volume = {25},
number = {1},
pages = {380},
pmid = {38632506},
issn = {1471-2164},
mesh = {Animals ; *Scrub Typhus/epidemiology/microbiology ; *Trombiculidae/genetics/microbiology ; *Wolbachia/genetics ; Phylogeny ; *Borrelia/genetics ; Multilocus Sequence Typing ; RNA, Ribosomal, 16S/genetics ; Saudi Arabia ; *Orientia tsutsugamushi/genetics ; Rodentia/genetics ; DNA ; *Microbiota ; Orientia ; },
abstract = {BACKGROUND: Trombiculid mites are globally distributed, highly diverse arachnids that largely lack molecular resources such as whole mitogenomes for the elucidation of taxonomic relationships. Trombiculid larvae (chiggers) parasitise vertebrates and can transmit bacteria (Orientia spp.) responsible for scrub typhus, a zoonotic febrile illness. Orientia tsutsugamushi causes most cases of scrub typhus and is endemic to the Asia-Pacific Region, where it is transmitted by Leptotrombidium spp. chiggers. However, in Dubai, Candidatus Orientia chuto was isolated from a case of scrub typhus and is also known to circulate among rodents in Saudi Arabia and Kenya, although its vectors remain poorly defined. In addition to Orientia, chiggers are often infected with other potential pathogens or arthropod-specific endosymbionts, but their significance for trombiculid biology and public health is unclear.

RESULTS: Ten chigger species were collected from rodents in southwestern Saudi Arabia. Chiggers were pooled according to species and screened for Orientia DNA by PCR. Two species (Microtrombicula muhaylensis and Pentidionis agamae) produced positive results for the htrA gene, although Ca. Orientia chuto DNA was confirmed by Sanger sequencing only in P. agamae. Metagenomic sequencing of three pools of P. agamae provided evidence for two other bacterial associates: a spirochaete and a Wolbachia symbiont. Phylogenetic analysis of 16S rRNA and multi-locus sequence typing genes placed the spirochaete in a clade of micromammal-associated Borrelia spp. that are widely-distributed globally with no known vector. For the Wolbachia symbiont, a genome assembly was obtained that allowed phylogenetic localisation in a novel, divergent clade. Cytochrome c oxidase I (COI) barcodes for Saudi Arabian chiggers enabled comparisons with global chigger diversity, revealing several cases of discordance with classical taxonomy. Complete mitogenome assemblies were obtained for the three P. agamae pools and almost 50 SNPs were identified, despite a common geographic origin.

CONCLUSIONS: P. agamae was identified as a potential vector of Ca. Orientia chuto on the Arabian Peninsula. The detection of an unusual Borrelia sp. and a divergent Wolbachia symbiont in P. agamae indicated links with chigger microbiomes in other parts of the world, while COI barcoding and mitogenomic analyses greatly extended our understanding of inter- and intraspecific relationships in trombiculid mites.},
}

Animals
*Scrub Typhus/epidemiology/microbiology
*Trombiculidae/genetics/microbiology
*Wolbachia/genetics
Phylogeny
*Borrelia/genetics
Multilocus Sequence Typing
RNA, Ribosomal, 16S/genetics
Saudi Arabia
*Orientia tsutsugamushi/genetics
Rodentia/genetics
DNA
*Microbiota
Orientia

@article {pmid38632488,
year = {2024},
author = {Pais, N and Ravishanker, N and Rajasekaran, S and Weinstock, G and Tran, DB},
title = {Randomized feature selection based semi-supervised latent Dirichlet allocation for microbiome analysis.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {8855},
pmid = {38632488},
issn = {2045-2322},
mesh = {Humans ; Algorithms ; *Microbiota ; *Gastrointestinal Microbiome ; },
abstract = {Health and disease are fundamentally influenced by microbial communities and their genes (the microbiome). An in-depth analysis of microbiome structure that enables the classification of individuals based on their health can be crucial in enhancing diagnostics and treatment strategies to improve the overall well-being of an individual. In this paper, we present a novel semi-supervised methodology known as Randomized Feature Selection based Latent Dirichlet Allocation (RFSLDA) to study the impact of the gut microbiome on a subject's health status. Since the data in our study consists of fuzzy health labels, which are self-reported, traditional supervised learning approaches may not be suitable. As a first step, based on the similarity between documents in text analysis and gut-microbiome data, we employ Latent Dirichlet Allocation (LDA), a topic modeling approach which uses microbiome counts as features to group subjects into relatively homogeneous clusters, without invoking any knowledge of observed health status (labels) of subjects. We then leverage information from the observed health status of subjects to associate these clusters with the most similar health status making it a semi-supervised approach. Finally, a feature selection technique is incorporated into the model to improve the overall classification performance. The proposed method provides a semi-supervised topic modelling approach that can help handle the high dimensionality of the microbiome data in association studies. Our experiments reveal that our semi-supervised classification algorithm is effective and efficient in terms of high classification accuracy compared to popular supervised learning approaches like SVM and multinomial logistic model. The RFSLDA framework is attractive because it (i) enhances clustering accuracy by identifying key bacteria types as indicators of health status, (ii) identifies key bacteria types within each group based on estimates of the proportion of bacteria types within the groups, and (iii) computes a measure of within-group similarity to identify highly similar subjects in terms of their health status.},
}

Humans
Algorithms
*Microbiota
*Gastrointestinal Microbiome

@article {pmid38632454,
year = {2024},
author = {},
title = {Video game unleashes millions of citizen scientists on microbiome research.},
journal = {Nature biotechnology},
volume = {},
number = {},
pages = {},
pmid = {38632454},
issn = {1546-1696},
}

@article {pmid38632445,
year = {2024},
author = {Marchal, I},
title = {Mapping the landscape of host-microbiome interactions.},
journal = {Nature biotechnology},
volume = {42},
number = {4},
pages = {571},
doi = {10.1038/s41587-024-02219-x},
pmid = {38632445},
issn = {1546-1696},
}