@article {pmid39423213,
year = {2024},
author = {Ma, J and Yang, X and He, J},
title = {Comprehensive gut microbiota composition and microbial interactions among the three age groups.},
journal = {PloS one},
volume = {19},
number = {10},
pages = {e0305583},
pmid = {39423213},
issn = {1932-6203},
mesh = {Humans ; *Gastrointestinal Microbiome ; Aged ; Aged, 80 and over ; Adult ; Middle Aged ; Male ; Aging ; Young Adult ; Microbial Interactions ; Female ; Bacteria/genetics/classification ; Age Factors ; Archaea/genetics ; },
abstract = {There is a growing interest in studying the microbiota associated with aging by integrating multiple longevity researches while minimizing the influence of confounding factors. Here, we reprocessed metagenomic sequencing data from four different aging research studies and evaluated potential confounding factors in order to minimize the batch effect. Subsequently, we detected the diversity and abundance of the gut microbiome in three different age cohorts. Out of 1053 different bacteria species, only four showed substantial depletion across different age groups: Ligilactobacillus ruminis, Turicibacter sp. H121, Blautia massiliensis, and Anaerostipes hadrus. Archaea accumulated more in young individuals compared to elderly and centenarians. Candida albicans was more prevalent in centenarians, but Nakaseomyces glabratus (also known as Candida glabrata) was more common in elderly adults. Shuimuvirus IME207 showed a significant increase in centenarians compared to both control groups. In addition, we utilized a Fisher's exact test to investigate topological properties of differentially abundant microbiota in the co-occurrence network of each age group. Microbial signatures specific to different age stages were identified based on the condition: the reads showing differential abundance were higher compared to the other age groups. Lastly, we selected Methanosarcina sp. Kolksee for the Y group, Prevotella copri for the E group and Shuimuvirus IME207 for the C group as representatives of age-related characteristics to study how their interactions change during the aging process. Our results provide crucial insights into the gut microbiome's ecological dynamics in relation to the aging process.},
}

Humans
*Gastrointestinal Microbiome
Aged
Aged, 80 and over
Adult
Middle Aged
Male
Aging
Young Adult
Microbial Interactions
Female
Bacteria/genetics/classification
Age Factors
Archaea/genetics

@article {pmid39422655,
year = {2024},
author = {Kumar, A and Quraishi, MN and Al-Hassi, HO and Elasrag, M and Segal, JP and Jain, M and Steed, H and Butterworth, J and Farmer, A and Mclaughlin, J and Beggs, AD and Brookes, MJ},
title = {The Effect of Colesevelam on the Microbiome in Postoperative Crohn's Disease.},
journal = {Inflammatory bowel diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/ibd/izae230},
pmid = {39422655},
issn = {1536-4844},
support = {//Bowel and Cancer Research/ ; },
abstract = {BACKGROUND: While surgery plays a pivotal role in the management of ileal Crohn's disease, the risk of endoscopic recurrence following an ileocaecal resection can be greater than 65% within 12 months of surgery. More than 90% of patients with Crohn's disease have a concomitant diagnosis of bile acid diarrhea following an ileal resection. This pilot study aimed to assess whether the use of bile acid sequestrants in patients with Crohn's disease who have undergone a primary terminal ileal resection with concomitant bile acid diarrhea can alter the microbiome and prevent disease recurrence.

METHODS: Patients with Crohn's disease who underwent a primary terminal ileal resection and had symptoms of diarrhea within 1-3 months of surgery underwent 75SeHCAT testing for bile acid diarrhea. If positive (75SeHCAT ≤ 15%), patients were treated with colesevelam and stool samples were collected at 4 weeks, 8 weeks, and 6-12 months posttreatment. If negative (75SeHCAT > 15%), treatment was not given and were reviewed in the clinic as per local guidelines. All patients underwent a 6-12 month postoperative colonoscopy where further stool samples and mucosal biopsies were taken. Disease activity was established using the endoscopic Rutgeert's score, with disease remission defined as Rutgeert's score
RESULTS: A total of 14 patients who completed the study, 10 of whom had a 75SeHCAT positive diagnosis of bile acid diarrhea and were started on treatment with colesevelam. Four patients did not require treatment as 3 were asymptomatic and 1 had a negative 75SeHCAT scan. Three of the fourteen patients had disease recurrence at their 6-12 month postoperative colonoscopy assessment, of which 1 patient was taking colesevelam and 2 patients were not taking colesevelam. A total of 44 fecal samples and 44 mucosal biopsies underwent 16S ribosomal RNA gene analysis to assess α/β-diversity and microbial composition. In the colesevelam treated patients there was no significant difference in α/β-diversity pre- and posttreatment. Pretreatment, the 3 most abundant bacterial classes in all patients were Bacteroidia, Clostridia, and Gammaproteobacteria. Following 6-12 months of treatment, out of the 9 patients on colesevelam, 5/9 (55.6%) had a reduction in Bacteroidia, 9/9 (100%) had an increase in Clostridia, and 7/9 (77.8%) had a reduction in Gammaproteobacteria. Of the 2 patients not given colesevelam, one showed a reduction in Bacteroidia, increase in Clostridia and a reduction in Gammaproteobacteria.

CONCLUSIONS: This small pilot study demonstrated that patients who were given colesevelam, were more likely to be in disease remission at their 6-12 months colonoscopy review compared with those not treated. Furthermore, treatment with colesevelam may have a role in altering the microbiome to help maintain remission states in postoperative Crohn's disease. Larger mechanistic studies are now needed to confirm these findings and demonstrate statistical significance as well as investigate whether this benefit may be present even in those patients with 75SeHCAT negative disease.},
}

@article {pmid39422492,
year = {2024},
author = {Lu, F and Huang, T and Chen, R and Yin, H},
title = {Multi-omics analysis reveals the interplay between pulmonary microbiome and host in immunocompromised patients with sepsis-induced acute lung injury.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0142424},
doi = {10.1128/spectrum.01424-24},
pmid = {39422492},
issn = {2165-0497},
abstract = {UNLABELLED: The mechanisms behind the high inflammatory state and immunocompromise in severe sepsis remain unclear. While microbiota's role in immune regulation is known, the impact of pulmonary microbiota on sepsis progression is not fully understood. This study aims to investigate pulmonary microbial characteristics in septic patients and their relationship with host immune-related genes and clinical features. Fifty-four sepsis patients were divided into the immunocompromised host (ICH) group (n = 18) and the control group (n = 36). Bronchoalveolar lavage fluid (BALF) was analyzed using metagenomic next-generation sequencing (mNGS) to assess the pulmonary microbiome, and transcriptomic sequencing evaluated host gene expression. The pulmonary microbiota network in the ICH group showed notable alterations. Symbiotic bacteria like Streptococcus salivarius and Streptococcus oralis were key taxa in the control group. In contrast, opportunistic pathogens such as Campylobacter concisus and Prevotella melaninogenica, typically linked to infections in various body sites, dominated in the ICH group. Transcriptomic analysis revealed differential genes between the two groups. The downregulated differential genes in the ICH group were primarily enriched in pathways related to T-cell activation and the Type I interferon signaling pathway, both crucial for the immune system. Further correlation analysis identified significant associations between certain microbes and host genes, as well as clinical indicators, particularly with species like Campylobacter concisus, Streptococcus salivarius, Streptococcus oralis, and several species of Veillonella. These findings suggest that alterations in the pulmonary microbiome, especially the presence of opportunistic pathogens, may contribute to immune dysregulation in immunocompromised septic patients, warranting further research to explore causal relationships.

IMPORTANCE: Recent research has substantiated the significant role of microbiota in immune regulation, which could influence high inflammatory state and immunocompromise in patients with severe sepsis, as well as provide new opportunities for acute lung injury induced by sepsis diagnosis and treatment. Our study identified some potential critical microbes (Campylobacter concisus and several species of Veillonella), which were correlated with immune-related genes and might be the novel target to regulate immunotherapy in sepsis.},
}

@article {pmid39421556,
year = {2024},
author = {Ren, W and Zhang, L and Tondre, B and Wang, X and Xu, T},
title = {The rootstock genotype shapes the diversity of pecan (Carya illinoinensis) rhizosphere microbial community.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1461685},
pmid = {39421556},
issn = {1664-302X},
abstract = {Pecans (Carya illinoinensis), one of the most valuable native North American nut crops, are commonly propagated through grafting to preserve the desired characteristics from parent trees. Since successful cultivation of pecan trees relies on the interplay among scion varieties, rootstocks, and soil conditions, this study investigated the microbial change to communities in the soils and roots of southern (87MX5-1.7) and northern (Peruque) rootstocks in a rootstock test orchard. Both grafted with the 'Pawnee' scion cultivar. Bacterial 16S ribosomal RNA and fungal ITS were amplified from both roots and rhizosphere soils of the two 10-year-grafted trees, then sequenced and annotated into trophic and nutrient-related groups to characterize the rhizosphere microbiota. The Peruque roots had a higher relative abundance of saprotroph fungi, while 87MX5-1.7 exhibited higher levels of symbiotroph fungi and nitrogen fixation-related bacteria. Among them, the presence of symbiotroph fungi, particularly ectomycorrhizal fungi, notably differed between these two rootstocks, with a significantly higher presence observed in the root of 87MX5-1.7 compared to Peruque. This variation likely leads to divergent pathways of nutrient translocation: Peruque was in favor of multiple fungi (Russula and Inocybe) to gain nutrition, while 87MX5-1.7 preferred a specific domain of fungi (Tuber) and nitrogen fixation-related bacteria (Bradyrhizobia) to form beneficial symbiosis. Moreover, the presence of pathogens suggested a potential risk of Fusarium patch and snow molds in 87MX5-1.7, while canker and black foot disease pose threats in Peruque. The findings of this study suggest that rootstocks from different origins shape rhizosphere microbes differently, potentially affecting nutrient uptake and nut yield. Exploring rootstock-microbe combinations could provide insights into optimizing scion growth and ultimately increasing nut yield. By understanding how different rootstock-microbe interactions influence pecan tree development, growers can strategically select combinations that promote beneficial symbiotic relationships, enhancing nutrient uptake, disease resistance, and overall tree vigor.},
}

@article {pmid39421460,
year = {2024},
author = {Gopinath, D and Pandiar, D and Li, Z and Panda, S},
title = {Rodent models for oral microbiome research: considerations and challenges- a mini review.},
journal = {Frontiers in oral health},
volume = {5},
number = {},
pages = {1439091},
pmid = {39421460},
issn = {2673-4842},
abstract = {Rodent models have been commonly employed in oral microbiota research to investigate the relationship between bacteria and oral disease. Nevertheless, to apply the knowledge acquired from studies conducted on rodents to a human context, it is crucial to consider the significant spatial and temporal parallels and differences between the oral microbiota of mice and humans. Initially, we outline the comparative physiology and microbiology of the oral cavity of rodents and humans. Additionally, we highlight the strong correlation between the oral microbiome of rodents and genetic makeup, which is influenced by factors including vendor, husbandry practices, and environmental conditions. All of these factors potentially impact the replicability of studies on rodent microbiota and the resulting conclusions. Next, we direct our attention toward the diversity in the microbiome within mice models of disease and highlight the diversity that may potentially affect the characteristics of diseases and, in turn, alter the ability to replicate research findings and apply them to real-world situations. Furthermore, we explore the practicality of oral microbial models for complex oral microbial diseases in future investigations by examining the concept of gnotobiotic and germ-free mouse models. Finally, we stress the importance of investigating suitable techniques for characterizing and managing genetically modified organisms. Future research should consider these aspects to improve oral microbiome research's translational potential.},
}

@article {pmid39421302,
year = {2024},
author = {Xin, Y and Peng, G and Song, W and Zhou, X and Huang, X and Cao, X},
title = {Gut microbiota as a prognostic biomarker for unresectable hepatocellular carcinoma treated with anti-PD-1 therapy.},
journal = {Frontiers in genetics},
volume = {15},
number = {},
pages = {1366131},
pmid = {39421302},
issn = {1664-8021},
abstract = {OBJECTIVE: To investigate the relationship between the gut microbiome and the response to anti-PD-1-based combination therapy in unresectable hepatocellular carcinoma (HCC). We aimed to identify potential non-invasive biomarkers and new strategies to modulate immunotherapy in HCC.

METHODS: In this study, fresh stool samples and clinical data were collected from unresectable HCC patients treated with anti-PD-1-based combination therapy at the Cancer Hospital of the Chinese Academy of Medical Sciences between January 2020 and December 2021. The patients were divided into two groups based on their response to treatment: the treatment responder group (R group) and the treatment non-responder group (NR group). The composition and diversity of the gut microbiome were bioinformatically analyzed by using the Whole Genome Shotgun strategy, including taxonomic composition analysis, Alpha diversity analysis, Beta diversity analysis, and differentially enriched bacterial taxa analysis. Differentially enriched bacterial taxa between R and NR groups were identified based on the magnitude of the linear discriminant analysis effect size (LEfSe) and analyzed for their impact on the survival of the patient.

RESULTS: A total of 45 eligible patients with unresectable HCC treated with anti-PD-1-based combination therapy participated in this study. The gut microbiological composition and Alpha diversity of patients were not statistically different, but there was a statistically significant difference in Beta diversity between the R and NR groups. (PERMANOVA tests, P = 0.006). We further identified 56 enriched bacterial taxa in the R group and 44 enriched bacterial taxa in the NR group based on the LEfSe analysis (LDA >2.66, P< 0.05). Patients with a high abundance of Collinsella genus, Ruminococcus_AM4211, and Ruminococcus_AF25_28AC had a longer median PFS and median OS compared to those with low abundance (P < 0.05). On the contrary, the median PFS and OS of patients with a high abundance of Bacteroides_AF20_13LB and Veillonella_atypica were significantly shorter than those of patients with low abundance (P < 0.05). The multivariate analysis showed that the abundance of Bacteroides_AF20_13LB and Ruminococcus_ AF25_28AC was independent related factors for PFS, and the abundance of Bacteroides_AF20_13LB was an independent related factor of OS.

CONCLUSION: The enrichment of specific gut microbiota affected clinical efficacy and survival benefits in HCC treated with anti-PD-1 therapy and may be a promising non-invasive gut microbial biomarker and a new strategy for modulating immunotherapy in HCC.},
}

@article {pmid39421256,
year = {2024},
author = {Badr, K and He, QP and Wang, J},
title = {Probing interspecies metabolic interactions within a synthetic binary microbiome using genome-scale modeling.},
journal = {Microbiome research reports},
volume = {3},
number = {3},
pages = {31},
pmid = {39421256},
issn = {2771-5965},
abstract = {Aim: Metabolic interactions within a microbial community play a key role in determining the structure, function, and composition of the community. However, due to the complexity and intractability of natural microbiomes, limited knowledge is available on interspecies interactions within a community. In this work, using a binary synthetic microbiome, a methanotroph-photoautotroph (M-P) coculture, as the model system, we examined different genome-scale metabolic modeling (GEM) approaches to gain a better understanding of the metabolic interactions within the coculture, how they contribute to the enhanced growth observed in the coculture, and how they evolve over time. Methods: Using batch growth data of the model M-P coculture, we compared three GEM approaches for microbial communities. Two of the methods are existing approaches: SteadyCom, a steady state GEM, and dynamic flux balance analysis (DFBA) Lab, a dynamic GEM. We also proposed an improved dynamic GEM approach, DynamiCom, for the M-P coculture. Results: SteadyCom can predict the metabolic interactions within the coculture but not their dynamic evolutions; DFBA Lab can predict the dynamics of the coculture but cannot identify interspecies interactions. DynamiCom was able to identify the cross-fed metabolite within the coculture, as well as predict the evolution of the interspecies interactions over time. Conclusion: A new dynamic GEM approach, DynamiCom, was developed for a model M-P coculture. Constrained by the predictions from a validated kinetic model, DynamiCom consistently predicted the top metabolites being exchanged in the M-P coculture, as well as the establishment of the mutualistic N-exchange between the methanotroph and cyanobacteria. The interspecies interactions and their dynamic evolution predicted by DynamiCom are supported by ample evidence in the literature on methanotroph, cyanobacteria, and other cyanobacteria-heterotroph cocultures.},
}

@article {pmid39421252,
year = {2024},
author = {Klaassens, ES and Baak, ML and Mekkes, NJ and Bongoni, R and Schaubeck, M},
title = {Effect of protein modification in synbiotic infant formula on probiotic metabolic activity and bacterial composition in an infant gut-model.},
journal = {Microbiome research reports},
volume = {3},
number = {3},
pages = {38},
pmid = {39421252},
issn = {2771-5965},
abstract = {Aim: Microbial colonization of the neonatal gut is pivotal in priming the infant's immune system. Human milk (HM) is the best nutrition for infants and supports the development of the microbiota due to prebiotic compounds and probiotic microorganisms. When exclusive breastfeeding is not possible, infant formula (IF) with probiotics is a strategy to support the infant's microbiome development. However, knowledge about the effects of the infant gut microbiota and different compounds in IF on individual probiotic strains is limited, as strain-level detection in a complex ecosystem is challenging. The aim of the present study was to show the effects of IF with different protein forms on the metabolic activity of two probiotic strains isolated from HM in a complex ecosystem. Methods: By using an ex-vivo infant gut model containing infant donor-microbiota, the effects of IF with either intact or extensively hydrolyzed protein on the metabolic activity of the donor microbiota, as well as two probiotic strains [Limosilactobacillus fermentum (L. fermentum) CECT 5716 (Lf) and Bifidobacterium breve (B. breve) DSM 32583 (Bb)], were analyzed. A new bioinformatic pipeline combined with a specific infant microbiome database was used to explore shotgun metagenome datasets (1200 Megabases) for taxonomic identification and strain-level tracking. Results: Both protein forms (i.e., intact or extensively hydrolyzed protein) in IF supported infant gut microbial metabolic activity equally, as evidenced by similar levels of short-chain fatty acids (SCFAs). Interestingly, gut microbial metabolic activity was found to be differently activated in a strain-dependent manner. Taxonomic profiling of the microbiome at the strain level enabled monitoring of the prevalence and abundance of both probiotic strains, even in a complex ecosystem. Conclusion: Food matrix and host microbiota interactions should be considered when evaluating strain-specific probiotic effects in the future.},
}

@article {pmid39421251,
year = {2024},
author = {Cattero, V and Roussel, C and Lessard-Lord, J and Roy, D and Desjardins, Y},
title = {Supplementation with a cranberry extract favors the establishment of butyrogenic guilds in the human fermentation SHIME system.},
journal = {Microbiome research reports},
volume = {3},
number = {3},
pages = {34},
pmid = {39421251},
issn = {2771-5965},
abstract = {Background: Proanthocyanidins (PAC) and oligosaccharides from cranberry exhibit multiple bioactive health properties and persist intact in the colon post-ingestion. They display a complex bidirectional interaction with the microbiome, which varies based on both time and specific regions of the gut; the nature of this interaction remains inadequately understood. Therefore, we aimed to investigate the impact of cranberry extract on gut microbiota ecology and function. Methods: We studied the effect of a cranberry extract on six healthy participants over a two-week supplementation period using the ex vivo artificial fermentation system TWIN-M-SHIME to replicate luminal and mucosal niches of the ascending and transverse colon. Results: Our findings revealed a significant influence of cranberry extract supplementation on the gut microbiota ecology under ex vivo conditions, leading to a considerable change in bacterial metabolism. Specifically, Bifidobacterium adolescentis (B. adolescentis) flourished in the mucus of the ascending colon, accompanied by a reduced adhesion of Proteobacteria. The overall bacterial metabolism shifted from acetate to propionate and, notably, butyrate production following PAC supplementation. Although there were variations in microbiota modulation among the six donors, the butyrogenic effect induced by the supplementation remained consistent across all individuals. This metabolic shift was associated with a rise in the relative abundance of several short-chain fatty acid (SCFA)-producing bacterial genera and the formation of a consortium of key butyrogenic bacteria in the mucus of the transverse colon. Conclusions: These observations suggest that cranberry extract supplementation has the potential to modulate the gut microbiota in a manner that may promote overall gut health.},
}

@article {pmid39421249,
year = {2024},
author = {Mueller, KD and Panzetta, ME and Davey, L and McCann, JR and Rawls, JF and Flores, GE and Valdivia, RH},
title = {Pangenomic analysis identifies correlations between Akkermansia species and subspecies and human health outcomes.},
journal = {Microbiome research reports},
volume = {3},
number = {3},
pages = {33},
pmid = {39421249},
issn = {2771-5965},
abstract = {Aim: Akkermansia are common members of the human gastrointestinal microbiota. The prevalence of these mucophilic bacteria, especially Akkermansia muciniphila (A. muciniphila), correlates with immunological and metabolic health. The genus Akkermansia in humans includes species with significantly larger genomes than A. muciniphila, leading us to postulate that this added genetic content may influence how they impact human metabolic and immunological health. Methods: We conducted a pangenomic analysis of 234 Akkermansia complete or near-complete genomes. We also used high-resolution species and subspecies assignments to reanalyze publicly available metagenomic datasets to determine if there are relationships between Akkermansia species and A. muciniphila clades with various disease outcomes. Results: Analysis of genome-wide average nucleotide identity, 16S rRNA gene identity, conservation of core Akkermansia genes, and analysis of the fatty acid composition of representative isolates support the partitioning of the genus Akkermansia into several species. In addition, A. muciniphila sensu stricto, the most prevalent Akkermansia species in humans, should be subdivided into two subspecies. For a pediatric cohort, we observed species-specific correlations between Akkermansia abundance with baseline obesity or after various interventions. For inflammatory bowel disease cohorts, we identified a decreased abundance of Akkermansia in patients with ulcerative colitis or Crohn's disease, which was species and subspecies-dependent. In patients undergoing immune checkpoint inhibitor therapies for non-small cell lung carcinoma, we observed a significant association between one A. muciniphila subspecies and survival outcomes. Conclusion: Our findings suggest that the prevalence of specific Akkermansia species and/or subspecies can be crucial in evaluating their association with human health, particularly in different disease contexts, and is an important consideration for their use as probiotics.},
}

@article {pmid39421247,
year = {2024},
author = {Wang, A and Fekete, EEF and Creskey, M and Cheng, K and Ning, Z and Pfeifle, A and Li, X and Figeys, D and Zhang, X},
title = {Assessing fecal metaproteomics workflow and small protein recovery using DDA and DIA PASEF mass spectrometry.},
journal = {Microbiome research reports},
volume = {3},
number = {3},
pages = {39},
pmid = {39421247},
issn = {2771-5965},
abstract = {Aim: This study aims to evaluate the impact of experimental workflow on fecal metaproteomic observations, including the recovery of small and antimicrobial proteins often overlooked in metaproteomic studies. The overarching goal is to provide guidance for optimized metaproteomic experimental design, considering the emerging significance of the gut microbiome in human health, disease, and therapeutic interventions. Methods: Mouse feces were utilized as the experimental model. Fecal sample pre-processing methods (differential centrifugation and non-differential centrifugation), protein digestion techniques (in-solution and filter-aided), data acquisition modes (data-dependent and data-independent, or DDA and DIA) when combined with parallel accumulation-serial fragmentation (PASEF), and different bioinformatic workflows were assessed. Results: We showed that, in DIA-PASEF metaproteomics, the library-free search using protein sequence database generated from DDA-PASEF data achieved better identifications than using the generated spectral library. Compared to DDA, DIA-PASEF identified more microbial peptides, quantified more proteins with fewer missing values, and recovered more small antimicrobial proteins. We did not observe any obvious impacts of protein digestion methods on both taxonomic and functional profiles. However, differential centrifugation decreased the recovery of small and antimicrobial proteins, biased the taxonomic observation with a marked overestimation of Muribaculum species, and altered the measured functional compositions of metaproteome. Conclusion: This study underscores the critical impact of experimental choices on metaproteomic outcomes and sheds light on the potential biases introduced at different stages of the workflow. The comprehensive methodological comparisons serve as a valuable guide for researchers aiming to enhance the accuracy and completeness of metaproteomic analyses.},
}

@article {pmid39421246,
year = {2024},
author = {Boyajian, JL and Islam, P and Abosalha, A and Schaly, S and Thareja, R and Kassab, A and Arora, K and Santos, M and Shum-Tim, C and Prakash, S},
title = {Probiotics, prebiotics, synbiotics and other microbiome-based innovative therapeutics to mitigate obesity and enhance longevity via the gut-brain axis.},
journal = {Microbiome research reports},
volume = {3},
number = {3},
pages = {29},
pmid = {39421246},
issn = {2771-5965},
abstract = {The global prevalence of obesity currently exceeds 1 billion people and is accompanied by an increase in the aging population. Obesity and aging share many hallmarks and are leading risk factors for cardiometabolic disease and premature death. Current anti-obesity and pro-longevity pharmacotherapies are limited by side effects, warranting the development of novel therapies. The gut microbiota plays a major role in human health and disease, with a dysbiotic composition evident in obese and aged individuals. The bidirectional communication system between the gut and the central nervous system, known as the gut-brain axis, may link obesity to unhealthy aging. Modulating the gut with microbiome-targeted therapies, such as biotics, is a novel strategy to treat and/or manage obesity and promote longevity. Biotics represent material derived from living or once-living organisms, many of which have therapeutic effects. Pre-, pro-, syn- and post-biotics may beneficially modulate gut microbial composition and function to improve obesity and the aging process. However, the investigation of biotics as next-generation therapeutics has only just begun. Further research is needed to identify therapeutic biotics and understand their mechanisms of action. Investigating the function of the gut-brain axis in obesity and aging may lead to novel therapeutic strategies for obese, aged and comorbid (e.g., sarcopenic obese) patient populations. This review discusses the interrelationship between obesity and aging, with a particular emphasis on the gut microbiome, and presents biotics as novel therapeutic agents for obesity, aging and related disease states.},
}

@article {pmid39421242,
year = {2024},
author = {Liu, L and Davidorf, B and Dong, P and Peng, A and Song, Q and He, Z},
title = {Decoding the mosaic of inflammatory bowel disease: Illuminating insights with single-cell RNA technology.},
journal = {Computational and structural biotechnology journal},
volume = {23},
number = {},
pages = {2911-2923},
pmid = {39421242},
issn = {2001-0370},
abstract = {Inflammatory bowel diseases (IBD), comprising ulcerative colitis (UC) and Crohn's disease (CD), are complex chronic inflammatory intestinal conditions with a multifaceted pathology, influenced by immune dysregulation and genetic susceptibility. The challenges in understanding IBD mechanisms and implementing precision medicine include deciphering the contributions of individual immune and non-immune cell populations, pinpointing specific dysregulated genes and pathways, developing predictive models for treatment response, and advancing molecular technologies. Single-cell RNA sequencing (scRNA-seq) has emerged as a powerful tool to address these challenges, offering comprehensive transcriptome profiles of various cell types at the individual cell level in IBD patients, overcoming limitations of bulk RNA sequencing. Additionally, single-cell proteomics analysis, T-cell receptor repertoire analysis, and epigenetic profiling provide a comprehensive view of IBD pathogenesis and personalized therapy. This review summarizes significant advancements in single-cell sequencing technologies for enhancing our understanding of IBD, covering pathogenesis, diagnosis, treatment, and prognosis. Furthermore, we discuss the challenges that persist in the context of IBD research, including the need for longitudinal studies, integration of multiple single-cell and spatial transcriptomics technologies, and the potential of microbial single-cell RNA-seq to shed light on the role of the gut microbiome in IBD.},
}

@article {pmid39420944,
year = {2024},
author = {Chen, X and Zou, T and Ding, G and Jiang, S},
title = {Findings and methodologies in oral phageome research: a systematic review.},
journal = {Journal of oral microbiology},
volume = {16},
number = {1},
pages = {2417099},
pmid = {39420944},
issn = {2000-2297},
abstract = {BACKGROUND: The oral microbiome serves as both an indicator and a mediator of oral health. Evidence indicates that bacteriophages (phages) are widely present in the oral microbiome and exhibit diverse classifications and interactions with human cells and other microbes. These phages constitute the oral phageome, which potentially exerts significant yet unexplored effects on the interplay between oral and general health.

METHODS: Three databases (PubMed/MEDLINE, Embase and Scopus) were searched for metagenomic analyses that investigated the oral phageome. Eligible studies were synthesized based on their methodological approaches and findings.

RESULTS: A total of 14 articles were included in this systematic review. Among the 14 articles included, there were six studies that discussed disease-related alterations, along with a discursive examination of additional variables such as sampling niches, external interventions and methodologies. The phages that infect Streptococcus Actinomyces Haemophilus, and Veillonella have been discovered to be associated with chronic periodontitis, caries, and pancreatic ductal carcinoma.

CONCLUSIONS: This systematic review focuses on findings and methodologies in oral phageome studies, which were conducted using highly heterogeneous methodologies that explored the oral phageome in multiple directions while placing constraints on quantitative statistics. Combining different kinds of sample types, utilizing the characteristics of different methods, involving both DNA and RNA phages, and differentiating lysogenic and lytic phages should be the distinction of further studies.},
}

@article {pmid39420635,
year = {2024},
author = {Li, C and Sun, L and Jia, Z and Tang, Y and Liu, X and Zhang, J and Müller, C},
title = {Microbial Inoculants Drive Changes in Soil and Plant Microbiomes and Improve Plant Functions in Abandoned Mine Restoration.},
journal = {Plant, cell & environment},
volume = {},
number = {},
pages = {},
doi = {10.1111/pce.15215},
pmid = {39420635},
issn = {1365-3040},
support = {//Jinchi Zhang acknowledges the funding support from Jiangsu Science and Technology Plan Project (BE2022420); the Innovation and Promotion of Forestry Science and Technology Program of Jiangsu Province (LYKJ[2021]30); the Scientific Research Project of Baishanzu National Park (2021ZDLY01); and the Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD). Chong Li is grateful for the partial financial support from the Postgraduate Research and Practice Innovation Program of Jiangsu Province (KYCX21_0915), and the China Scholarship Council (202108320300)./ ; },
abstract = {The application of microbial inoculants holds promise for the sustainable restoration of abandoned mine sites by affecting soil nutrients and microbial communities. However, the responses of plant microbial communities to microbial inoculants in mine restoration remain largely unknown. To bridge this knowledge gap, we conducted a 4-year field experiment at an abandoned carbonate mine site to assess the impacts of microbial inoculants on the soil-plant microbiome. Our findings revealed that microbial inoculants significantly changed roots, fine root bacterial and fungal communities. Further, no significant correlations were observed between the soil-plant nutrient content (Z-score) and microbial alpha diversity. However, a significantly positive correlation was found between the relative abundance of the keystone ecological cluster (Module #1) and soil-plant nutrient content. The application of microbial inoculants also increased complexity, albeit decreased stability of plant microbiome networks, alongside a reduction in stochastic assembly. Conversely, they decreased the complexity but increased the stability of soil microbiome networks, accompanied by an increase in stochastic assembly. Notably, the number of specifically enriched microbiome functional traits of roots and root nodules under the microbial inoculant treatments surpassed that of the control. In summary, our findings underscored the potential of microbial inoculants to enhance soil-plant functionality at abandoned mine restoration sites.},
}

@article {pmid39420603,
year = {2024},
author = {Poupard, L and Page, G and Thoreau, V and Kaouah, Z},
title = {Relationships between Gut Microbiota and Autism Spectrum Disorders: Development and Treatment.},
journal = {Clinical psychopharmacology and neuroscience : the official scientific journal of the Korean College of Neuropsychopharmacology},
volume = {22},
number = {4},
pages = {554-564},
pmid = {39420603},
issn = {1738-1088},
abstract = {Many studies have demonstrated the impact of intestinal microbiota on normal brain development. Moreover, the gut microbiota (GM) is impacted by multiple endogenous and environmental factors that may promote gut dysbiosis (GD). An increasing number of studies are investigating the possible role of the GD in the development of neurological and behavioral disorders. For autism spectrum disorders (ASD), specific intestinal bacterial signatures have been identified, knowing that gastrointestinal symptoms are frequently found in ASD. In this review, the peri and post-natal factors modulating the GM are described and the specific gut bacterial signature of ASD children is detailed. Through bidirectional communication between the GM and the brain, several mechanisms are involved in the development of ASD, such as cytokine-mediated neuroinflammation and decreased production of neuroprotective factors such as short-chain fatty acids by the GM. Imbalance of certain neurotransmitters such as serotonin or gamma-aminobutyric acid could also play a role in these gut-brain interactions. Some studies show that this GD in ASD is partly reversible by treatment with pre- and probiotics, or fecal microbiota transplantation with promising results. However, certain limitations have been raised, in particular concerning the short duration of treatment, the small sample sizes and the diversity of protocols. The development of standardized therapeutics acting on GD in large cohort could rescue the gastrointestinal symptoms and behavioral impairments, as well as patient management.},
}

@article {pmid39420595,
year = {2024},
author = {Xing, H and Zhang, Y and Li, R and Ruzicka, HM and Hain, C and Andersson, J and Bozdogan, A and Henkel, M and Knippschild, U and Hasler, R and Kleber, C and Knoll, W and Kissmann, AK and Rosenau, F},
title = {A Blautia producta specific gFET-based aptasensor for quantitative monitoring of microbiome quality.},
journal = {Nanoscale horizons},
volume = {},
number = {},
pages = {},
doi = {10.1039/d4nh00281d},
pmid = {39420595},
issn = {2055-6764},
abstract = {The use of health-relevant bacteria originating from human microbiomes for the control or therapy of diseases, including neurodegenerative disorders or diabetes, is currently gaining increasing importance in medicine. Directed and successful engineering of microbiomes via probiotic supplementation requires subtle, precise as well as, more importantly, easy, fast and convenient monitoring of its success, e.g., in patients' gut. Based on a previously described polyclonal SELEX aptamer library evolved against the human gut bacterium Blautia producta, we finally isolated three individual aptamers that proved their performance concerning affinity, specificity and robustness in reliably labeling the target bacterium and in combination with "contaminating" control bacteria. Using biofunctionalization molecules on gFETs, we could specifically quantify 10[1]-10[6] cells per mL, retrace their number in mixtures and determine aptamer Kd-values around 2 nM. These measurements were possible even in the context of a real human stool sample. Our results qualify gFETs in combination with BL2, BL7 and BL8 aptamers as a promising foundation for the construction of respective sensing devices, which will open new avenues towards developing an intended monitoring technique for probiotic therapy and microbiome engineering approaches.},
}

@article {pmid39420474,
year = {2024},
author = {Dilhari, A and Campbell, PM and Munasinghe, A and Brown, H and Kaluarachchi, TDJ and Gunasekara, C and Pathirage, S and Fernando, N and Weerasekara, D and Humphreys, GJ and McBain, AJ and Weerasekera, M},
title = {Biofilms and Microbiome Profiles in Chronic Wounds: Links to Antibiotic Use and Wound Severity in a Sri Lankan Cohort.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxae262},
pmid = {39420474},
issn = {1365-2672},
abstract = {AIMS: We have characterized the microbiome of infected chronic diabetic wounds (CDWs), exploring associations with antibiotic use and wound severity in a Sri Lankan cohort.

METHODS AND RESULTS: Fifty CDW patients were enrolled, 38 of whom received antibiotics. Tissue biopsies were analyzed by microbiome profiling, and wounds were graded using the University of Texas Wound Grading System. Biofilm presence was assessed in 20 wounds. The microbiome was largely dominated by Enterobacteriaceae, Pseudomonadaceae, Streptococcaceae, and Corynebacteriaceae. Proteobacteria levels were significantly higher in antibiotic-treated wounds (p = 0.019), with increased Pseudomonas abundance. Wounds were categorized as grade 1 (10), grade 2 (29), and grade 3 (11). Alpha diversity varied by wound grade (p = 0.015), with grade 2 wounds showing the highest diversity and grade 3 the lowest. All 20 tested wounds were biofilm-positive, and community composition varied more in antibiotic-treated wounds (p = 0.004).

CONCLUSIONS: CDW microbiomes were dominated by Enterobacteriaceae and Pseudomonadaceae, with elevated Proteobacteria in antibiotic-treated wounds. Alpha diversity correlated with wound severity, peaking in grade 2 wounds. The high prevalence of biofilms in wounds underscores the need for management of CDWs that address microbial complexity.},
}

@article {pmid39420423,
year = {2024},
author = {Boukadida, C and Peralta-Prado, A and Chávez-Torres, M and Romero-Mora, K and Rincon-Rubio, A and Ávila-Ríos, S and Garrido-Rodríguez, D and Reyes-Terán, G and Pinto-Cardoso, S},
title = {Alterations of the gut microbiome in HIV infection highlight human anelloviruses as potential predictors of immune recovery.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {204},
pmid = {39420423},
issn = {2049-2618},
mesh = {Humans ; *Gastrointestinal Microbiome ; *HIV Infections/virology/immunology/complications ; *Feces/microbiology/virology ; Cross-Sectional Studies ; Male ; Longitudinal Studies ; Adult ; *HIV-1 ; Female ; *Anelloviridae/isolation & purification/genetics ; *Dysbiosis/virology ; Middle Aged ; CD4 Lymphocyte Count ; Bacteriophages/isolation & purification/genetics ; Bacteria/classification/isolation & purification/genetics ; CD4-Positive T-Lymphocytes/immunology ; Virome ; },
abstract = {BACKGROUND: HIV-1 infection is characterized by a massive depletion of mucosal CD4 T cells that triggers a cascade of events ultimately linking gut microbial dysbiosis to HIV-1 disease progression and pathogenesis. The association between HIV infection and the enteric virome composition is less characterized, although viruses are an essential component of the gut ecosystem. Here, we performed a cross-sectional analysis of the fecal viral (eukaryotic viruses and bacteriophages) and bacterial microbiome in people with HIV (PWH) and in HIV-negative individuals. To gain further insight into the association between the gut microbiome composition, HIV-associated immunodeficiency, and immune recovery, we carried out a longitudinal study including 14 PWH who initiated antiretroviral therapy (ART) and were followed for 24 months with samplings performed at baseline (before ART) and at 2, 6, 12, and 24 months post-ART initiation.

RESULTS: Our data revealed a striking expansion in the abundance and prevalence of several human virus genomic sequences (Anelloviridae, Adenoviridae, and Papillomaviridae) in stool samples of PWH with severe immunodeficiency (CD4 < 200). We also noted a decreased abundance of sequences belonging to two plant viruses from the Tobamovirus genus, a reduction in bacterial alpha diversity, and a decrease in Inoviridae bacteriophage sequences. Short-term ART (24 months) was linked to a significant decrease in human Anelloviridae sequences. Remarkably, the detection of Anellovirus sequences at baseline independently predicted poor immune recovery, as did low CD4 T cell counts. The bacterial and bacteriophage populations were unique to each PWH with individualized trajectories; we found no discernable pattern of clustering after 24 months on ART.

CONCLUSION: Advanced HIV-1 infection was associated with marked alterations in the virome composition, in particular a remarkable expansion of human anelloviruses, with a gradual restoration after ART initiation. In addition to CD4 T cell counts, anellovirus sequence detection might be useful to predict and monitor immune recovery. This study confirms data on the bacteriome and expands our knowledge on the viral component of the gut microbiome in HIV-1 infection. Video Abstract.},
}

Humans
*Gastrointestinal Microbiome
*HIV Infections/virology/immunology/complications
*Feces/microbiology/virology
Cross-Sectional Studies
Male
Longitudinal Studies
Adult
*HIV-1
Female
*Anelloviridae/isolation & purification/genetics
*Dysbiosis/virology
Middle Aged
CD4 Lymphocyte Count
Bacteriophages/isolation & purification/genetics
Bacteria/classification/isolation & purification/genetics
CD4-Positive T-Lymphocytes/immunology
Virome

@article {pmid39420420,
year = {2024},
author = {Kasule, GW and Hermans, S and Semugenze, D and Wekiya, E and Nsubuga, J and Mwachan, P and Kabugo, J and Joloba, M and García-Basteiro, AL and Ssengooba, W and , },
title = {Non-sputum-based samples and biomarkers for detection of Mycobacterium tuberculosis: the hope to improve childhood and HIV-associated tuberculosis diagnosis.},
journal = {European journal of medical research},
volume = {29},
number = {1},
pages = {502},
pmid = {39420420},
issn = {2047-783X},
mesh = {Humans ; *Biomarkers/analysis ; *Mycobacterium tuberculosis/isolation & purification ; *HIV Infections/complications/diagnosis ; *Tuberculosis/diagnosis/microbiology ; Child ; Sputum/microbiology ; Saliva/microbiology ; },
abstract = {In 2014, the World Health Organisation (WHO) published target product profiles (TPP) for development of novel tuberculosis (TB) diagnostics. One of the key highlights is the need for point-of-care non-sputum-based tests capable of detecting all forms of TB through identification of characteristic biomarkers or biosignatures. Compared to the limitations associated with sputum-based TB tests, non-sputum samples are easy to collect, non-invasive, with potential to improve TB diagnosis among children and among people living with HIV/AIDS (PLHIV). This review gives an overview of the existing evidence on TB diagnostic studies of non-sputum-based samples collected non-invasively from or through the oral-gastrointestinal tract (GI) and nasal pharynx regions of humans and the biomarkers detected. We further summarized evidence of these biomarkers and sample types from research done in paediatric and PLHIV. The review identified; saliva, cough aerosols, oral swabs, oral wash, dental plaque, tongue swabs, face mask sampling, exhaled breath, and stool, as the non-sputum samples investigated. These biomarkers can be categorized into Deoxyribose Nucleic Acid (DNA), Ribonucleic Acid (RNA), inflammatory, antigen-antibody, volatile and non-volatile compounds, microbiome and microbiota. The biomarkers identified were derived both from the host and pathogen. Similar biomarkers were identified in the general population, children and among PLHIV. These biomarkers have been detected by either already approved simple point of care or sophisticated devices. Differences in methodology and sample types investigated, small sample size of children and PLHIV populations, bias due to confounding factors, were some of the identified challenges in these studies. There is need to conduct larger and standardized multi centre studies to evaluate non-sputum-based biomarker-based tests in children and PLHIV.},
}

Humans
*Biomarkers/analysis
*Mycobacterium tuberculosis/isolation & purification
*HIV Infections/complications/diagnosis
*Tuberculosis/diagnosis/microbiology
Child
Sputum/microbiology
Saliva/microbiology

@article {pmid39420006,
year = {2024},
author = {Dricot, CEMK and Erreygers, I and Cauwenberghs, E and De Paz, J and Spacova, I and Verhoeven, V and Ahannach, S and Lebeer, S},
title = {Riboflavin for women's health and emerging microbiome strategies.},
journal = {NPJ biofilms and microbiomes},
volume = {10},
number = {1},
pages = {107},
pmid = {39420006},
issn = {2055-5008},
support = {Lacto-Be//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; },
mesh = {*Riboflavin/biosynthesis/metabolism ; Humans ; Female ; *Probiotics ; *Microbiota ; *Women's Health ; Lactobacillus/metabolism ; Vagina/microbiology ; Dietary Supplements ; Riboflavin Deficiency ; },
abstract = {Riboflavin (vitamin B2) is an essential water-soluble vitamin that serves as a precursor of flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD). FMN and FAD are coenzymes involved in key enzymatic reactions in energy metabolism, biosynthesis, detoxification and electron scavenging pathways. Riboflavin deficiency is prevalent worldwide and impacts women's health due to riboflavin demands linked to urogenital and reproductive health, hormonal fluctuations during the menstrual cycle, pregnancy, and breastfeeding. Innovative functional foods and nutraceuticals are increasingly developed to meet women's riboflavin needs to supplement dietary sources. An emerging and particularly promising strategy is the administration of riboflavin-producing lactic acid bacteria, combining the health benefits of riboflavin with those of probiotics and in situ riboflavin production. Specific taxa of lactobacilli are of particular interest for women, because of the crucial role of Lactobacillus species in the vagina and the documented health effects of other Lactobacillaceae taxa in the gut and on the skin. In this narrative review, we synthesize the underlying molecular mechanisms and clinical benefits of riboflavin intake for women's health, and evaluate the synergistic potential of riboflavin-producing lactobacilli and other microbiota.},
}

*Riboflavin/biosynthesis/metabolism
Humans
Female
*Probiotics
*Microbiota
*Women's Health
Lactobacillus/metabolism
Vagina/microbiology
Dietary Supplements
Riboflavin Deficiency

@article {pmid39419849,
year = {2024},
author = {Gutierrez, A and Rébufa, C and Farnet Da Silva, AM and Davidson, S and Foli, L and Combet-Blanc, Y and Martinez, M and Christen, P},
title = {Biochemical and microbial characterization of a forest litter-based bio-fertilizer produced in batch culture by fermentation under different initial oxygen concentrations.},
journal = {World journal of microbiology & biotechnology},
volume = {40},
number = {11},
pages = {353},
pmid = {39419849},
issn = {1573-0972},
mesh = {*Oxygen/metabolism/analysis ; *Fermentation ; *Forests ; *Fertilizers/analysis ; *Ethanol/metabolism ; Batch Cell Culture Techniques ; Acetates/metabolism ; Microbiota ; Bacteria/metabolism/classification/isolation & purification ; Fungi/metabolism/isolation & purification ; Carbon Dioxide/metabolism/analysis ; Anaerobiosis ; Hydrogen-Ion Concentration ; },
abstract = {This work focused on the physico-chemical, biochemical and microbiological characterization of a new organic fertilizer based on fermented forest litter (FFL) mixed with agro-industrial by-products, on the culture realized in airtight glass bottle. Under strict anaerobiosis (0% initial oxygen concentration (IOC)), after a 16-day batch culture, the bottle-headspace analysis showed that the specific CO2 production rate was low (0.014 mL/h.g dry matter) compared to those reached under aerobic conditions (e.g. 0.464 mL/h.g dm at 21% IOC). Moreover, the culture displayed a slight fermented fruity odour, mainly due to ethanol and ethyl acetate detected in the headspace (335 µL and 58.6 µL accumulated, respectively). The FFL organic matter degradation followed by infrared spectroscopy and catabolic potential and diversity characterized by BIOLOG[®] EcoPlates were poor and pH dropped to 4.54. The microbiome's metabolism was oriented toward lactic fermentation with medium acidification, enrichment in lactic acid bacteria (LAB), depletion in fungi and absence of pathogens. By increasing IOC from 0 to 21%, the respirometric activity, and the catabolic potential and diversity increased. However, some enterobacteria were detected above 5% IOC. Ethanol and ethyl acetate decreased strongly with IOC, and aromatics and proteins contained in the solid matrix remained in the culture. This study showed the importance of oxygen on the final product. A 2% IOC was found to ensure an optimal balance between LAB development, preservation of functional catabolic diversity and bio-product free of microbial pathogens.},
}

*Oxygen/metabolism/analysis
*Fermentation
*Forests
*Fertilizers/analysis
*Ethanol/metabolism
Batch Cell Culture Techniques
Acetates/metabolism
Microbiota
Bacteria/metabolism/classification/isolation & purification
Fungi/metabolism/isolation & purification
Carbon Dioxide/metabolism/analysis
Anaerobiosis
Hydrogen-Ion Concentration

@article {pmid39419819,
year = {2024},
author = {Nichols, B and Russell, RK and Short, B and Papadopoulou, R and Focht, G and Ijaz, UZ and Walters, TD and Sladek, M and Hansen, R and Mack, DR and Wine, E and Griffiths, AM and Turner, D and Gerasimidis, K},
title = {Gut Microbial Signatures in Pediatric Crohn's Disease Vary According to Disease Activity Measures and Are Influenced by Proxies of Gastrointestinal Transit Time: An ImageKids Study.},
journal = {Inflammatory bowel diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/ibd/izae199},
pmid = {39419819},
issn = {1536-4844},
support = {//Glasgow Children's Hospital Charity/ ; },
abstract = {INTRODUCTION: We investigated relationships between disease activity measures and the gut microbiome in children with Crohn's disease (CD) and how these were confounded by gastrointestinal transit time.

METHODS: Microbiome was profiled (16S rRNA sequencing) in feces from 196 children with CD. Sixty participants also provided samples after 18 months. Mural inflammation (Pediatric Inflammatory Crohn's Magnetic Resonance Enterography Index, PICMI), the simple endoscopic score for CD, and the weighted pediatric Crohn's disease activity index (wPCDAI) were assessed. Fecal calprotectin, plasma C-reactive protein (CRP), and fecal water content (FWC), a proxy of gastrointestinal transit time, were measured too.

RESULTS: Microbiome α diversity, clustering, and differential taxa were related to disease status, but varied remarkably by disease activity measure used. The strongest relationships between microbiome and disease activity status were observed using wPCDAI; fewer or no relationships were seen using more objective measures like PICMI. Taxa predictive of disease activity status were dependent on the disease activity measure used with negligible overlap. Active disease was associated with more pathobionts (eg, Viellonella, Enterobacterales) and fewer fiber-fermenting organisms. The effect FWC had on microbiome superseded the effect of active disease for all disease activity measures, particularly with wPCDAI. Accounting for FWC, the differences in microbial signatures explained by disease activity status were attenuated or lost.

CONCLUSIONS: In CD, microbiome signatures fluctuate depending on the measure used to assess disease severity; several of these signals might be secondary disease effects linked with changes in gut motility in active disease. PICMI appears to be less influenced when studying relationships between microbiome and mural inflammation in CD.},
}

@article {pmid39419784,
year = {2024},
author = {Roman, A and Koenraadt, CJM and Raymond, B},
title = {Asaia spp. Accelerate development of the yellow fever mosquito, Aedes aegypti, via interactions with the vertically transmitted larval microbiome.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxae261},
pmid = {39419784},
issn = {1365-2672},
abstract = {AIMS: A wide range of vector control programs rely on the efficient production and release of male mosquito. Asaia bacteria are described as potential symbionts of several mosquito species but their relationship with Aedes aegypti has never been rigorously tested. Here we aimed to quantify the benefits of three Asaia species on host development in Ae. aegypti, and the ability of these bacteria to form a stable symbiotic association with growing larvae.

METHODS AND RESULTS: In order to disentangle direct and indirect effects of Asaia inoculation on host development, experiments used insects with an intact microbiome and those reared in near-aseptic conditions, while we characterized bacterial communities and Asaia densities with culture dependent and independent methods (16S rRNA amplicon sequencing). Neonate larvae were inoculated with Asaia spp. for 24 hours, or left as uninoculated controls, all were reared on sterile food. Aseptic larvae were produced by surface sterilization of eggs. Although all Asaia were transient members of the gut community, two species accelerated larval development relative to controls. The two mutualistic species had lasting impacts on the larval microbiome, largely by altering the relative abundance of dominant bacteria, namely Klebsiella and Pseudomonas. Axenic larvae were dominated by Asaia when inoculated with this species but showed slower development than conventionally reared insects, indicating that Asaia alone could not restore normal development.

CONCLUSIONS: Our results reveal Asaia as a poor mutualist for Ae. aegypti, but with a species-specific positive effect on improving host performance mediated by interactions with other bacteria.},
}

@article {pmid39419781,
year = {2024},
author = {Qiao, Y and Mei, J and Ma, ZS},
title = {Species Diversity and Network Diversity in the Human Lung Cancer Tissue Microbiomes.},
journal = {FEMS microbiology letters},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsle/fnae087},
pmid = {39419781},
issn = {1574-6968},
abstract = {This study explores the relationship between microbial diversity and disease status in human lung cancer tissue microbiomes, using a sample size of 1,212. Analysis divided the data into primary tumor (PT) and normal tissue (NT) categories. Differences in microbial diversity between PT and NT were significant in 57% of comparisons, although dataset dependence was a factor in the diversity levels. Shared species analysis (SSA) indicated no significant differences between PT and NT in over 90% of comparisons. Network diversity assessments revealed significant differences between NT and PT regarding species relative abundances and network link abundances for q=0-3. Additionally, at q=0, significant variations were found between NT and LUSC in network link probabilities, illustrating the diversity in species interactions. Our findings suggest a stable overall microbiome diversity and composition in lung cancer patients' lung tissues despite patients with diagnosed lung tumors, indicating modified microbial interactions within the tumor. These results highlight an association between altered microbiome interaction patterns and lung tumors, offering new insights into the ecological dynamics of lung cancer microbiomes.},
}

@article {pmid39419665,
year = {2024},
author = {Sharma, S},
title = {Crafting friendly microbiomes as plant bodyguards against pests.},
journal = {Trends in plant science},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tplants.2024.10.001},
pmid = {39419665},
issn = {1878-4372},
abstract = {Research has shown that acclimatizing plant-associated microbiomes through repeated cycles of selection pressure can enhance plant resilience to abiotic stresses. A recent study by Enders et al. expanded this concept by selecting plant-associated microbiomes for insect resistance, paving the way for microbiome engineering to enhance plant fitness.},
}

@article {pmid39419539,
year = {2024},
author = {Scher, JU and Nayak, R and Clemente, JC},
title = {Microbiome research in autoimmune and immune-mediated inflammatory diseases: lessons, advances and unmet needs.},
journal = {Annals of the rheumatic diseases},
volume = {},
number = {},
pages = {},
doi = {10.1136/ard-2024-225735},
pmid = {39419539},
issn = {1468-2060},
abstract = {The increasing prevalence of autoimmune and immune-mediated diseases (AIMDs) underscores the need to understand environmental factors that contribute to their pathogenesis, with the microbiome emerging as a key player. Despite significant advancements in understanding how the microbiome influences physiological and inflammatory responses, translating these findings into clinical practice remains challenging. This viewpoint reviews the progress and obstacles in microbiome research related to AIMDs, examining molecular techniques that enhance our understanding of microbial contributions to disease. We discuss significant discoveries linking specific taxa and metabolites to diseases such as rheumatoid arthritis, systemic lupus erythematosus and spondyloarthritis, highlighting the role of gut dysbiosis and host-microbiome interactions. Furthermore, we explore the potential of microbiome-based therapeutics, including faecal microbiota transplantation and pharmacomicrobiomics, while addressing the challenges of identifying robust microbial targets. We advocate for integrative, transdisease studies and emphasise the need for diverse cohort research to generalise findings across populations. Understanding the microbiome's role in AIMDs will pave the way for personalised medicine and innovative therapeutic strategies.},
}

@article {pmid39419356,
year = {2024},
author = {Medina-Rodriguez, EM and Han, D and Zeltzer, SE and Moraskie Alvarez-Tabío, MP and O'Connor, G and Daunert, S and Beurel, E},
title = {Stress-induced VIPergic activation mediates microbiota/Th17cell-dependent depressive-like behaviors.},
journal = {Brain, behavior, and immunity},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.bbi.2024.10.016},
pmid = {39419356},
issn = {1090-2139},
abstract = {Chronic stress often has deleterious effects leading to the development of psychiatric diseases. The gut-brain axis represents a novel avenue for stress research. The negative effects of stress on the gut physiology have been well-described, whereas the pathways whereby stress controls microbial composition to modulate behaviors remains mainly unknown. We discovered that vasoactive intestinal peptide (VIP) activation promoted stress-induced microbial changes leading to increased infiltration of T helper (Th) 17 cells and microglial activation in the hippocampus and depressive-like behaviors, uncovering a close crosstalk between intestinal VIPergic release and the gut microbiota during stress and providing a new interaction between the nervous system and the gut microbiome after stress. Neutralization of the signature cytokine of Th17 cells, interleukin (IL)-17A, was sufficient to block depressive-like behaviors, reduce neuronal VIPergic activation and microglia activation induced by VIPergic activation after stress, opening new potential therapeutic targets for depression.},
}

@article {pmid39419226,
year = {2024},
author = {Liu, J and Zhu, M and Shi, X and Hui, C and Sun, Y and Zhang, R and Jin, D and Li, Z and Chen, H and Zhao, Z},
title = {Cascading impacts of nitrogen deposition on soil microbiome and herbivore communities in desert steppes.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {176892},
doi = {10.1016/j.scitotenv.2024.176892},
pmid = {39419226},
issn = {1879-1026},
abstract = {Human activities in the last century have intensified global nitrogen deposition, resulting in the degradation of ecosystem function and loss of biodiversity worldwide. Nitrogen addition is a crucial method for examining the effects of atmospheric nitrogen deposition on species composition and structure of soil microbiome and biotic community, as exogenous nitrogen inputs can trigger cascading effects on ecosystem functions. In a 6-year experiment, we evaluated the impact of nitrogen addition on soil microbial-plant-insect systems in desert steppes. Our results show that nitrogen addition significantly altered soil microbial composition and ecological function, leading to a decrease in nitrogen-fixing bacteria and an increase in saprophytic fungi. High levels of nitrogen addition increased total plant biomass while decreasing species diversity. Additionally, high nitrogen addition levels suppressed below-ground biomass of gramineae and legumes compared to low nitrogen addition. Nitrogen addition also increased herbivore abundance by altering insect community structure, particularly benefiting chewing pests over sucking pests, thus heightening the risk of biological disasters through trophic cascading effects. Consequently, excessive nitrogen addition may destabilize desert steppe ecosystems by disturbing soil microbial-plant-insect interactions, hindering the maintenance of biotic community diversity and steppe productivity.},
}

@article {pmid39419209,
year = {2024},
author = {Dong, L and Liu, Z and Xin, Z and Song, C and Bai, X and Li, J and Zhang, Y and Valverde-Pérez, B and Zhang, C},
title = {Runoff variation alters estuarine sediment microbiome and nitrogen removal processes by affecting salinity.},
journal = {The Science of the total environment},
volume = {},
number = {},
pages = {176880},
doi = {10.1016/j.scitotenv.2024.176880},
pmid = {39419209},
issn = {1879-1026},
abstract = {Runoff variations shape the dynamics of the estuarine environmental factors, profoundly influencing the nitrogen cycle in estuarine sediments. However, our understanding of how these changes regulate microbially-mediated nitrogen removal processes remains limited. In this study, the impacts of changes in environmental factors caused by normal and low runoffs on denitrification and anammox in sediments of the Liao River Estuary in China, were investigated, using continuous-flow experiments combined with [15]N tracing techniques and molecular methods. Results indicated that denitrification was the main nitrogen removal process in estuarine sediments under both runoff conditions. Elevated salinity under low runoff condition increased the abundance of nitrifying bacteria (Nitrospina, Nitrosomonas and Nitrosomonadaceae), thereby promoting the coupled nitrification-denitrification nitrogen removal process. Furthermore, seawater intrusion under low runoff contributed to dilute nitrite concentrations, resulting in decreased denitrification rates in sediments. Overall, this study highlighted the impacts of runoff variations on biological nitrogen removal process through affecting environmental factors, gene abundance and microbial community in the estuary.},
}

@article {pmid39419193,
year = {2024},
author = {Chen, H and Zeng, M and Batool, SS and Zhao, Y and Yu, Z and Zhou, J and Liu, K and Huang, J},
title = {Metagenomic analysis reveals effects of gut microbiome in response to neoadjuvant chemoradiotherapy in advanced rectal cancer.},
journal = {Genomics},
volume = {116},
number = {6},
pages = {110951},
doi = {10.1016/j.ygeno.2024.110951},
pmid = {39419193},
issn = {1089-8646},
abstract = {Neoadjuvant chemoradiotherapy can enhance survival rate of patients with advanced rectal cancer, but its effectiveness varies considerably. Previous studies have indicated that gut microbes may serve as biomarkers for predicting treatment efficacy. However, the specific roles of the gut microbiome in patients who have good response to nCRT remains unclear. In this study, shotgun metagenomic sequencing technology was used to analyze the fecal microbiome of patients with varying responses to nCRT. Our findings revealed that beneficial intestinal bacteria and genes from different metabolic pathways (carbohydrate metabolism, amino acid metabolism, and sulfur metabolism) were significantly enriched in patients with good response. Additionally, causal relationship in which microbial-derived GDP-D-rhamnose and butyrate could influence the response to nCRT was clarified. Our results offered new insights into the different response to nCRT, and provided valuable reference points for improving the effectiveness of nCRT in patients with advanced colorectal cancer.},
}

@article {pmid39418819,
year = {2024},
author = {Zhou, Y and Wang, NL and Cen, JQ and Han, JT and Tang, YX and Xu, ZQ and Zeng, H and Houf, K and Yu, Z},
title = {Comparative analyses of bacterial contamination and microbiome of broiler carcasses in wet market and industrial processing environments.},
journal = {International journal of food microbiology},
volume = {426},
number = {},
pages = {110937},
doi = {10.1016/j.ijfoodmicro.2024.110937},
pmid = {39418819},
issn = {1879-3460},
abstract = {The slaughtering environment is crucial for the food hygiene and safety of poultry products. Despite the global dominance of industrial processing, live bird slaughtering in wet markets persists due to cultural, religious, and economic reasons. This study aims to reveal the correlation between hygiene scales in wet markets and bacterial contamination levels on broiler carcasses, with a particular focus on pathobiont transmission risks and microbiome characteristics. Wet markets were categorized based on home-made ratings and the Hygiene and Biosecurity Assessment Tool (HABT). The study assessed total aerobic bacterial (TAB) levels, food spoilage and hygiene indicators (Pseudomonas and E. coli), foodborne pathogen Salmonella, and the microbiome of broiler carcasses, intestinal contents, and slaughtering facilities. Comparative analyses were conducted between market and industrial processing environments. TAB levels on broiler carcasses showed a significant negative correlation with hygiene scores, indicating that both HABT and home-made rating tools effectively assess and improve processing hygiene. Industrial processing consistently reduced bacterial contamination compared to wet markets. Although Salmonella spp. prevalence was lower in market-processed carcasses, the study identified significant cross-transmission of pathobionts and variations in bacterial composition with hygiene improvements. Notably, the microbiome analysis revealed overlaps in amplicon sequence variants (ASVs) between carcasses and contamination vectors, highlighting pathobiont transmission risks. The present study confirmed the scales of hygiene standards among wet markets reflect bacterial contamination on broiler carcasses. Enhancing slaughter practices to meet industrial hygiene standards is essential for reducing the transmission of foodborne pathogens and pathobionts, and improving food safety.},
}

@article {pmid39418776,
year = {2024},
author = {Xie, Q and Sun, J and Sun, M and Wang, Q and Wang, M},
title = {Perturbed microbial ecology in neuromyelitis optica spectrum disorder: Evidence from the gut microbiome and fecal metabolome.},
journal = {Multiple sclerosis and related disorders},
volume = {92},
number = {},
pages = {105936},
doi = {10.1016/j.msard.2024.105936},
pmid = {39418776},
issn = {2211-0356},
abstract = {BACKGROUND: Neuromyelitis optica spectrum disorder (NMOSD) is a central nervous system inflammatory demyelinating immune-mediated ailment, which is influenced by genetic, epigenetic, and environmental elements. The escalating incidence of NMOSD in recent years implies alterations in environmental risk factors. Recent research has established a correlation between gut microbiomes and the development of NMOSD.

METHODS: Metagenomic shotgun sequencing and gas chromatography-mass spectrometry (GC-MS) were employed to assess alterations of the structure and function in the fecal microbiome, as well as levels of short-chain fatty acids (SCFAs) in fecal and blood samples, among individuals with neuromyelitis optica spectrum disorder (NMOSD) during the acute phase (n = 25), the remission phase (n = 11), and a group of healthy controls (HCs) (n = 24). We further explored the correlation between gut microbiota and the pathogenesis of NMOSD through fecal microbiota transplantation (FMT). The gut microbiome from human donors diagnosed with NMOSD or HCs was transplanted into germ-free mice, followed by an analysis of the alterations in the structure and functionality of the transplanted mice's gut microbiome. Additionally, the impact of microbiome transfer on the immunity and spinal cord of germ-free mice was assessed through various techniques, including ELISA, flow cytometry, western blot, histopathology, and transcriptome sequencing.

RESULTS: (1) At the taxonomic levels of genus and species, there were significant differences in the α-diversity of the microbiome between HCs and NMOSD patients in the acute phase, with NMOSD patients having higher species diversity. (2) In the acute phase, the gut microbiota of NMOSD patients was characterized by Ruminococcaceae_unclassified, Campylobacter, Parabacteroides, Lactobacillus, Akkermansia, Streptococcus oralis, Clostridium leptum, Clostridium asparagiforme, Firmicutes bacterium CAG 238, and Lactobacillus fermentum. (3) The relative abundances of Coprobacter, Turicimonas, Gemmiger, Enterobacter, Roseburia sp.CAG 471, Veillonella tobetsuensis, Proteobacteria bacterium CAG 139, Ruminococcus bicirculans, Lactococcus lactis, Flavonifractor plautii, and Streptococcus cristatus were notably lower in patients experiencing remission compared to NMOSD patients in the acute phase, On the other hand, the relative abundances of Flavonifractor (P = 0.049) and Clostridium aldenense (P = 0.049) were significantly higher. Following medication, the gut microbiome distribution in NMOSD patients during remission closely resembled that of healthy controls (HCs). (4) Compared with HCs, acetate levels in the feces of patients with NMOSD in the acute phase were significantly lower. (5) In addition, we transplanted feces from NMOSD patients into germ-free mice and revealed a significant increase in the levels of IL-6, IL-17A, and IL-23 in the blood of mice belonging to the NMOSD fecal transplantation (NFMT) group. Additionally, the IL-10 level exhibited a significant reduction. Moreover, the proportion of Th17 cells displayed a significant increase, while the proportion of Treg cells exhibited a significant decrease in the spleens of NFMT mice.

CONCLUSION: Patients in the acute phase of neuromyelitis optica spectrum disorder (NMOSD) exhibited imbalances in their gut microbiota and a deficiency in short-chain fatty acids (SCFAs). Following drug treatment, the composition of intestinal microbes in NMOSD patients during the remission phase closely resembled that of the healthy control population. The FMT experiment provided evidence of the significant association between intestinal flora and the pathogenesis of NMOSD. Consequently, investigating gut microbiota and identifying novel microbial markers hold promise for the diagnosis and treatment of NMOSD patients.},
}

@article {pmid39418324,
year = {2024},
author = {Freudenthal, J and Dumack, K and Schaffer, S and Schlegel, M and Bonkowski, M},
title = {Algae-fungi symbioses and bacteria-fungi co-exclusion drive tree species-specific differences in canopy bark microbiomes.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrae206},
pmid = {39418324},
issn = {1751-7370},
abstract = {With over 3 trillion trees, forest ecosystems comprise nearly one-third of the terrestrial surface of the Earth. Very little attention has been given to the exploration of the above-ground plant microbiome of trees, its complex trophic interactions, and variations among tree species. To address this knowledge gap, we applied a primer-independent shotgun metatranscriptomic approach to assess the entire living canopy bark microbiome comprising prokaryotic and eukaryotic primary producers, decomposers, and various groups of consumers. With almost 1500 genera, we found a high microbial diversity on three tree species with distinct bark textures: oak (Quercus robur), linden (Tilia cordata), both with rough bark, and maple (Acer pseudoplatanus) with smooth bark. Core co-occurrence network analysis revealed a rich food web dominated by algal primary producers, and bacterial and fungal decomposers, sustaining a diverse community of consumers, including protists, microscopic metazoans and predatory bacteria. Whereas maple accommodated a depauperate microbiome, oak and linden accommodated a richer microbiome mainly differing in their relative community composition: Bacteria exhibited an increased dominance on linden, whereas co-occurring algae and fungi dominated on oak, highlighting the importance of algal-fungal lichen symbioses even at the microscopic scale. Further, due to bacteria-fungi co-exclusion, bacteria on bark are not the main beneficiaries of algae-derived carbon compounds as it is known from aquatic systems.},
}

@article {pmid39418297,
year = {2024},
author = {Yadav, A and Devi, P and Kumari, P and Shamim, U and Tarai, B and Budhiraja, S and Pandey, R},
title = {Metatranscriptomic insights into the dengue patient blood microbiome: Enhanced microbial diversity and metabolic activity in severe patients.},
journal = {PLoS neglected tropical diseases},
volume = {18},
number = {10},
pages = {e0012589},
doi = {10.1371/journal.pntd.0012589},
pmid = {39418297},
issn = {1935-2735},
abstract = {BACKGROUND: Dengue is the most re-emergent infection, with approximately 100 million new cases reported annually, yet no effective treatment or vaccine exists. Here, we aim to define the microbial community structure and their functional profiles in the dengue positive patients with varying disease severity.

Hospital admitted 112 dengue-positive patients blood samples were analyzed by dual RNA-sequencing to simultaneously identify the transcriptionally active microbes (TAMs), their expressed genes and associated pathways. Results highlight that patients with severe dengue exhibited increased microbial diversity and presence of opportunistic species (unique and core) which includes Bacillus cereus, Burkholderia pseudomallei, Streptococcus suis, and Serratia marcescens. The functional profile analysis revealed enriched metabolic pathways such as protein degradation, nucleotide biosynthesis, ion transport, cell shape integrity, and ATP formation in severe cases, indicating the high energy demands and adaptability of these microbes.

CONCLUSION: Our metatranscriptomic approach provides a species-level characterization of blood microbiome composition and reveals a heightened diversity of TAMs in patients with severe dengue, underscoring the need for further research into the role of blood microbiota in disease progression. Comparing the microbial signatures across the severity classes early in the disease offers unique potential for convenient and early diagnosis of dengue infection.},
}

@article {pmid39418241,
year = {2024},
author = {Song, C and Liu, F and Mei, Y and Cai, W and Cheng, K and Guo, D and Liu, Y and Shi, H and Duan, DD and Liu, Z},
title = {Integrated metagenomic and metabonomic mechanisms for the therapeutic effects of Duhuo Jisheng decoction on intervertebral disc degeneration.},
journal = {PloS one},
volume = {19},
number = {10},
pages = {e0310014},
pmid = {39418241},
issn = {1932-6203},
mesh = {Animals ; *Intervertebral Disc Degeneration/drug therapy/metabolism/microbiology ; *Drugs, Chinese Herbal/pharmacology/therapeutic use ; *Metabolomics/methods ; Rats ; *Gastrointestinal Microbiome/drug effects ; Male ; *Rats, Sprague-Dawley ; *Metagenomics/methods ; Metabolome/drug effects ; Feces/microbiology ; Disease Models, Animal ; },
abstract = {Intervertebral disc degeneration (IVDD) is a prevalent orthopedic condition with lower back pain as the predominant clinical presentation that challenges clinical treatment with few therapeutic options. Duhuo Jisheng Decoction (DHJSD) has been proven effective in the therapy of IVDD, but the precise underlying mechanisms remain not fully elucidated. The current study was designed to test our hypothesis that DHJSD may systematically correct the phenotypic disruption of the gut microbiota and changes in the serum metabolome linked to IVDD. Analysis of the active ingredients of DHJSD by ultra high performance liquid chromatography. An integrated metagenomic and metabonomic approach was used to analyze feces and blood samples from normal and IVDD rats. Compared to the control group, fiber ring pinning on the caudal 3 to caudal 5 segments of the rats caused IVDD and significantly altered the compositions of the intestinal microbiota and serum metabolites. Integrated analysis revealed commonly-altered metabolic pathways shared by both intestinal microbiota and serum metabolome of the IVDD rats. DHJSD inhibited the degenerative process and restored the compositions of the perturbed gut microbiota, particularly the relative abundance of commensal microbes of the Prevotellaceae family. DHJSD also corrected the altered metabolic pathways involved in the metabolism of glycine, serine, threonine, valine, the citric acid cycle, and biosynthesis of leucine and isoleucine. DHJSD inhibited the disc degeneration process by an integrated metagenomic and metabonomic mechanism to restore the microbiome profile and normalize the metabonomic pathways.},
}

Animals
*Intervertebral Disc Degeneration/drug therapy/metabolism/microbiology
*Drugs, Chinese Herbal/pharmacology/therapeutic use
*Metabolomics/methods
Rats
*Gastrointestinal Microbiome/drug effects
Male
*Rats, Sprague-Dawley
*Metagenomics/methods
Metabolome/drug effects
Feces/microbiology
Disease Models, Animal

@article {pmid39417900,
year = {2024},
author = {Mitchell, LK and Heussler, HS and Burgess, CJ and Rehman, A and Steinert, RE and Davies, PSW},
title = {Gastrointestinal, Behaviour and Anxiety Outcomes in Autistic Children Following an Open Label, Randomised Pilot Study of Synbiotics vs Synbiotics and Gut-Directed Hypnotherapy.},
journal = {Journal of autism and developmental disorders},
volume = {},
number = {},
pages = {},
pmid = {39417900},
issn = {1573-3432},
abstract = {Alterations of the microbiome-gut-brain (MGB) axis have been associated with autism spectrum disorder (ASD) and disorders of gut-brain interaction (DGBI). DGBI are highly prevalent in autistic children and are associated with worsening behaviour and anxiety. Treatments such as probiotics, prebiotics and gut-directed hypnotherapy (GDH) have shown efficacy in improving gut symptoms in children. The primary objective of the study was to compare changes in gastrointestinal (GI) scores following a 12-week intervention of synbiotics (prebiotic + probiotic) +/- GDH with a follow-up at 24 weeks. Secondary objectives included changes in behavioural and anxiety symptoms, while changes in gut microbiome composition were assessed as an exploratory objective. Children diagnosed with ASD aged 5.00-10.99 years (n = 40) were recruited and randomised (1:1) to a 12-week intervention of either synbiotics (SYN group) or synbiotics + GDH (COM group). Both the SYN and COM group experienced significant reductions in total GI scores post-intervention and at follow-up (p < 0.001), with no superiority of the COM treatment over the SYN treatment. The COM group showed beneficial reductions in anxiety scores (p = 0.002) and irritability behaviours (p < 0.001) which were not present in the SYN group. At follow-up, only those in the COM group maintained significant reductions in GI pain scores (p < 0.001). There were significant changes in gut microbiota such as increases in Bifidobacterium animalis and Dialister in both groups over time. In conclusion, synbiotics with or without GDH may help support standard care for autistic children who suffer comorbid DGBI. The trial was prospectively registered at clinicialtrials.gov on 16 November 2020 (NCTO4639141).},
}

@article {pmid39417540,
year = {2024},
author = {Ginatt, AA and Berihu, M and Castel, E and Medina, S and Carmi, G and Faigenboim-Doron, A and Sharon, I and Tal, O and Droby, S and Somera, T and Mazzola, M and Eizenberg, H and Freilich, S},
title = {A metabolic modeling-based framework for predicting trophic dependencies in native rhizobiomes of crop plants.},
journal = {eLife},
volume = {13},
number = {},
pages = {},
pmid = {39417540},
issn = {2050-084X},
support = {US-5390-21//United States-Israel Binational Agricultural Research and Development Fund/ ; },
mesh = {*Rhizosphere ; *Malus/microbiology/metabolism ; *Microbiota ; Plant Roots/microbiology/metabolism ; Soil Microbiology ; Bacteria/metabolism/genetics/classification ; Crops, Agricultural/microbiology ; Metabolomics/methods ; Models, Biological ; },
abstract = {The exchange of metabolites (i.e., metabolic interactions) between bacteria in the rhizosphere determines various plant-associated functions. Systematically understanding the metabolic interactions in the rhizosphere, as well as in other types of microbial communities, would open the door to the optimization of specific predefined functions of interest, and therefore to the harnessing of the functionality of various types of microbiomes. However, mechanistic knowledge regarding the gathering and interpretation of these interactions is limited. Here, we present a framework utilizing genomics and constraint-based modeling approaches, aiming to interpret the hierarchical trophic interactions in the soil environment. 243 genome scale metabolic models of bacteria associated with a specific disease-suppressive vs disease-conducive apple rhizospheres were drafted based on genome-resolved metagenomes, comprising an in silico native microbial community. Iteratively simulating microbial community members' growth in a metabolomics-based apple root-like environment produced novel data on potential trophic successions, used to form a network of communal trophic dependencies. Network-based analyses have characterized interactions associated with beneficial vs non-beneficial microbiome functioning, pinpointing specific compounds and microbial species as potential disease supporting and suppressing agents. This framework provides a means for capturing trophic interactions and formulating a range of testable hypotheses regarding the metabolic capabilities of microbial communities within their natural environment. Essentially, it can be applied to different environments and biological landscapes, elucidating the conditions for the targeted manipulation of various microbiomes, and the execution of countless predefined functions.},
}

*Rhizosphere
*Malus/microbiology/metabolism
*Microbiota
Plant Roots/microbiology/metabolism
Soil Microbiology
Bacteria/metabolism/genetics/classification
Crops, Agricultural/microbiology
Metabolomics/methods
Models, Biological

@article {pmid39417122,
year = {2024},
author = {Atugonza, C and Muwonge, A and Najjuka, CF and Kateete, DP and Katagirya, E and Mwesigwa, S and Asiimwe, B},
title = {Early changes in the gut microbiome among HIV-infected Individuals in Uganda initiating daily TMP/SMX.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.10.07.24315002},
pmid = {39417122},
abstract = {Daily cotrimoxazole (TMP/SXT) prophylaxis is part of the HIV treatment package for all new HIV-infected individuals in Uganda. Although this treatment has shown reduced morbidity and mortality in HIV, it remains controversial due to its contribution to developing antibiotic-resistant bacteria. Moreover, the effects of daily use of a broad-spectrum antibiotic on the gut microbiome remain unknown. To study the early effects, we analysed shotgun metagenome sequence data from stool samples of five newly HIV-infected individuals initiating TMP/SXT prophylaxis longitudinally for the first 30 days of treatment. Using shotgun metagenomics sequencing, we generated both taxonomic and functional profiles from each patient and compared gut microbial changes Pre-TMP/SXT and post-TMP/SXT on Day 5, Day 14, and Day 30. Daily TMP/SXT prophylaxis resulted in a shift characterised by an enrichment of Prevetollea and Ruminococcus genera members and the depletion of Lactococcus and Bacteroides genera members. Furthermore, these microbial shifts were associated with changes in the functional profile revealed by a differential abundance of pathways of amino acid metabolism, carbohydrate metabolism, and nucleotide biosynthesis linked to members of the Bacteroidaceae and Enterobacteriaceae families. TMP/SXT daily prophylaxis in HIV-infected individuals is associated with dramatic changes in microbial composition and functional profiles; however, other factors such as Age, Gender, HIV clinical stage, and ART regiment are at play. Further investigation is needed to examine the implication of these shifts on clinical management and outcomes among HIV patients.},
}

@article {pmid39417117,
year = {2024},
author = {Jorgensen, JA and Choo-Kang, C and Wang, L and Issa, L and Gilbert, JA and Ecklu-Mensah, G and Luke, A and Bedu-Addo, K and Forrester, T and Bovet, P and Lambert, EV and Rae, D and Argos, M and Kelly, TN and Sargis, RM and Dugas, LR and Dai, Y and Layden, BT},
title = {Toxic Metals Impact Gut Microbiota and Metabolic Risk in Five African-Origin Populations.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.10.07.24315016},
pmid = {39417117},
abstract = {Exposure to toxic metals impacts obesity and type 2 diabetes (T2DM) risk. Yet, the underlying mechanisms remain largely unknown. Gut microbiota has been strongly associated with progression of cardiometabolic risk. To determine whether high metal exposures and gut dysbiosis interact to promote metabolic dysregulation and cardiometabolic risk, we assessed relationships between these factors. We analyzed cross-sectional associations between arsenic, lead, mercury, cadmium, and cardiometabolic health markers in 178 randomly selected African-origin adults (52% female, 51% obese, mean age=43.0±6.4 years) from Ghana, South Africa, Seychelles, Jamaica, and USA. Metal levels were dichotomized to high or low at the median level of each metal. We analyzed associations between gut microbiome taxa, metal levels, clinical measures (BMI, fasting blood glucose, and blood pressure) and diagnoses (hypertension, obesity, and diabetes status). High vs. low lead and arsenic exposures had a significant effect on beta diversity (p <0.05). 71 taxa were associated with high lead levels: 30 with elevated BMI, 22 with T2DM, and 23 with elevated fasting blood glucose (p<0.05). 115 taxa were associated with high arsenic levels: 32 with elevated BMI, 33 with T2DM, and 26 with elevated blood glucose (p<0.05). Of the taxa associated with high lead and arsenic exposure and either elevated BMI or fasting blood glucose, porphyrin metabolism was the most enriched metabolic pathway. These data collectively provide the first findings in a human study that the gut microbiome may drive the association between lead and arsenic exposure and obesity and T2DM risk.},
}

@article {pmid39417072,
year = {2024},
author = {Luo, X and Yan, G and Wang, Q and Xing, Y},
title = {Community structure, diversity and function of endophytic and soil microorganisms in boreal forest.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1410901},
pmid = {39417072},
issn = {1664-302X},
abstract = {INTRODUCTION: Despite extensive studies on soil microbial community structure and functions, the significance of plant-associated microorganisms, especially endophytes, has been overlooked. To comprehensively anticipate future changes in forest ecosystem function under future climate change scenarios, it is imperative to gain a thorough understanding of the community structure, diversity, and function of both plant-associated microorganisms and soil microorganisms.

METHODS: In our study, we aimed to elucidate the structure, diversity, and function of leaf endophytes, root endophytes, rhizosphere, and soil microbial communities in boreal forest. The microbial structure and composition were determined by high-throughput sequencing. FAPROTAX and FUNGuild were used to analyze the microbial functional groups.

RESULTS: Our findings revealed significant differences in the community structure and diversity of fungi and bacteria across leaves, roots, rhizosphere, and soil. Notably, we observed that the endophytic fungal or bacterial communities associated with plants comprised many species distinct from those found in the soil microbial communities, challenging the assumption that most of endophytic fungal or bacterial species in plants originate from the soil. Furthermore, our results indicated noteworthy differences in the composition functional groups of bacteria or fungi in leaf endophytes, root endophytes, rhizosphere, and soil, suggesting distinct roles played by microbial communities in plants and soil.

DISCUSSION: These findings underscore the importance of recognizing the diverse functions performed by microbial communities in both plant and soil environments. In conclusion, our study emphasizes the necessity of a comprehensive understanding of the structure and function microbial communities in both plants and soil for assessing the functions of boreal forest ecosystems.},
}

@article {pmid39417049,
year = {2024},
author = {Bilal, M and Nashwan, AJ},
title = {Challenges in integrating traditional Chinese medicine and gut microbiota research for insomnia treatment.},
journal = {World journal of clinical cases},
volume = {12},
number = {29},
pages = {6271-6274},
pmid = {39417049},
issn = {2307-8960},
abstract = {The gut microbiome is an extensive variety of bacteria with a range of metabolic capabilities that can be pathogenic, beneficial, or opportunistic. Changes in the gut microbiota's composition can affect the link between gut integrity and host health as well as cause disruptions to numerous neurological systems. The second most prevalent mental health problem, insomnia has a negative social and economic impact. Currently, it is becoming increasingly obvious how crucial it is to preserve the delicate balance of gut microbiota to treat illness-related symptoms like insomnia. Although traditional Chinese medicine has proposed an effective strategy against insomnia through gut microbiota alteration in animal models, studies in human models are limited. This decreases the predictive value of the studies in terms of human outcomes. This editorial places an emphasis on cultural sensitivity rather than scientific reasoning that promotes the use of traditional Chinese medicine (TCM). We aim to emphasize the concern that promoting TCM could divert resources from conventional medical research, leading to suboptimal care.},
}

@article {pmid39416793,
year = {2024},
author = {Zhu, W and Chi, J and Zhang, Y and Wu, D and Xia, X and Liao, X and Xu, K and Shi, W and Hu, H and Wang, W and Lu, Z and Zhang, Z and Liu, Y},
title = {Global hotspots and trends in gut mycological research: a visual analytics and bibliometric approach.},
journal = {Frontiers in immunology},
volume = {15},
number = {},
pages = {1457913},
pmid = {39416793},
issn = {1664-3224},
mesh = {*Bibliometrics ; Humans ; *Gastrointestinal Microbiome ; *Fungi ; Biomedical Research/trends ; },
abstract = {BACKGROUND: Recent findings highlight the significant impact of intestinal fungi on the complex makeup of the gut microbiota and human health, challenging past oversights. However, a lack of thorough systematic and quantitative analyses remains. This study aims to address this gap by thoroughly examining the current research on gut fungi. Through analyzing developments and unique features in this area, our goal is to foster a deeper understanding and identify future research pathways.

METHODS: We performed an extensive bibliometric analysis on documents from 2000 to 2023, sourced from the Web of Science Core Collection (WoSCC). Utilizing advanced visualization tools such as VOSviewer, CiteSpace, and Bibliometrix R, we meticulously examined and illustrated the data in scientific landscapes and networks.

RESULTS: A total of 1434 papers were analyzed, revealing a substantial increase in publication volume over the past two decades, particularly in 2020. Contributions came from 67 countries, 2178 institutions, and 8,479 authors. China led in publication output with 468 articles, followed by the University of California with 84 articles, and ZHANG F as the most prolific author with 17 articles. Emerging research areas such as "Fungal-Bacteria Interactions," "Gut Fungus and Gut-Brain Axis," and "Gut Fungus and Immunity" are expected to attract growing interest in the future.

CONCLUSION: This extensive bibliometric analysis offers a current overview of scholarly efforts concerning intestinal fungi, highlighting the predominant landscape in this field. These insights can assist scholars in identifying appropriate publication avenues, forming collaborative relationships, and enhancing understanding of key themes and emerging areas, thereby stimulating future research endeavors.},
}

*Bibliometrics
Humans
*Gastrointestinal Microbiome
*Fungi
Biomedical Research/trends

@article {pmid39416478,
year = {2024},
author = {Kaundal, A and Srivastava, AK and Yadav, D},
title = {Editorial: The role of the microbiome in plant and soil health in a changing climate.},
journal = {Frontiers in plant science},
volume = {15},
number = {},
pages = {1491438},
pmid = {39416478},
issn = {1664-462X},
}

@article {pmid39416467,
year = {2024},
author = {Costantini, MS and Videvall, E and Foster, JT and Medeiros, MCI and Gillece, JD and Paxton, EH and Crampton, LH and Mounce, HL and Wang, AX and Fleischer, RC and Campana, MG and Reed, FA},
title = {The Role of Geography, Diet, and Host Phylogeny on the Gut Microbiome in the Hawaiian Honeycreeper Radiation.},
journal = {Ecology and evolution},
volume = {14},
number = {10},
pages = {e70372},
pmid = {39416467},
issn = {2045-7758},
abstract = {The animal gut microbiome can have a strong influence on the health, fitness, and behavior of its hosts. The composition of the gut microbial community can be influenced by factors such as diet, environment, and evolutionary history (phylosymbiosis). However, the relative influence of these factors is unknown in most bird species. Furthermore, phylosymbiosis studies have largely focused on clades that diverged tens of millions of years ago, and little is known about the degree of gut microbiome divergence in more recent species radiations. This study explores the drivers of microbiome variation across the unique and recent Hawaiian honeycreeper radiation (Fringillidae: Drepanidinae). Fecal samples were collected from 14 extant species spanning the main islands of the Hawaiian archipelago and were sequenced using three metabarcoding markers to characterize the gut microbiome, invertebrate diet, and plant diet of Hawaiian honeycreepers. We then used these metabarcoding data and the honeycreeper host phylogeny to evaluate their relative roles in shaping the gut microbiome. Microbiome variation across birds was highly individualized; however, source island had a small but significant effect on microbiome structure. The microbiomes did not recapitulate the host phylogenetic tree, indicating that evolutionary history does not strongly influence microbiome structure in the honeycreeper clade. These results expand our understanding of the roles of diet, geography, and phylogeny on avian microbiome structure, while also providing important ecological information about the diet and gut microbiota of wild Hawaiian honeycreepers.},
}

@article {pmid39416140,
year = {2024},
author = {Majernik, SN and Beaver, L and Bradley, PH},
title = {Small amounts of misassembly can have disproportionate effects on pangenome-based metagenomic analyses.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.10.11.617902},
pmid = {39416140},
issn = {2692-8205},
abstract = {Individual genes from microbiomes can drive host-level phenotypes. To help identify such candidate genes, several recent tools estimate microbial gene copy numbers directly from metagenomes. These tools rely on alignments to pangenomes, which in turn are derived from the set of all individual genomes from one species. While large-scale metagenomic assembly efforts have made pangenome estimates more complete, mixed communities can also introduce contamination into assemblies, and it is unknown how robust pangenome-based metagenomic analyses are to these errors. To gain insight into this problem, we re-analyzed a case-control study of the gut microbiome in cirrhosis, focusing on commensal Clostridia previously implicated in this disease. We tested for differentially prevalent genes in the Lachnospiraceae , then investigated which were likely to be contaminants using sequence similarity searches. Out of 86 differentially prevalent genes, we found that 33 (38%) were probably contaminants originating in taxa such as Veillonella and Haemophilus , unrelated genera that were independently correlated with disease status. Our results demonstrate that even small amounts of contamination in metagenome assemblies, below typical quality thresholds, can threaten to overwhelm gene-level metagenomic analyses. However, we also show that such contaminants can be accurately identified using a method based on gene-to-species correlation. After removing these contaminants, we observe that several flagellar motility gene clusters in the Lachnospira eligens pangenome are associated with cirrhosis status. We have integrated our analyses into an analysis and visualization pipeline, PanSweep, that can automatically identify cases where pangenome contamination may bias the results of gene-resolved analyses.},
}

@article {pmid39416120,
year = {2024},
author = {Richardson, M and Zhao, S and Sheth, RU and Lin, L and Qu, Y and Lee, J and Moody, T and Ricaurte, D and Huang, Y and Velez-Cortes, F and Urtecho, G and Wang, HH},
title = {SAMPL-seq reveals micron-scale spatial hubs in the human gut microbiome.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.10.08.617108},
pmid = {39416120},
issn = {2692-8205},
abstract = {UNLABELLED: The local arrangement of microbes can profoundly impact community assembly, function, and stability. To date, little is known about the spatial organization of the human gut microbiome. Here, we describe a high-throughput and streamlined method, dubbed SAMPL-seq, that samples microbial composition of micron-scale sub-communities with split-and-pool barcoding to capture spatial colocalization in a complex consortium. SAMPL-seq analysis of the gut microbiome of healthy humans identified bacterial taxa pairs that consistently co-occurred both over time and across multiple individuals. These colocalized microbes organize into spatially distinct groups or "spatial hubs" dominated by Bacteroideceae , Ruminococceae , and Lachnospiraceae families. From a dietary perturbation using inulin, we observed reversible spatial rearrangement of the gut microbiome, where specific taxa form new local partnerships. Spatial metagenomics using SAMPL-seq can unlock new insights to improve the study of microbial communities.

ONE SENTENCE SUMMARY: High throughput micron-scale subcommunity sampling and sequencing identifies distinct spatial associations of gut bacteria within and across individuals.},
}

@article {pmid39416080,
year = {2024},
author = {Wang, Q and Wang, BY and Williams, S and Xie, H},
title = {Diversity and characteristics of the oral microbiome influenced by race and ethnicity.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.10.07.617037},
pmid = {39416080},
issn = {2692-8205},
abstract = {UNLABELLED: Periodontitis disproportionately affects racial/ethnic populations. Besides social determinants contributing to disparities in periodontal health, variations of oral microbial communities may also be a key factor influencing oral immune responses. To characterize the oral microbiome from different racial/ethnic populations, we collected 161 dental plaque samples from African Americans (AAs), Caucasian Americans (CAs), and Hispanic Americans (HAs) with clinical gingival health or biofilm-induced gingivitis on an intact periodontium. Using metagenomic sequencing, we found significant difference in diversity and abundance of microbial taxa in the dental plaque samples from AA, CA, and HA groups and unique microbial species that can only be detected in a particular racial/ethnic group. Moreover, we revealed racial/ethnic associated variations in functional potential of the oral microbiome, showing that diversity and abundance of antibiotic resistant genes were greater in the oral microbiome of the AAs than those in CAs or HAs, and that the AAs exhibited higher levels of genes involving in modification of glycoconjugates, oligo- and polysaccharides. These findings indicate more complex and higher virulence potential oral microbiome in AA and HA populations, which likely contributes to higher prevalence of periodontitis in AAs and HAs.

IMPORTANCE: Recognizing the variations in the oral microbiome among racial/ethnic populations offers insight into the microbial determinants contributing to oral health disparities. In the study presented here, we found a higher level of bleeding on probing (BOP), an indicator of tissue inflammatory response, in the AA group, which is correspondence with a more complex oral microbiome detected in this group. Our observations suggest that the variations of the oral microbiome associated with racial/ethnic backgrounds may directly relate to their virulence potential including their abilities to induce host immune responses and to resist antibiotic treatment. Therefore, these finding can be a stepping stone for developing precision medicine and personalized periodontal prevention/treatment and for reducing oral health disparities.},
}

@article {pmid39416066,
year = {2024},
author = {Powell, CE and McCurry, MD and Quevedo, SF and Ventura, L and Krishnan, K and Dave, M and Mahmood, SD and Specht, K and Bordia, R and Pratt, DS and Korzenik, JR and Devlin, AS},
title = {Cultured Bacteria Isolated from Primary Sclerosing Cholangitis Patient Bile Induce Inflammation and Cell Death.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.10.08.617321},
pmid = {39416066},
issn = {2692-8205},
abstract = {BACKGROUND: Primary sclerosing cholangitis (PSC) is a chronic liver disease characterized by inflammation and progressive fibrosis of the biliary tree. The pathogenesis of PSC remains poorly understood, and there are no effective therapeutic options. Previous studies have observed associations between changes in the colonic and biliary microbiome and PSC. We aimed to determine whether bacterial isolates cultured from PSC patient bile induced disease-associated phenotypes in cells.

METHODS: Bile was collected from PSC patients (n=10) by endoscopic retrograde cholangiography and from non-PSC controls (n=3) undergoing cholecystectomies. Biliary bacteria were cultured anaerobically, and 50 colonies per sample were identified by 16S rRNA sequencing. The effects of supernatants from seven PSC-associated bacterial strains on cellular phenotypes were characterized using human colonic (Caco-2), hepatic (HepG2), and biliary (EGI-1) cells.

RESULTS: No bacteria were isolated from non-PSC controls, while bacteria were cultured from most PSC patients. The PSC bile microbiomes exhibited reduced diversity compared to the gut or oral cavity, with one or two bacterial strains predominating. Overall, PSC-associated bacteria produced factors that were cytotoxic to hepatic and biliary cells. Enterococcus faecalis , and to a lesser extent Veillonella parvula , induced epithelial permeability, while Escherichia coli, Fusobacterium necrophorum , and Klebsiella pneumoniae induced inflammatory cytokines in biliary cells.

CONCLUSIONS: Our data suggest that bacteria cultured from PSC bile induce cellular changes that may contribute to PSC disease pathogenesis. Enterococcus may promote intestinal permeability, facilitating bacterial migration to the biliary tree. Once there, Escherichia, Fusobacterium and Klebsiella , may cause inflammation and damage in biliary and liver cells.},
}

@article {pmid39416028,
year = {2024},
author = {Lawore, DC and Jena, S and Berard, AR and Birse, K and Lamont, A and Mackelprang, RD and Noel-Romas, L and Perner, M and Hou, X and Irungu, E and Mugo, N and Knodel, S and Muwonge, TR and Katabira, E and Hughes, SM and Levy, C and Calienes, FL and Baeten, JM and Celum, C and Hladik, F and Lingappa, JR and Burgener, AD and Green, LN and Brubaker, DK},
title = {Computational Microbiome Pharmacology Analysis Elucidates the Anti-Cancer Potential of Vaginal Microbes and Metabolites.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2024.10.10.616351},
pmid = {39416028},
issn = {2692-8205},
abstract = {The vaginal microbiome's role in risk, progression, and treatment of female cancers has been widely explored. Yet, there remains a need to develop methods to understand the interaction of microbiome factors with host cells and to characterize their potential therapeutic functions. To address this challenge, we developed a systems biology framework we term the Pharmacobiome for microbiome pharmacology analysis. The Pharmacobiome framework evaluates similarities between microbes and microbial byproducts and known drugs based on their impact on host transcriptomic cellular signatures. Here, we apply our framework to characterization of the Anti-Gynecologic Cancer Vaginal Pharmacobiome. Using published vaginal microbiome multi-omics data from the Partners PrEP clinical trial, we constructed vaginal epithelial gene signatures associated with each profiled vaginal microbe and metabolite. We compared these microbiome-associated host gene signatures to post-drug perturbation host gene signatures associated with 35 FDA-approved anti-cancer drugs from the Library of Integrated Network-based Cellular Signatures database to identify vaginal microbes and metabolites with high statistical and functional similarity to these drugs. We found that Lactobacilli and their metabolites can regulate host gene expression in ways similar to many anti-cancer drugs. Additionally, we experimentally tested our model prediction that taurine, a metabolite produced by L. crispatus, kills cancerous breast and endometrial cancer cells. Our study shows that the Pharmacobiome is a powerful framework for characterizing the anti-cancer therapeutic potential of vaginal microbiome factors with generalizability to other cancers, microbiomes, and diseases.},
}

@article {pmid39416003,
year = {2024},
author = {Jacoby, C and Scorza, K and Ecker, L and McMillin, M and Ramaswamy, R and Sundararajan, A and Sidebottom, AM and Lin, H and Dufault-Thompson, K and Hall, B and Jiang, X and Light, SH},
title = {Gut Bacteria Metabolize Natural and Synthetic Steroid Hormones via the Reductive OsrABC Pathway.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {39416003},
issn = {2692-8205},
abstract = {Steroid hormone metabolism by the gut microbiome has multiple implications for mammalian physiology, but the underlying mechanisms and broader significance of this activity remains largely unknown. Here, we isolate a novel human gut bacterium, Clostridium steroidoreducens [T] strain HCS.1, that reduces cortisol, progesterone, testosterone, and related steroid hormones to 3β,5β-tetrahydrosteroid products. Through transcriptomics and heterologous enzyme profiling, we identify and biochemically characterize the C. steroidoreducens OsrABC reductive steroid hormone pathway. OsrA is a 3-oxo-Δ [1] -steroid hormone reductase that selectively targets the Δ [1] -bond present in synthetic steroid hormones, including the anti-inflammatory corticosteroids prednisolone and dexamethasone. OsrB is a promiscuous 3-oxo-Δ [4] -steroid hormone reductase that converts steroid hormones to 5β-dihydrosteroid intermediates. OsrC is a 3-oxo-5β-steroid hormone oxidoreductase that reduces 5β-intermediates to 3β,5β-tetrahydro products. We find that osrA and osrB homologs predict steroid hormone reductase activity in diverse gut bacteria and are enriched in Crohn's disease fecal metagenomes. These studies thus identify the basis of reductive steroid hormone metabolism in the gut and establish a link between inflammatory disease and microbial enzymes that deplete anti-inflammatory corticosteroids.},
}

@article {pmid39415953,
year = {2024},
author = {Sonnega, S and Sheriff, MJ},
title = {Harnessing the gut microbiome: a potential biomarker for wild animal welfare.},
journal = {Frontiers in veterinary science},
volume = {11},
number = {},
pages = {1474028},
pmid = {39415953},
issn = {2297-1769},
abstract = {The welfare of wild animal populations is critically important to conservation, with profound implications for ecosystem health, biodiversity, and zoonotic disease transmission. Animal welfare is typically defined as the accumulated affective mental state of an animal over a particular time period. However, the assessment of animal welfare in the wild poses unique challenges, primarily due to the lack of universally applicable biomarkers. This perspective explores the potential role of the gut microbiome, a dynamic and non-invasive biomarker, as a novel avenue for evaluating animal welfare in wild animals. The gut microbiome, through interactions with the host's physiology, behavior, and cognition, offers a promising opportunity to gain insights into the well-being of animals. In this synthesis, we discuss the distinction between fitness and welfare, the complexities of assessing welfare in wild populations, and the linkages between the gut microbiome and aspects of animal welfare such as behavior and cognition. We lastly elucidate how the gut microbiome could serve as a valuable tool for wildlife managers, with the potential to serve as a non-invasive yet informative window into the welfare of wild animals. As this nascent field evolves, it presents unique opportunities to enhance our understanding of the well-being of wild animals and to contribute to the preservation of ecosystems, biodiversity, and human health.},
}

@article {pmid39415222,
year = {2024},
author = {Raymo, G and Januario, F and Ali, A and Ahmed, RO and Al-Tobasei, R and Salem, M},
title = {Fecal microbiome analysis uncovers hidden stress effects of low stocking density on rainbow trout.},
journal = {Animal microbiome},
volume = {6},
number = {1},
pages = {57},
pmid = {39415222},
issn = {2524-4671},
support = {2023-67015-39742//National Institute of Food and Agriculture/ ; },
abstract = {BACKGROUND: Recirculating aquaculture systems can cause chronic stress in fish when stocking density is too high. However, this study tested whether low stocking density can cause fish stress. Adult rainbow trout, with an average weight of 1.517 kg (± 0.39), were subjected to low (12 kg/m3 ± 0.94) and moderate (43 kg/m3 ± 2.03) stocking densities for 24 days in a recirculating system maintained at 15 °C. At the end of the experiment, fecal microbiome analysis was carried out using a 16S rRNA amplicon sequencing. Additionally, an untargeted plasma metabolomics analysis was conducted.

RESULTS: The moderate stocking density group harboured greater numbers of commensals, such as C. somerae, R. lituseburensis, and L. plantarum. In contrast, detrimental species such as S. putrifacens and P. putida were abundant in the low-stocking density fish. Functional microbiome profiling revealed vitamin B12 salvage and synthesis in moderate stocking densities, which may support intestinal tight junction function. Additionally, vitamin B1 biosynthesis pathways were more abundant in the moderate stocking density group, which may function towards oxidative energy metabolism and protect against oxidative stress. A complementary plasma metabolomics study, although done at slightly different stocking densities and duration, confirmed the presence of blood metabolic stress markers. Elevated levels of L-lactic acid and L-Norvaline, L-Valine, and L-glutamine, indicate low stocking density fish were under stress. Furthermore, a P4HA2 stress gene biomarker confirmed the occurrence of stress in low-density fish. This study suggests that low stocking density can induce stress in fish. Moreover, moderate stocking density leads to a distinct and beneficial fecal microbiome profile.

CONCLUSION: Our study highlights the potential benefits of optimizing the stocking density of fish in recirculating aquaculture systems. This can improve fish health and welfare, promoting a more resilient fecal microbiome.},
}

@article {pmid39415218,
year = {2024},
author = {Lahrach, Z and Legeay, J and Ahmed, B and Hijri, M},
title = {The composition of the arbuscular mycorrhizal fungal bacteriome is species dependent.},
journal = {Environmental microbiome},
volume = {19},
number = {1},
pages = {77},
pmid = {39415218},
issn = {2524-6372},
abstract = {BACKGROUND: In addition to their role as endosymbionts for plant roots, arbuscular mycorrhizal fungi (AMF) engage in complex interactions with various soil microorganisms, the rhizosphere, and the root endosphere of host plants. They also host diverse prokaryotic groups within their mycelia, contributing to what is termed multipartite symbiosis. In this study, we examined the impact of three AMF species-Rhizophagus irregularis, R. clarus, and R. cerebriforme-combined with microbial bioaugmentation on the diversity and composition of bacterial communities in the mycelia and hyphosphere. Using a microcosm design to separate the influence of host plant roots from AMF mycelia and Illumina MiSeq amplicon sequencing to analyze the bacterial communities.

RESULTS: Our results revealed that, while AMF identity and microbial bioaugmentation did not affect the structure of bacterial communities in the hyphosphere soil, they significantly altered the communities associated with their mycelia. Although all three AMF species belong to the same genus, with R. irregularis and R. clarus being closely related compared to R. cerebriforme, we observed variations in the bacterial communities associated with their mycelia. Interestingly, the mycelial bacterial community of R. cerebriforme contained 60 bacteriome core taxa exclusive to it, while R. clarus and R. irregularis had 25 and 9 exclusive taxa, respectively.

CONCLUSION: This study suggests that organismal phylogeny influences the bacterial communities associated with AMF mycelia. These findings provide new insights into AMF and bacterial interactions, which are crucial for the successful deployment of AMF inoculants. The taxonomic diversity of AMF inoculants is important for engineering the plant microbiome and enhancing ecosystem services.},
}

@article {pmid39415203,
year = {2024},
author = {Tong, X and Luo, D and Leung, MHY and Lee, JYY and Shen, Z and Jiang, W and Mason, CE and Lee, PKH},
title = {Diverse and specialized metabolic capabilities of microbes in oligotrophic built environments.},
journal = {Microbiome},
volume = {12},
number = {1},
pages = {198},
pmid = {39415203},
issn = {2049-2618},
support = {BK20230230//Jiangsu Science and Technology Programme/ ; 11214721//Hong Kong Research Grants Council, General Research Fund/ ; R1016-20F//Hong Kong Research Grants Council, Research Impact Fund/ ; },
mesh = {Humans ; Hong Kong ; *Microbiota ; *Built Environment ; *Metagenome ; *Phylogeny ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Skin/microbiology ; Micrococcus luteus/genetics/metabolism ; Genome, Bacterial ; },
abstract = {BACKGROUND: Built environments (BEs) are typically considered to be oligotrophic and harsh environments for microbial communities under normal, non-damp conditions. However, the metabolic functions of microbial inhabitants in BEs remain poorly understood. This study aimed to shed light on the functional capabilities of microbes in BEs by analyzing 860 representative metagenome-assembled genomes (rMAGs) reconstructed from 738 samples collected from BEs across the city of Hong Kong and from the skin surfaces of human occupants. The study specifically focused on the metabolic functions of rMAGs that are either phylogenetically novel or prevalent in BEs.

RESULTS: The diversity and composition of BE microbiomes were primarily shaped by the sample type, with Micrococcus luteus and Cutibacterium acnes being prevalent. The metabolic functions of rMAGs varied significantly based on taxonomy, even at the strain level. A novel strain affiliated with the Candidatus class Xenobia in the Candidatus phylum Eremiobacterota and two novel strains affiliated with the superphylum Patescibacteria exhibited unique functions compared with their close relatives, potentially aiding their survival in BEs and on human skins. The novel strains in the class Xenobia possessed genes for transporting nitrate and nitrite as nitrogen sources and nitrosative stress mitigation induced by nitric oxide during denitrification. The two novel Patescibacteria strains both possessed a broad array of genes for amino acid and trace element transport, while one of them carried genes for carotenoid and ubiquinone biosynthesis. The globally prevalent M. luteus in BEs displayed a large and open pangenome, with high infraspecific genomic diversity contributed by 11 conspecific strains recovered from BEs in a single geographic region. The versatile metabolic functions encoded in the large accessory genomes of M. luteus may contribute to its global ubiquity and specialization in BEs.

CONCLUSIONS: This study illustrates that the microbial inhabitants of BEs possess metabolic potentials that enable them to tolerate and counter different biotic and abiotic conditions. Additionally, these microbes can efficiently utilize various limited residual resources from occupant activities, potentially enhancing their survival and persistence within BEs. A better understanding of the metabolic functions of BE microbes will ultimately facilitate the development of strategies to create a healthy indoor microbiome. Video Abstract.},
}

Humans
Hong Kong
*Microbiota
*Built Environment
*Metagenome
*Phylogeny
*Bacteria/classification/genetics/metabolism/isolation & purification
Skin/microbiology
Micrococcus luteus/genetics/metabolism
Genome, Bacterial

@article {pmid39415150,
year = {2024},
author = {Ma, J and Wang, F and Zhu, Y and Tian, Y and Du, C and Yan, L and Ding, C and Wang, D},
title = {Oral microbiome dysbiosis may be associated with intra cranial aneurysms.},
journal = {BMC oral health},
volume = {24},
number = {1},
pages = {1235},
pmid = {39415150},
issn = {1472-6831},
support = {2021J01217//Fujian Provincial Nature Foundation/ ; 2021Y2001//Technology Platform Construction Project of Fujian Province/ ; },
mesh = {Humans ; *Intracranial Aneurysm/microbiology ; Female ; Male ; Middle Aged ; *Dysbiosis/microbiology ; *Microbiota ; Case-Control Studies ; *Saliva/microbiology ; Mouth/microbiology ; RNA, Ribosomal, 16S/analysis ; Adult ; Aged ; High-Throughput Nucleotide Sequencing ; },
abstract = {BACKGROUND: Although the etiology of aneurysms remains elusive, recent advances in high-throughput sequencing technology and ongoing human microbiome investigations suggest a potential link between microbiome composition and the onset of various human diseases.

OBJECTIVE: This study aimed to utilize high-throughput 16 S rRNA gene sequencing to analyze the oral flora bacterial profiles of individuals, comparing patients with intracranial aneurysms to a healthy control group. Importantly, we sought to identify differences in the oral microbiota and offer novel insights and methods for early diagnosis and identification of intracranial aneurysms.

METHOD: Saliva samples were collected from 60 patients with cerebral aneurysms (case group) and 130 healthy individuals (control group). The V3-V4 region of the bacterial 16 S rRNA gene was amplified and sequenced using the HiSeq high-throughput sequencing platform to establish the bacterial profile. Sequencing data were analyzed using QIIME2 and Metastats software to compare composition differences and relative abundance at the phylum and genus levels in the oral microbiota of the two groups.

RESULTS: Significant differences in oral microbiota composition were observed between patients in the case and control groups (P < 0.05). Genus-level identification highlighted key positions occupied by Eubacterium, Saccharimonadaceae, Rothia, Gemella, Streptococcus, Lactobacillales, Phocaeicola, Bacteroides, Saccharimonadales, and Abiotrophia.

CONCLUSION: This study revealed noteworthy distinctions in the composition, abundance, and diversity of oral microbiota between intracranial aneurysm patients and healthy controls. These disparities suggest a potential correlation between oral microbiota and the development of intracranial aneurysms, offering new avenues for early diagnosis and intervention. However, limitations such as a small sample size, lack of prospective design, and absence of causal inference warrant further validation and exploration.},
}

Humans
*Intracranial Aneurysm/microbiology
Female
Male
Middle Aged
*Dysbiosis/microbiology
*Microbiota
Case-Control Studies
*Saliva/microbiology
Mouth/microbiology
RNA, Ribosomal, 16S/analysis
Adult
Aged
High-Throughput Nucleotide Sequencing

@article {pmid39415135,
year = {2024},
author = {Shariatmadari, F and Motaghi, A and Arjmand Shabestari, A and Hashemi, SM and Almasi-Hashiani, A},
title = {The effect of synbiotics in the treatment of drug-resistant epilepsy and the parental burden of caregivers: a single-arm pretest-posttest trial.},
journal = {BMC pediatrics},
volume = {24},
number = {1},
pages = {666},
pmid = {39415135},
issn = {1471-2431},
mesh = {Humans ; Female ; Male ; *Synbiotics/administration & dosage ; Child, Preschool ; Child ; *Drug Resistant Epilepsy/drug therapy ; *Caregiver Burden ; Adolescent ; Caregivers/psychology ; Anticonvulsants/therapeutic use ; Gastrointestinal Microbiome ; Infant ; Parents/psychology ; Iran ; },
abstract = {BACKGROUND: In patients with drug-resistant epilepsy (DRE), the composition of the gut microbiome changes compared to drug-sensitive patients and healthy individuals. Synbiotics, a mixture of probiotics and prebiotics, aim to improve the balance of bacteria in the gut microbiome. This study aimed to assess the effect of synbiotics on the treatment of DRE and the burden on caregivers.

METHODS: This one-group pretest-posttest quasi-experimental study was conducted in Arak, Iran. Thirty children with DRE, diagnosed by a pediatric neurologist and meeting the inclusion criteria in 2021-22, were included in the study. In addition to anticonvulsant drugs, infants were administered PediLact at a dose of 5-15 drops per day for eight weeks, and KidiLact at a dose of one sachet per day for eight weeks for children aged 2-15 years. Both PediLact and KidiLact are synbiotics. To investigate the burden on caregivers (parents), the Zarit Caregiver Burden Interview was conducted. In addition, the number of epileptic seizures was assessed from mothers before and immediately after the intervention over one month.

RESULTS: The mean age of the participants in the study was 8.6 years (SD: 3.4). Eighteen participants (60%) were boys, and 12 (40%) were girls. The results of the study showed a statistically significant decrease in the mean burden on caregivers, from 34.20 (SD: 14.4) before the intervention to 30.26 (SD: 15.8) after the intervention (P = 0.017). The mean frequency of seizures decreased significantly, from 15.83 (SD: 12.9) before the intervention to 12.73 (SD: 12.8) after the intervention (P = 0.001). Following the intervention, the seizure frequency stopped in two patients, decreased by 50% in six patients, increased in one patient, and remained unchanged in 21 patients.

CONCLUSION: The results suggest that Symbiotics in DRE patients are associated with a lower parental burden of caregivers and seizure frequency. Well-designed randomized clinical trial studies are recommended to generate rigorous causal evidence and conclusions.},
}

Humans
Female
Male
*Synbiotics/administration & dosage
Child, Preschool
Child
*Drug Resistant Epilepsy/drug therapy
*Caregiver Burden
Adolescent
Caregivers/psychology
Anticonvulsants/therapeutic use
Gastrointestinal Microbiome
Infant
Parents/psychology
Iran

@article {pmid39414875,
year = {2024},
author = {Darwesh, MK and Bakr, W and Omar, TEI and El-Kholy, MA and Azzam, NF},
title = {Unraveling the relative abundance of psychobiotic bacteria in children with Autism Spectrum Disorder.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {24321},
pmid = {39414875},
issn = {2045-2322},
mesh = {Humans ; *Autism Spectrum Disorder/microbiology ; *Gastrointestinal Microbiome ; Child ; Male ; Female ; Child, Preschool ; Probiotics/therapeutic use ; Lactobacillus ; Bifidobacterium/isolation & purification ; Feces/microbiology ; },
abstract = {Autism Spectrum Disorder (ASD) is a complex neurodevelopmental disorder characterized by social deficits. Accumulated evidence has shown a link between alterations in the composition of gut microbiota and both neurobehavioural and gastrointestinal symptoms in children with ASD which are related to the genera Lactobacillus and Bifidobacterium. These genera have been recently categorized as "psychobiotics". Moreover, this study aimed to compare the relative abundance of psychobiotics (L. plantarum, L. reuteri, and B. longum) to the total gut microbiome in typically developing (TD) children and those with ASD in order to correlate the distribution of psychobiotic with the severity and sensory impairments in autism. The ASD children were assessed using the Childhood Autism Rating Scale (CARS), while sensory impairments were evaluated using the Short Sensory Profile (SSP). Furthermore, the gut microbiome was analyzed using the quantitative real-time PCR. The study revealed a statistically significant increase in the relative abundance of L. reuteri and L. plantarum in the TD group in comparison to ASD children. Regarding the SSP total score of ASD children, a statistically significant negative correlation was found between both Lactobacillus and L. plantarum with the under-responsive subscale. For the Autism Treatment Evaluation Checklist (ATEC) score, B. longum and Lactobacillus showed a significant positive correlation with Health/Physical/Behaviour.},
}

Humans
*Autism Spectrum Disorder/microbiology
*Gastrointestinal Microbiome
Child
Male
Female
Child, Preschool
Probiotics/therapeutic use
Lactobacillus
Bifidobacterium/isolation & purification
Feces/microbiology

@article {pmid39414857,
year = {2024},
author = {Villela, LB and da Silva-Lima, AW and Moreira, APB and Aiube, YRA and Ribeiro, FV and Villela, HDM and Majzoub, ME and Amario, M and de Moura, RL and Thomas, T and Peixoto, RS and Salomon, PS},
title = {Bacterial and Symbiodiniaceae communities' variation in corals with distinct traits and geographical distribution.},
journal = {Scientific reports},
volume = {14},
number = {1},
pages = {24319},
pmid = {39414857},
issn = {2045-2322},
support = {310057/2022-1//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; },
mesh = {Animals ; *Anthozoa/microbiology ; *Microbiota ; *Coral Reefs ; *RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification ; Brazil ; Symbiosis ; Phylogeny ; Dinoflagellida/genetics/physiology ; High-Throughput Nucleotide Sequencing ; Ecosystem ; },
abstract = {Coral microbiomes play crucial roles in holobiont homeostasis and adaptation. The host's ability to populate broad ecological niches and to cope with environmental changes seems to be related to the flexibility of the coral microbiome. By means of high-throughput DNA sequencing we characterized simultaneously both bacterial (16S rRNA) and Symbiodiniaceae (ITS2) communities of four reef-building coral species (Mussismilia braziliensis, Mussismilia harttii, Montastraea cavernosa, and Favia gravida) that differ in geographic distribution and niche specificity. Samples were collected in a marginal reef system (Abrolhos, Brazil) in four sites of contrasting irradiance and turbidity. Biological filters governed by the host are important in shaping corals' microbiome structure. More structured associated microbial communities by reef site tend to occur in coral species with broader geographic and depth ranges, especially for Symbiodiniaceae, whereas the endemic and habitat-specialist host, M. braziliensis, has relatively more homogenous bacterial communities with more exclusive members. Our findings lend credence to the hypothesis that higher microbiome flexibility renders corals more adaptable to diverse environments, a trend that should be investigated in more hosts and reef areas.},
}

Animals
*Anthozoa/microbiology
*Microbiota
*Coral Reefs
*RNA, Ribosomal, 16S/genetics
*Bacteria/genetics/classification
Brazil
Symbiosis
Phylogeny
Dinoflagellida/genetics/physiology
High-Throughput Nucleotide Sequencing
Ecosystem

@article {pmid39414750,
year = {2024},
author = {Olaniyi, KS and Mackraj, I and Moodley, J and Moodley, R},
title = {Evaluation of the Human Placental Microbiota in Early- and Late-Onset Pre-Eclampsia.},
journal = {High blood pressure & cardiovascular prevention : the official journal of the Italian Society of Hypertension},
volume = {},
number = {},
pages = {},
pmid = {39414750},
issn = {1179-1985},
abstract = {INTRODUCTION: Despite many decades of research, the exact etiology of pre-eclampsia (PE) remains unknown. Several etiopathologies have been suggested, including the role of the placental microbiota. However, the existence of placental microbiota and its possible contribution to pregnancy complications, particularly PE has remained controversial.

AIM: The present study was designed to identify different microbes that co-exist the placenta of women with early- and late-onset PE.

METHODS: Thirty age-matched normotensive and early-onset as well as age-matched normotensive and late-onset pre-eclamptic women respectively, were recruited. After obtaining an informed consent, the placental tissues were obtained through caesarian section with sterile and standardized clinical procedures. DNA was extracted from each tissue and microbiome analysis was conducted using a targeted 16 S analysis and the reads were analyzed with bioinformatics.

RESULTS: There was a significance difference between the blood pressure of early-/late-onset PE compared with age-matched normotensive controls, respectively. In addition, the reads from placencental samples were classified as belonging to the phyla, Actinobacteria, Firmicutes, Bacteroidetes, Proteobacteria, with Proteobacteria dominated by the classes Pseudomonadales and Gammaproteobacteria with smaller amounts of Actinobacteria and Bacteroidetes. There was no significant difference between the placental bacterial species of early-/late-onset PE compared with age-matched normotensive controls, respectively. Further analysis found no correlation between bacterial species and early- or late-onset PE.

CONCLUSION: The present results demonstrate a low biomass of bacterial species, which might further indicate that the placental samples had very low levels of bacteria species and there is no correlation between the bacterial composition and early- or late-onset PE.},
}

@article {pmid39414684,
year = {2024},
author = {Siqueira, JS and de Carvalho, LAL and Santos, CHB and Frezarin, ET and Pinheiro, DG and Nicodemo, D and Desoignies, N and Rigobelo, EC},
title = {Influence of Growth Support on the Diversity, Composition, and Functionality of Microbial Communities Associated with Tillandsia recurvata.},
journal = {Microbial ecology},
volume = {87},
number = {1},
pages = {129},
pmid = {39414684},
issn = {1432-184X},
mesh = {*Microbiota ; *Bacteria/classification/genetics/isolation & purification ; *Plant Roots/microbiology ; *Plant Leaves/microbiology ; Fungi/classification/genetics/isolation & purification/physiology ; Biodiversity ; Trees/microbiology ; Soil Microbiology ; },
abstract = {Tillandsia recurvata is an epiphytic plant commonly found in tropical regions and colonizes tree trunks, fences, and power wires. This plant plays an important role in interacting with trees, sharing microorganisms, and performing specific functions in the process of tree colonization. The objective of this study was to evaluate and compare the microbiomes of T. recurvata collected from two different locations (trees and fences) and two plant tissues (leaves and roots). The hypothesis of this study was that the microbiome of T. recurvata is composed of microorganisms that would provide nutritional support to compensate for the lack of nutrients in a particular growth support. The results showed significant differences in microbial diversity between trees and fences, with trees exhibiting higher richness and more complex microbial networks. Proteobacteria was the most prevalent bacterial phylum, with Actinobacteria and Sphingomonas also playing key roles in nitrogen fixation and plant growth. Fungal communities were similar across locations, with Ascomycota and Basidiomycota being predominant, but Paraconiothyrium and Nigrospora showed significant differences in abundance between trees and fences. Functional analysis indicated similar metabolic profiles across leaf and root samples, with key functions for T. recurvata including carbohydrate and amino acid metabolism, stress control, and biofertilization.},
}

*Microbiota
*Bacteria/classification/genetics/isolation & purification
*Plant Roots/microbiology
*Plant Leaves/microbiology
Fungi/classification/genetics/isolation & purification/physiology
Biodiversity
Trees/microbiology
Soil Microbiology

@article {pmid39414630,
year = {2024},
author = {Córdoba-Agudelo, M and Arboleda-Rivera, JC and Borrego-Muñoz, DA and Ramírez-Cuartas, CA and Pérez-Jaramillo, JE},
title = {Key Chemical Soil Parameters for the Assembly of Rhizosphere Bacteria Associated with Avocado Cv Hass Grafted on Landrace Rootstocks.},
journal = {Current microbiology},
volume = {81},
number = {12},
pages = {412},
pmid = {39414630},
issn = {1432-0991},
mesh = {*Persea/microbiology ; *Rhizosphere ; *Soil Microbiology ; *Bacteria/classification/genetics/isolation & purification/metabolism ; *Soil/chemistry ; *Microbiota ; *RNA, Ribosomal, 16S/genetics ; *Plant Roots/microbiology ; Colombia ; Phylogeny ; },
abstract = {Avocado cultivation holds significant economic importance in many countries, ranking Colombia as the fifth largest global producer. Particularly, the Hass cultivar plays a pivotal role in Colombia's avocado industry, especially in the Department of Antioquia, the primary export region. This cultivar is grown under diverse soil and climate conditions and exhibits considerable genetic polymorphism due to the hybridization of varieties of agronomic significance, leading to a diverse array of landrace rootstocks. However, the role of soil conditions and rootstock genotype in structuring rhizosphere bacterial communities is still lacking. In addressing this knowledge gap, we investigated the influence of two soil conditions on the structure of rhizosphere bacterial communities associated with two landrace genotypes of Persea americana cv. Hass, utilizing 16S rRNA sequencing. Notably, no significant differences related to genotypes were observed. This study reports that the rhizosphere bacterial microbiome remains consistent across avocado landrace rootstocks, while variations in key parameters such as phosphorus, pH, Mg, and Ca drive distinct rhizosphere effects. Our results reveal that despite the soils having similar management, increases in these crucial parameters can lead to bacterial communities with lower alpha diversity and a more complex co-occurrence network. In addition, we found substantial variations in beta diversity, bacterial composition, and metagenome predictions between the two farms, underscoring the role of soil variables in shaping the bacterial microbiome. These findings provide valuable insights into the factors influencing the bacterial communities that may play a role in the health and productivity of crops with agro-industrial potential, such as Hass avocado.},
}

*Persea/microbiology
*Rhizosphere
*Soil Microbiology
*Bacteria/classification/genetics/isolation & purification/metabolism
*Soil/chemistry
*Microbiota
*RNA, Ribosomal, 16S/genetics
*Plant Roots/microbiology
Colombia
Phylogeny

@article {pmid39414535,
year = {2024},
author = {Feng, B and Lu, Y and Zhang, B and Zhu, Y and Su, Z and Tang, L and Yang, L and Wang, T and He, C and Li, C and Zhao, J and Zheng, X and Zheng, G},
title = {Integrated microbiome and metabolome analysis reveals synergistic efficacy of basil polysaccharide and gefitinib in lung cancer through modulation of gut microbiota and fecal metabolites.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {135992},
doi = {10.1016/j.ijbiomac.2024.135992},
pmid = {39414535},
issn = {1879-0003},
abstract = {Emerging evidence suggests that gut microbiota and its metabolites significantly influence the effectiveness of EGFR-TKIs (e.g., gefitinib, erlotinib) in lung cancer treatment. Plant polysaccharides can interact with gut microbiota, leading to changes in the host-microbe metabolome that may affect drug metabolism and therapeutic outcomes. Our previous research demonstrated the efficacy of basil polysaccharide (BPS) in treating various cancers by regulating hypoxic microenvironment and inhibiting epithelial-mesenchymal transition process. However, the potential impact of BPS on gut microbiota has not been thoroughly explored. In this study, we employed an immunodeficient gefitinib-resistant xenograft mouse model to explore whether BPS enhances the antitumor effects of gefitinib. A multi-omics approach, including 16S rDNA amplicon sequencing and LC-MS, was used to elucidate these synergistic effects. Our findings indicate that BPS can enhance tumor responsiveness to gefitinib by modulating the gut microbiota and its metabolites through multiple metabolic pathways. These changes in gut microbiota and metabolites could potentially affect cancer related signaling pathway and lung resistance-related protein, which are pivotal in determining the efficacy of EGFR-TKIs in cancer treatment.},
}

@article {pmid39414243,
year = {2024},
author = {Chantarangkul, C and Phuengmaung, P and Leelahavanichkul, A and Piewngam, P and Otto, M and Taweechotipatr, M},
title = {Lipid-lowering and antioxidant properties of probiotic Bifidobacterium animalis MSMC83 in rats on a high-fat diet.},
journal = {Beneficial microbes},
volume = {},
number = {},
pages = {1-16},
doi = {10.1163/18762891-bja00043},
pmid = {39414243},
issn = {1876-2891},
abstract = {Hyperlipidaemia, the abnormally high concentration of lipids such as cholesterol in the body, has a series of deleterious effects on health that are least in part are due to increased inflammation and oxidative stress. Probiotics are living microorganisms that possess the efficacy to improve health. Among the many effects that have been ascribed to probiotics is the potential to lower the body lipid content. Here, we used a rat model of induced hyperlipidaemia to assess the lipid-lowering and antioxidant properties of the probiotic strain Bifidobacterium animalis MSMC83 as well as its impact on intestinal barrier immunity and the intestinal microbiota. Oral probiotic intake led to a reduction of body weight, fasting blood glucose, and lipid levels, and increased expression of cholesterol-7α-hydroxylase and antioxidant enzymes. Additionally, B. animalis MSMC83 decreased the levels of liver enzymes and pro-inflammatory cytokines, leading to reduced hepatic steatosis. Furthermore, it re-established intestinal barrier integrity as shown by restoration of the tight junction protein zonula occludens-1 amount and reduced pathogen-induced inflammation in the intestinal epithelium as shown by readjusted expression of toll-like receptors (TLRs). Moreover B. animalis MSMC83 contributed to the maintenance of a balanced, diverse microbiome. Thus, our results indicate that B. animalis MSMC83 alleviates risk factors associated with hyperlipidaemia, suggesting its use as a probiotic to counter the effects associated with unhealthy diets.},
}

@article {pmid39414067,
year = {2024},
author = {Gou, Y and Lin, F and Dan, L and Zhang, D},
title = {Exposure to toluene diisocyanate induces dysbiosis of gut-lung homeostasis: Involvement of gut microbiota.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {363},
number = {Pt 1},
pages = {125119},
doi = {10.1016/j.envpol.2024.125119},
pmid = {39414067},
issn = {1873-6424},
abstract = {Toluene diisocyanate (TDI) is a major industrial compound that induces occupational asthma with steroid-resistant properties. Recent studies suggest that the gastrointestinal tract may be an effective target for the treatment of respiratory diseases. However, the alterations of the gut-lung axis in TDI-induced asthma remain unexplored. Therefore, in this study, a model of stable occupational asthma caused by TDI exposure was established to detect the alteration of the gut-lung axis. Exposure to TDI resulted in dysbiosis of the gut microbiome, with significant decreases in Barnesiella_intestinihominis, Faecalicoccus_pleomorphus, Lactobacillus_apodemi, and Lactobacillus_intestinalis, but increases in Alistipes_shahii and Odoribacter_laneus. The largest change in abundance was in Barnesiella_intestinihominis, which decreased from 12.14 per cent to 6.18 per cent. The histopathological abnormalities, including shorter length of intestinal villi, thinner thickness of muscularis, reduced number of goblet cells and inflammatory cell infiltration, were found in TDI-treated mice compared to control mice. In addition, increased permeability (evidenced by significantly reduced levels of ZO-1, Occludin and Claudin-1) and activation of TLR4/NF-κB signaling were observed in the intestine of these TDI-exposed mice. Concurrently, exposure to TDI resulted in airway hyperresponsiveness, overt cytokine production (e.g., IL-4, IL-5, IL-13, IL-25, and IL-33), and elevated IgE level within the respiratory tract. The expression of tight junction proteins is reduced and TLR4/NF-κB signaling is activated in the lung following TDI treatment. In addition, correlation analyses showed that changes in the gut microbiota were correlated with TDI exposure-induced airway inflammation. In conclusion, the present study suggests that the immune gut-lung axis may be involved in the development of TDI-induced asthma, which may have implications for potential interventions against steroid-resistant asthma.},
}

@article {pmid39414049,
year = {2024},
author = {Utembe, W and Kamng'ona, AW},
title = {Inhalation exposure to chemicals, microbiota dysbiosis and adverse effects on humans.},
journal = {The Science of the total environment},
volume = {955},
number = {},
pages = {176938},
doi = {10.1016/j.scitotenv.2024.176938},
pmid = {39414049},
issn = {1879-1026},
abstract = {As revealed by culture-independent methodologies, disruption of the normal lung microbiota (LM) configuration (LM dysbiosis) is a potential mediator of adverse effects from inhaled chemicals. LM, which consists of microbiota in the upper and lower respiratory tract, is influenced by various factors, including inter alia environmental exposures. LM dysbiosis has been associated with multiple respiratory pathologies such as asthma, lung cancer, idiopathic pulmonary fibrosis (IPF), chronic obstructive pulmonary disease (COPD) and cystic fibrosis (CF). Chemically-induced LM dysbiosis appears to play significant roles in human respiratory diseases, as has been shown for some air pollutants, cigarette smoke and some inhalable chemical antibiotics. Lung microbiota are also linked with the central nervous system (CNS) in the so-called lung-brain axis. Inhaled chemicals that undergo mucociliary clearance may be linked to respiratory conditions through gut microbiota (GM) dysbiosis in the so-called Gut-Lung axis. However, current linkages of various disease states to LM appears to be associative, with causal linkages requiring further studies using more robust approaches, methods and techniques that are different from those applied in studies involving (GM). Most importantly, the sampling techniques determine the level of risk of cross contamination. Furthermore, the development of continuous or semi-continuous systems designed to replicate the lung microbiome will go a long way to further LM dysbiosis studies. These challenges notwithstanding, the preponderance of evidence points to the significant role of LM-mediated chemical toxicity in human disease and conditions.},
}

@article {pmid39413617,
year = {2024},
author = {Zhang, S and Sun, Z and Li, Y and Du, X and Qian, K and Yang, L and Jia, G and Yin, J and Liao, S and Zhou, Z},
title = {Agmatine attenuates the severity of immunometabolic disorders by suppressing macrophage polarization: an in vivo study using an ulcerative colitis mouse model.},
journal = {Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie},
volume = {180},
number = {},
pages = {117549},
doi = {10.1016/j.biopha.2024.117549},
pmid = {39413617},
issn = {1950-6007},
abstract = {Agmatine, an endogenous polyamine generated by the gut microbiota, positively affects host lifespan by regulating mononuclear cell or macrophage function. Although the regulatory pathways governing monocyte/macrophage differentiation have been well studied, the influence of the microbiome and its metabolites on monocyte/macrophage function have not been fully elucidated. To address this, we aimed to investigate the mechanisms whereby agmatine inhibits immunometabolic disorders using the colon of ulcerative colitis (UC) model mice. Agmatine (10 mM) attenuated pathological damage to colonic tissue and significantly improved the survival rate of UC model mice. In particular, treatment of UC model mice with 0.4, 2, and 10 mM agmatine resulted in mortality rates of 70 %, 20 %, 10 %, and 0 %, respectively. In a macrophage-depletion model, agmatine regulated the inflammatory microenvironment by affecting macrophages: it reduced the proportion of M1 macrophages and increased that of M2 macrophages in UC model mice. In cultured macrophages, agmatine inhibited lipopolysaccharide-induced inflammatory cytokine and NO secretion, as detected by enzyme-linked immunosorbent assay and the Griess assay, respectively. Agmatine partially reduced inflammatory factor production by inhibiting histone deacetylase, as detected by fluorometric assay. These findings provide evidence that agmatine efficiently suppresses macrophage polarization in UC mice, highlighting its potential as an anti-inflammatory agent against UC.},
}

@article {pmid39413077,
year = {2024},
author = {Lin, B and Pathak, JL and Gao, H and Zhou, Z and Ser, HL and Wu, L and Lee, LH and Wang, L and Chen, J and Zhong, M},
title = {A pilot study examining periodontally healthy middle-aged humans and monkeys display different levels of alveolar bone resorption, gingival inflammatory infiltrate, and salivary microbiota profile.},
journal = {PloS one},
volume = {19},
number = {10},
pages = {e0311282},
pmid = {39413077},
issn = {1932-6203},
mesh = {Humans ; Animals ; *Saliva/microbiology ; Male ; Pilot Projects ; Female ; *Microbiota ; Middle Aged ; *Alveolar Bone Loss/microbiology/pathology/diagnostic imaging ; Adult ; RNA, Ribosomal, 16S/genetics ; Gingivitis/microbiology/pathology ; Gingiva/microbiology/pathology ; Periodontitis/microbiology/pathology ; },
abstract = {BACKGROUND: Monkeys are an appropriate model for periodontal research owing to their similar dental anatomy and physiology unlike humans. Extensive literature exists on pathological periodontitis in monkeys and humans, although concerns regarding whether healthy middle-aged monkeys and humans display the same periodontal and oral microbial status remains unclear.

AIMS AND OBJECTIVES: The current study aimed to compare alveolar bone resorption, gingival inflammatory infiltrate, and salivary microbiota profile in periodontally healthy middle-aged humans and monkeys.

METHODS: CBCT examination and histological analysis were performed to compare the periodontal status in middle-aged healthy humans and monkeys. Oral saliva16S rRNA sequencing was performed to analyze the oral microbial profile.

RESULTS: The alveolar resorption was compared between humans and monkeys, to determine the periodontal health. The percentage attachment of attachment loss was more around the posteriors teeth in humans when compared to monkeys (p<0.05). The degree of gingival inflammation was analyzed in both the groups, the expression of CD 34,45was higher in humans. 16S rRNA analysis demonstrated less diversity of salivary microorganisms in humans than in monkeys. The relative abundance of Aggregatibacter, Haemophilus, Gemella, and Porphyromonas at the genus level was significantly less in humans than in monkeys (p(<0.05).

CONCLUSION: The periodontally healthy middle-aged humans and monkeys display different alveolar bone resorption and gingival inflammatory infiltrate levels. Furthermore, the salivary microbiota profile showed distinctly different oral microbiomes in these two primates. Our results suggest that the difference in alveolar bone status and gingival inflammatory infiltrate in healthy humans and monkeys might be associated with the diversity of the oral microbiome.},
}

Humans
Animals
*Saliva/microbiology
Male
Pilot Projects
Female
*Microbiota
Middle Aged
*Alveolar Bone Loss/microbiology/pathology/diagnostic imaging
Adult
RNA, Ribosomal, 16S/genetics
Gingivitis/microbiology/pathology
Gingiva/microbiology/pathology
Periodontitis/microbiology/pathology

@article {pmid39412697,
year = {2024},
author = {Kim, G and Kim, S and Jung, H and Kang, S and Park, G and Shin, H},
title = {The Impact of Makgeolli Consumption on Gut Microbiota: An Enterotype-Based Preliminary Study.},
journal = {Journal of microbiology (Seoul, Korea)},
volume = {},
number = {},
pages = {},
pmid = {39412697},
issn = {1976-3794},
support = {2023R1A6C101A045//Ministry of Education/ ; 2022R1A6A1A03055869//Ministry of Education/ ; 321034-5//Korea Institute of Planning and Evaluation for Technology in Food, Agriculture and Forestry/ ; },
abstract = {Makgeolli, a traditional Korean liquor, contains components such as lactic acid bacteria and dietary fiber, which can induce changes in the gut microbiome. Since variations in microbiome responses may exist between enterotypes-classifications based on the dominant bacterial populations in the gut-we hypothesized that the consumption of makgeolli leads to enterotype-dependent differences in gut microbial structures among healthy participants. This study aimed to determine the effect of makgeolli consumption on gut microbial structures by stratifying all participants into two enterotype groups: Bacteroides-dominant type (B-type, n = 7) and Prevotella-dominant type (P-type, n = 4). The B-type showed an increase in alpha diversity, while no significant difference was observed in the P-type following makgeolli consumption. The composition of gut microbiota significantly changed in the B-type, whereas no noticeable alteration was observed in the P-type after makgeolli consumption. Notably, Prevotella exhibited the most significant changes only in the P-type. In line with the increased abundance of Prevotella, the genes associated with carbohydrate metabolism, including pentose/glucuronate interconversions, fructose/mannose metabolism, starch/sucrose metabolism and amino sugar/nucleotide sugar metabolism were significantly enriched following makgeolli consumption in the P-type. These findings suggest that makgeolli consumption induces enterotype-dependent alterations in gut microbial composition and metabolic pathways, highlighting the potential for personalized dietary interventions.},
}

@article {pmid39412663,
year = {2024},
author = {Gogoi, K and Gogoi, H and Borgohain, M and Saikia, R and Chikkaputtaiah, C and Hiremath, S and Basu, U},
title = {The molecular dynamics between reactive oxygen species (ROS), reactive nitrogen species (RNS) and phytohormones in plant's response to biotic stress.},
journal = {Plant cell reports},
volume = {43},
number = {11},
pages = {263},
pmid = {39412663},
issn = {1432-203X},
support = {FBR0203010//CSIR-North East Institute of Science and Technology/ ; },
mesh = {*Reactive Oxygen Species/metabolism ; *Plant Growth Regulators/metabolism ; *Reactive Nitrogen Species/metabolism ; *Stress, Physiological ; *Plants/metabolism/parasitology/microbiology/immunology ; Plant Immunity ; Signal Transduction ; Plant Diseases/microbiology/parasitology/immunology ; Host-Pathogen Interactions ; Oxidation-Reduction ; },
abstract = {Reactive oxygen species (ROS) and reactive nitrogen species (RNS) are critical for plant development as well as for its stress response. They can function as signaling molecules to orchestrate a well-defined response of plants to biotic stress. These responses are further fine-tuned by phytohormones, such as salicylic acid, jasmonic acid, and ethylene, to modulate immune response. In the past decades, the intricacies of redox and phytohormonal signaling have been uncovered during plant-pathogen interactions. This review explores the dynamic interplay of these components, elucidating their roles in perceiving biotic threats and shaping the plant's defense strategy. Molecular regulators and sites of oxidative burst have been explored during pathogen perception. Further, the interplay between various components of redox and phytohormonal signaling has been explored during bacterial, fungal, viral, and nematode infections as well as during insect pest infestation. Understanding these interactions highlights gaps in the current knowledge and provides insights into engineering crop varieties with enhanced resistance to pathogens and pests. This review also highlights potential applications of manipulating regulators of redox signaling to bolster plant immunity and ensure global food security. Future research should explore regulators of these signaling pathways as potential target to develop biotic stress-tolerant crops. Further insights are also needed into roles of endophytes and host microbiome modulating host ROS and RNS pool for exploiting them as biocontrol agents imparting resistance against pathogens in plants.},
}

*Reactive Oxygen Species/metabolism
*Plant Growth Regulators/metabolism
*Reactive Nitrogen Species/metabolism
*Stress, Physiological
*Plants/metabolism/parasitology/microbiology/immunology
Plant Immunity
Signal Transduction
Plant Diseases/microbiology/parasitology/immunology
Host-Pathogen Interactions
Oxidation-Reduction

@article {pmid39412514,
year = {2024},
author = {Han, M and Wang, X and Su, L and Pan, S and Liu, N and Li, D and Liu, L and Cui, J and Zhao, H and Yang, F},
title = {Intestinal microbiome dysbiosis increases Mycobacteria pulmonary colonization in mice by regulating the Nos2-associated pathways.},
journal = {eLife},
volume = {13},
number = {},
pages = {},
pmid = {39412514},
issn = {2050-084X},
support = {242102521045//Science and Technology Research Project of Henan Province/ ; 242102310202//Science and Technology Research Project of Henan Province/ ; LHGJ20230525//Project of Health Commission of Henan Province/ ; Open Project of the Institute of Tuberculosis XYJHB20210//Xinxiang Medical University/ ; Tuberculosis Capacity Improvement Project 2023-68//Henan Provincial Health Commission/ ; },
mesh = {Animals ; *Dysbiosis/microbiology ; *Gastrointestinal Microbiome/physiology ; Mice ; *Lung/microbiology ; *Nitric Oxide Synthase Type II/metabolism/genetics ; Mice, Inbred C57BL ; Mycobacterium tuberculosis ; Tuberculosis/microbiology ; },
abstract = {Increasing researches reveal gut microbiota was associated with the development of tuberculosis (TB). How to prevent or reduce Mycobacterium tuberculosis colonization in the lungs is a key measure to prevent TB. However, the data on gut microbiota preventing Mycobacterium colonization in the lungs were scarce. Here, we established the clindamycin-inducing intestinal microbiome dysbiosis and fecal microbial transplantation models in mice to identify gut microbiota's effect on Mycobacterium's colonization in the mouse lungs and explore its potential mechanisms. The results showed that clindamycin treatment altered the diversity and composition of the intestinal bacterial and fungal microbiome, weakened the trans-kingdom network interactions between bacteria and fungi, and induced gut microbiome dysbiosis in the mice. Gut microbiota dysbiosis increases intestinal permeability and enhances the susceptibility of Mycobacterium colonization in the lungs of mice. The potential mechanisms were gut microbiota dysbiosis altered the lung transcriptome and increased Nos2 expression through the 'gut-lung axis'. Nos2 high expression disrupts the intracellular antimicrobial and anti-inflammatory environment by increasing the concentration of nitric oxide, decreasing the levels of reactive oxygen species and Defb1 in the cells, and promoting Mycobacteria colonization in the lungs of mice. The present study raises a potential strategy for reducing the risks of Mycobacteria infections and transmission by regulating the gut microbiome balance.},
}

Animals
*Dysbiosis/microbiology
*Gastrointestinal Microbiome/physiology
Mice
*Lung/microbiology
*Nitric Oxide Synthase Type II/metabolism/genetics
Mice, Inbred C57BL
Mycobacterium tuberculosis
Tuberculosis/microbiology

@article {pmid39412394,
year = {2024},
author = {Isokääntä, H and Pinto da Silva, L and Karu, N and Kallonen, T and Aatsinki, AK and Hankemeier, T and Schimmel, L and Diaz, E and Hyötyläinen, T and Dorrestein, PC and Knight, R and Orešič, M and Kaddurah-Daouk, R and Dickens, AM and Lamichhane, S},
title = {Correction to "Comparative Metabolomics and Microbiome Analysis of Ethanol versus OMNImet/gene•GUT Fecal Stabilization".},
journal = {Analytical chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.analchem.4c05417},
pmid = {39412394},
issn = {1520-6882},
}

@article {pmid39412349,
year = {2024},
author = {Wang, HS and Shih, SY and Huang, YL and Chang, CC and Tsai, H},
title = {Full-length 16S rRNA gene amplicon analysis of gut microbiota in pigs fed with different diets in growing and finishing stages.},
journal = {Animal biotechnology},
volume = {35},
number = {1},
pages = {2414299},
doi = {10.1080/10495398.2024.2414299},
pmid = {39412349},
issn = {1532-2378},
mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; *RNA, Ribosomal, 16S/genetics ; Swine ; *Animal Feed/analysis ; *Diet/veterinary ; Feces/microbiology/chemistry ; Bacteria/classification/genetics/isolation & purification ; Dietary Proteins/metabolism ; },
abstract = {The present study utilized full-length 16S rRNA gene sequencing to investigate the impact of dietary protein content on the composition and function of gut microbiota, and to analyze the gut microbiota of pigs in the growing (30 kg) and finishing (120 kg) stages under different feeding conditions. The results indicated that the gut microbiota was significantly different between pigs fed high- and low-protein diets. Comparing fecal samples from pigs at 30 and 120 kg, pigs at 30 kg showed a significant increase in the relative abundance of Clostridium butyricum, whereas at 120 kg, the abundance of Lactobacillus reuteri and Lactobacillus johnsonii decreased. To access the functional profiles and metabolic pathways based on amplicon sequence variants (ASVs), the microbiome of the 120 kg exhibited significant enrichments in Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways related to metabolism-related category, including Alanine, aspartate and glutamate metabolism, Tyrosine and Thiamin metabolism, and Inositol phosphate metabolism. Meanwhile, analysis using the MetaCyc database showed that the metabolic pathways of the 30 kg group were significantly distinct when compared to the 120 kg of fecal samples. Overall, the findings indicated that the gut microbiota composition and function in the 30 and 120 kg fecal samples were markedly shaped by different dietary protein levels.},
}

Animals
*Gastrointestinal Microbiome/physiology
*RNA, Ribosomal, 16S/genetics
Swine
*Animal Feed/analysis
*Diet/veterinary
Feces/microbiology/chemistry
Bacteria/classification/genetics/isolation & purification
Dietary Proteins/metabolism

@article {pmid39412260,
year = {2024},
author = {Mu, C and Kesler, M and Chen, X and Shearer, J and Teskey, GC and Rho, JM},
title = {Exogenous ketones exert antiseizure effects and modulate the gut microbiome and mycobiome in a clinically relevant murine model of epilepsy.},
journal = {Epilepsia},
volume = {},
number = {},
pages = {},
doi = {10.1111/epi.18150},
pmid = {39412260},
issn = {1528-1167},
support = {//Alberta Children's Hospital Research Institute/ ; FRN-162177/CAPMC/CIHR/Canada ; },
abstract = {OBJECTIVE: Despite growing interest in the potential use of exogenous ketones for the treatment of epilepsy, their impact on seizures and the gut microbiome and mycobiome remain unclear.

METHODS: Here, we examined the effects of both oral gavage and subcutaneous (SC) injection of a ketone ester (KE) in spontaneously epileptic Kcna1-null (KO) mice that model seminal aspects of human temporal lobe epilepsy. Electroencephalographic recordings and biochemical analyses were performed in KE-treated KO mice. Fecal microbial and fungal communities were profiled to determine whether the antiseizure activity of KE involves changes in the gut microbiome.

RESULTS: We found that exogenous KE administration by SC injection was more effective than oral gavage in terms of rendering antiseizure effects while generating similar degrees of ketonemia. However, reductions in mean daily seizure counts were accompanied by overall alterations in the fecal bacterial microbiome. Either oral or SC injection imposed a greater impact on the microbiome in male than female mice. In males, oral KE decreased Bacteroidota phylum and genera of Ligilactobacillus and Muribaculaceae, whereas SC injection decreased Bacteroides, Lactobacillus, and Lachnospiraceae. The fecal mycobiome was affected by KE injection to a greater degree than by oral gavage, and more in females than in males, as reflected by an increase in Ascomycota and Saccharomyces. Correlation analysis between microbiome and seizure counts revealed that in mice receiving KE injection, the seizure count was positively correlated with an amplicon sequencing variant of Lactobacillus (Spearman rho = .64, p = .03) and tended toward a negative correlation with Saccharomyces (Spearman rho = -.57, p = .057).

SIGNIFICANCE: Our findings demonstrate that exogenous ketone administration alone can induce antiseizure effects equally via different routes of administration, and that they induce differential shifts in both the bacterial microbiome and mycobiome.},
}

@article {pmid39386691,
year = {2024},
author = {Gustafson, KL and Rodriguez, TR and McAdams, ZL and Coghill, LM and Ericsson, AC and Franklin, CL},
title = {Failure of colonization following gut microbiota transfer exacerbates DSS-induced colitis.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {39386691},
issn = {2692-8205},
support = {T32 GM008396/GM/NIGMS NIH HHS/United States ; T32 OD011126/OD/NIH HHS/United States ; U42 OD010918/OD/NIH HHS/United States ; },
abstract = {To study the impact of differing specific pathogen-free gut microbiomes (GMs) on a murine model of inflammatory bowel disease, selected GMs were transferred using embryo transfer (ET), cross-fostering (CF), and co-housing (CH). Prior work showed that the GM transfer method and the microbial composition of donor and recipient GMs can influence microbial colonization and disease phenotypes in dextran sodium sulfate-induced colitis. When a low richness GM was transferred to a recipient with a high richness GM via CH, the donor GM failed to successfully colonize, and a more severe disease phenotype resulted when compared to ET or CF, where colonization was successful. By comparing CH and gastric gavage for fecal material transfer, we isolated the microbial component of this effect and determined that differences in disease severity and survival were associated with microbial factors rather than the transfer method itself. Mice receiving a low richness GM via CH and gastric gavage exhibited greater disease severity and higher expression of pro-inflammatory immune mediators compared to those receiving a high richness GM. This study provides valuable insights into the role of GM composition and colonization in disease modulation.},
}

@article {pmid39412235,
year = {2024},
author = {Huang, MH and Liu, CX and Huang, YS and He, TY and Dong, ZQ},
title = {Genetic association of gut microbiota with osteoarthritis: a multivariable Mendelian randomization study considering medication use.},
journal = {Journal of medical microbiology},
volume = {73},
number = {10},
pages = {},
doi = {10.1099/jmm.0.001920},
pmid = {39412235},
issn = {1473-5644},
mesh = {Humans ; *Mendelian Randomization Analysis ; *Gastrointestinal Microbiome/genetics/drug effects ; *Genome-Wide Association Study ; *Osteoarthritis/microbiology/drug therapy/epidemiology/genetics ; *Polymorphism, Single Nucleotide ; },
abstract = {Background. The interplay among human gut microbiota (GM) composition, osteoarthritis (OA) and OA-related medication use has been extensively discussed. However, to date, there has been no exploration of the genetic correlation among these three factors.Hypothesis/Gap. The potential causal link between GM and OA), and whether medications influence this relationship, remains unclear.Methods. We utilized bidirectional Mendelian randomization (MR) to explore the genetic associations between GM and OA. We leveraged genome-wide association study (GWAS) summary statistics from the MiBioGen and GO consortia, which provided data on GM taxa and OA cases, respectively. We identified outlier single-nucleotide polymorphisms using radial-MR and assessed causal associations using inverse variance weighting (IVW), weighted median and MR-Egger methods. Robust outcomes, consistent across these methods, were reported. We addressed potential biases through tests for horizontal pleiotropy and heterogeneity, supplemented by the Mendelian randomization pleiotropy residual sum and outlier method. Multivariable MR techniques were applied to adjust for OA medication use using UK Biobank data.Results. IVW estimates revealed a significant increase in hip OA risk for Gordonibacter and Eubacterium (brachy group) [odds ratio (OR): 1.09, 95% confidence interval (CI): 1.04-1.15, P=7.82E-04; OR: 1.09, 95% CI: 1.03-1.16, P=4.67E-03, respectively]. Conversely, Senegalimassilia, Slackia and Streptococcus exhibited protective effects (OR: 0.88, P=2.14E-02; OR: 0.88, P=3.33E-02; 0.91, P=4.29E-02). Sutterella increased the risk of knee OA (OR=1.15, 95% CI: 1.07-1.25, P=4.06E-04), while Haemophilus decreased it (OR=0.94, 95% CI: 0.88-1.00, P=4.26E-02). No significant heterogeneity or horizontal pleiotropy was observed in the results. Even after accounting for the potential confounding effect of medication, the results remained consistent. No reverse causation was detected.Conclusions. Our MR study reveals gut microbiome links to OA risk. Associations hold after adjusting for medication, indicating a potential causal connection between GM and OA.},
}

Humans
*Mendelian Randomization Analysis
*Gastrointestinal Microbiome/genetics/drug effects
*Genome-Wide Association Study
*Osteoarthritis/microbiology/drug therapy/epidemiology/genetics
*Polymorphism, Single Nucleotide

@article {pmid39411833,
year = {2024},
author = {Hall, CV and Hepsomali, P and Dalile, B and Scapozza, L and Gurry, T},
title = {Effects of a diverse prebiotic fibre blend on inflammation, the gut microbiota and affective symptoms in metabolic syndrome: a pilot open-label randomised controlled trial.},
journal = {The British journal of nutrition},
volume = {},
number = {},
pages = {1-12},
doi = {10.1017/S0007114524002186},
pmid = {39411833},
issn = {1475-2662},
abstract = {Emerging evidence suggests that low-grade systemic inflammation plays a key role in altering brain activity, behaviour and affect. Modulation of the gut microbiota using prebiotic fibre offers a potential therapeutic tool to regulate inflammation, mediated via the production of short-chain fatty acids (SCFA). However, the impact of prebiotic consumption on affective symptoms and the possible contribution from inflammation, gut symptoms and the gut microbiome are currently underexamined. In this 12-week study, the effects of a diverse prebiotic blend on inflammation, gut microbiota profiles and affective symptoms in a population with metabolic syndrome (MetS) were examined. Sixty males and females with MetS meeting the criteria for MetS were randomised into a treatment group (n 40), receiving 10 g per day of a diverse prebiotic blend and healthy eating advice, and a control group (n 20), receiving healthy eating advice only. Our results showed a significant reduction in high sensitivity C-reactive protein (hs-CRP) in the treatment (-0·58 [-9·96 to-2·63]) compared with control (0·37 [-3·64 to-3·32]), alongside significant improvements in self-reported affective scores in the treatment compared with the control group. While there were no differences in relative abundance between groups at week 12, there was a significant increase from baseline to week 12 in fecal Bifidobacterium and Parabacteroides in the treatment group, both of which are recognised as SCFA producers. Multivariate regression analyses further revealed an association between gastrointestinal symptoms and hs-CRP with affective scores. Together, this study provides preliminary support for a diverse prebiotic blend for mood, stress and anxiety.},
}

@article {pmid39411786,
year = {2024},
author = {Vacca, F and Mules, TC and Camberis, M and Lavender, B and Noble, SL and Cait, A and Maclean, K and Mamum, J and Yumnam, B and Te Kawa, T and Ferrer-Font, L and Tang, JS and Gasser, O and Le Gros, G and Inns, S},
title = {Controlled infection with cryopreserved human hookworm induces CTLA-4 expression on Tregs and upregulates tryptophan metabolism.},
journal = {Gut microbes},
volume = {16},
number = {1},
pages = {2416517},
pmid = {39411786},
issn = {1949-0984},
mesh = {Humans ; *T-Lymphocytes, Regulatory/immunology ; *Tryptophan/metabolism ; Animals ; *CTLA-4 Antigen/metabolism/genetics ; *Cryopreservation ; *Hookworm Infections/immunology/parasitology ; *Larva/immunology ; Up-Regulation ; Adult ; Female ; Feces/parasitology/microbiology ; Ancylostomatoidea/immunology ; Male ; },
abstract = {Infecting humans with controlled doses of helminths, such as human hookworm (termed hookworm therapy), is proposed to prevent or treat various intestinal and extraintestinal diseases. However, full-scale clinical trials examining hookworm therapy are limited by the inability to scale-up the production of hookworm larvae to infect sufficient numbers of patients. With the aim of overcoming this challenge, this study infected four healthy individuals with hookworm larvae that had been reanimated from cryopreserved eggs to examine their viability and immunogenicity. We demonstrate that reanimated cryopreserved hookworm larvae establish a viable hookworm infection and elicit a similar immune response to larvae cultured from fresh stool. Furthermore, a refined understanding of the therapeutic mechanisms of hookworm is imperative to determine which diseases to target with hookworm therapy. To investigate potential therapeutic mechanisms, this study assessed changes in the immune cells, microbiome, and plasma metabolome in the four healthy individuals infected with cryopreserved hookworm larvae and another nine individuals infected with larvae cultured from freshly obtained stool. We identified potential immunoregulatory mechanisms by which hookworm may provide a beneficial effect on its host, including increased expression of CTLA-4 on regulatory T cells (Tregs) and upregulation of tryptophan metabolism. Furthermore, we found that a participant's baseline microbiome predicted the severity of symptoms and intestinal inflammation experienced during a controlled hookworm infection. In summary, our findings demonstrate the feasibility of full-scale clinical trials examining hookworm therapy by minimizing the reliance on human donors and optimizing the culturing process, thereby enabling viable hookworm larvae to be mass-produced and enabling on-demand inoculation of patients. Furthermore, this study provides insights into the complex interactions between helminths and their host, which could inform the development of novel therapeutic strategies.},
}

Humans
*T-Lymphocytes, Regulatory/immunology
*Tryptophan/metabolism
Animals
*CTLA-4 Antigen/metabolism/genetics
*Cryopreservation
*Hookworm Infections/immunology/parasitology
*Larva/immunology
Up-Regulation
Adult
Female
Feces/parasitology/microbiology
Ancylostomatoidea/immunology
Male

@article {pmid39411443,
year = {2024},
author = {Peng, Y and Liu, Y and Liu, Y and Wang, J},
title = {Comprehensive data optimization and risk prediction framework: machine learning methods for inflammatory bowel disease prediction based on the human gut microbiome data.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1483084},
pmid = {39411443},
issn = {1664-302X},
abstract = {Over the past decade, the prevalence of inflammatory bowel disease (IBD) has significantly increased, making early detection crucial for improving patient survival rates. Medical research suggests that changes in the human gut microbiome are closely linked to IBD onset, playing a critical role in its prediction. However, the current gut microbiome data often exhibit missing values and high dimensionality, posing challenges to the accuracy of predictive algorithms. To address these issues, we proposed the comprehensive data optimization and risk prediction framework (CDORPF), an ensemble learning framework designed to predict IBD risk based on the human gut microbiome, aiding early diagnosis. The framework comprised two main components: data optimization and risk prediction. The data optimization module first employed triple optimization imputation (TOI) to impute missing data while preserving the biological characteristics of the microbiome. It then utilized importance-weighted variational autoencoder (IWVAE) to reduce redundant information from the high-dimensional microbiome data. This process resulted in a complete, low-dimensional representation of the data, laying the foundation for improved algorithm efficiency and accuracy. In the risk prediction module, the optimized data was classified using a random forest (RF) model, and hyperparameters were globally optimized using improved aquila optimizer (IAO), which incorporated multiple strategies. Experimental results on IBD-related gut microbiome datasets showed that the proposed framework achieved classification accuracy, recall, and F1 scores exceeding 0.9, outperforming comparison models and serving as a valuable tool for predicting IBD onset risk.},
}

@article {pmid39411438,
year = {2024},
author = {Lv, J and Huo, C and Zhang, J and Huang, Y and Su, Y and Lv, Y and Xie, X and Chen, Z},
title = {Host genotype and age shape the microbial community in the rhizosphere soils of Camellia forests.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1440255},
pmid = {39411438},
issn = {1664-302X},
abstract = {Microbiota living in the rhizosphere influences plant growth and fitness, from the opposite perspective; whether host genotypes control its root microbiota is of great interest to forest breeders and microbiologists. To improve low-yield plantations and promote sustainable management of Camellia oleifera, high-throughput sequencing was used to study the chemical properties and microbiome in rhizosphere soil of Camellia forests under three genotypes (common C. oleifera, local C. gauchowensis, and C. chekiangoleosa) and three growth stages (sapling stage at 4-year-old, primary fruit stage at 7-year-old, and full fruiting stage at 11-year-old). The results showed that the rhizosphere soil organic matter (OM), nutrient concentrations, diversity, and community composition of the microbiome were significantly varied among different Camellia genotypes. The relative abundance of symbiotic and pathotrophic fungi in the rhizosphere soil of C. chekiangoleosa was significantly higher than that of C. gauchowensis. Concentrations of OM, available phosphorus (AP), and bacterial alpha diversity increased with tree age. Fungi of Saitozyma, Mortierella, and Glomeromycota and bacteria of Burkholderia-Caballeronia-Paraburkholderia and Vicinamibacterales had potential for fertilizer development for Camellia plantation. Camellia genotypes and growth stages were significantly correlated with the rhizosphere soil pH, OM, and available potassium (AK). Soil pH and OM were key factors that affected the microbiome in the Camellia rhizosphere soils. In conclusion, tree genotypes and growth stages shaped microbial communities in Camellia rhizosphere soils, and some plant growth-promoting rhizobacteria were identified as preliminary candidates for improving Camellia plantation growth.},
}

@article {pmid39411429,
year = {2024},
author = {Xiao, P and Wu, Y and Zuo, J and Grossart, HP and Sun, R and Li, G and Jiang, H and Cheng, Y and Wang, Z and Geng, R and Zhang, H and Ma, Z and Yan, A and Li, R},
title = {Differential microbiome features in lake-river systems of Taihu basin in response to water flow disturbance.},
journal = {Frontiers in microbiology},
volume = {15},
number = {},
pages = {1479158},
pmid = {39411429},
issn = {1664-302X},
abstract = {INTRODUCTION: In riverine ecosystems, dynamic interplay between hydrological conditions, such as flow rate, water level, and rainfall, significantly shape the structure and function of bacterial and microeukaryotic communities, with consequences for biogeochemical cycles and ecological stability. Lake Taihu, one of China's largest freshwater lakes, frequently experiences cyanobacterial blooms primarily driven by nutrient over-enrichment and hydrological changes, posing severe threats to water quality, aquatic life, and surrounding human populations. This study explored how varying water flow disturbances influence microbial diversity and community assembly within the interconnected river-lake systems of the East and South of Lake Taihu (ET&ST). The Taipu River in the ET region accounts for nearly one-third of Lake Taihu's outflow, while the ST region includes the Changdougang and Xiaomeigang rivers, which act as inflow rivers. These two rivers not only channel water into Lake Taihu but can also cause the backflow of lake water into the rivers, creating distinct river-lake systems subjected to different intensities of water flow disturbances.

METHODS: Utilizing high-throughput sequencing, we selected 22 sampling sites in the ET and ST interconnected river-lake systems and conducted seasonally assessments of bacterial and microeukaryotic community dynamics. We then compared differences in microbial diversity, community assembly, and co-occurrence networks between the two regions under varying hydrological regimes.

RESULTS AND DISCUSSION: This study demonstrated that water flow intensity and temperature disturbances significantly influenced diversity, community structure, community assembly, ecological niches, and coexistence networks of bacterial and eukaryotic microbes. In the ET region, where water flow disturbances were stronger, microbial richness significantly increased, and phylogenetic relationships were closer, yet variations in community structure were greater than in the ST region, which experienced milder water flow disturbances. Additionally, migration and dispersal rates of microbes in the ET region, along with the impact of dispersal limitations, were significantly higher than in the ST region. High flow disturbances notably reduced microbial niche width and overlap, decreasing the complexity and stability of microbial coexistence networks. Moreover, path analysis indicated that microeukaryotic communities exhibited a stronger response to water flow disturbances than bacterial communities. Our findings underscore the critical need to consider the effects of hydrological disturbance on microbial diversity, community assembly, and coexistence networks when developing strategies to manage and protect river-lake ecosystems, particularly in efforts to control cyanobacterial blooms in Lake Taihu.},
}

@article {pmid39410889,
year = {2024},
author = {Kumar, A and Hussain, S and Srivastava, N and Singh, G and Gulati, M and Kumar, R},
title = {Bridging the GAP: Probiotic Douches Redefining the Feminine Hygiene.},
journal = {Current pharmaceutical biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.2174/0113892010322564240929204907},
pmid = {39410889},
issn = {1873-4316},
abstract = {Vaginal douching is a centuries-old practice which is still in use, especially among adolescents. "Probiotic douches" are the vaginal douches that are formulated with probiotics and are intended to restore or maintain the vaginal microbiome balance. Probiotic douches are a new type of feminine hygiene product that claims to promote a balanced vaginal microbiome and improve overall well-being. However, the evidence supporting the use of probiotics for vaginal health is limited because of the variability in probiotic strains and dosages studied, and the lack of more comprehensive, long-term clinical trials. Most of the existing scientific literature on probiotics focuses on oral probiotic supplements and vaginal probiotic suppositories. Some potential benefits of probiotic douches include restoring a balanced vaginal microbiota, preventing, or managing infections, supporting local immune function, reducing odor and discharge, and enhancing overall vaginal comfort. However, it is important to note that these benefits have not been definitively proven and remain a subject of ongoing research. There are also potential risks associated with their use including disruption of the natural vaginal ecosystem by introducing foreign substances, risk of infection, and stability issues with the formulation that may lead to negative consequences. This review attempts to comprehend the critical need for robust scientific research to guide the safe and effective incorporation of probiotic douches into modern feminine hygiene practices, revolutionizing women's health, and well-being.},
}

@article {pmid39410868,
year = {2024},
author = {Atefi, N and Mohammadi, M and Bodaghabadi, M and Mehrali, M and Behrangi, E and Ghassemi, M and Jafarzadeh, A and Goodarzi, A},
title = {Evaluating the Effectiveness of Probiotic Supplementation in Combination With Doxycycline for the Treatment of Moderate Acne: A Randomized Double-Blind Controlled Clinical Trial.},
journal = {Journal of cosmetic dermatology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jocd.16614},
pmid = {39410868},
issn = {1473-2165},
abstract = {BACKGROUND: Acne is a chronic inflammatory skin disease that negatively affects patients' quality of life. Increasing antibiotic resistance is making acne less responsive to treatment. Probiotics are live microorganisms that can provide health benefits by fighting pathogens and maintaining intestinal homeostasis and skin microbiome balance. This study investigates the effects of probiotics in the treatment of acne vulgaris.

METHODS: In this randomized controlled clinical trial, 80 patients with moderate acne were divided into two groups of 40. All patients received the same topical treatment, which consisted of a daily antibacterial face wash and Adapalene gel every other night. The control group received one capsule of doxycycline (100 mg) daily, whereas the intervention group received one probiotic capsule daily in addition to doxycycline. Patients underwent photography of facial acne lesions, and treatment response was assessed using the global acne grading system (GAGS) and acne grading method at baseline, as well as during follow-up visits at 1, 2, and 3 months.

RESULTS: The global acne grading system indicated that both groups showed improvement. However, analyses revealed that outcomes were significantly better in the doxycycline plus probiotics group for the forehead (p = 0.018), chin (p = 0.021), and nose (p = 0.021). No significant differences were observed for the left and right cheeks, back, and chest areas, with the mean GAGS score reduction between the two groups differing by only 2%. Treatment with probiotics significantly reduced the severity of lesions compared to the control group (p < 0.001). The acne grading method also indicated that the intervention group had a significantly better treatment response than the control group (p < 0.001). Furthermore, treatment with probiotics did not result in any side effects.

CONCLUSION: Probiotics can serve as an effective and safe treatment option, enhancing the outcomes of routine acne treatments, particularly for patients with acne on the forehead, chin, and nose.},
}

@article {pmid39410854,
year = {2024},
author = {Khorashadizadeh, S and Abbasifar, S and Yousefi, M and Fayedeh, F and Moodi Ghalibaf, A},
title = {The Role of Microbiome and Probiotics in Chemo-Radiotherapy-Induced Diarrhea: A Narrative Review of the Current Evidence.},
journal = {Cancer reports (Hoboken, N.J.)},
volume = {7},
number = {10},
pages = {e70029},
pmid = {39410854},
issn = {2573-8348},
mesh = {Humans ; *Probiotics/administration & dosage/therapeutic use ; *Diarrhea/chemically induced/microbiology/prevention & control/etiology ; *Gastrointestinal Microbiome/drug effects/radiation effects ; Animals ; *Neoplasms/therapy/radiotherapy/drug therapy ; Chemoradiotherapy/adverse effects/methods ; Antineoplastic Agents/adverse effects ; },
abstract = {BACKGROUND: In this article, we review the most recent research on probiotics effects on diarrhea in both human and animal models of the condition along with the therapeutic potential of these compounds based on their findings.

RECENT FINDINGS: Nearly 50%-80% of cancer patients experience chemotherapy-induced diarrhea (CID), serious gastrointestinal toxicity of chemotherapeutic and radiation regimens that leads to prolonged hospitalizations, cardiovascular problems, electrolyte imbalances, disruptions in cancer treatment, poor cancer prognosis, and death. CID is typically categorized as osmotic diarrhea. The depletion of colonic crypts and villi by radiotherapy and chemotherapy agents interferes with the absorptive function of the intestine, thereby decreasing the absorption of chloride and releasing water into the intestinal lumen. Probiotic supplements have been found to be able to reverse the intestinal damage caused by chemo-radiation therapy by promoting the growth of crypt and villi and reducing inflammatory pathways. In addition, they support the modulation of immunological and angiogenesis responses in the gut as well as the metabolism of certain digestive enzymes by altering the gut microbiota.

CONCLUSION: Beyond the benefits of probiotics, additional clinical research is required to clarify the most effective strain combinations and dosages for preventing chemotherapy and radiotherapy diarrhea.},
}

Humans
*Probiotics/administration & dosage/therapeutic use
*Diarrhea/chemically induced/microbiology/prevention & control/etiology
*Gastrointestinal Microbiome/drug effects/radiation effects
Animals
*Neoplasms/therapy/radiotherapy/drug therapy
Chemoradiotherapy/adverse effects/methods
Antineoplastic Agents/adverse effects

@article {pmid39410847,
year = {2024},
author = {Fialova, L and Bartos, A and Kalousova, M and Noskova, L and Zelenkova, M and Slukova, M and Zima, T},
title = {Serum neurofilament light chain in response to probiotics in bi-center, double-blind, randomized, placebo-controlled clinical trial (CleverAge Biota).},
journal = {Biomedical papers of the Medical Faculty of the University Palacky, Olomouc, Czechoslovakia},
volume = {},
number = {},
pages = {},
doi = {10.5507/bp.2024.032},
pmid = {39410847},
issn = {1804-7521},
abstract = {BACKGROUND AND AIMS: Neurodegenerative disorders affecting the brain and spinal cord are caused by a large number of factors. More recently, imbalances in gut microbiota are found to be one factor linked directly to neurological dysfunction. Probiotics prevent cognitive decline. For the first time, the effect of probiotics was assessed by monitoring the concentrations of the neurodegeneration biomarker neurofilament light chains (NfL) in a well-defined group of community-dwelling individuals. The aim of this study was to determine whether administration of our new probiotics could reduce NfL concentrations.

METHODS: The serum NfL concentrations were measured in total of 190 serum samples of 85 older community-dwelling individuals. The participants were randomly divided into two groups: the PROPLA group and the PLAPRO group. Individuals in the PROPLA group started with a three-month use of probiotics and continued with a three-month use of placebo while the order was reversed in the PLAPRO group. The participants underwent detailed examinations at three time points: at baseline, in three and six months. The serum NfL concentrations were determined using ultrasensitive single-molecule array (SIMOA) assay.

RESULTS: Longitudinal comparisons of NfL concentrations between samplings at different time points in the PROPLA and PLAPRO groups showed no statistically significant differences. Baseline NfL concentrations at the beginning of the study and in the succeeding samplings were not significantly different for the two groups in cross-sectional comparisons.

CONCLUSIONS: Serum NfL concentrations were not influenced by the three-month use of probiotics.},
}

@article {pmid39410728,
year = {2024},
author = {Moreno-Arrones, OM and Béa-Ardebol, S and Galiano-Mejías, S and Turrión-Merino, L and de Perosanz-Lobo, D and Perez-Brocal, V and Moya, A and Rios-Buceta, L},
title = {Locally advanced basal cell carcinoma associated with distinct gut microbiome signature.},
journal = {Journal der Deutschen Dermatologischen Gesellschaft = Journal of the German Society of Dermatology : JDDG},
volume = {},
number = {},
pages = {},
doi = {10.1111/ddg.15588},
pmid = {39410728},
issn = {1610-0387},
}

@article {pmid39410714,
year = {2024},
author = {Ji, XY and Ye, C and Kang, W and Luan, W and Liu, Y and He, X and Yang, M and Sun, L and Sun, W and Huang, H and Zhu, Y and Zhu, S},
title = {Interspecific Allelopathic Interaction Primes Direct and Indirect Resistance of Neighbor Plant in Agroforestry System.},
journal = {Plant communications},
volume = {},
number = {},
pages = {101173},
doi = {10.1016/j.xplc.2024.101173},
pmid = {39410714},
issn = {2590-3462},
abstract = {Agroforestry system with high biodiversity augments ecosystem stability and minimizes its vulnerability to environmental disturbances and disease. Deciphering the underlying mechanisms of interspecies allelopathic interactions in disease suppression in agroforestry offer a sustainable strategy for plant disease management. Here, we utilized Panax ginseng cultivated under Pinus koraiensis forests, where the occurrences of Alternaria leaf spot are low, as a research model to investigate the role of allelochemicals in disease suppression. Our findings demonstrate that foliar application of leachates from the needles of P. koraiensis effectively enhanced the resistance of P. ginseng against Alternaria leaf spot. Through GC-MS analysis, we identified and quantified endo-borneol as a key compound in the leachates of P. koraiensis, and validated its capacity to prime resistance in its neighbor P. ginseng. We discovered that endo-borneol not only directly activates defense-related pathways of P. ginseng to induce resistance, but also indirectly recruits its rhizospheric beneficial microbiota by enhancing the secretion of ginsenosides, thereby triggering induced systemic resistance (ISR). Importantly, the higher concentrations of endo-borneol from 10 to 100 mg/L demonstrated a stronger capacity to induce plant resistance and enhance root secretion to recruit more microbiota compared with the lower concentrations from 0.01 to 1 mg/L. Moreover, endo-borneol exhibited antifungal activity against the growth of the pathogen Alternaria panax when its concentrations exceeding 10 mg/L. These results reveal the multifaceted functions of allelochemical endo-borneol in disease suppression in agroforestry system and highlight its potential as an environmental-friendly compound for sustainable agriculture.},
}

@article {pmid39410228,
year = {2024},
author = {Kim, S and Kang, JY and Nguyen, QA and Lee, JS},
title = {Effects of Prebiotic Dietary Fibers on the Stimulation of the Mucin Secretion in Host Cells by In Vitro Gut Microbiome Consortia.},
journal = {Foods (Basel, Switzerland)},
volume = {13},
number = {19},
pages = {},
pmid = {39410228},
issn = {2304-8158},
support = {NRF-2021R1A2C1005811//National Research Foundation of Korea/ ; NRF-2023K2A9A1A01098813, FY2023//National Research Foundation of Korea/ ; KRIBB Research Initiative Program grant (KGM5482423)//Korea Research Institute of Bioscience and Biotechnology/ ; },
abstract = {The gastrointestinal microbiota are important for human health. Dietary intake may modulate the composition and metabolic function of the gut microbiome. We examined how the breakdown of prebiotic dietary fibers by the gut microbiome affects mucin secretion by intestinal epithelial cells. Metagenomic analyses of in vitro gut microbiome consortia revealed taxonomic profiles and genetic diversity of carbohydrate-active enzymes that digest polysaccharides. Two independent consortia exhibited different abilities to produce acetic acid, propionic acid, and butyric acid via the fermentation of polysaccharides derived from dietary fibers of grains and mushrooms. Although acetic acid generally had the highest concentration, the ratios of butyric acid and propionic acid to acetic acid varied depending on the polysaccharide source. These short-chain fatty acids affected morphological differentiation and mucin secretion in HT-29 human intestinal epithelial cells. These results suggest that prebiotic dietary fibers can be digested and metabolized by the gut microbiome to short-chain fatty acids, which can affect gut epithelial cells both directly and indirectly via the modulation of the gut microbiota and their enzymes.},
}

@article {pmid39410212,
year = {2024},
author = {Yang, R and Zhu, F and Mo, W and Li, H and Zhu, D and He, Z and Ma, X},
title = {A New Plant Active Polysaccharide from Nicotiana Improves the Lead-Led Impairment of Spatial Memory in Mice by Modulating the Gut Microbiota and IL-6.},
journal = {Foods (Basel, Switzerland)},
volume = {13},
number = {19},
pages = {},
pmid = {39410212},
issn = {2304-8158},
support = {JZ2019YYPY0029//the Fundamental Research Funds for the Central Universities of China/ ; },
abstract = {Active polysaccharides from plants are broadly applied in the food and health industry. The purpose of this study is to identify a new plant active polysaccharide and to investigate its role in modulating spatial memory. Ultrasonics and DEAE-52 chromatography were used to separate and purify the plant active polysaccharide (PAP). Mice were exposed to 100 ppm of lead acetate from birth to 7 weeks old to establish the memory impairment model. PAPs with concentrations of 200 or 400 ppm were fed to the subject mice each day after weaning in a spatiotemporally separated fashion. At the end of the intervention, mice were examined using the Morris water maze test, microbiome sequencing, cytokine profiling and protein analysis. The derived active polysaccharide was constituted by β-anomeric carbon, indicating a new form of PAP. The PAP significantly ameliorates the memory impairment caused by postnatal lead exposure, as evidenced by the preferred coverage of the test mouse in the hidden platform, demonstrating salient neuroregulatory activity. In terms of the gut microbiome in response to PAP treatment, it was found that the 400 ppm PAP reversed the gut dysbiosis, producing a comparable structure to the intact animals, represented by the relative abundance of Firmicutes and Muribaculum, Desulfovibrio, etc. For cytokines, the PAP reversed the plasma levels of IL-6, suggesting an anti-inflammatory trend in the context of proinflammation caused by lead invasion. By injecting an IL-6 antagonist, Tocilizumab, into the deficient mice, the spatial memory was significantly repaired, which demonstrates the central roles of IL-6 in mediating the positive effect of the PAP. Finally, a histone modification mark, H3K27me3, was found to be potent in responding to the signals conveyed by the PAP. The PAP could improve the memory deficits by remodeling the gut-brain axis centered at the microbiota and IL-6, which is regarded as an important cytokine-modulating brain activity. This is an intriguing instance linking neuromodulation with the active polysaccharide, shedding light on the innovative applications of plant polysaccharides due to the scarcity of similar phenotypic connections.},
}

@article {pmid39410136,
year = {2024},
author = {Katimbwa, DA and Kim, Y and Kim, MJ and Jeong, M and Lim, J},
title = {Solubilized β-Glucan Supplementation in C57BL/6J Mice Dams Augments Neurodevelopment and Cognition in the Offspring Driven by Gut Microbiome Remodeling.},
journal = {Foods (Basel, Switzerland)},
volume = {13},
number = {19},
pages = {},
pmid = {39410136},
issn = {2304-8158},
support = {NRF-2021R1F1A105044//National Research Foundation of Korea/ ; },
abstract = {A maternal diet rich in dietary fiber, such as β-glucan, plays a crucial role in the offspring's acquisition of gut microbiota and the subsequent shaping of its microbiome profile and metabolome. This in turn has been shown to aid in neurodevelopmental processes, including early microglial maturation and immunomodulation via metabolites like short chain fatty acids (SCFAs). This study aimed to investigate the effects of oat β-glucan supplementation, solubilized by citric acid hydrolysis, from gestation to adulthood. Female C57BL/6J mice were orally supplemented with soluble oat β-glucan (ObG) or carboxymethyl cellulose (CMC) via drinking water at 200 mg/kg body weight during breeding while the control group received 50 mg/kg body weight of carboxymethyl cellulose. ObG supplementation increased butyrate production in the guts of both dams and 4-week-old pups, attributing to alterations in the gut microbiota profile. One-week-old pups from the ObG group showed increased neurodevelopmental markers similar to four-week-old pups that also exhibited alterations in serum markers of metabolism and anti-inflammatory cytokines. Notably, at 8 weeks, ObG-supplemented pups exhibited the highest levels of spatial memory and cognition compared to the control and CMC groups. These findings suggest a potential enhancement of neonatal neurodevelopment via shaping of early-life gut microbiome profile, and the subsequent increased later-life cognitive function.},
}

@article {pmid39410045,
year = {2024},
author = {Patel, NM and Patel, PH and Bhogal, RH and Harrington, KJ and Singanayagam, A and Kumar, S},
title = {Altered Microbiome Promotes Pro-Inflammatory Pathways in Oesophago-Gastric Tumourigenesis.},
journal = {Cancers},
volume = {16},
number = {19},
pages = {},
pmid = {39410045},
issn = {2072-6694},
abstract = {INTRODUCTION: The upper gastrointestinal microbiome is a dynamic entity that is involved in numerous processes including digestion, production of vitamins and protection against pathogens. Many external and intrinsic factors may cause changes in the proportions of bacteria within the microbial community, termed 'dysbiosis'. A number of these have been identified as risk factors for a range of diseases, including oesophago-gastric carcinoma.

MATERIALS AND METHODS: A narrative review was conducted to elucidate the current evidence on the role of the microbiome in promoting oesophago-gastric tumourigenesis. Significant causes of dysbiosis including age, medications and GORD were examined and key pro-inflammatory pathways implicated in tumourigenesis and their interaction with the microbiome were described.

RESULTS AND DISCUSSION: An association between microbial dysbiosis and development of oesophago-gastric cancer may be mediated via activation of pro-inflammatory pathways, the inflammasome and the innate immune system. Advances in sequencing technology allow microbial communities to be fingerprinted by sequencing the 16S rRNA gene, enabling a deeper understanding of the genera that may be implicated in driving tumourigenesis.

CONCLUSIONS: Developing a greater understanding of the influence of the microbiota on oesophago-gastric tumourigenesis may enable advances to be made in the early detection of malignancy and in the development of novel systemic therapies, leading to improved rates of survival.},
}

@article {pmid39410035,
year = {2024},
author = {Dorobisz, K and Dorobisz, T and Pazdro-Zastawny, K},
title = {Assessment of Prognostic Factors, Clinical Features Including the Microbiome, and Treatment Outcomes in Patients with Cancer of Unknown Primary Site.},
journal = {Cancers},
volume = {16},
number = {19},
pages = {},
pmid = {39410035},
issn = {2072-6694},
support = {Grant No. SUBK.C250.22.013//Wroclaw Medical University/ ; },
abstract = {INTRODUCTIONS: cancer of unknown primary site (CUP) is a heterogeneous group of cancers in which metastases are found, and the primary tumor is not detected with available diagnostic methods. CUP is a disease that has not been fully researched, and its biology is unclear. The clinical characteristics of CUP are variable, but the prognosis of patients is usually unfavorable, and the possibilities of radical treatment are limited. The microbiome is the genes and gene products of microorganisms residing in a human body. In recent years, thanks to the use of next-generation sequencing, it is possible to assess the impact of the microbiome on human body functions. Head and neck cancers, due to the rich microbiome of this area, are influenced by it, and dysbiosis may be a risk factor for the development of cancer. Objective of this work: the aim of this study was to evaluate prognostic factors, clinical features including the microbiome, and treatment outcomes in patients with cancer of unknown primary site.

RESULTS: in the study group, increased numbers of bacteria of the phyla Bacteroides, Fusobacteria, Bacillota, Actinomycetota, Actinobacteria, and Candidatus were detected, while Firmicutes and Proteobacteria were detected in smaller numbers. Independent predictors of CUP occurrence were the following: leukocyte count of at most 6.49 × 10[3]/mm, bacteria from the Proteobacteria phylum in the microbiome below 11.6%, Firmicutes below 22.1%, and Actinobacteria at least 11.0%. Increased numbers of Porphyromonas and Fusobacterium bacteria were associated with the risk of radiotherapy complications and shortened survival rate.

CONCLUSIONS: clinical diagnosis and treatment of patients with CUP is complicated and difficult due to the lack of consensus on this issue. Treatment and prognosis of patients with CUP is unsatisfactory. The clinical value of the influence of the microbiome on the development, course, and treatment of cancer is becoming increasingly important. The microbiome may become a marker of response to anticancer treatment and the risk of its complications. Immunity modulation with the microbiome provides opportunities for further research on improving the effectiveness of oncological treatment. Fusobacterium and Porphyromonas seem to be the bacteria most important for the development of cancer, also worsening the prognosis of patients by increasing the risk of complications of radiotherapy and shortening the survival rate of patients. Streptococcus and Lactobacillus seem to be bacteria that reduce the risk of cancer, reduce the risk of complications, and improve the prognosis of patients. Total protein deficiency and elevated inflammatory markers are also important predictors of cancer risk.},
}

@article {pmid39410033,
year = {2024},
author = {Plaza-Diaz, J and Ruiz-Ojeda, FJ and López-Plaza, B and Brandimonte-Hernández, M and Álvarez-Mercado, AI and Arcos-Castellanos, L and Feliú-Batlle, J and Hummel, T and Palma-Milla, S and Gil, A},
title = {Effect of a Novel Food Rich in Miraculin on the Oral Microbiome of Malnourished Oncologic Patients with Dysgeusia.},
journal = {Cancers},
volume = {16},
number = {19},
pages = {},
pmid = {39410033},
issn = {2072-6694},
support = {Ref. IDI-20210622. (Science and Education Ministry, Spain).//Center for Industrial Technological Development (CDTI), "Cervera" Transfer R&D Projects./ ; },
abstract = {BACKGROUND/OBJECTIVES: Dysgeusia contributes to the derangement of nutritional status in patients with cancer as well as worsening the quality of life. There has been a lack of effective treatments for taste disorders provided by the pharmaceutical industry.

METHODS: This was a pilot randomized, parallel, triple-blind, and placebo-controlled intervention clinical trial in which 31 malnourished patients with cancer and dysgeusia receiving antineoplastic treatment were randomized into three arms [standard dose of DMB (150 mg DMB/tablet), high dose of DMB (300 mg DMB/tablet) or placebo (300 mg freeze-dried strawberry)] for three months. Patients consumed a DMB or placebo tablet before each main meal. Using the nanopore methodology, we analyzed the oral microbiome of patients with cancer using saliva samples.

RESULTS: All patients with cancer and dysgeusia had dysbiosis in terms of lower bacterial diversity and richness. DMB consumption was associated with changes in oral microbiome composition. Neither selected bacteria nor taste perception, type of diet, and cytokine levels were associated with mucositis. Likewise, alcohol and tobacco consumption as well as general and digestive toxicity due to systemic therapy were not associated with specific changes of the oral microbiome, according to logistic binary regression. The standard dose of DMB resulted in a lower abundance of Veillonella compared with the high DMB dose and placebo at 3 months after intervention with DMB. In particular, some species such as Streptococcus parasanguinis, Veillonella parvula, and Streptococcus mutans were less abundant in the DMB standard-dose group. Additionally, the consumption of a standard dose of DMB revealed a negative association between the concentrations of TNF-α and the abundance of species such as Streptococcus thermophilus, Streptococcus pneumoniae, Streptococcus dysgalactiae and Streptococcus agalactiae.

CONCLUSIONS: Accordingly, regular DMB consumption could modify the oral microbiome in patients with cancer and dysgeusia, which may contribute to maintaining an appropriate immune response. However, as the present pilot study involved a small number of participants, further studies are necessary to draw robust conclusions from the data.},
}

@article {pmid39409962,
year = {2024},
author = {Belaid, A and Roméo, B and Rignol, G and Benzaquen, J and Audoin, T and Vouret-Craviari, V and Brest, P and Varraso, R and von Bergen, M and Hugo Marquette, C and Leroy, S and Mograbi, B and Hofman, P},
title = {Impact of the Lung Microbiota on Development and Progression of Lung Cancer.},
journal = {Cancers},
volume = {16},
number = {19},
pages = {},
doi = {10.3390/cancers16193342},
pmid = {39409962},
issn = {2072-6694},
support = {ANR-23-IAHU-007//ANR/ ; },
abstract = {The past several years have provided a more profound understanding of the role of microbial species in the lung. The respiratory tract is a delicate ecosystem of bacteria, fungi, parasites, and viruses. Detecting microbial DNA, pathogen-associated molecular patterns (PAMPs), and metabolites in sputum is poised to revolutionize the early diagnosis of lung cancer. The longitudinal monitoring of the lung microbiome holds the potential to predict treatment response and side effects, enabling more personalized and effective treatment options. However, most studies into the lung microbiota have been observational and have not adequately considered the impact of dietary intake and air pollutants. This gap makes it challenging to establish a direct causal relationship between environmental exposure, changes in the composition of the microbiota, lung carcinogenesis, and tumor progression. A holistic understanding of the lung microbiota that considers both diet and air pollutants may pave the way to improved prevention and management strategies for lung cancer.},
}

@article {pmid39409925,
year = {2024},
author = {Moe, KT and Tan, KS},
title = {Mechanistic Insights on Microbiota-Mediated Development and Progression of Esophageal Cancer.},
journal = {Cancers},
volume = {16},
number = {19},
pages = {},
pmid = {39409925},
issn = {2072-6694},
support = {A-8000685-00-00 and A-8000629-00-00//Yong Loo Lin School of Medicine, National University of Singapore/ ; },
abstract = {Esophageal cancer (EC) is one of the most common malignant tumors worldwide, and its two major types, esophageal adenocarcinoma (EAC) and esophageal squamous cell carcinoma (ESCC), present a severe global public health problem with an increasing incidence and mortality. Established risk factors include smoking, alcohol consumption, and dietary habits, but recent research has highlighted the substantial role of oral microbiota in EC pathogenesis. This review explores the intricate relationship between the microbiome and esophageal carcinogenesis, focusing on the following eight significant mechanisms: chronic inflammation, microbial dysbiosis, production of carcinogenic metabolites, direct interaction with epithelial cells, epigenetic modifications, interaction with gastroesophageal reflux disease (GERD), metabolic changes, and angiogenesis. Certain harmful bacteria, such as Porphyromonas gingivalis and Fusobacterium nucleatum, are specifically implicated in sustaining irritation and tumor progression through pathways including NF-κB and NLRP3 inflammasome. Additionally, the review explores how microbial byproducts, including short-chain fatty acids (SCFAs) and reactive oxygen species (ROS), contribute to DNA harm and disease advancement. Furthermore, the impact of reflux on microbiota composition and its role in esophageal carcinogenesis is evaluated. By combining epidemiological data with mechanistic understanding, this review underscores the potential to target the microbiota-immune system interplay for novel therapeutic and diagnostic strategies to prevent and treat esophageal cancer.},
}

@article {pmid39409832,
year = {2024},
author = {Kang, HJ and Kim, SW and Kim, SM and La, TM and Hyun, JE and Lee, SW and Kim, JH},
title = {Altered Gut Microbiome Composition in Dogs with Hyperadrenocorticism: Key Bacterial Genera Analysis.},
journal = {Animals : an open access journal from MDPI},
volume = {14},
number = {19},
pages = {},
pmid = {39409832},
issn = {2076-2615},
abstract = {Hyperadrenocorticism (HAC) is a common endocrine disorder in dogs, which is associated with diverse metabolic abnormalities. We hypothesized that elevated cortisol levels in dogs with HAC disrupt the gut microbiome (GM), and this disruption persists even after trilostane treatment. This study explored GM composition in dogs with HAC. We included 24 dogs, 15 with HAC and 9 healthy controls, and followed up with 5 dogs with HAC who received trilostane treatment. The GM analysis revealed significant compositional changes in dogs with HAC, including reduced microbiome diversity compared to healthy controls, particularly in rare taxa, as indicated by the Shannon index (p = 0.0148). Beta diversity analysis further showed a distinct clustering of microbiomes in dogs with HAC, separating them from healthy dogs (p < 0.003). Specifically, an overrepresentation of Proteobacteria (Pseudomonadota), Actinobacteria, Bacteroides, Enterococcus, Corynebacterium, Escherichia, and Proteus populations occurred alongside a decreased Firmicutes (Bacillota) population. Despite trilostane treatment, gut dysbiosis persisted in dogs with HAC at a median of 41 d post treatment, suggesting its potential role in ongoing metabolic issues. We identified GM dysbiosis in dogs with HAC by examining key bacterial genera, offering insights into potential interventions like probiotics or fecal microbiota transplants for better HAC management.},
}

@article {pmid39409735,
year = {2024},
author = {Qin, B and Li, Z and Zhu, Q and Chen, T and Lan, W and Cui, Y and Azad, MAK and Kong, X},
title = {Dietary Fermented Blueberry Pomace Supplementation Improves Small Intestinal Barrier Function and Modulates Cecal Microbiota in Aged Laying Hens.},
journal = {Animals : an open access journal from MDPI},
volume = {14},
number = {19},
pages = {},
pmid = {39409735},
issn = {2076-2615},
support = {SXHZ2020007//City-School Cooperation Project of the Special Funds of Science and Technology in Fuyang City/ ; 092GJHZ2022044FN//Future Partner Special Fund of Chinese Academy of Sciences/ ; },
abstract = {This study aimed to investigate the effects of fermented blueberry pomace (FBP) on the intestinal barrier function and cecal microbiome of aged laying hens. A total of 320 Yukou Jingfen No. 8 laying hens (345-day-old) were randomly divided into a control group, 0.25% FBP group, 0.5% FBP group, or 1.0% FBP group. The results showed that the villus height (VH) in the jejunum of the 0.25-0.5% FBP groups and villus surface area in the jejunum of the 0.25% FBP group were higher (p < 0.05), while 0.25% FBP supplementation displayed a higher (p = 0.070) VH in the ileum compared to the control group. Mucin-2 expression was upregulated (p < 0.05) in the jejunum of the 0.5% FBP group and the ileum of the 0.25-0.5% FBP groups. Compared to the control group, interleukin (IL)-4 and IL-13 expressions were upregulated (p < 0.05) in the 1.0% FBP group. Microbiota analysis revealed that Prevotella abundance in the cecum of the 0.5-1.0% FBP groups was higher (p < 0.05) than in the 0.25% FBP group. In addition, microbial function prediction analysis showed that cecal microbiota in the 0.25% FBP group were mainly enriched by alanine/aspartate/glutamate metabolism and methane metabolism. Moreover, Spearman's correlation analysis revealed the potential correlations between the abundance of the cecal microbiota and intestinal-barrier-function-related gene expressions, as well as the short-chain fatty acid content, of laying hens. In summary, dietary FBP supplementation enhanced intestinal barrier function by improving intestinal morphology, upregulating gene expressions related to barrier function, and altering the cecal microbiota of aged laying hens.},
}

@article {pmid39409729,
year = {2024},
author = {Chen, Z and Yan, Z and Xia, S and Wang, K and Han, Q and Zhou, M and Wang, D and Yin, J and Yin, Y},
title = {Dietary Isatidis Root Residue Improves Diarrhea and Intestinal Function in Weaned Piglets.},
journal = {Animals : an open access journal from MDPI},
volume = {14},
number = {19},
pages = {},
pmid = {39409729},
issn = {2076-2615},
abstract = {Weaning stress can trigger diarrhea, cause intestinal damage, and disrupt the intestinal flora of piglets, ultimately resulting in retarded growth or even the death of the animals. Traditional Chinese medicine residues encompass numerous bioactive compounds and essential nutrients; however, their efficient utilization remains a challenge. Consequently, our study sought to explore the impact of traditional Chinese medicine residues, specifically Isatidis Root residue (IRR), on the growth performance, intestinal function, and occurrence of weaning diarrhea in newly weaned piglets. Forty healthy, castrated Duroc × Landrace × Yorkshire males, weaned at 21 days old and exhibiting similar body conditions, were randomly allocated into five groups, with eight piglets in each group. The results indicated that the dietary inclusion of IRR at concentrations ranging from 0.5% to 4.0% notably decreased the incidence of diarrhea in weaned piglets compared to the control group (p < 0.05). Serum LDL-C and globulin (GLB) contents were reduced in response to dietary IRR concentrations (0.5% to 4.0%), while serum albumin (ALB) and albumin/globulin (A/G) contents were enhanced (p < 0.05). Dietary 0.5%, 1.0%, and 2.0% IRR resulted in significant increases in villus height (VH) and villus height/crypt depth (V/C) ratios in the jejunum, V/C ratios in the ileum, and the number of villi goblet cells both in the jejunum and ileum. IRR also led to a significant decrease in the crypt depth (CD) of the jejunum and ileum (p < 0.05). Furthermore, the expression of IL-6 in the jejunum was significantly increased in IRR-fed piglets (0.5% to 4.0%) (p < 0.05). IRR demonstrated inhibitory effects on harmful bacteria in the gastrointestinal microbiome, including Campylobacter, Actinobacillus minor, and Ralstonia pickettii, indicating its broad-spectrum bacteriostatic properties. In conclusion, dietary IRR alleviated diarrhea in weaned piglets and improved gut function and microbial compositions.},
}

@article {pmid39409573,
year = {2024},
author = {Cen, X and Li, H and Zhang, Y and Huang, L and Luo, Y},
title = {Isolation and Plant Growth Promotion Effect of Endophytic Siderophore-Producing Bacteria: A Study on Halophyte Sesuvium portulacastrum.},
journal = {Plants (Basel, Switzerland)},
volume = {13},
number = {19},
pages = {},
pmid = {39409573},
issn = {2223-7747},
support = {2022YFC3103700//National Key Research & Development Program of China/ ; },
abstract = {The objective of the present study was to isolate endophytes from the roots of the halophyte Sesuvium portulacastrum, which is applied for aquatic phytoremediation. From these endophytes, siderophore-producing bacteria were specifically isolated for their potential capacity to promote plant growth. The siderophore production capacity of the isolated bacteria was quantified, and a high-yield siderophore-producing strain was selected for further investigation. A total of 33 endophytic bacteria were successfully isolated and identified using a culturable approach. Of these, 10 siderophore-producing bacteria were identified using the selective agar assay, displaying siderophore unit (SU) values ranging from 11.90% to 80.39%. It is noteworthy that Erwinia sp. QZ-E9 exhibited the highest siderophore production capacity, achieving an SU of 80.39%. A microcosm co-cultivation experiment was conducted with the strain QZ-E9 in iron-deficient conditions (2 μmol/L Fe[3][+]). The results demonstrated that strain QZ-E9 significantly enhanced the growth of S. portulacastrum, by increases in both fresh weight (1.41 g) and root length (18.7 cm). Furthermore, fluorescence in situ hybridization (FISH) was utilized to ascertain the colonization pattern of strain QZ-E9 within the plant roots. The analysis demonstrated that strain QZ-E9 exhibited extensive colonization of the epidermal and outer cortical cells of S. portulacastrum roots, as well as the intercellular spaces and vascular tissues. This colonization indicated that Erwinia sp. QZ-E9 plays a crucial role in promoting the growth of S. portulacastrum, presumably through its siderophore-mediated iron acquisition mechanism.},
}

@article {pmid39409556,
year = {2024},
author = {Zhu, Y and Xing, Y and Li, Y and Jia, J and Ying, Y and Shi, W},
title = {The Role of Phosphate-Solubilizing Microbial Interactions in Phosphorus Activation and Utilization in Plant-Soil Systems: A Review.},
journal = {Plants (Basel, Switzerland)},
volume = {13},
number = {19},
pages = {},
pmid = {39409556},
issn = {2223-7747},
support = {2022YFD2201500//National Science and Technology Council/ ; 32271971 & 32171879//Natural Science Foundation Committee of China/ ; },
abstract = {To address the issue of phosphorus limitation in agricultural and forestry production and to identify green and economical alternatives to chemical phosphorus fertilizers, this paper reviews the utilization of phosphorus in plant-soil systems and explores the considerable potential for exploiting endogenous phosphorus resources. The application of phosphate-solubilizing microorganisms (PSMs) is emphasized for their role in phosphorus activation and plant growth promotion. A focus is placed on microbial interactions as an entry point to regulate the functional rhizosphere microbiome, introducing the concept of synthetic communities. This approach aims to deepen the understanding of PSM interactions across plant root, soil, and microbial interfaces, providing a theoretical foundation for the development and application of biological regulation technologies to enhance phosphorus utilization efficiency.},
}