@article {pmid39656273, year = {2024}, author = {Zhang, Z and Jiang, N and Zhang, Y and Yu, Q and Jiang, Y and Li, F and Wang, X}, title = {Unveiling the skin microbial guardians and assailants in psoriasis subtypes: a Mendelian randomization study.}, journal = {Archives of dermatological research}, volume = {317}, number = {1}, pages = {95}, pmid = {39656273}, issn = {1432-069X}, mesh = {Humans ; *Psoriasis/microbiology/genetics/diagnosis ; *Mendelian Randomization Analysis ; *Skin/microbiology/pathology ; *Genome-Wide Association Study ; *Microbiota/genetics ; Risk Factors ; Bayes Theorem ; }, abstract = {Previous studies have shown an association between skin microbiota and psoriasis, but the causal relationship between skin microbiota and different psoriasis subtypes remains unexplored. Our study employed the Mendelian randomization (MR) method, using summary statistics from Genome-Wide Association Studies, to investigate the causal relationships between skin microbiota and different subtypes of psoriasis. The inverse variance weighted (IVW) method served as the primary method in our MR study. The MR-Egger intercept test, Cochran's Q test, MR-PRESSO test, and leave-one-out analysis were conducted for sensitive analyses. Bayesian weighted Mendelian randomization (BWMR) method was conducted to enhance our results. For psoriasis vulgaris, our results showed that asv016 [Enhydrobacter (unc.)], alphaproteobacteria, and asv070 [Veillonella (unc.)] may serve as protective factors. Meanwhile, asv009 [D. nitroreducens], asv010 [Staphylococcus (unc.)], Neisseriaceae, and clostridiales were found to be risk factors. For guttate psoriasis, our findings suggested that asv023 [C. kroppenstedtii], asv039 [Acinetobacter (unc.)], bacteroidales, paracoccus, and betaproteobacteria may serve as protective factors, while asv008 [Staphylococcus (unc.)], asv061 [S. mitis], asv086 [A. johnsonii], finegoldia, and flavobacteriaceae emerged as potential risk factors. For generalized pustular psoriasis, our findings identified asv039 [Acinetobacter (unc.)], asv009 [D. nitroreducens], and Staphylococcus as potential protective factors, whereas asv016 [Enhydrobacter (unc.)], asv006 [S. hominis], bacteroidales, and bacteroides emerged as potential risk factors. For psoriatic arthropathies, our findings suggested that Propionibacterium, asv053 [Streptococcus (unc.)], asv093 [Staphylococcus (unc.)], rothia may serve as protective factors, while asv012 [S. hominis], corynebacterium, clostridiales, flavobacteriaceae, anaerococcus, asv013 [S. epidermidis] were associated with increased risk. Our findings suggest potential causal relationships between certain skin microbiota and different subtypes of psoriasis, highlighting their potential as novel biomarkers for diagnosing different subtypes of psoriasis, and offering promising avenues for developing microbiome-based diagnostics and targeted therapies for diverse psoriasis subtypes.}, }
@article {pmid39656168, year = {2024}, author = {Moustafa, A and Li, W and Anderson, EL and MWong, EH and Dulai, PS and Sandborn, WJ and Biggs, W and Yooseph, S and Jones, MB and Venter, CJ and Nelson, KE and Chang, JT and Telenti, A and Boland, BS}, title = {Correction to: Genetic Risk, Dysbiosis, and Treatment Stratification Using Host Genome and Gut Microbiome in Inflammatory Bowel Disease.}, journal = {Clinical and translational gastroenterology}, volume = {}, number = {}, pages = {}, doi = {10.14309/ctg.0000000000000796}, pmid = {39656168}, issn = {2155-384X}, }
@article {pmid39656018, year = {2024}, author = {de Oliveira, ACFM and Vieira, BD and de Felício, R and Silva, LdS and Veras, AAdO and Graças, DAd and Silva, A and Azevedo Baraúna, R and Barretto Barbosa Trivella, D and Schneider, MPC}, title = {A metabologenomics approach reveals the unexplored biosynthetic potential of bacteria isolated from an Amazon Conservation Unit.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0099624}, doi = {10.1128/spectrum.00996-24}, pmid = {39656018}, issn = {2165-0497}, abstract = {The Amazon, an important biodiversity hotspot, remains poorly explored in terms of its microbial diversity and biotechnological potential. The present study characterized the metabolic potential of Gram-positive strains of the Actinomycetes and Bacilli classes isolated from soil samples of an Amazon Conservation Unit. The sequencing of the 16S rRNA gene classified the strains ACT015, ACT016, and FIR094 within the genera Streptomyces, Rhodococcus, and Brevibacillus, respectively. Genome mining identified 33, 17, and 14 biosynthetic gene clusters (BGCs) in these strains, including pathways for the biosynthesis of antibiotic and antitumor agents. Additionally, 40 BGCs (62,5% of the total BGCs) were related to unknown metabolites. The OSMAC approach and untargeted metabolomics analysis revealed a plethora of metabolites under laboratory conditions, underscoring the untapped chemical diversity and biotechnological potential of these isolates. Our findings illustrated the efficacy of the metabologenomics approach in elucidating secondary metabolism and selecting BGCs with chemical novelty.IMPORTANCEThe largest rainforest in the world is globally recognized for its biodiversity. However, until now, few studies have been conducted to prospect natural products from the Amazon microbiome. In this work, we isolated three free-living bacterial species from the microbiome of pristine soils and used two high-throughput technologies to reveal the vast unexplored repertoire of secondary metabolites produced by these microorganisms.}, }
@article {pmid39656008, year = {2024}, author = {Ishizaka, A and Tamura, A and Koga, M and Mizutani, T and Yamayoshi, S and Iwatsuki-Horimoto, K and Yasuhara, A and Yamamoto, S and Nagai, H and Adachi, E and Suzuki, Y and Kawaoka, Y and Yotsuyanagi, H}, title = {Dysbiosis of gut microbiota in COVID-19 is associated with intestinal DNA phage dynamics of lysogenic and lytic infection.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0099824}, doi = {10.1128/spectrum.00998-24}, pmid = {39656008}, issn = {2165-0497}, abstract = {This study compared intestinal DNA phage dynamics and gut microbiota changes observed at the onset of coronavirus disease 2019 (COVID-19). The study participants included 19 healthy individuals and 19 patients with severe acute respiratory syndrome coronavirus 2 infection. Significant differences were observed in the diversity of the intestinal DNA virome after the onset of COVID-19 compared with that in healthy individuals. Classification by their tail morphology resulted in the order Caudovirales, a double-stranded DNA phage, accounting for >95% of all participants. In classifying phages based on host bacteria, a decreased number of phages infecting mainly the Clostridia class was observed immediately after the onset of COVID-19 and recovered over time. After the onset of COVID-19, two distinct movement patterns of intestinal phages and their host bacteria were observed: phage- and bacteria-predominant. The abundance of obligate anaerobes, such as Clostridium_sense_strict_1, Fusicatenibacter, and Romboutsia, and the phages hosting these bacteria decreased immediately after the onset of COVID-19, and faster phage recovery was observed compared with bacterial recovery. In contrast, the genus Staphylococcus, a facultative anaerobic bacterium, increased immediately after the onset of COVID-19, whereas the phages infecting Staphylococcus decreased. Furthermore, immediately after the onset of COVID-19, the percentage of lytic phages increased, whereas that of temperate phages decreased. These observations suggest that the gut microbiota dysbiosis observed immediately after the onset of COVID-19 may be linked to phage dynamics that control gut microbiota and may also affect the recovery from dysbiosis.IMPORTANCEBacteriophages infect and replicate with bacteria and archaea and are closely associated with intestinal bacteria. The symbiotic relationship between gut microbiota and bacteriophages is of interest, but it is challenging to study their dynamics in the human body over time. SARS-CoV-2 infection has been reported to alter the gut microbiota, which is involved in gut immune regulation and pathophysiology, although changes in the intestinal phages of patients with SARS-CoV-2 and their dynamic relationship with the gut microbiota remain unclear. SARS-CoV-2 infection, which follows a transient pathological course from disease onset to cure, may provide a reliable model to investigate these interactions in the gut environment. Therefore, this study aimed to elucidate the correlation between gut microbiota and intestinal DNA virome dynamics in COVID-19 pathogenesis. This study found that the dysbiosis observed in SARS-CoV-2 infection involves a growth strategy that depends on the phage or bacterial dominance.}, }
@article {pmid39656003, year = {2024}, author = {Yunusbayev, B and Bogdanova, A and Nadyrchenko, N and Danilov, L and Bogdanov, V and Sergeev, G and Altinbaev, R and Bilalov, F and Yunusbaeva, M}, title = {Gut dysbiosis narrative in psoriasis: matched-pair approach identifies only subtle shifts correlated with elevated fecal calprotectin.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0138224}, doi = {10.1128/spectrum.01382-24}, pmid = {39656003}, issn = {2165-0497}, abstract = {UNLABELLED: Many studies have reported gut microbiome alterations in psoriasis patients, suggesting dysbiosis. While evidence for dysbiosis and its link to pathogenesis remains inconclusive, murine models of psoriasis suggest that gut microbiome alterations develop in response to psoriasis-like inflammation. Hence, the dominant narrative about gut microbiome alterations' impact on disease should be evaluated critically with more data and a well-powered approach. In this case-control study, we used deep sequencing of fecal samples from 53 psoriasis patients and 47 healthy donors to reconstruct the strain/species-level content of the gut microbiome. Unlike previous studies, we first identified matched pairs for each patient with healthy donors to adjust for microbiome variability and increase power. We found no evidence for depleted gut community diversity and apparent divergence in structure between patients and healthy individuals. However, our matched-pair approach identified a subtle but systematic increase in select bacteria among patients, e.g., Megasphaera elsdenii and Eubacterium CAG 180. We next showed that these enriched species were correlated with elevated biomarkers of intestinal and systemic inflammation and liver function. Functionally, one of the top species, Megasphaera elsdenii, is a potent lactate utilizer in the context of intestinal lactic acidosis and inflammation. While our findings hardly support overt dysbiosis in the large intestine, the observed microbial changes correlate with moderately elevated calprotectin, albeit at levels not enough to diagnose ongoing inflammation. Hence, the sources of elevated inflammatory markers in patients' intestines remain unclear and warrant further investigation to clarify their cause-and-effect relationship with the disease.<br><br>IMPORTANCE: With sufficient taxonomic resolution and sample size, this study critically evaluates new and published data on the gut microbiome in psoriasis patients. It shows that observed taxonomic changes in patients are modest and do not meet strict criteria for gut dysbiosis, at least in the large intestine. Instead, observed taxonomic changes in psoriasis patients can be explained by the microbial response to possible low-grade inflammation with unknown localization in the intestine and unclear impact on the host. The authors point out that published endoscopic data point to the small intestine as the site of gut inflammation. Therefore, further research focused on the small intestine would be informative to clarify the hypothetical gut-psoriasis link.}, }
@article {pmid39655940, year = {2024}, author = {Zhang, H and Wang, W and Honnas, L and Mazzola, M and Somera, T}, title = {Evaluating the stability of nursery-established arbuscular mycorrhizal fungal associations in apple rootstocks.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0193724}, doi = {10.1128/aem.01937-24}, pmid = {39655940}, issn = {1098-5336}, abstract = {Arbuscular mycorrhizal fungi (AMF) are promoted as commercial bioinoculants for sustainable agriculture. Little is known, however, about the survival of AMF inoculants in soil and their impacts on native or pre-established AMF communities in root tissue. The current study was designed to assess the stability of pre-existing/nursery-derived AMF in apple rootstocks after being planted into soil containing a known community of AMF with a limited number of species. Root-associated endophytic communities (bacteria and fungi) are known to differ depending on apple rootstock genotype. Thus, an additional aim of this study was to explore the effect of apple rootstock genotype on AMF community structure. A greenhouse experiment was conducted in which a variety of apple rootstock genotypes (G.890, G.935, M.26, and M.7) were inoculated with a commercially available, multi-species AMF consortium. Nursery-derived AMF communities were sequenced, and changes to AMF community structure following cultivation in pasteurized soil (inoculated and non-inoculated) were assessed using a Glomeromycota-specific phylogenetic tree, which included 91 different AMF species from 24 genera. Results show that inoculant colonization potential was limited and that apple rootstocks serve as a significant source of inoculum from the nursery where they are produced. Rootstocks established relationships with introduced AMF in a genotype-specific manner. Regardless of colonization success, however, the inoculant caused alterations to the resident AMF communities of both Geneva and Malling rootstocks, particularly low abundance taxa. In addition, phylogeny-based analysis revealed a unique, well-supported clade of unknown taxonomy, highlighting the importance of using phylogenetic-based classification for accurate characterization of AMF communities.IMPORTANCEUnderstanding the impacts of introduced AMF on residential AMF communities is essential to improving plant productivity in nursery and orchard systems. In general, there is a dearth of data on the interactions of commercial AMF inoculants with pre-established AMF communities living in symbiosis with the host plant. The interplay between apple rootstock genotype and the endophytic root microbiome is also an area where more research is needed. This study demonstrates the potential for nursery-established AMF associations to be maintained when transplanted into the field. In addition to providing insight into rootstock/AMF associations, our study calls attention to the current issues attendant with relying on web-based databases for determining AMF identity. The use of phylogenetic tools represents one possible solution and may be of value to industry practitioners in terms of improving product composition and consistency.}, }
@article {pmid39655934, year = {2024}, author = {Cui, Y and Xiao, Y and Wang, Z and Ji, P and Zhang, C and Li, Y and Fang, J and Yu, X}, title = {Microbial community structure and functional traits involved in the adaptation of culturable bacteria within the gut of amphipods from the deepest ocean.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0072324}, doi = {10.1128/spectrum.00723-24}, pmid = {39655934}, issn = {2165-0497}, abstract = {UNLABELLED: The Hadal Zone is acknowledged for its extreme environmental conditions, especially high hydrostatic pressures. The dominant scavengers in the Hadal Zone, Hadal amphipods, fulfill vital roles in the Hadal food web and ecological niches. However, research on the gut microbiota of amphipods related to ecological functions and environmental adaptation is still limited. Here, we used 16S rRNA sequencing technology and a culture-dependent method to analyze the composition of the gut microbiota in Amphipoda living in the Mariana Trench. A total of 16 bacterial genera were identified. Among them, Firmicutes and Proteobacteria were the predominant phyla. The adaptability of gut probiotics to the environment was investigated. Pediococcus pentosaceus XY62 was picked up as the representative strain to elucidate the ecological functions of gut microbes in amphipods. The ProBio database and the K-B agar diffusion method indicated that P. pentosaceus XY62 exhibited the highest probiotic activity compared with all other isolated strains. Specific metabolic pathways and transporter systems that contribute to a range of environmental adaptation strategies have been revealed by genomic analysis of P. pentosaceus XY62. The environmental response genes and a specialized KDP transport system allow it to adapt to the challenging conditions of the Hadal Zone. In addition, the presence of antibacterial compounds and antibiotic resistance genes, as well as the ability to form a biofilm, facilitated the successful colonization of P. pentosaceus XY62 in the gut environment.<br><br>IMPORTANCE: Amphipods are widely distributed in the Hadal trenches, and the study of their gut microbes has garnered considerable scientific interest. Our research breaks away from traditional omics approaches, innovatively combining sequencing technologies with culture-dependent methods to analyze the gut microbiome structure of amphipods from the Mariana Trench. This not only complements the current omics-dominated field but also paves the way for future resource development of extreme microbes. Furthermore, by conducting genomic analyses and functional validations on a representative strain, we have uncovered its probiotic effects and strategies for adapting to extreme environments. This provides new insights into the theoretical study of the ecological functions of deep-sea bacteria. Overall, our findings offer a fresh perspective on the microbial community structure and environmental adaptation strategies of gut microorganisms in the Hadal Zone.}, }
@article {pmid39655923, year = {2024}, author = {Rivera-Lopez, EO and Huertas-Miranda, J and Rios-Velazquez, C}, title = {Characterization of the microbial communities in paddy soils in Lajas, Puerto Rico using 16S rRNA gene.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0100824}, doi = {10.1128/mra.01008-24}, pmid = {39655923}, issn = {2576-098X}, abstract = {The microbiota in the paddy soils of the Lajas Agricultural Experimental Station at the University of Puerto Rico (LAES-UPR) plays a crucial role in agricultural ecosystems. Despite being at an experimental station, these soils represent natural environments supporting rice cultivation. Microbial diversity was evaluated during pre-harvest and post-harvest periods.}, }
@article {pmid39655747, year = {2024}, author = {Yamamoto, FY and Older, CE and Khoo, LH and Romano, N and Richardson, BM and Ott, BD and Wise, DJ and Ware, C and Goodman, PM and Reifers, JG and Griffin, MJ}, title = {Dietary Iron Fortification Did Not Affect the Intestinal Microbiome for Channel Catfish (Ictalurus punctatus) Juveniles, but Decreased Their Resistance Against Edwardsiella ictaluri.}, journal = {Journal of fish diseases}, volume = {}, number = {}, pages = {e14060}, doi = {10.1111/jfd.14060}, pmid = {39655747}, issn = {1365-2761}, support = {//U.S. Department of Agriculture/ ; //Agricultural Research Service/ ; //Mississippi Agricultural and Forestry Experiment Station, Mississippi State University/ ; }, }
@article {pmid39655703, year = {2024}, author = {DeCandia, AL and Lu, J and Hamblen, EE and Brenner, LJ and King, JL and Gagorik, CN and Schamel, JT and Baker, SS and Ferrara, FJ and Booker, M and Bridges, A and Carrasco, C and vonHoldt, BM and Koepfli, KP and Maldonado, JE}, title = {Phylosymbiosis and Elevated Cancer Risk in Genetically Depauperate Channel Island Foxes.}, journal = {Molecular ecology}, volume = {}, number = {}, pages = {e17610}, doi = {10.1111/mec.17610}, pmid = {39655703}, issn = {1365-294X}, support = {//Georgetown University/ ; //Friends of the Island Fox/ ; //National Museum of the American Latino/ ; //Smithsonian Institution/ ; //Smithsonian's National Zoo and Conservation Biology Institute/ ; }, abstract = {Examination of the host-associated microbiome in wildlife can provide critical insights into the eco-evolutionary factors driving species diversification and response to disease. This is particularly relevant for isolated populations lacking genomic variation, a phenomenon that is increasingly common as human activities create habitat 'islands' for wildlife. Here, we characterised the gut and otic microbial communities of one such species: Channel Island foxes (Urocyon littoralis). The gut microbiome provided evidence of phylosymbiosis by reflecting the host phylogeny, geographic proximity, history of island colonisation and contemporary ecological differences, whereas the otic microbiome primarily reflected geography and disease. Santa Catalina Island foxes are uniquely predisposed to ceruminous gland tumours following infection with Otodectes cynotis ear mites, while San Clemente and San Nicolas Island foxes exhibit ear mite infections without evidence of tumours. Comparative analyses of otic microbiomes revealed that mite-infected Santa Catalina and San Clemente Island foxes exhibited reduced bacterial diversity, skewed abundance towards the opportunistic pathogen Staphylococcus pseudintermedius and disrupted microbial community networks. However, Santa Catalina Island foxes uniquely harboured Fusobacterium and Prevotella bacteria as potential keystone taxa. These bacteria have previously been associated with colorectal cancer and may predispose Santa Catalina Island foxes to an elevated cancer risk. In contrast, mite-infected San Nicolas Island foxes maintained high bacterial diversity and robust microbial community networks, suggesting that they harbour more resilient microbiomes. Considered together, our results highlight the diverse eco-evolutionary factors influencing commensal microbial communities and their hosts and underscore how the microbiome can contribute to disease outcomes.}, }
@article {pmid39655692, year = {2024}, author = {Smith, KM and Francisco, SG and Zhu, Y and LeRoith, T and Davis, ML and Crott, JW and Barger, K and Greenberg, AS and Smith, DE and Taylor, A and Yeruva, L and Rowan, S}, title = {Dietary prevention of antibiotic-induced dysbiosis and mortality upon aging in mice.}, journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology}, volume = {38}, number = {23}, pages = {e70241}, doi = {10.1096/fj.202402262R}, pmid = {39655692}, issn = {1530-6860}, support = {M2017147//BrightFocus Foundation (BFF)/ ; 2016-08885//USDA | National Institute of Food and Agriculture (NIFA)/ ; 8050-51000-101-01S//USDA | Agricultural Research Service (ARS)/ ; 6026-51000-012-000D//USDA | Agricultural Research Service (ARS)/ ; P30DK2022-6708-37186//HHS | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)/ ; T32DK124170//HHS | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)/ ; }, mesh = {Animals ; *Dysbiosis/chemically induced ; Mice ; *Anti-Bacterial Agents/pharmacology ; *Gastrointestinal Microbiome/drug effects ; *Aging ; Male ; Mice, Inbred C57BL ; Diet ; }, abstract = {Oral antibiotic use is both widespread and frequent in older adults and has been linked to dysbiosis of the gut microbiota, enteric infection, and chronic diseases. Diet and nutrients, particularly prebiotics, may modify the susceptibility of the gut microbiome to antibiotic-induced dysbiosis. We fed 12-month-old mice a high glycemic (HG) or low glycemic (LG) diet with or without antibiotics (ampicillin and neomycin) for an additional 11 months. The glycemic index was modulated by the ratio of rapidly digested amylopectin starch to slowly digested amylose, a type-2-resistant starch. We observed a significant decrease in survival of mice fed a HG diet containing antibiotics (HGAbx) relative to those fed a LG diet containing antibiotics (LGAbx). HGAbx mice died with an enlarged and hemorrhagic cecum, which is associated with colonic hyperplasia and goblet cell depletion. Gut microbiome analysis revealed a pronounced expansion of Proteobacteria and a near-complete loss of Bacteroidota and Firmicutes commensal bacteria in HGAbx, whereas the LGAbx group maintained a population of Bacteroides and more closely resembled the LG microbiome. The predicted functional capacity for bile salt hydrolase activity was lost in HGAbx mice but retained in LGAbx mice. An LG diet containing amylose may therefore be a potential therapeutic to prevent antibiotic-induced dysbiosis and morbidity.}, }
@article {pmid39655437, year = {2024}, author = {Feng, Y and Chen, R}, title = {Phosphorus Cycling as a Function of Soil Microbiome.}, journal = {Global change biology}, volume = {30}, number = {12}, pages = {e17611}, doi = {10.1111/gcb.17611}, pmid = {39655437}, issn = {1365-2486}, support = {42177297//National Natural Science Foundation of China/ ; }, }
@article {pmid39655222, year = {2024}, author = {Deng, L and Tang, Y and Zhang, X and Chen, J}, title = {Structure-adaptive canonical correlation analysis for microbiome multi-omics data.}, journal = {Frontiers in genetics}, volume = {15}, number = {}, pages = {1489694}, pmid = {39655222}, issn = {1664-8021}, abstract = {Sparse canonical correlation analysis (sCCA) has been a useful approach for integrating different high-dimensional datasets by finding a subset of correlated features that explain the most correlation in the data. In the context of microbiome studies, investigators are always interested in knowing how the microbiome interacts with the host at different molecular levels such as genome, methylol, transcriptome, metabolome and proteome. sCCA provides a simple approach for exploiting the correlation structure among multiple omics data and finding a set of correlated omics features, which could contribute to understanding the host-microbiome interaction. However, existing sCCA methods do not address compositionality, and its application to microbiome data is thus not optimal. This paper proposes a new sCCA framework for integrating microbiome data with other high-dimensional omics data, accounting for the compositional nature of microbiome sequencing data. It also allows integrating prior structure information such as the grouping structure among bacterial taxa by imposing a "soft" constraint on the coefficients through varying penalization strength. As a result, the method provides significant improvement when the structure is informative while maintaining robustness against a misspecified structure. Through extensive simulation studies and real data analysis, we demonstrate the superiority of the proposed framework over the state-of-the-art approaches.}, }
@article {pmid39655221, year = {2024}, author = {Contreras-Peruyero, H and Nuñez, I and Vazquez-Rosas-Landa, M and Santana-Quinteros, D and Pashkov, A and Carranza-Barragán, ME and Perez-Estrada, R and Guerrero-Flores, S and Balanzario, E and Muñiz Sánchez, V and Nakamura, M and Ramírez-Ramírez, LL and Sélem-Mojica, N}, title = {CAMDA 2023: Finding patterns in urban microbiomes.}, journal = {Frontiers in genetics}, volume = {15}, number = {}, pages = {1449461}, pmid = {39655221}, issn = {1664-8021}, abstract = {The Critical Assessment of Massive Data Analysis (CAMDA) addresses the complexities of harnessing Big Data in life sciences by hosting annual competitions that inspire research groups to develop innovative solutions. In 2023, the Forensic Challenge focused on identifying the city of origin for 365 metagenomic samples collected from public transportation systems and identifying associations between bacterial distribution and other covariates. For microbiome classification, we incorporated both taxonomic and functional annotations as features. To identify the most informative Operational Taxonomic Units, we selected features by fitting negative binomial models. We then implemented supervised models conducting 5-fold cross-validation (CV) with a 4:1 training-to-validation ratio. After variable selection, which reduced the dataset to fewer than 300 OTUs, the Support Vector Classifier achieved the highest F1 score (0.96). When using functional features from MIFASER, the Neural Network model outperformed other models. When considering climatic and demographic variables of the cities, Dirichlet regression over Escherichia, Enterobacter, and Klebsiella bacteria abundances suggests that population increase is indeed associated with a rise in the mean of Escherichia while decreasing temperature is linked to higher proportions of Klebsiella. This study validates microbiome classification using taxonomic features and, to a lesser extent, functional features. It shows that demographic and climatic factors influence urban microbial distribution. A Docker container and a Conda environment are available at the repository: GitHub facilitating broader adoption and validation of these methods by the scientific community.}, }
@article {pmid39654976, year = {2024}, author = {Nishizaki, N and Oshiro, S and Tohya, M and Watanabe, S and Okazaki, T and Takahashi, K and Kirikae, T and Shimizu, T}, title = {Propionimicrobium lymphophilum in urine of children with monosymptomatic nocturnal enuresis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1377992}, pmid = {39654976}, issn = {2235-2988}, mesh = {Humans ; Child ; *Nocturnal Enuresis/microbiology/urine ; Male ; Female ; *RNA, Ribosomal, 16S/genetics ; Urine/microbiology ; Anti-Bacterial Agents/therapeutic use ; Urinary Tract Infections/microbiology/diagnosis ; Adolescent ; Actinobacteria/isolation &amp; purification/genetics ; DNA, Bacterial/genetics ; Real-Time Polymerase Chain Reaction ; Sequence Analysis, DNA ; }, abstract = {BACKGROUND: Despite a unique microbiome in urine, the relationship between nocturnal enuresis and the urobiome remains unclear. This study aimed to compare the presence of specific bacterial species in the urine of children with and without nocturnal enuresis.<br><br>METHODS: We used 16S ribosomal RNA gene sequencing to analyze the urobiome in urine samples obtained from the two groups of children. The presence of Propionimicrobium lymphophilum was examined using real-time PCR in the urine of 25 children diagnosed with monosymptomatic nocturnal enuresis (MNE), and 17 children without this condition.<br><br>RESULTS: Children with MNE exhibited a significantly higher prevalence of P. lymphophilum: 16 out of 25 (64.0%) compared to 4 out of 17 (23.5%) in the control group. Among children with frequent bedwetting, there was a significantly higher prevalence of P. lymphophilum;15 out of 16 (93.8%) compared to 2 out of 9 (22.2%) in those with infrequent bedwetting. Bacterial culture tests confirmed the anaerobic growth of P. lymphophilum isolates from urine samples of two PCR-positive patients with MNE. These isolates were found to be susceptible to ampicillin.<br><br>CONCLUSION: These findings suggest that P. lymphophilum may be associated with chronic urinary tract infections and potentially contribute to the development of MNE in children.}, }
@article {pmid39654975, year = {2024}, author = {Jarmukhanov, Z and Mukhanbetzhanov, N and Vinogradova, E and Kozhakhmetov, S and Kushugulova, A}, title = {Gut metagenomic features of frailty.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1486579}, pmid = {39654975}, issn = {2235-2988}, mesh = {*Gastrointestinal Microbiome/genetics ; Humans ; *Frailty/microbiology/metabolism ; Male ; Female ; Aged ; Middle Aged ; *Feces/microbiology ; *Metagenomics/methods ; Kazakhstan ; Adult ; Metagenome ; Bacteria/classification/genetics/isolation &amp; purification/metabolism ; Aged, 80 and over ; Metabolic Networks and Pathways/genetics ; }, abstract = {This study investigates the relationship between frailty severity and gut microbiome characteristics in adults in Kazakhstan. We analyzed 158 participants across four frailty severity (mild to very severe) using metagenomic sequencing of stool samples. Frailty was significantly correlated with age, weight, and functional measures like walking speed and grip strength. Microbial diversity decreased significantly with increasing frailty. Beta diversity analysis revealed distinct clustering patterns based at phylum level. Taxonomically, we observed a significant inverse correlation between Firmicutes abundance and frailty. Classes like Clostridia and Erysipelotrichia decreased with frailty, while Bacteroidia and Actinobacteria increased. At the family level, Oscillospiraceae showed a positive correlation with frailty. Functionally, we identified significant correlations between frailty measures and specific metabolic pathways. The frailty index negatively correlated with pathways involved in cobalamin, arginine and molybdenum cofactor biosynthesis and positively correlated with folate biosynthesis. Physical performance measures strongly correlated with pathways related to nucleotide biosynthesis, and one-carbon metabolism. We propose these identified features may constitute a "frailty-associated metabolic signature" in the gut microbiome. This signature suggests multiple interconnected mechanisms through which the microbiome may influence frailty development, including modulation of inflammation, alterations in energy metabolism, and potential impacts on muscle function through microbial metabolites.}, }
@article {pmid39654856, year = {2024}, author = {Subramanian, A and J, A and T, T and Kumarasamy, V and Begum, MY and Sekar, M and Subramaniyan, V and Wong, LS and Al Fatease, A}, title = {Exploring the Connections: Autophagy, Gut Microbiota, and Inflammatory Bowel Disease Pathogenesis.}, journal = {Journal of inflammation research}, volume = {17}, number = {}, pages = {10453-10470}, pmid = {39654856}, issn = {1178-7031}, abstract = {Inflammatory Bowel Disease (IBD), which includes Crohn's disease and ulcerative colitis, represents a complex and growing global health issue with a multifaceted origin. This review delves into the intricate relationship between gut microbiota, autophagy, and the development of IBD. The gut microbiota, a diverse community of microorganisms, plays a vital role in maintaining gut health, while imbalances in this microbial community, known as dysbiosis, are linked to IBD. Autophagy, a process by which cells recycle their components, is essential for gut homeostasis and the regulation of immune responses. When autophagy is impaired and dysbiosis occurs, they individually contribute to IBD, with their combined impact intensifying inflammation. The interconnectedness of gut microbiota, autophagy, and the host's immune system is central to the onset of IBD. The review also examines how diet influences gut microbiota and its subsequent effects on IBD. It highlights the therapeutic potential of targeting the microbiota and modulating autophagic pathways as treatment strategies for IBD. Understanding these interactions could lead to personalized therapies within the rapidly advancing fields of microbiome research and immunology.}, }
@article {pmid39654779, year = {2024}, author = {Veneruso, I and Mennitti, C and Gentile, A and Di Bonito, G and Ulisse, J and Scarano, C and Lombardo, B and Terracciano, D and Pero, R and D'Alicandro, G and Frisso, G and D'Argenio, V and Scudiero, O}, title = {Effect of elite sport activity on salivary microbiota: The case of water polo.}, journal = {Heliyon}, volume = {10}, number = {23}, pages = {e40663}, pmid = {39654779}, issn = {2405-8440}, abstract = {It has been well established that the human gut microbiota plays a pivotal role in humans' health, since it is involved in nutrients' uptake, vitamins' synthesis, energy harvest, inflammatory modulation, and host immune responses. Moreover, gut microbiota alterations have been associated to an increasing number of diseases and its composition can be affected by several factors, including physical exercise. In particular, it has been reported that intense physical activity can induce metabolic changes which translate in alterations of specific biomarkers that can lead to the onset of infections, inflammation and hepatic or kidney disorders. Recently, the oral microbiota has shown its relevance not only for the health of oral cavity but also for human host's health, emerging as an ecological niche with a great potential for the study of gut microbiome alterations due also to its accessibility respect to other tracts that can be inferred through fecal samples analysis. Thus, the purpose of this study has been to assess the effect of intense physical activity, i.e., elite water polo, on the human salivary microbiota. Thirteen professional water polo players and nineteen sedentary controls were recruited for this study. The salivary microbiota analysis was performed in oral rinse collected from both controls and athletes three months after the beginning of the agonist season. Our results showed significant differences in the salivary microbiota between athletes and controls. In particular, three species, namely Oribacterium sinus, Oribacterium parvum and Oribacterium asaccharolyticum, were found to be significantly increased in the water polo players compared to controls. Even if these data have to be further validated, also to assess the role of these identified species, they strengthen the hypothesis that elite sports can influence and alter the status of the gut microbiota. Moreover, the saliva is confirmed as a suitable sample for microbiome evaluations that may improve athletes' status evaluation and monitoring.}, }
@article {pmid39654676, year = {2024}, author = {Han, H and Choi, YH and Kim, SY and Park, JH and Chung, J and Na, HS}, title = {Optimizing microbiome reference databases with PacBio full-length 16S rRNA sequencing for enhanced taxonomic classification and biomarker discovery.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1485073}, pmid = {39654676}, issn = {1664-302X}, abstract = {BACKGROUND: The study of the human microbiome is crucial for understanding disease mechanisms, identifying biomarkers, and guiding preventive measures. Advances in sequencing platforms, particularly 16S rRNA sequencing, have revolutionized microbiome research. Despite the benefits, large microbiome reference databases (DBs) pose challenges, including computational demands and potential inaccuracies. This study aimed to determine if full-length 16S rRNA sequencing data produced by PacBio could be used to optimize reference DBs and be applied to Illumina V3-V4 targeted sequencing data for microbial study.<br><br>METHODS: Oral and gut microbiome data (PRJNA1049979) were retrieved from NCBI. DADA2 was applied to full-length 16S rRNA PacBio data to obtain amplicon sequencing variants (ASVs). The RDP reference DB was used to assign the ASVs, which were then used as a reference DB to train the classifier. QIIME2 was used for V3-V4 targeted Illumina data analysis. BLAST was used to analyze alignment statistics. Linear discriminant analysis Effect Size (LEfSe) was employed for discriminant analysis.<br><br>RESULTS: ASVs produced by PacBio showed coverage of the oral microbiome similar to the Human Oral Microbiome Database. A phylogenetic tree was trimmed at various thresholds to obtain an optimized reference DB. This established method was then applied to gut microbiome data, and the optimized gut microbiome reference DB provided improved taxa classification and biomarker discovery efficiency.<br><br>CONCLUSION: Full-length 16S rRNA sequencing data produced by PacBio can be used to construct a microbiome reference DB. Utilizing an optimized reference DB can increase the accuracy of microbiome classification and enhance biomarker discovery.}, }
@article {pmid39654106, year = {2024}, author = {Xiao, C and Feng, X and Zhao, T and Ding, G and Gao, Y}, title = {Research trends and hotspots of intratumor microbiome: A comprehensive visualization and bibliometric study from 2012 to 2024.}, journal = {Chinese medical journal}, volume = {}, number = {}, pages = {}, pmid = {39654106}, issn = {2542-5641}, }
@article {pmid39653980, year = {2024}, author = {Budzinski, L and Sempert, T and Lietz, L and Maier, R and Kang, GU and von Stuckrad, ASL and Goetzke, CC and Roth, M and Shah, A and Abbas, A and Lehman, K and Necke, K and Bartsch, S and Hoffmann, U and Mashreghi, MF and Biesen, R and Kallinich, T and Chang, HD}, title = {Age-stratification reveals age-specific intestinal microbiota signatures in juvenile idiopathic arthritis.}, journal = {Molecular and cellular pediatrics}, volume = {11}, number = {1}, pages = {12}, pmid = {39653980}, issn = {2194-7791}, abstract = {OBJECTIVE: Juvenile Idiopathic Arthritis (JIA) comprises diverse chronic inflammatory conditions driven by malfunction of the immune system. The intestinal microbiota is considered a crucial environmental factor correlating with chronic inflammatory diseases, and for JIA certain alterations in the microbiota have already been described.<br><br>METHODS: Here, we have characterized intestinal microbiota samples from 54 JIA patients and 38 pediatric healthy controls by conventional 16S rRNA sequencing and by single-cell analysis for phenotypic features by multi-parameter microbiota flow cytometry (mMFC), which complements the population-based taxonomic profiling with the characterization of individual bacterial cells.<br><br>RESULTS: We found age to be a crucial confounder in microbiota analyses of JIA patients. Age stratification revealed specific microbiota alterations neglected by the general comparison of JIA patients and pediatric controls.<br><br>CONCLUSION: Age groups presented distinct taxonomic profiles and microbiota phenotypic signatures which transitioned with age, highlighting changes in the microbiota-immune system interaction with age.}, }
@article {pmid39653811, year = {2024}, author = {Zhou, Z and Kleis, L and Depetris-Chauvin, A and Jaskulski, S and Damerell, V and Michels, KB and Gigic, B and Nöthlings, U and Panagiotou, G}, title = {Beneficial microbiome and diet interplay in early-onset colorectal cancer.}, journal = {EMBO molecular medicine}, volume = {}, number = {}, pages = {}, pmid = {39653811}, issn = {1757-4684}, support = {01KD2101//Bundesministerium f&#xfc;r Bildung und Forschung (BMBF)/ ; 390713860//Deutsche Forschungsgemeinschaft (DFG)/ ; CA189184//HHS | National Institutes of Health (NIH)/ ; }, abstract = {Colorectal cancer (CRC) is the third most commonly diagnosed cancer and the second leading cause of cancer-related deaths worldwide. Although the risk of developing CRC increases with age, approximately 10% of newly diagnosed cases occur in individuals under the age of 50. Significant changes in dietary habits in young adults since industrialization create a favorable microenvironment for colorectal carcinogenesis. We aim here to shed light on the complex interplay between diet and gut microbiome in the pathogenesis and prevention of early-onset CRC (EO-CRC). We provide an overview of dietary risk factors associated with EO-CRC and contrast them with the general trends for CRC. We delve into gut bacteria, fungi, and phages with potential benefits against CRC and discuss the underlying molecular mechanisms. Furthermore, based on recent findings from human studies, we offer insights into how dietary modifications could potentially enhance gut microbiome composition to mitigate CRC risk. All together, we outline the current research landscape in this area and propose directions for future investigations that could pave the way for novel preventive and therapeutic strategies.}, }
@article {pmid39653763, year = {2024}, author = {Forrester, JV and McMenamin, PG}, title = {Evolution of the ocular immune system.}, journal = {Eye (London, England)}, volume = {}, number = {}, pages = {}, pmid = {39653763}, issn = {1476-5454}, abstract = {The evolution of the ocular immune system should be viewed within the context of the evolution of the immune system, and indeed organisms, as a whole. Since the earliest time, the most primitive responses of single cell organisms involved molecules such as anti-microbial peptides and behaviours such as phagocytosis. Innate immunity took shape ~2.5 billion years ago while adaptive immunity and antigen specificity appeared with vertebrate evolution ~ 500 million years ago. The invention of the microscope and the germ theory of disease precipitated debate on cellular versus humoral immunity, resolved by the discovery of B and T cells. Most recently, our understanding of the microbiome and consideration of the host existing symbiotically with trillions of microbial genes (the holobiont), suggests that the immune system is a sensor of homoeostasis rather than simply a responder to pathogens. Each tissue type in multicellular organisms, such as vertebrates, has a customised response to immune challenge, with powerful reactions most evident in barrier tissues such as the skin and gut mucosa, while the eye and brain occupy the opposite extreme where responses are attenuated. The experimental background which historically led to the concept of immune privilege is discussed in this review; however, we propose that the ocular immune response should not be viewed as unique but simply an example of how the tissues variably respond in nature, more or less to the same challenge (or danger).}, }
@article {pmid39653697, year = {2024}, author = {Palladino, G and Nanetti, E and Scicchitano, D and Cinti, N and Foresto, L and Cozzi, A and Gonzalez Vara Rodriguez, A and Interino, N and Fiori, J and Turroni, S and Candela, M and Rampelli, S}, title = {Zonation of the Vitis vinifera microbiome in Vino Nobile di Montepulciano PDO production area.}, journal = {Communications biology}, volume = {7}, number = {1}, pages = {1626}, pmid = {39653697}, issn = {2399-3642}, support = {818290//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; }, mesh = {*Vitis/microbiology ; *Microbiota/genetics ; Italy ; *Wine/microbiology ; Soil Microbiology ; Bacteria/genetics/classification/metabolism/isolation &amp; purification ; Fungi/genetics/classification/metabolism ; Rhizosphere ; }, abstract = {The microbial dimension of the terroir is crucial for wine quality, as microbiomes contribute to plant biofertilization, stress tolerance and pathogen suppression. While microbial terroir can act as a biological signature at large scale, data for local contexts is lacking, hindering the characterization of regional microbial diversity in vineyards. Here, we define the microbial terroir of vineyards across the 12 sub-areas (Additional Geographic Units -AGUs) of the "Consorzio del Vino Nobile di Montepulciano DOCG" PDO area (Italy), a world-renowned wine-producing region. Rhizospheres of Vitis vinifera cultivar Sangiovese and soil samples were collected throughout the 2022 viticultural season and analyzed through an integrated metabarcoding/shotgun metagenomic approach, targeting bacteria and fungi. Wine metabolomics was also perfomed, projecting compositional and functional variations of the microbial terroir at the AGUs level into a corresponding variation in the product metabolic profile. Our findings reveal a unique taxonomic configuration of the Vino Nobile di Montepulciano terroir compared to other vineyards, with microbiomes being "AGU-specific" in taxonomic abundances and plant growth-promoting functions, confirming the potential relevance of characterizing and preserving the microbial terroir to safeguard high-quality traditional wines.}, }
@article {pmid39653637, year = {2024}, author = {Lepcha, A and Kumar, R and Dindhoria, K and Bhargava, B and Pati, AM and Kumar, R}, title = {Metagenomic insights into the functional potential of non-sanitary landfill microbiomes in the Indian Himalayan region, highlighting key plastic degrading genes.}, journal = {Journal of hazardous materials}, volume = {484}, number = {}, pages = {136642}, doi = {10.1016/j.jhazmat.2024.136642}, pmid = {39653637}, issn = {1873-3336}, abstract = {Solid waste management in the Indian Himalayan Region (IHR) is a growing challenge, intensified by increasing population and tourism, which strain non-sanitary landfills. This study investigates microbial diversity and functional capabilities within these landfills using a high-throughput shotgun metagenomic approach. Physicochemical analysis revealed that the Manali and Mandi landfill sites were under heavy metal contamination and thermal stress. Taxonomic annotation identified a dominance of bacterial phyla, including Proteobacteria, Actinobacteria, Bacteroidetes, and Firmicutes, with genera like Pseudomonas and Bacillus prevalent. Squeezemeta analysis generated 9,216,983 open reading frames (ORFs) across the sampling sites, highlighting diverse metabolic potentials for heavy metal resistance and degrading organic, xenobiotics and plastic wastes. Hierarchical clustering and principal component analysis (PCA) identified distinct gene clusters in Manali and Mandi landfill sites, reflecting differences in pollution profiles. Functional redundancy of landfill microbiome was observed with notable xenobiotic and plastic degradation pathways. This is the first comprehensive metagenomic assessment of non-sanitary landfills in the IHR, providing valuable insights into the microbial roles in degrading persistent pollutants, plastic waste, and other contaminants in these stressed environments.}, }
@article {pmid39653531, year = {2024}, author = {Wang, W and Wang, FR and Guo, Y and Zhang, HB and Jiang, FF}, title = {[Characteristics of airway microbiome co-occurrence network in patients with type 2 and non-type 2 asthma].}, journal = {Zhonghua jie he he hu xi za zhi = Zhonghua jiehe he huxi zazhi = Chinese journal of tuberculosis and respiratory diseases}, volume = {47}, number = {12}, pages = {1121-1129}, doi = {10.3760/cma.j.cn112147-20241015-00611}, pmid = {39653531}, issn = {1001-0939}, mesh = {Humans ; *Asthma/microbiology/metabolism ; Female ; Male ; Middle Aged ; Adult ; Prospective Studies ; *Microbiota ; *Nitric Oxide/metabolism ; Sputum/microbiology ; Case-Control Studies ; Respiratory System/microbiology/metabolism ; Breath Tests ; }, abstract = {Objective: To study the characteristics of the airway microbiome co-occurrence network in patients with type 2 and non-type 2 asthma. Methods: In a prospective study based on a cohort of asthma patients, respiratory induced sputum samples were collected from 55 asthma patients [25 males and 30 females, with a median age of 47.7 years (age range 34.3-63.0 years)] admitted to the Department of Respiratory and Critical Care, Beijing Chaoyang Hospital, Capital Medical University and 12 healthy controls from the Physical Examination Centre of Beijing Chaoyang Hospital, Capital Medical University, from May 2021 to May 2022. According to the level of exhaled breath nitric oxide (FeNO), the asthma patients were divided into 22 cases in the high FeNO group (FeNO≥40 ppb, i.e., type 2 asthma group) and 33 cases in the low FeNO group (FeNO<40 ppb, i.e., non-type 2 asthma group). All induced sputum samples were subjected to second-generation macrogenomic sequencing and bioinformatic analyses of microbial community diversity, compositional characteristics, symbiotic network characteristics and metabolic function prediction. The Kruskal-Wallis rank sum test was used for between-group comparisons, and the linear discriminant analysis (LEfSe) method was used to compare the differences in flora composition between groups. The R language was used for microbial network analysis. In addition, PICRUSt was used to predict the metabolic-functional characteristics of the microbial communities. Results: The microbial communities in the healthy control group had a lower proportion of p_Firmicutes and p_Proteobacteria than asthma patients, 29% and 21%, respectively; 37% and 33% in the low FeNO group and 42% and 26% in the high FeNO group. The microbial network in the low FeNO group had 64 pairs of edges forming 16 communities, and about 75% of the nodes had eigenvector centrality values between 0 and 0.05, and 25% of the nodes had eigenvector centrality values between 0.10 and 0.45. There were four layers of κ-nucleosynthesis, and about 42% of the vertices were in the centre of the two layers. The microbial network of the high-FeNO group had 80 pairs of edges forming 18 clusters, and 81% of the nodes had eigenvector centrality values between 0 and 0.05, and 19% of the nodes had eigenvector centrality values between 0.10 and 0.35. The κ-nucleus decomposition had eight layers, and 21% of the vertices were located in the centre's two layers. The main functional differences between the low and high FeNO groups were shown in metabolic pathways (including sugar, lipid, amino acid, and energy metabolism), drug resistance, biofilm transport, signalling, intercellular communication, and cellular repair. Conclusions: Compared with non-type 2 asthmatics, type 2 asthmatics had a higher alpha diversity of respiratory microbiota, lower levels of microorganisms in the p_Proteobacteria, and a more aggregated microbial network. There was a significant difference in the predicted metabolic function of the two endotypes of asthmatics.}, }
@article {pmid39652612, year = {2024}, author = {Mac Cann, R and Newman, E and Devane, D and Sabin, C and Cotter, AG and Landay, A and O'Toole, PW and Mallon, PW}, title = {HIV, the gut microbiome and clinical outcomes, a systematic review.}, journal = {PloS one}, volume = {19}, number = {12}, pages = {e0308859}, pmid = {39652612}, issn = {1932-6203}, mesh = {Humans ; *Gastrointestinal Microbiome ; *HIV Infections/microbiology/drug therapy ; *Dysbiosis/microbiology ; Cardiovascular Diseases/microbiology ; }, abstract = {BACKGROUND: Effective antiretroviral therapy (ART) has improved the life expectancy of people with HIV (PWH). However, this population is now experiencing accelerated age-related comorbidities, contributed to by chronic immune activation and inflammation, with dysbiosis of the gut microbiome also implicated.<br><br>METHOD: We conducted a systematic literature search of PubMed, Embase, Scopus, Cochrane reviews and international conference abstracts for articles that examined for the following non-communicable diseases (NCDs); cardiovascular disease, cancer, frailty, metabolic, bone, renal and neurocognitive disease, in PWH aged >18 years. Studies were included that measured gut microbiome diversity and composition, microbial translocation markers or microbial metabolite markers.<br><br>RESULTS: In all, 567 articles were identified and screened of which 87 full-text articles were assessed for eligibility and 56 were included in the final review. The data suggest a high burden NCD, in particular cardiovascular and metabolic disease in PWH. Alterations in bacterial diversity and structure varied by NCD type, but a general trend in reduced diversity was seen together with alterations in bacterial abundances between different NCD. Lipopolysaccharide was the most commonly investigated marker of microbial translocation across NCD followed by soluble CD14. Short-chain fatty acids, tryptophan and choline metabolites were associated with cardiovascular outcomes and also associated with chronic liver disease (CLD).<br><br>CONCLUSIONS: This systematic review is the first to summarise the evidence for the association between gut microbiome dysbiosis and NCDs in PWH. Understanding this interaction will provide insights into the pathogenesis of many NCD and help develop novel diagnostic and therapeutic strategies for PWH.}, }
@article {pmid39652543, year = {2024}, author = {Heras-Molina, A and Estellé, J and Vázquez-Gómez, M and López-García, A and Pesantez-Pacheco, JL and Astiz, S and Garcia-Contreras, C and Escudero, R and Isabel, B and Gonzalez-Bulnes, A and Óvilo, C}, title = {The impact of host genetics on porcine gut microbiota composition excluding maternal and postnatal environmental influences.}, journal = {PloS one}, volume = {19}, number = {12}, pages = {e0315199}, pmid = {39652543}, issn = {1932-6203}, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Swine/microbiology ; Female ; Genotype ; Feces/microbiology ; Male ; Fatty Acids, Volatile/metabolism ; }, abstract = {The gut microbiota of the pig is being increasingly studied due to its implications for host homeostasis and the importance of the pig as a meat source and biomedical model of human diseases. However, most studies comparing the microbiome between different breeds do not consider the influence of maternal environment during the colonization of the microbiota. The aim of the present study was to compare the gut microbiota during postnatal growth between two pig genotypes (purebred Iberian vs. crossbreds Iberian x Large White pigs), gestated in a single maternal environment (pure Iberian mothers) inseminated with heterospermic semen. Postnatally, piglets were maintained in the same environmental conditions, and their microbiota was studied at 60 and 210 days old. Results showed that age had the greatest influence on alpha and beta diversity, and genotype also affected beta diversity at both ages. There were differences in the microbiome profile between genotypes at the ASV and genus levels when jointly analyzing the total number of samples, which may help to explain phenotypical differences. When each time-point was analyzed individually, there were more differences at 210 days-old than 60 days-old. Fecal short-chain fatty acids (SCFA) were also affected by age, but not by genotype. These results may be a basis for further research on host genotype interactions with the gut microbiota.}, }
@article {pmid39652457, year = {2024}, author = {Zhao, A and Li, Q and Meng, P and Liu, P and Wu, S and Lang, Z and Song, Y and Macho, AP}, title = {Reduced content of gamma-aminobutyric acid enhances resistance to bacterial wilt disease in tomato.}, journal = {Plant biotechnology journal}, volume = {}, number = {}, pages = {}, doi = {10.1111/pbi.14539}, pmid = {39652457}, issn = {1467-7652}, support = {XDB27040204//Chinese Academy of Sciences/ ; //Chinese 1000 talents program/ ; 2022YFD2100100//National Key Research and Development Program of China/ ; }, abstract = {Bacteria within the Ralstonia solanacearum species complex cause devastating diseases in numerous crops, causing important losses in food production and industrial supply. Despite extensive efforts to enhance plant tolerance to disease caused by Ralstonia, efficient and sustainable approaches are still missing. Before, we found that Ralstonia promotes the production of gamma-aminobutyric acid (GABA) in plant cells; GABA can be used as a nutrient by Ralstonia to sustain the massive bacterial replication during plant colonization. In this work, we used CRISPR-Cas9-mediated genome editing to mutate SlGAD2, which encodes the major glutamate decarboxylase responsible for GABA production in tomato, a major crop affected by Ralstonia. The resulting Slgad2 mutant plants show reduced GABA content, and enhanced tolerance to bacterial wilt disease upon Ralstonia inoculation. Slgad2 mutant plants did not show altered susceptibility to other tested biotic and abiotic stresses, including drought and heat. Interestingly, Slgad2 mutant plants showed altered microbiome composition in roots and soil. We reveal a strategy to enhance plant resistance to Ralstonia by the manipulation of plant metabolism leading to an impairment of bacterial fitness. This approach could be particularly efficient in combination with other strategies based on the manipulation of the plant immune system, paving the way to a sustainable solution to Ralstonia in agricultural systems.}, }
@article {pmid39652259, year = {2024}, author = {Gamba, G and Colonetti, T and Uggioni, MLR and Elibio, LU and Balbinot, EL and Heinzen, R and Macedo, ACL and Grande, AJ and da Rosa, MI}, title = {Gut microbiota and breast cancer: systematic review and meta-analysis.}, journal = {Breast cancer (Tokyo, Japan)}, volume = {}, number = {}, pages = {}, pmid = {39652259}, issn = {1880-4233}, abstract = {BACKGROUND: The gastrointestinal microbiota can modulate systemic estrogens, potentially influencing estrogen-induced breast neoplasia development. This study aimed to assess alterations in the gut microbiota in breast cancer patients.<br><br>METHODS: A search strategy was developed using the terms: "Microbiota," "Gastrointestinal Microbiome," "Breast Cancer," and synonyms. Ten observational studies were included.<br><br>RESULTS: The total sample was 1730 women (929 cases and 801 controls). The meta-analysis of alpha diversity, assessed by the Shannon index, displayed that in the breast cancer group, the diversity of the gut microbiota was reduced compared to controls, with a standardized mean difference (SMD) of -&#xa0;0.34 (95% CI -&#xa0;0.59, -&#xa0;0.10, I[2]&#x2009;=&#x2009;68%, p&#x2009;=&#x2009;0.007). Regarding the premenopausal population, there was a significant reduction in the breast cancer group (SMD -&#xa0;0.67, 95% CI -&#xa0;1.06, -&#xa0;0.28, I[2]&#x2009;=&#x2009;77%, p&#x2009;=&#x2009;0.0009). In women with a body mass index (BMI) between overweight or obesity, no statistically significant difference was observed (SMD -&#xa0;0.20; 95% CI -&#xa0;0.51, 0.11; I[2] 52%, p&#x2009;=&#x2009;0.20). However, in women with a BMI greater than or equal to 18.5 and less than 25.0, there was lower diversity in women with breast cancer compared to controls (SMD -&#xa0;0.49, 95% CI -&#xa0;0.94, -&#xa0;0.04; I[2] 78%, p&#x2009;=&#x2009;0.03).<br><br>CONCLUSIONS: The study found a significant difference in gut microbiota diversity between women with breast cancer and controls, supporting the growing evidence that the gut microbiota may play a role in mammary carcinogenesis.}, }
@article {pmid39651993, year = {2024}, author = {Poncet, R and Gargominy, O}, title = {In the Shadow of Medicine: The Glaring Absence of Occurrence Records of Human-Hosted Biodiversity.}, journal = {Online journal of public health informatics}, volume = {16}, number = {}, pages = {e60140}, doi = {10.2196/60140}, pmid = {39651993}, issn = {1947-2579}, abstract = {Microbial diversity is vast, with bacteria playing a crucial role in human health. However, occurrence records (location, date, observer, and host interaction of human-associated bacteria) remain scarce. This lack of information hinders our understanding of human-microbe relationships and disease prevention. In this study, we show that existing solutions such as France's Système d'Information sur le Patrimoine Naturel framework, can be used to efficiently collect and manage occurrence data on human-associated bacteria. This user-friendly system allows medical personnel to easily share and access data on bacterial pathogens. By adopting similar national infrastructures and treating human-associated bacteria as biodiversity data, we can significantly improve public health management and research, and our understanding of the One Health concept, which emphasizes the interconnectedness of human, animal, and environmental health.}, }
@article {pmid39651929, year = {2024}, author = {Liu, F and Wan, H and Fan, H and Zhang, Z and Dai, H and He, H}, title = {Complexation of starch and konjac glucomannan during screw extrusion exhibits obesity-reducing effects by modulating the intestinal microbiome and its metabolites.}, journal = {Food &amp; function}, volume = {}, number = {}, pages = {}, doi = {10.1039/d4fo04275a}, pmid = {39651929}, issn = {2042-650X}, abstract = {Dietary interventions have been shown to improve gut health by altering the gut flora, preventing obesity, and mitigating inflammatory disorders. This study investigated the benefits of a rice starch-konjac glucomannan (ERS-KGM) complex, produced via screw extrusion, for gut health and obesity prevention. Analyzed through in vitro starch digestion, scanning electron microscopy, and structural analysis, the ERS-KGM complex exhibited a notable increase in resistant starch content due to its well-ordered structure. When administered to mice on a high-fat diet for 8 weeks, the ERS-KGM complex significantly reduced body weight, white adipose tissue mass, adipocyte size, and food intake while increasing water consumption. It also improved glucose metabolism, insulin sensitivity, and lipid profiles by lowering serum triglycerides and total glycerol content. Enhanced metabolic biomarkers and enzyme activities were observed, specifically involving glycerophospholipid metabolism. It decreased the activities of aldehyde dehydrogenase, lactate dehydrogenase, and amino acid transaminase while increasing antioxidant enzymes like glutathione peroxidase and superoxide dismutase. Additionally, it elevated glycogen and positively altered gut microbiota by enriching Firmicutes, Desulfobacterota, and Bifidobacterium. This change enhanced the ability to degrade specific compounds and elevated the concentrations of short-chain fatty acids in feces. These findings suggest that the ERS-KGM complex could serve as a dietary supplement for obesity prevention.}, }
@article {pmid39651911, year = {2024}, author = {Rocha, ST and Shah, DD and Zhu, Q and Shrivastava, A}, title = {The prevalence of motility-related genes within the human oral microbiota.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0126424}, doi = {10.1128/spectrum.01264-24}, pmid = {39651911}, issn = {2165-0497}, abstract = {The human oral and nasal microbiota contains approximately 770 cultivable bacterial species. More than 2,000 genome sequences of these bacteria can be found in the expanded Human Oral Microbiome Database (eHOMD). We developed HOMDscrape, a freely available Python software tool to programmatically retrieve and process amino acid sequences and sequence identifiers from BLAST results acquired from the eHOMD website. Using the data obtained through HOMDscrape, the phylogeny of proteins involved in bacterial type 9 secretion system (T9SS)-driven gliding motility, flagellar motility, and type IV pilus-driven twitching motility was constructed. A comprehensive phylogenetic analysis was conducted for all components of the rotary T9SS, a machinery responsible for secreting various enzymes, virulence factors, and enabling bacterial gliding motility. Results revealed that the T9SS outer membrane β-barrel protein SprA of human oral bacteria underwent horizontal evolution. Overall, we catalog motile bacteria that inhabit the human oral microbiota and document their evolutionary connections. These results will serve as a guide for further studies exploring the impact of motility on the shaping of the human oral microbiota.IMPORTANCEThe human oral microbiota has been extensively studied, and many of the isolated bacteria have genome sequences stored on the human oral microbiome database (eHOMD). Spatial distribution and polymicrobial biofilms are observed in the oral microbiota, but little is understood on how they are influenced by motility. To bridge this gap, we developed a software tool to identify motile bacteria from eHOMD. The results enabled the cataloging of motile bacteria present in the oral microbiota but also provided insight into their evolutionary relationships. This information can guide future research to better understand how bacterial motility shapes the human oral microbiota.}, }
@article {pmid39401017, year = {2024}, author = {Yang, T and Liu, Y and Yin, J and Yv, T and Zhou, F and Li, Y and Yang, L and Han, L and Huang, X}, title = {Transplantation of fecal microbiota from different breeds improved intestinal barrier condition and modulated ileal microflora of recipient pigs.}, journal = {Journal of animal science}, volume = {102}, number = {}, pages = {}, doi = {10.1093/jas/skae314}, pmid = {39401017}, issn = {1525-3163}, mesh = {Animals ; *Fecal Microbiota Transplantation ; *Ileum/microbiology ; Swine ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; Intestinal Mucosa/microbiology ; }, abstract = {In this study, we investigated the effects of transplanting Ningxiang pig fecal bacteria on the ileum microflora and intestinal barrier of Duroc × Landrace × Large White (DLY) pigs. Thirty-two DLY pigs at 90-d-old were equally assigned to either control groups (fed the basal diet) or test groups (fed the basal diet + 10 mL fecal microbiota suspension from Ningxiang pig). Results showed that fecal microbiota transplantation (FMT) did not influence the growth performance, but increased the number of ileum goblet cells and the expression level of mucin-2. Additionally, the mucosal levels of anti-inflammatory cytokines interlukin-4 and interlukin-10 were upregulated, but the level of pro-inflammatory cytokine interferon-γ was downregulated by FMT. Moreover, FMT increased the expression level of porcine β defensin-114 in ileum mucus. 16S rRNA gene sequencing of ileal digesta showed that FMT modulated the diversity and composition of ileal microbiota of DLY pigs by increasing the relative abundances of beneficial bacteria, while decreasing the abundance of the pathogenic bacterium Streptococcus. Taken together, the study showed that FMT of Ningxiang pigs could improve the intestinal barrier condition of DLY pigs by improving intestinal microflora and promoting intestinal health.}, }
@article {pmid39651880, year = {2024}, author = {Plata, G and Srinivasan, K and Krishnamurthy, M and Herron, L and Dixit, P}, title = {Designing host-associated microbiomes using the consumer/resource model.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0106824}, doi = {10.1128/msystems.01068-24}, pmid = {39651880}, issn = {2379-5077}, abstract = {UNLABELLED: A key step toward rational microbiome engineering is in silico sampling of realistic microbial communities that correspond to desired host phenotypes, and vice versa. This remains challenging due to a lack of generative models that simultaneously capture compositions of host-associated microbiomes and host phenotypes. To that end, we present a generative model based on the mechanistic consumer/resource (C/R) framework. In the model, variation in microbial ecosystem composition arises due to differences in the availability of effective resources (inferred latent variables), while species' resource preferences remain conserved. Simultaneously, the latent variables are used to model phenotypic states of hosts. In silico microbiomes generated by our model accurately reproduce universal and dataset-specific statistics of bacterial communities. The model allows us to address three salient questions in host-associated microbial ecologies: (i) which host phenotypes maximally constrain the composition of the host-associated microbiomes? (ii) how context-specific are phenotype/microbiome associations, and (iii) what are plausible microbiome compositions that correspond to desired host phenotypes? Our approach aids the analysis and design of microbial communities associated with host phenotypes of interest.<br><br>IMPORTANCE: Generative models are extremely popular in modern biology. They have been used to model the variation of protein sequences, entire genomes, and RNA sequencing profiles. Importantly, generative models have been used to extrapolate and interpolate to unobserved regimes of data to design biological systems with desired properties. For example, there has been a boom in machine-learning models aiding in the design of proteins with user-specified structures or functions. Host-associated microbiomes play important roles in animal health and disease, as well as the productivity and environmental footprint of livestock species. However, there are no generative models of host-associated microbiomes. One chief reason is that off-the-shelf machine-learning models are data hungry, and microbiome studies usually deal with large variability and small sample sizes. Moreover, microbiome compositions are heavily context dependent, with characteristics of the host and the abiotic environment leading to distinct patterns in host-microbiome associations. Consequently, off-the-shelf generative modeling has not been successfully applied to microbiomes.To address these challenges, we develop a generative model for host-associated microbiomes derived from the consumer/resource (C/R) framework. This derivation allows us to fit the model to readily available cross-sectional microbiome profile data. Using data from three animal hosts, we show that this mechanistic generative model has several salient features: the model identifies a latent space that represents variables that determine the growth and, therefore, relative abundances of microbial species. Probabilistic modeling of variation in this latent space allows us to generate realistic in silico microbial communities. The model can assign probabilities to microbiomes, thereby allowing us to discriminate between dissimilar ecosystems. Importantly, the model predictively captures host-associated microbiomes and the corresponding hosts' phenotypes, enabling the design of microbial communities associated with user-specified host characteristics.}, }
@article {pmid39651862, year = {2024}, author = {Su, Q and Zhang, X and Chen, X and Yu, Z and Wu, W and Xiang, Q and Yang, C and Zhao, J and Chen, L and Xu, Q and Liu, C}, title = {Integrating microbial profiling and machine learning for inference of drowning sites: a forensic investigation in the Northwest River.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0132124}, doi = {10.1128/spectrum.01321-24}, pmid = {39651862}, issn = {2165-0497}, abstract = {Drowning incidents present significant challenges for forensic investigators in determining the exact site of occurrence. Traditional forensic methods often rely on physical evidence and circumstantial clues, but the emerging field of forensic microbiology offers a promising avenue for enhancing precision and reliability in site inference. Our study investigates the application of microbiome analysis in inferring drowning sites, focusing on microbial diversity in water samples and lung tissues of drowned animals from different sites in the Northwest River. We utilized 16S rDNA sequencing to analyze microbial diversity in water samples and lung tissues, revealing distinct microbial signatures associated with drowning sites. Our findings highlight variations in species richness and diversity across different sampling points, indicating the influence of environmental factors on microbial community structure. Machine learning models trained on microbial data from lung tissues demonstrated high accuracy in predicting drowning sites, with cross-validation accuracy ranging from 83.53% ± 3.99% to 95.07% ± 3.17%. Notably, the Gradient Boosting Machine (GBM) method achieved a classification accuracy of 95.07% ± 3.17% for different sampling points at a submersion time of 1 day. Moreover, our cross-species site inference results revealed that utilizing data from drowned mice to predict the drowning sites of rabbits in location W5 achieved an accuracy of 72.22%. In conclusion, our study underscores the potential of microbiome analysis in forensic investigations of drowning incidents. By integrating microbial data with traditional forensic techniques, there is significant potential to enhance the reliability of scene inferences, thereby making substantial contributions to case investigations and judicial trials.IMPORTANCEBy employing advanced techniques like microbial profiling and machine learning, the study aims to enhance the accuracy of determining drowning sites, which is crucial for both legal proceedings. By analyzing microbial diversity in water samples and drowned animal lung tissues, the study sheds light on how environmental factors and victim-related variables influence microbial communities. The findings not only advance our understanding of forensic microbiology but also offer practical implications for improving investigative techniques in cases of drowning.}, }
@article {pmid39651854, year = {2024}, author = {Jiang, C and Wang, F and Tian, J and Zhang, W and Xie, K}, title = {Two rice cultivars recruit different rhizospheric bacteria to promote aboveground regrowth after mechanical defoliation.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0125424}, doi = {10.1128/spectrum.01254-24}, pmid = {39651854}, issn = {2165-0497}, abstract = {Plants have evolved the ability to regrow after mechanical defoliation and environmental stresses. However, it is unclear whether and how defoliated plants exploit beneficial microbiota from the soil to promote aboveground regrowth. Here, we compared the defoliation-triggered changes in the root exudation and bacterial microbiome of two rice cultivars (Oryza sativa L ssp.), indica/xian cultivar Minghui63 and japonica/geng cultivar Nipponbare. The results show that reciprocal growth promotion existed between defoliated Minghui63 seedlings and soil bacteria. After the leaves were removed, the Minghui63 seedlings displayed approximately 1.5- and 2.1-fold higher root exudation and leaf regrowth rates, respectively, than did the Nipponbare seedlings. In field trials, Minghui63 and Nipponbare enriched taxonomically and functionally distinct bacteria in the rhizosphere and root. In particular, Minghui63 rhizosphere and root communities depleted bacteria whose functions are related to xenobiotics biodegradation and metabolism. The microbiome data implied that the bacterial family Rhodocyclaceae was specifically enriched during the regrowth of defoliated Minghui63 rice. We further isolated a Rhodocyclaceae strain, Uliginosibacterium gangwonense MDD1, from rice root. Compared with germ-free conditions, MDD1 inoculation promoted the aboveground regrowth of defoliated Minghui63 by 61% but had a weaker effect on Nipponbare plants, suggesting cultivar-specific associations between regrowth-promoting bacteria and rice. This study provides novel insight into microbiota‒root‒shoot communication, which is implicated in the belowground microbiome and aboveground regrowth in defoliated rice. These data will be helpful for microbiome engineering to increase rice resilience to defoliation and environmental stresses.IMPORTANCEAs sessile organisms, plants face a multitude of abiotic and biotic stresses which often result in defoliation. To survive, plants have evolved the ability to regrow leaves after stresses and wounding. Previous studies revealed that the rhizosphere microbiome affected plant growth and stress resilience; however, how belowground microbiota modulates the aboveground shoot regrowth is unclear. To address this question, we used rice, an important crop worldwide, to analyze the role of rhizosphere microbiota in leaf regrowth after defoliation. Our data indicate mutual growth promotion between defoliated rice and rhizosphere bacteria and such beneficial effect is cultivar specific. The microbiome analysis also led us to find a Uliginosibacterium gangwonense strain that promoted rice cv. MH63 leaf regrowth. Our findings therefore present a novel insight into plant-microbiome function and provide beneficial strains that potentially enhance rice stress resilience.}, }
@article {pmid39651758, year = {2024}, author = {Duong, V and Pooladanda, V and Mitchell, C}, title = {Tissue Processing and Isolation of Primary Fibroblasts from the Human Vagina.}, journal = {Journal of visualized experiments : JoVE}, volume = {}, number = {213}, pages = {}, doi = {10.3791/65864}, pmid = {39651758}, issn = {1940-087X}, mesh = {Humans ; Female ; *Fibroblasts/cytology ; *Vagina/cytology/surgery ; Aged ; *Pelvic Organ Prolapse/surgery ; Middle Aged ; }, abstract = {Pelvic organ prolapse is a disorder that seriously impacts the quality of life of women. It occurs when muscles and ligaments weaken and cause pelvic organs to drop lower in the pelvis, creating a bulge in the vagina. Surgery to correct pelvic organ prolapse has been a mainstay treatment. Recently, there has been growing interest in studying the tissue composition of patients with prolapse at the cellular level. There is currently little consensus regarding the effect of donor or patient age on cell-based therapies. Current published protocols for vaginal fibroblast isolation either concentrate on premenopausal tissue or neglect to comment on the age of donor tissue. Most existing protocols use animal models. The consistency of human vaginal tissue is denser than the tissues used in most protocols. In this study, human vaginal tissue was obtained primarily from older donors, which likely contributed to the failure of existing protocols. The aim of this study is to describe a standard protocol for reliably acquiring human vaginal fibroblasts, regardless of donor age and menopausal status. Results were reproduced using tissue from nine separate donors who underwent pelvic organ prolapse surgery. Six patients were postmenopausal, with the oldest donor being 78 years old. The median age of the tissue donors was 59. Here, we describe a reliable method for generating a fibroblast-enriched single-cell suspension using a combination of enzymatic and mechanical dissociation and cell suspension pooling of multiple vaginal biopsies from a single donor. Reliable isolation of human vaginal primary fibroblasts may be useful in the study of pelvic organ prolapse as well as microbiome-host interactions.}, }
@article {pmid39651351, year = {2024}, author = {Wei, TJ and Li, G and Cui, YR and Xie, J and Teng, X and Wang, YJ and Li, ZH and Guan, FC and Liang, ZW}, title = {Compost mediates the recruitment of core bacterial communities in alfalfa roots to enhance their productivity potential in saline-sodic soils.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1502536}, doi = {10.3389/fmicb.2024.1502536}, pmid = {39651351}, issn = {1664-302X}, abstract = {INTRODUCTION: Composting is one of the effective environmental protection and sustainable measures for improving soil quality and increasing crop yield. However, due to the special physical and chemical properties of saline-sodic soil and the complex rhizosphere microecological environment, the potential mechanism of regulating plant growth after applying compost in saline-sodic soil remains elusive.<br><br>METHODS: Here, we investigated the effects of different compost addition rates (0, 5, 15, 25%) on plant growth traits, soil chemical properties, and rhizosphere bacterial community structure.<br><br>RESULTS: The results showed that compost promoted the accumulation of plant biomass and root growth, increased soil nutrients, and enhanced the diversity and complexity of the rhizosphere bacterial communities. Moreover, the enriched core bacterial ASVs (Amplicon Sequence Variants) in compost treatment could be reshaped, mainly including dominant genera, such as Pseudomonas, Devosia, Novosphingobium, Flavobacterium, and Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium. The functions of these ASVs were energy resources and nitrogen cycle functions, suggesting the roles of these ASVs in improving plant root nutrient resource acquisition for alfalfa growth. The contents of available potassium, available phosphorus, total nitrogen, and organic carbon of the soil surrounding the roots, the root length, root surface area, root volume, and root tips affected the abundance of the core bacterial ASVs, and the soil chemical properties contributed more to the effect of plant biomass.<br><br>DISCUSSION: Overall, our study strengthens the understanding of the potentially important taxa structure and function of plant rhizosphere bacteria communities, and provides an important reference for developing agricultural microbiome engineering techniques to improve root nutrient uptake and increase plant productivity in saline-sodic soils.}, }
@article {pmid39651277, year = {2024}, author = {Sharma, S and Woodworth, B and Yang, B and Duan, N and Pheko, M and Moutsopoulos, N and Emiola, A}, title = {Quantitative mapping of pseudouridines in bacteria RNA.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.11.26.625507}, pmid = {39651277}, issn = {2692-8205}, abstract = {RNA pseudouridylation is one of the most prevalent post-transcriptional modifications, occurring universally across all organisms. Although pseudouridines have been extensively studied in bacterial tRNAs and rRNAs, their presence and role in bacterial mRNA remain poorly characterized. Here, we used a bisulfite-based sequencing approach to provide a comprehensive and quantitative measurement of bacteria pseudouridines. As a proof of concept in E. coli, we identified 1,954 high-confidence sites in 1,331 transcripts, covering almost 30% of the transcriptome. Furthermore, pseudouridine mapping enabled the detection of differentially expressed genes associated with stress response that were unidentified using conventional RNA-seq approach. We also demonstrate that in addition to pseudouridine profiling, our approach can facilitate the discovery of previously unidentified transcripts. As an example, we identified a small RNA transcribed from the antisense strand of tRNA-Tyr which represses expression of distal genes. Finally, we mapped pseudouridines in oral microbiome samples of human subjects, demonstrating the broad applicability of our approach in complex microbiomes. Altogether, our work highlights the advantages of mapping bacterial pseudouridines and provides a tool to study posttranscription regulation in microbial communities.}, }
@article {pmid39651251, year = {2024}, author = {Jeong, S and Tollison, T and Brochu, H and Chou, H and Huntress, I and Yount, KS and Zheng, X and Darville, T and O'Connell, CM and Peng, X}, title = {Cervicovaginal microbial features predicts Chlamydia trachomatis spread to the upper genital tract of infected women.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.11.26.625070}, pmid = {39651251}, issn = {2692-8205}, abstract = {INTRODUCTION: Chlamydia trachomatis (CT) infection can lead to pelvic inflammatory disease, infertility and other reproductive sequelae when it ascends to the upper genital tract. Factors including chlamydial burden, co-infection with other sexually-transmitted bacterial pathogens and oral contraceptive use influence risk for upper genital tract spread. Cervicovaginal microbiome composition influences CT susceptibility and we investigated if it contributes to spread by analyzing amplicon sequence variants (ASVs) derived from the V4 region of 16S rRNA genes in vaginal samples collected from women at high risk for CT infection and for whom endometrial infection had been determined.<br><br>RESULTS: Participants were classified as CT negative (CT-, n=77), CT positive at the cervix (Endo-, n=77), or CT positive at both cervix and endometrium (Endo+, n=66). Although we were unable to identify many significant differences between CT infected and uninfected women, differences in abundance of ASVs representing Lactobacillus iners and L. crispatus subspecies but not dominant lactobacilli were detected. Twelve informative ASVs predicted endometrial chlamydial infection (AUC=0.74), with CT ASV abundance emerging as a key predictor. We also observed a positive correlation between levels of cervically secreted cytokines previously associated with CT ascension and abundance of the informative ASVs.<br><br>CONCLUSION: Our findings suggest that vaginal microbial community members may influence chlamydial spread directly by nutrient limitation and/or disrupting endocervical epithelial integrity and indirectly by modulating pro-inflammatory signaling and/or homeostasis of adaptive immunity. Further investigation of these predictive microbial factors may lead to cervicovaginal microbiome biomarkers useful for identifying women at increased risk for disease.}, }
@article {pmid39651214, year = {2024}, author = {Barekat, K and Ricciotti, E and Ghosh, S and Herrmann, C and Keat, K and Assenmacher, CA and Tanes, C and Wilson, N and Sengupta, A and Das, U and Joshi, R and Ritchie, M and Bittinger, K and Weljie, A and Cadwell, K and Bushman, FD and Wu, G and FitzGerald, GA}, title = {Concomitant suppression of COX-1 and COX-2 is insufficient to induce enteropathy associated with chronic NSAID use.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.11.22.624882}, pmid = {39651214}, issn = {2692-8205}, abstract = {Nonsteroidal anti-inflammatory drugs (NSAIDs) are the most widely used medications for the management of chronic pain; however, they are associated with gastrointestinal (GI) adverse events. Although many mechanisms have been suggested, NSAID-induced enteropathy has been thought to be primarily due to inhibition of both cyclooxygenases (COX) -1 and -2, which results in suppression of prostaglandin synthesis. Here we report that concomitant postnatal deletion of Cox-1 and -2 over 10 months failed to cause intestinal injury in mice unless they were treated with naproxen or its structural analog, phenylpropionic acid, which is not a COX inhibitor. Cox double knockout mice exhibit a distinct gut microbiome composition, and cohousing them with controls rescues their dysbiosis and delays the onset of NSAID-induced GI bleeding. Suppression of bile acid synthesis is also protective. In both the UK Biobank and All of Us human cohorts, coadministration of antibiotics with NSAIDs is associated with an increased frequency of GI bleeding. These results show that prostaglandin suppression plays a trivial role in NSAID-induced enteropathy. However, Cox deletion causes dysbiosis of the gut microbiome that amplifies the enteropathic response to NSAIDs.}, }
@article {pmid39651120, year = {2024}, author = {Xu, K and Covila-Corona, I and Frutos, MD and Núñez-Sánchez, M&#xc1; and Makhanasa, D and Shah, PV and Guzman, G and Ramos-Molina, B and Priyadarshini, M and Khan, MW}, title = {Hepatic HKDC1 Deletion Alleviates Western Diet-Induced MASH in Mice.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.11.26.625530}, pmid = {39651120}, issn = {2692-8205}, abstract = {The global prevalence of Metabolic dysfunction-associated steatohepatitis (MASH) has been rising sharply, closely mirroring the increasing rates of obesity and metabolic syndrome. MASH exhibits a strong sexual dimorphism where females are affected with more severe forms after menopause. Hexokinase domain-containing protein 1 (HKDC1) has recently been recognized for its role in liver diseases, where its expression is minimal under normal conditions but significantly increases in response to metabolic stressors like obesity and liver injury. This selective upregulation suggests HKDC1's potential specialization in hepatic glucose and lipid dysregulation, linking it closely to the progression of MASLD and MASH. This study aims to clarify the role of HKDC1 in Western diet-induced MASH in female mice by examining its impact on hepatic glucose and lipid metabolism, offering insights into its potential as a therapeutic target and addressing the need for sex-specific research in liver disease. This study reveals that HKDC1 expression is elevated in obese women with MASH and correlates with liver pathology. In a mouse model, liver-specific HKDC1 knockout (HKDC1 [LKO]) protected against Western diet-induced obesity, glucose intolerance, and MASH features, including steatosis, inflammation, and fibrosis. Transcriptomic analysis showed that HKDC1 deletion reduced pro-inflammatory and pro-fibrotic gene expression, while gut microbiome analysis indicated a shift toward MASH-protective bacteria. These findings suggest that HKDC1 may exacerbate MASH progression through its role in metabolic and inflammatory pathways, making it a potential therapeutic target.}, }
@article {pmid39651062, year = {2024}, author = {Kaundal, S and Patil, AN and Ks, L and Sharma, V and Arora, A and Singh, C and Jandial, A and Jain, A and Prakash, G and Khadwal, A and Malhotra, P and Lad, DP}, title = {A role for diet and gut microbiota metabolites in autologous hematopoietic cell transplant recipients.}, journal = {Blood cell therapy}, volume = {7}, number = {4}, pages = {101-105}, doi = {10.31547/bct-2024-007}, pmid = {39651062}, issn = {2432-7026}, abstract = {INTRODUCTION: The gut microbiome has an established role in allogeneic hematopoietic cell transplantation (allo-HCT), but not in an auto-HCT setting. We have hypothesized that fecal short-chain fatty acids (SCFA) and urinary 3-indoxyl sulfate (3-IS), which are metabolites derived from the action of the gut microbiome on dietary fiber, play a role in auto-HCT outcomes.<br><br>METHODS: This was a single-center prospective study involving auto-HCT recipients. Baseline patient and disease details, diet diaries, and antibiotic exposure were recorded in consenting patients. Serial (pre-HCT, week two, and week four post-HCT) SCFA and urine 3-IS levels were measured using liquid chromatography-mass spectrometry/mass spectrometry (LC-MS/MS). HCT outcomes were correlated with these metabolites.<br><br>RESULTS: Thirty patients (myeloma, n=13; lymphoma, n=17) were analyzed. The levels of urinary 3-IS, fecal acetate, propionate, and butyrate were found to be decreased at week two and were recovered by week four post-HCT. Those with low median nadir fecal butyrate levels at week two also had significantly lower pre-HCT and week four butyrate levels. Recipients with low butyrate levels had more grade &#x2265;2 mucositis (80% vs. 33%, p=0.01) and low fiber intake (10.4 g vs. 13.6 g, p=0.04). They also had more carbapenem exposure (93% vs. 47%, p=0.005) and prolonged antibiotics (11 days vs. 8 days, p=0.008). There were no differences in the time to neutrophil or platelet engraftment, mortality, or disease response.<br><br>CONCLUSION: Low pre-HCT fecal butyrate levels tend to persist post-HCT and they are associated with mucositis, dietary fiber intake, and antibiotic exposure. The gut microbiome and its modulation may play a role in auto-HCT settings.}, }
@article {pmid39651029, year = {2024}, author = {Suresh, SB and Malireddi, A and Abera, M and Noor, K and Ansar, M and Boddeti, S and Nath, TS}, title = {Gut Microbiome and Its Role in Parkinson's Disease.}, journal = {Cureus}, volume = {16}, number = {11}, pages = {e73150}, doi = {10.7759/cureus.73150}, pmid = {39651029}, issn = {2168-8184}, abstract = {Parkinson's disease (PD) afflicted more than 8.5 million people globally in 2019, as the prevalence of the condition more than doubled during the preceding 25 years. Both non-motor symptoms, such as mood disorders and cognitive impairment, and motor symptoms, such as tremors and rigidity, are indicative of this progressive neurodegenerative disease. Recent data indicates a significant role for the gut microbiome in PD pathogenesis and progression, emphasizing the microbiota-gut-brain axis. In compliance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) 2020 statement, this systematic review summarizes our current knowledge about the function of the gut microbiome in PD, highlighting recurrent microbial alterations and assessing microbiome-based treatment strategies. The review revealed several consistent patterns in the gut microbiota of PD patients, including reduced microbial diversity and specific taxonomic alterations, including a drop in Firmicutes abundance and an increase in Proteobacteria abundance. Functional changes in the gut microbiome, such as altered short-chain fatty acid (SCFA) production and tryptophan metabolism, were also noted. These microbial changes were observed even in early-stage and drug-naïve PD patients, suggesting they are not merely a consequence of disease progression or medication use. The review highlighted potential mechanisms linking gut microbiome alterations to PD, including increased intestinal permeability, neuroinflammation, and modulation of alpha-synuclein aggregation. Probiotics, prebiotics, and fecal microbiota transplantation are a few interventions that try to modify the gut microbiome and might be possible to halt the advancement of PD and enhance patients' quality of life with the condition. Future research should focus on establishing causality through large-scale longitudinal studies, standardizing microbiome analysis methods, and exploring personalized microbiome-based therapies.}, }
@article {pmid39650132, year = {2024}, author = {Cui, K and Xia, X and Wang, Y and Zhang, Y and Zhang, Y and Cao, J and Xu, J and Dong, F and Liu, X and Pan, X and Zheng, Y and Wu, X}, title = {Thiophanate-methyl and its major metabolite carbendazim weaken rhizobacteria-mediated defense responses in cucumbers against Fusarium wilt.}, journal = {aBIOTECH}, volume = {5}, number = {4}, pages = {417-430}, doi = {10.1007/s42994-024-00181-5}, pmid = {39650132}, issn = {2662-1738}, abstract = {UNLABELLED: The effect of fungicides on the plant-rhizosphere microbiome is a subject of ongoing debate, but whether any alteration in the rhizosphere microbiome could affect plant health is an issue that has not been thoroughly investigated. To address this deficiency, we analyzed the rhizosphere microbiome of wilt disease-resistant and disease-susceptible cucumber cultivars to determine whether (and which) plant-associated microorganisms have a role in disease resistance. We further assessed whether the fungicides thiophanate-methyl and carbendazim affect the rhizosphere microbiome, which may contribute to the plant's immune response. Based on results acquired with both radicle-inoculation and soil-inoculation methods, cultivars Longyuanxiuchun (LYXC) and Shuyan2 (SY2) were identified as being disease resistant, whereas Zhongnong6 (ZN6) and Zhongnong38 (ZN38) were susceptible. The microbiome structure differed substantially between the resistant and susceptible plants, with LYXC and SY2 each having a significantly greater Shannon index than Zhongnong38. These results revealed that the disease-resistant cucumber cultivars recruited more beneficial bacteria, i.e., Bacillus, in their rhizosphere soil; as such, Bacillus was identified as a keystone genus in the microbial co-occurrence network. Thus, the presence of Bacillus may help cucumbers defend against fungal pathogens within the rhizosphere. Bacillus subtilis strain LD15, which was isolated from LYXC rhizosphere soil, could suppress pathogen growth, in vitro, and reduce disease severity in pot assays. Moreover, evidence also confirmed the accumulation of LD1 in the rhizosphere soil of resistant cucumber cultivars. For LYXC, application of thiophanate-methyl or carbendazim altered the microbiome structure, decreased bacterial diversity, and reduced the abundance of Bacillus species. Finally, pot assays verified that fungicide application decreased the proportion of LD15 in rhizosphere soil. From a microbial perspective, thiophanate-methyl and carbendazim may weaken the rhizobacteria-mediated defense response of cucumbers against cucumber Fusarium wilt disease. Our findings reveal a role for the rhizosphere microbiome in protecting plants from pathogens and constitute a reference for assessing the ecotoxicological risk of pesticides to non-target soil microorganisms.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s42994-024-00181-5.}, }
@article {pmid39650028, year = {2024}, author = {Miccoli, FE and Galarza, RI and Juliano, N and Ferreyra, S and Maresca, S and López-Valiente, S and Guerrero, LD and Palladino, RA and Albornoz, RI}, title = {Oro-ruminal sampling device and technique for rapid collection of rumen content and improved recovery of solid fractions for microbiome analysis.}, journal = {JDS communications}, volume = {5}, number = {6}, pages = {563-567}, doi = {10.3168/jdsc.2023-0536}, pmid = {39650028}, issn = {2666-9102}, abstract = {Rumen fistulation is a widely used procedure that allows for collection of ruminal contents. However, fistulation is an invasive and costly procedure that generally limits the number of animals that can be recruited for experiments, thus encouraging the use of alternative techniques such as the intra-esophageal tube technique. One of the challenges of this technique is the limited ability to collect solid fractions from the rumen content pool, which may affect the microbial community structure in the sample, particularly affecting the recovery and characterization of solid adherent bacteria. We developed an intra-esophageal tube rumen sampling technique and device referred to as the "Rumen Sampler MG" with the aim of increasing the recovery of solid fractions from rumen content compared with other oro-ruminal sampling methods. The Rumen Sampler MG device consists of a manual pump fitted with a barometer and an intra-esophageal flexible polyvinyl chloride (PVC) tube with beveled terminal edge allowing for minimal clogging of the sampling tubing and a rapid flux of contents being sampled. Nine lactating Holstein-Friesian dairy cows (554.6 ± 25.2 kg of BW; 8.3 ± 3.3 DIM; ± SD) were recruited to evaluate the proposed method. During the procedure, animals were safely restrained in a chute and administered with a low dosage of a neuroleptic drug to reduce animal stress during sampling. An endoscopic camera was inserted into the reticulo-rumen through the esophagus to identify the sampling location and determine the length of the sampling tube necessary to reach the desired location. Following, the intra-esophageal sampling tube connected to a manual pump was inserted for collection of rumen contents. Samples collected did not present visual evidence of saliva contamination (e.g., high viscosity) and their pH ranged within expected values (6.33-7.04) for samples collected from the reticulo-rumen. Each sample contained 35% to 40% wet solids volume. Individual dry matter intake and milk production of cows continued to increase after sampling as expected for cows in the early postpartum period, suggesting that the sampling procedure did not affect cow performance. Results from microbiome analysis of rumen content samples suggest that the relative abundances of the main bacterial phyla are consistent with those from samples collected from dairy cows via rumen fistula in previous studies. The device and technique proposed allow for adequate samples of ruminal liquid and solid contents to be collected for microbiome analysis without disruption of animal performance.}, }
@article {pmid39650020, year = {2024}, author = {Vermeersch, AS and Van Nieuwerburgh, F and Gansemans, Y and Ali, M and Ducatelle, R and Geldhof, P and Deforce, D and Callens, J and Opsomer, G}, title = {Multi-omics analysis elucidates the host-microbiome interplay in severe udder cleft dermatitis lesions in dairy cows.}, journal = {JDS communications}, volume = {5}, number = {6}, pages = {598-601}, doi = {10.3168/jdsc.2023-0537}, pmid = {39650020}, issn = {2666-9102}, abstract = {Udder cleft dermatitis is a skin disease in dairy cattle that is characterized by painful, large open wounds between the udder halves or at the front udder attachment. Its impact on animal welfare and production warrants an in-depth investigation of its pathogenesis. The present study delves into the pathophysiology of severe udder cleft dermatitis, employing a multi-omics approach by integrating transcriptomic and metagenomic data obtained from samples of severe udder cleft dermatitis lesions and healthy udder skin of dairy cattle. All dominant features selected from the virulence factor, taxonomic, and transcriptomic datasets, except for the facultative pathogen Streptococcus pyogenes, form a network that could be associated with the healthy udder skin. The severe udder cleft dermatitis-associated Streptococcus pyogenes exhibited a negative correlation with these virulence factors and genes, but was not correlated with the other commensal bacteria in the analysis. Examining the different components interacting with each other could advance our understanding of the pathogenesis of severe udder cleft dermatitis.}, }
@article {pmid39650005, year = {2024}, author = {Morita, Y and Yachida, M and Tokimitsu, K and Itoh, M}, title = {Analysis of gut microbiota with cryptosporidiosis based on fecal condition in neonatal dairy calves on a farm in Japan.}, journal = {JDS communications}, volume = {5}, number = {6}, pages = {649-653}, doi = {10.3168/jdsc.2023-0539}, pmid = {39650005}, issn = {2666-9102}, abstract = {Cryptosporidiosis is a major cause of diarrhea and is associated with high morbidity in calves. Changes in the gut microbiota exacerbate diarrhea caused by Cryptosporidium parvum infection in neonatal and weaned calves. However, information on the gut microbiota of neonatal calves with C. parvum infection is scarce, and research into the microbiome of calves is essential for developing preventive and therapeutic interventions. This study aimed to elucidate the gut microbiota of neonatal calves with cryptosporidiosis. We collected 31 fecal samples from 31 neonatal calves on a dairy farm with or without C. parvum antigen [CP(+) or CP(-)] using a kit and analyzed the differences in the microbiota between diarrheal (D) and normal (N) fecal samples with C. parvum infection based on the fecal score. The analyses revealed the α diversity indexes of fecal microbiota in CP(+)-N samples were higher than that in CP(+)-D samples. Megasphaera spp. and other rumen microbes were identified, and significantly associated with CP(+)-N samples compared with CP(+)-D samples by linear discriminant analysis effect size (LEfSe). We conclude that the specific gut microbiota could characterize fecal microbiota in calves with neonatal cryptosporidiosis without clinical symptoms.}, }
@article {pmid39649904, year = {2024}, author = {Banisefid, E and Nasiri, E and Pourebrahimian Leilabadi, S and Hamzehzadeh, S and Akbarzadeh, MA and Hosseini, MS}, title = {The paradox of Helicobacter pylori: how does H. pylori infection protect against esophageal cancer?.}, journal = {Annals of medicine and surgery (2012)}, volume = {86}, number = {12}, pages = {7221-7226}, doi = {10.1097/MS9.0000000000002674}, pmid = {39649904}, issn = {2049-0801}, abstract = {Helicobacter pylori is a microaerophilic gram-negative bacterium infecting around half of the world's population. Despite its well-known role in gastric malignancies, its impact on esophageal cancer comes with a complex paradox. Several mechanisms have been proposed to explain its observed lack of carcinogenic activity in the esophagus, including the trigger of anti-inflammatory pathways, promoting atrophic gastritis, and esophageal microbiome modulation. However, recent studies have highlighted a significantly more complicated interplay, where H. pylori, typically considered a pathogen, may even deliver a protective effect against esophageal carcinogenesis. This paper aims to evaluate the prevalence of H. pylori infection among patients with esophageal carcinoma, discussing the underlying mechanisms of the paradoxical effects of H. pylori on esophageal cancer.}, }
@article {pmid39649811, year = {2024}, author = {Jung, J and Ahn, S and Kim, DH and Riu, M}, title = {Triple interactions for induced systemic resistance in plants.}, journal = {Frontiers in plant science}, volume = {15}, number = {}, pages = {1464710}, doi = {10.3389/fpls.2024.1464710}, pmid = {39649811}, issn = {1664-462X}, abstract = {Induced systemic resistance (ISR) is a crucial concept in modern agriculture, explaining plant defense mechanisms primed by rhizosphere stimuli and activated by subsequent infections. Biological factors contributing to ISR generally include plant growth-promoting microbes3 (PGPM). Bacillus spp., Pseudomonas spp., and Trichoderma spp. have been extensively studied for their plant growth-promoting characteristics and ISR effect against above-ground pathogens and insect infestations. These phenomena elucidate the bottom-up effects of how beneficial rhizosphere microbes help plants resist above-ground attacks. Conversely, soil microbiome analysis in the rhizosphere of plants infected by above-ground pathogens has shown increased beneficial microbes in the soil, a phenomenon termed 'soil legacy effects'. This represents the top-down effects of above-ground attackers on plants' rhizosphere environments. Interestingly, recent studies have shown that above-ground stimuli not only recruit PGPM in the rhizosphere but also that these PGPM influence plant defense responses against subsequent pathogen infections. This can be seen as a four-step plant defense mechanism involving above-ground attackers, host plants, rhizosphere microbes, and subsequent attacks. This represents an active defense mechanism that overcomes the limitations of sessile plants. This review summarizes plant ISR mechanisms in terms of triple inter-organism interactions and provides molecular evidence for each step.}, }
@article {pmid39649683, year = {2024}, author = {Bature, I and Xiaohu, W and Ding, X}, title = {The roles of phytogenic feed additives, trees, shrubs, and forages on mitigating ruminant methane emission.}, journal = {Frontiers in veterinary science}, volume = {11}, number = {}, pages = {1475322}, doi = {10.3389/fvets.2024.1475322}, pmid = {39649683}, issn = {2297-1769}, abstract = {Ruminant animals naturally emit methane gas owing to anaerobic microbial fermentation in the rumen, and these gases are considered major contributors to global warming. Scientists worldwide are attempting to minimize methane emissions from ruminant animals. Some of these attempts include the manipulation of rumen microbes using antibiotics, synthetic chemicals, dietary interventions, probiotics, propionate enhancers, stimulation of acetogens, manipulation of rumination time, vaccination, and genetic selection of animals that produce low methane (CH4). The majority of synthetic additives are harmful to both beneficial rumen microbes and the host or only temporarily affect methanogenesis. Phytogenic feed additives (PFAs) have recently emerged as the best alternatives to antibiotics and synthetic chemicals because of growing public concerns regarding drug resistance and the negative impacts of antibiotics and synthetic chemicals on humans, livestock, and the environment. These additives reduce methane production and improve the volatile fatty acid profile. In this review, we provide an overview of PFA sources and how their bioactive components affect the rumen microbiome to reduce methane emissions. Additionally, we highlight the mechanisms of action of PFAs as a whole, as well as some of their bioactive components. We also review some selected trees, herbs, shrubs, and forages and their roles in reducing methane emissions.}, }
@article {pmid39649549, year = {2024}, author = {Tong, HX and Ye, Y}, title = {Insights and future directions in studying intestinal microbiota post-transjugular intrahepatic portosystemic shunt for hepatitis B virus-related portal hypertension.}, journal = {World journal of gastroenterology}, volume = {30}, number = {45}, pages = {4855-4858}, doi = {10.3748/wjg.v30.i45.4855}, pmid = {39649549}, issn = {2219-2840}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Hypertension, Portal/microbiology/diagnosis/etiology/surgery ; *Portasystemic Shunt, Transjugular Intrahepatic/adverse effects ; *Hepatitis B virus/isolation &amp; purification/pathogenicity ; *Hepatic Encephalopathy/microbiology/etiology ; *Liver Cirrhosis/microbiology/virology/surgery/diagnosis ; Hepatitis B/diagnosis/microbiology/complications/virology ; Treatment Outcome ; China/epidemiology ; Hepatitis B, Chronic/microbiology/complications/diagnosis ; }, abstract = {The gut microbiota (GM) plays a major role in the progression and treatment response of liver diseases, with diverse compositions based on different etiologies. In China, hepatitis B virus (HBV) infection is the leading cause of cirrhosis and affects the GM composition in patients with cirrhosis-related portal hypertension (PH). However, a few studies have been conducted on GM alterations after transjugular intrahepatic portosystemic shunt (TIPS) in patients with HBV-related PH. A recent study investigated the changes in the GM in these patients after TIPS. This study found an increase in potentially pathogenic bacteria and a decrease in beneficial bacteria post-TIPS, particularly in patients with hepatic encephalopathy (HE), indicating the potential role of the GM in HE prediction and management post-TIPS. Nevertheless, the study had several limitations, including a small sample size, limited follow-up, a single time point for sample collection, and inadequate analysis of the correlation between intestinal flora, HBV infection status, and clinical parameters. Future research should address these limitations by expanding the sample size, prolonging the follow-up duration, collecting samples at multiple time points, and conducting comprehensive analyses to confirm the findings and evaluate the effectiveness of individualized microbiome-based therapies.}, }
@article {pmid39649211, year = {2024}, author = {Banerjee, T and Goswami, AG and Basu, S}, title = {Biliary microbiome and gallstones: A silent friendship.}, journal = {World journal of gastrointestinal surgery}, volume = {16}, number = {11}, pages = {3395-3399}, pmid = {39649211}, issn = {1948-9366}, abstract = {With increasing evidence, the biliary tract and the gallbladder mucosa are no longer considered sterile environments devoid of bacteria. Rather a profound biofilm of resident bacterial flora is associated with the mucosal surface. The bile too harbors a resident flora. It is when a dysbiotic process ensues, that this bacterial flora either becomes opportunist or is replaced by a pathogenic one that has a strong ability to survive the challenges of the biliary environment. Although once believed a metabolic problem, recent evidence indicates a complex interaction between different species of bacteria and gallbladder mucosa and bile which may culminate in calculus formation. The resident microbiota and its several enzymes dictate the type of gallstone by the mere interplay of the constituting type of bacteria in the biofilm, even without any evidence of infection. Dysbiosis is often mediated by either intestinal dysbiosis or less probably by oral dysbiosis. The gallstones, in turn, provide a haven for the resident microbiota in which they can form their own defined niche enriched with the biofilm that can resist the biliary defense mechanisms and survive the hostile biliary environment in the background of biliary stasis and local infection. However, this process of silent friendship is more complex than said, and further research is needed to define the relationship between the two.}, }
@article {pmid39649169, year = {2024}, author = {Bowser, S and Chapartegui-González, I and Torres, AG}, title = {Fecal Microbiome Alterations of Mice Following Immunization with Gold Nanoparticle Vaccines Against Enterohemorrhagic Escherichia coli.}, journal = {Research square}, volume = {}, number = {}, pages = {}, doi = {10.21203/rs.3.rs-5146579/v1}, pmid = {39649169}, issn = {2693-5015}, abstract = {Background. Enterohemorrhagic Escherichia coli (EHEC), a group of enteric pathogenic bacteria that is a major cause of human diarrheal disease, must interact with the diverse intestinal microbiome during colonization and subsequently overcome the environmental challenges to survive and cause disease. While this relationship, and how the microbiome modulates infection of EHEC, has been studied, it is less understood how the microbiome is impacted during treatment for an EHEC infection. One area that is notably lacking in knowledge is how vaccination can impact the intestinal microbiome composition, and therefore, influence vaccine efficacy. We previously developed vaccine formulations consisting of gold nanoparticles (AuNPs) conjugated to various EHEC antigens and tested them in small animal infection models using both EHEC and its murine counterpart Citrobacter rodentium . The goal of this study was to evaluate the relationship between these EHEC vaccines and their effects on the gut microbiome. Results. We found that immunization with the vaccines or adjuvant-only control did not lead to major alterations in the composition of the fecal microbiome; however, there were measurable variations in individual mice within the same vaccine group housed in separate cages. Finally, immunization with one vaccine (AuNP-EscC) did prevent a decrease in the diversity of the fecal microbiome and an increase in detectable C. rodentium following infection compared to the control animals. Conclusions. Overall, our small study argues in favor of evaluating the intestinal microbiome during vaccine development not just for EHEC, but for other enteric pathogens as well.}, }
@article {pmid39649167, year = {2024}, author = {Eggers, S and Hoggarth, ZE and Nagdeo, K and Banas, MJ and Lane, JM and Rechtman, E and Gennings, C and O'Neal, E and Peppard, PE and Sethi, AK and Safdar, N and Malecki, KM and Schultz, AA and Midya, V}, title = {Food Insecurity Modifies the Association Between the Gut Microbiome and the Risk of Cognitive Impairment in Adults.}, journal = {Research square}, volume = {}, number = {}, pages = {}, doi = {10.21203/rs.3.rs-5486286/v1}, pmid = {39649167}, issn = {2693-5015}, abstract = {Background Recent studies have shown associations between relative abundances of specific gut microbes and cognitive function; however, few studies have explored the potential interplay between the gut microbiome and food insecurity in association with the risk of cognitive impairment (RCI). This study investigated the role of food insecurity as an effect modifier between the gut microbiome, including groups of gut microbes (microbial cliques), and RCI. Methods Data came from the Survey of the Health of Wisconsin and its ancillary Wisconsin Microbiome Study. The analytical sample (n = 360) included adult participants with complete data on food insecurity, RCI, and 16S rRNA sequencing data from stool samples. A "mini-cog" memory test was implemented to assess RCI. Food insecurity was assessed using a set of survey-based questions. Alpha diversity and individual taxa associations with RCI were estimated using linear regression. Microbial cliques associated with RCI were identified using an interpretable machine-learning-based algorithm. All analyses were stratified by food insecurity level, and regression models were adjusted for relevant confounders. Results Food insecurity status was weakly associated with RCI (b = 0.06, 95%CI=[0.00, 0.12]). Gut microbiome a-diversity had an inverse association with RCI in both the food secure (b=-0.08, 95%CI=[-0.15, -0.02]) and insecure groups (b=-0.09, 95%CI=[-0.26, 0.07]). Bacteroides sp. was associated with RCI in the food secure group only (b = 0.09, 95%CI= [0.05, 1.36]. We identified two microbial cliques whose associations with RCI were modified by food insecurity status. The presence of the microbial clique with either Eisenbergiella or Eubacterium was more strongly associated with RCI for the food-insecure group (β = 0.29, p < 0.0001) than the food-secure group (β = 0.05, p < 0.001). Alternatively, a microbial clique representing the presence of Ruminococcus torques , Bacteroides , CAG-352F, and/or Eubacterium had a stronger association with RCI for the food-secure group (β = 0.1, p < 0.0001) than the food-insecure group (β = 0.07, p = 0.01). Conclusions Food insecurity may modify the relationship between the gut microbiome and RCI. These findings suggest environmental and lifestyle factors in potential prevention strategies against RCI.}, }
@article {pmid39649015, year = {2024}, author = {Basnet, J and Eissa, MA and Cardozo, LLY and Romero, DG and Rezq, S}, title = {Impact of Probiotics and Prebiotics on Gut Microbiome and Hormonal Regulation.}, journal = {Gastrointestinal disorders (Basel, Switzerland)}, volume = {6}, number = {4}, pages = {801-815}, pmid = {39649015}, issn = {2624-5647}, abstract = {The gut microbiome plays a crucial role in human health by influencing various physiological functions through complex interactions with the endocrine system. These interactions involve the production of metabolites, signaling molecules, and direct communication with endocrine cells, which modulate hormone secretion and activity. As a result, the microbiome can exert neuroendocrine effects and contribute to metabolic regulation, adiposity, and appetite control. Additionally, the gut microbiome influences reproductive health by altering levels of sex hormones such as estrogen and testosterone, potentially contributing to conditions like polycystic ovary syndrome (PCOS) and hypogonadism. Given these roles, targeting the gut microbiome offers researchers and clinicians novel opportunities to improve overall health and well-being. Probiotics, such as Lactobacillus and Bifidobacterium, are live beneficial microbes that help maintain gut health by balancing the microbiota. Prebiotics, non-digestible fibers, nourish these beneficial bacteria, promoting their growth and activity. When combined, probiotics and prebiotics form synbiotics, which work synergistically to enhance the gut microbiota balance and improve metabolic, immune, and hormonal health. This integrated approach shows promising potential for managing conditions related to hormonal imbalances, though further research is needed to fully understand their specific mechanisms and therapeutic potential.}, }
@article {pmid39648983, year = {2024}, author = {Bjørgen, H and Koppang, EO and Nowak, BF}, title = {Gill Health in Fish Farmed in Recirculating Aquaculture Systems (RAS): A Review.}, journal = {Journal of fish diseases}, volume = {}, number = {}, pages = {e14057}, doi = {10.1111/jfd.14057}, pmid = {39648983}, issn = {1365-2761}, abstract = {Recirculating Aquaculture Systems (RAS) have been proposed as the future of aquaculture, because they can be used anywhere regardless of access to water, they offer high level of control over farming environment, including biosecurity, and are considered to be sustainable. However, despite of continuous development, there can be still issues with water quality affecting gill health of fish farmed in these systems. This review provides an overview of fish gill structure and gill immune response, and discusses the known impacts of RAS on gill health. Several experimental studies have inadequately reported conditions, particularly water quality, making it difficult to determine if the observed effects were due to water quality issues or RAS system itself. It is crucial for studies investigating the impact of RAS on fish to report water quality during the study. Furthermore, assessments of RAS effects on gill health should include sufficient independent replicates and flow through controls using a common water source. Various methods have been used to assess gill health in RAS, including gill histology, presence of pathogens, gene expression in the gills and gill microbiome analysis. Differences in gill health in fish from RAS and a flow through system have been shown for a number of freshwater and marine fish species. However, these results have been inconsistent across studies, and some results have been challenging to interpret as indicators of gill health. Holistic studies including a number of different methods to assess fish gills would give more conclusive results. More research is needed, in particular, on brackish and marine RAS, to fully understand their impacts on gill health.}, }
@article {pmid39648789, year = {2024}, author = {Wu, W and Sun, Y and Niu, S and Li, X and Chen, L and Xie, S and Chang, L and Wei, S and Jing, M and Li, H and Zhao, Y}, title = {Integrated Microbiome and Metabolomic to Explore the Mechanism of Coptisine in Alleviating Ulcerative Colitis.}, journal = {Phytotherapy research : PTR}, volume = {}, number = {}, pages = {}, doi = {10.1002/ptr.8389}, pmid = {39648789}, issn = {1099-1573}, support = {82192915//Major Program of the National Natural Science Foundation of China/ ; 2020-4-5033//Capital's Funds for Health Improvement and Research/ ; }, abstract = {Coptisine (COP), a naturally occurring alkaloid, is known for its diverse pharmacological effects and its supportive role in intestinal health. Despite this, the detailed mechanisms behind its therapeutic benefits are not yet fully understood. The objective of this study is to investigate the therapeutic potential of COP for the treatment of Ulcerative Colitis (UC) and to delineate the critical pathways by which it exerts its therapeutic effects. To assess COP's therapeutic effectiveness, mice were administered COP and monitored for clinical symptoms, activity, and disease activity index (DAI) changes. Intestinal histopathology, mucosal barrier function, and gut microbiota structure were evaluated, along with metabolic profiling, focusing on Prenol lipids in the colon to identify COP-induced metabolic shifts. Mice treated with COP exhibited significant relief from diarrhea and bleeding, along with increased activity and a marked reduction in DAI scores. Histopathological evaluation revealed a reduction in intestinal inflammation, and the intestinal mucosal barrier function was notably enhanced. The gut microbiota composition in COP-treated mice showed improvements. Additionally, the levels of Prenol lipids in the colon were elevated by COP treatment, which is crucial for the recovery of intestinal function. Our study demonstrates that COP effectively ameliorates colitis symptoms by modulating colon Prenol lipids metabolism, particularly under the influence of key bacterial species. The findings of this study provide novel insights into the therapeutic mechanisms of COP in the treatment of UC.}, }
@article {pmid39648093, year = {2024}, author = {McConkey, DJ and Barb, JJ and Smith, AK and Sears, CL}, title = {Microbiome-based Therapeutics: Cutting-edge Innovation or Perpetual Promise?.}, journal = {European urology focus}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.euf.2024.11.008}, pmid = {39648093}, issn = {2405-4569}, abstract = {Recent preclinical and clinical research has established that the microbiome affects response to immunotherapy, and other work has shown that our diet has strong and rapid effects on the microbiome. Together, these findings have generated strong enthusiasm for the development of therapeutic approaches to exploit these effects. However, inconsistencies in sample collection and data analyses have made it challenging to evaluate the true impact of these interventions. We suggest that the research community needs to develop technical best practices before the true potential of therapeutic microbiome modulation can be realized.}, }
@article {pmid39647763, year = {2024}, author = {Huo, L and Zhang, H and Hou, S and Li, W and Meng, Q and Li, C and Ma, X and Huang, L and He, J and Zhao, B}, title = {Low-dose IL-2 restores metabolic dysfunction and immune dysregulation in mice with type 2 diabetes induced by a high-fat, high-sugar diet and streptozotocin.}, journal = {International journal of biological macromolecules}, volume = {}, number = {}, pages = {138468}, doi = {10.1016/j.ijbiomac.2024.138468}, pmid = {39647763}, issn = {1879-0003}, abstract = {Interleukin-2 (IL-2) is pivotal in immune regulation, particularly in the promotion of regulatory T (Treg) cells and the maintenance of immune tolerance. While its efficacy in autoimmune diseases is well established, its role in type 2 diabetes (T2D) remains largely unexplored. This study investigates the effects of low-dose IL-2 in a KM mouse model of T2D induced by streptozotocin (STZ) and a high-fat, high-sugar (HFHS) diet. We found that low-dose IL-2 administration significantly improved fasting plasma glucose (FPG), glycosylated hemoglobin (HbA1c) levels, and glucose tolerance, indicating better glycemic control. Additionally, IL-2 treatment improved insulin sensitivity, enhanced insulin secretion, and ameliorated lipid metabolism, as evidenced by reduced cholesterol and triglyceride levels. These metabolic improvements were associated with a modulation of inflammation, including a reduction in pro-inflammatory cytokines (TNF-α, IL-1β) and an increase in anti-inflammatory cytokines (IL-10). Importantly, IL-2 also altered the gut microbiome, reducing intestinal inflammation and endotoxin levels, which suggests a broader impact on metabolic health beyond immune regulation. These findings support the potential of low-dose IL-2 as an immunotherapeutic approach for improving metabolic dysfunction and inflammation in T2D.}, }
@article {pmid39647571, year = {2024}, author = {Sharma, A and Kapur, S and Kancharla, P and Yang, T}, title = {Sex Differences in Gut Microbiota, Hypertension, and Cardiovascular Risk.}, journal = {European journal of pharmacology}, volume = {}, number = {}, pages = {177183}, doi = {10.1016/j.ejphar.2024.177183}, pmid = {39647571}, issn = {1879-0712}, abstract = {The intricate ecosystem of the gut microbiome exhibits sex-specific differences, influencing the susceptibility to cardiovascular diseases (CVD). Imbalance within the gut microbiome compromises the gut barrier, activates inflammatory pathways, and alters the production of metabolites, all of which initiate chronic diseases including CVD. In particular, the interplay between lifestyle choices, hormonal changes, and metabolic byproducts uniquely affects sex-specific gut microbiomes, potentially shaping the risk profiles for hypertension and CVD differently in men and women. Understanding the gut microbiome's role in CVD risk offers informative reasoning behind the importance of developing tailored preventative strategies based on sex-specific differences in CVD risk. Furthermore, insight into the differential impact of social determinants and biological factors on CVD susceptibility emphasizes the necessity for more nuanced approaches. This review also outlines specific dietary interventions that may enhance gut microbiome health, offering a glimpse into potential therapeutic avenues for reducing CVD risk that require greater awareness. Imbalance in natural gut microbiomes may explain etiologies of chronic diseases; we advocate for future application to alter the gut microbiome as possible treatment of the aforementioned diseases. This review mentions the idea of altering the gut microbiome through interventions such as fecal microbiota transplantation (FMT), a major application of microbiome-based therapy that is first-line for Clostridium difficile infections and patient-specific probiotics highlights more innovative approaches to hypertension and CVD prevention. Through increased analysis of gut microbiota compositions along with patient-centric probiotics and microbiome transfers, this review advocates for future preventative strategies for hypertension.}, }
@article {pmid39647502, year = {2024}, author = {Porcari, S and Mullish, BH and Asnicar, F and Ng, SC and Zhao, L and Hansen, R and O'Toole, PW and Raes, J and Hold, G and Putignani, L and Hvas, CL and Zeller, G and Koren, O and Tun, H and Valles-Colomer, M and Collado, MC and Fischer, M and Allegretti, J and Iqbal, T and Chassaing, B and Keller, J and Baunwall, SM and Abreu, M and Barbara, G and Zhang, F and Ponziani, FR and Costello, SP and Paramsothy, S and Kao, D and Kelly, C and Kupcinskas, J and Youngster, I and Franceschi, F and Khanna, S and Vehreschild, M and Link, A and De Maio, F and Pasolli, E and Miguez, AB and Brigidi, P and Posteraro, B and Scaldaferri, F and Stojanovic, MR and Megraud, F and Malfertheiner, P and Masucci, L and Arumugam, M and Kaakoush, N and Segal, E and Bajaj, J and Leong, R and Cryan, J and Weersma, RK and Knight, R and Guarner, F and Shanahan, F and Cani, PD and Elinav, E and Sanguinetti, M and de Vos, WM and El-Omar, E and Dorè, J and Marchesi, J and Tilg, H and Sokol, H and Segata, N and Cammarota, G and Gasbarrini, A and Ianiro, G}, title = {International consensus statement on microbiome testing in clinical practice.}, journal = {The lancet. Gastroenterology &amp; hepatology}, volume = {}, number = {}, pages = {}, doi = {10.1016/S2468-1253(24)00311-X}, pmid = {39647502}, issn = {2468-1253}, abstract = {There is growing interest in the potential exploitation of the gut microbiome as a diagnostic tool in medicine, but evidence supporting its clinical usefulness is scarce. An increasing number of commercial providers offer direct-to-consumer microbiome diagnostic tests without any consensus on their regulation or any proven value in clinical practice, which could result in considerable waste of individual and health-care resources and potential drawbacks in the clinical management of patients. We convened an international multidisciplinary expert panel to standardise best practices of microbiome testing for clinical implementation, including recommendations on general principles and minimum requirements for their provision, indications, pre-testing protocols, method of analyses, reporting of results, and potential clinical value. We also evaluated current knowledge gaps and future directions in this field. We aimed to establish a framework to regulate the provision of microbiome testing and minimise the use of inappropriate tests and pave the way for the evidence-based development and use of human microbiome diagnostics in clinical medicine.}, }
@article {pmid39647412, year = {2024}, author = {He, T and Xie, J and Jin, L and Zhao, J and Zhang, X and Liu, H and Li, XD}, title = {Seasonal dynamics of the phage-bacterium linkage and associated antibiotic resistome in airborne PM2.5 of urban areas.}, journal = {Environment international}, volume = {194}, number = {}, pages = {109155}, doi = {10.1016/j.envint.2024.109155}, pmid = {39647412}, issn = {1873-6750}, abstract = {Inhalable microorganisms in airborne fine particulate matter (PM2.5), including bacteria and phages, are major carriers of antibiotic resistance genes (ARGs) with strong ecological linkages and potential health implications for urban populations. A full-spectrum study on ARG carriers and phage-bacterium linkages will shed light on the environmental processes of antibiotic resistance from airborne dissemination to the human lung microbiome. Our metagenomic study reveals the seasonal dynamics of phage communities in PM2.5, their impacts on clinically important ARGs, and potential implications for the human respiratory microbiome in selected cities of China. Gene-sharing network comparisons show that air harbours a distinct phage community connected to human- and water-associated viromes, with 57 % of the predicted hosts being potential bacterial pathogens. The ARGs of common antibiotics, e.g., peptide and tetracycline, dominate both the antibiotic resistome associated with bacteria and phages in PM2.5. Over 60 % of the predicted hosts of vARG-carrying phages are potential bacterial pathogens, and about 67 % of these hosts have not been discovered as direct carriers of the same ARGs. The profiles of ARG-carrying phages are distinct among urban sites, but show a significant enrichment in abundance, diversity, temperate lifestyle, and matches of CRISPR (short for 'clustered regularly interspaced short palindromic repeats') to identified bacterial genomes in winter and spring. Moreover, phages putatively carry 52 % of the total mobile genetic element (MGE)-ARG pairs with a unique 'flu season' pattern in urban areas. This study highlights the role that phages play in the airborne dissemination of ARGs and their delivery of ARGs to specific opportunistic pathogens in human lungs, independent of other pathways of horizontal gene transfer. Natural and anthropogenic stressors, particularly wind speed, UV index, and level of ozone, potentially explained over 80 % of the seasonal dynamics of phage-bacterial pathogen linkages on antibiotic resistance. Therefore, understanding the phage-host linkages in airborne PM2.5, the full-spectrum of antibiotic resistomes, and the potential human pathogens involved, will be of benefit to protect human health in urban areas.}, }
@article {pmid39647374, year = {2024}, author = {Liu, L and Li, X and Luo, X and Wang, X and Liu, L and Yuan, Z and Sun, C and Zheng, H and Xu, EG and Li, F}, title = {Phthalates esters disrupt demersal fish behavior: Unveiling the brain-gut axis impact.}, journal = {Ecotoxicology and environmental safety}, volume = {289}, number = {}, pages = {117470}, doi = {10.1016/j.ecoenv.2024.117470}, pmid = {39647374}, issn = {1090-2414}, abstract = {The widespread use of plasticizers like phthalate esters (PAEs) has led to environmental and health concerns. The neurobehavioral toxicity of these compounds in marine environments, particularly regulated by the "brain-gut" axis, remains unclear, especially concerning wild demersal fish of high ecological value. Our investigation into the behavioral effects of three common PAEs, i.e., dimethyl phthalate (DMP), di-n-butyl phthalate (DBP), and di(2-ethylhexyl) phthalate (DEHP), and their molecular mechanisms on juvenile Sebastes schlegelii, revealed alarming results from molecular to population levels. After a 20-day foodborne exposure at a low marine environmental concentration (1.0 μg g[-1]), we observed that all three PAEs significantly increased the thigmotaxis (behavioral tendency to stay close to physical boundaries) and mobility of juvenile fish by 28.2-59.4 % and 23.3-74.5 %, respectively, indicating anxiety-like behavior of fish. DEHP exhibited the most pronounced effects, followed by DBP and DMP. PAEs accumulated in the juvenile fish in the order of brain > liver > gut > muscle, with DEHP showing the highest brain concentrations (23.2 ± 2.98 μg g[-1]). This accumulation led to oxidative damage, inflammatory responses, and neurodegenerative changes in the optic tectum, resulting in cholinergic system dysfunction. In the gut, PAEs caused inflammatory lesions, disrupted the gut barrier, and altered the gut microbiome, exacerbating the neurotoxicity via "brain-gut" communication. These findings underscore the significant neurobehavioral toxicity of PAEs, emphasizing their critical impact on fish behavior. We also stress the crucial need for further research on fish and other marine species beyond the laboratory scale to fully understand the broader implications of PAE exposure in marine ecosystems and to guide future conservation efforts.}, }
@article {pmid39647263, year = {2024}, author = {Fu, Y and Gou, W and Zhong, H and Tian, Y and Zhao, H and Liang, X and Shuai, M and Zhuo, LB and Jiang, Z and Tang, J and Ordovas, JM and Chen, YM and Zheng, JS}, title = {Diet-gut microbiome interaction and its impact on host blood glucose homeostasis: a series of nutritional n-of-1 trials.}, journal = {EBioMedicine}, volume = {111}, number = {}, pages = {105483}, doi = {10.1016/j.ebiom.2024.105483}, pmid = {39647263}, issn = {2352-3964}, abstract = {BACKGROUND: The interplay between diet and gut microbiome substantially influences host metabolism, but uncertainties remain regarding their relationships tailored for each subject given the huge inter-individual variability. Here we aim to investigate diet-gut microbiome interaction at single-subject resolution and explore its effects on blood glucose homeostasis.<br><br>METHODS: We conducted a series of nutritional n-of-1 trials (NCT04125602), in which 30 participants were assigned high-carbohydrate (HC) and low-carbohydrate (LC) diets in a randomized sequence across 3 pair of cross-over periods lasting 72 days. We used shotgun metagenomic sequencing and continuous glucose monitoring systems to profile the gut microbiome and blood glucose, respectively. An independent cohort of 1219 participants with available metagenomics data are included as a validation cohort.<br><br>FINDINGS: We demonstrated that the gut microbiome exhibited both intra-individually dynamic and inter-individually personalized signatures during the interventions. At the single-subject resolution, we observed person-specific response patterns of gut microbiota to interventional diets. Furthermore, we discovered a personal gut microbial signature represented by a carb-sensitivity score, which was closely correlated with glycemic phenotypes during the HC intervention, but not LC intervention. We validate the role of this score in the validation cohort and find that it reflects host glycemic sensitivity to the personal gut microbiota profile when sensing the dietary carbohydrate inputs.<br><br>INTERPRETATION: Our finding suggests that the HC diet modulates gut microbiota in a person-specific manner and facilitates the connection between gut microbiota and glycemic sensitivity. This study represents a new paradigm for investigating the diet-microbiome interaction in the context of precision nutrition.<br><br>FUNDING: This work was supported by the National Key R&amp;D Program of China, National Natural Science Foundation of China and Zhejiang Provincial Natural Science Foundation of China.}, }
@article {pmid39645423, year = {2024}, author = {Singh, A and Chauhan, S and Trivedi, PK}, title = {Unlocking microbial reservoirs for antimicrobial peptides and beyond.}, journal = {Trends in plant science}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tplants.2024.11.013}, pmid = {39645423}, issn = {1878-4372}, abstract = {Recently, Santos-Júnior et al. utilized a machine learning approach to identify nearly a million novel antimicrobial peptides (AMPs) from the global microbiome. Here we explore the untapped potential of plant- and soil-associated microbiomes as a source of novel peptides, highlighting their promising applications in advancing agricultural innovation and sustainability.}, }
@article {pmid39645285, year = {2024}, author = {Catassi, G and Lener, E and Grattagliano, MM and Motuz, S and Zavarella, MA and Bibbò, S and Cammarota, G and Gasbarrini, A and Ianiro, G and Catassi, C}, title = {The role of microbiome in the development of gluten-related disorders.}, journal = {Best practice &amp; research. Clinical gastroenterology}, volume = {72}, number = {}, pages = {101951}, doi = {10.1016/j.bpg.2024.101951}, pmid = {39645285}, issn = {1532-1916}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Celiac Disease/microbiology/immunology/diet therapy ; *Glutens/adverse effects/immunology ; *Dysbiosis ; *Diet, Gluten-Free ; *Wheat Hypersensitivity/immunology/diet therapy/diagnosis ; Probiotics/administration &amp; dosage/therapeutic use ; }, abstract = {Gluten-related disorders (GRD) include celiac disease (CD), non celiac gluten sensitivity (NCGS) and wheat allergy (WA), conditions that are associated with the ingestion of gluten-containing food. Gut microbiota composition and function may be involved in the pathogenesis of GRD. In untreated CD the microbiota is characterized by a reduction in beneficial microbes like Lactobacillus and Bifidobacterium and an increase in pathogenic ones such as Bacteroides and E. coli. Dysbiosis is a hallmark of CD, persists across various disease stages and is only partially corrected by a gluten-free diet. NCGS patients show a different microbial profile, with a notable decrease in microbial richness, and an increase of Ruminococcaceae and decrease of Bacteroidetes and Fusobacteria. The increase of certain bacterial groups such as Clostridium and Anaerobacter, in contrast with the decline of Bacteroides and Clostridium XVIII, marks a distinctive microbial signature associated with allergic responses to food. Mechanisms linking the gut microbiota to the development of GRD include effects on the gut barrier function, microbiota-mediated immune response to gluten, and an impact of microbial metabolites on gluten digestion and tolerance. Although the gluten-free diet is the primary therapy of GRDs, treatment with probiotics may contribute to improve the natural history of these disorders, for instance by minimizing the damaging effects of gluten contamination and accelerating the catch-up growth at the beginning of the dietary treatment of CD. Additional high-quality trials are still needed to identify and standardize the use of probiotics/prebiotics in GRDs.}, }
@article {pmid39645284, year = {2024}, author = {Dean, NJ and d'Arienzo, PD and Ibraheim, H and Lee, KA and Olsson-Brown, AC and Pinato, DJ and Powell, N}, title = {The role of the gut microbiome in regulating the response to immune checkpoint inhibitor therapy.}, journal = {Best practice &amp; research. Clinical gastroenterology}, volume = {72}, number = {}, pages = {101944}, doi = {10.1016/j.bpg.2024.101944}, pmid = {39645284}, issn = {1532-1916}, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects/physiology ; *Immune Checkpoint Inhibitors/therapeutic use/pharmacology ; *Neoplasms/drug therapy/microbiology/immunology ; Immunotherapy/methods ; Treatment Outcome ; Anti-Bacterial Agents/therapeutic use/pharmacology ; }, abstract = {Immune checkpoint inhibitors (ICIs) have revolutionised cancer therapy, yet the proportion of patients who achieve long-term disease control remain suboptimal. Over the past decade, the gut microbiome has been shown to influence immune-mediated tumour suppression as well as responses to ICI therapies. Compositional differences in gut microbiome may account for the differences in outcomes from immune checkpoint blockade. Identifying microbiota species associated with favourable/unfavourable outcomes and modelling their dynamics throughout the course of ICI treatment could help develop predictive biomarkers of immunotherapy response, and manipulating the gut microbiome represent a novel approach to enhancing ICI effectiveness. Clinically, this raises the prospect of using gut microbiome-based therapies to overcome primary resistance to ICIs, mitigate the effects of microbiome-altering drugs such as antibiotics or proton pump inhibitors, and improve overall survival in patients across numerous different cancer types.}, }
@article {pmid39645282, year = {2024}, author = {Józefczuk, P and Biliński, J and Minkowska, A and Łaguna, P}, title = {Gut microbiome in children undergoing hematopoietic stem cell transplantation.}, journal = {Best practice &amp; research. Clinical gastroenterology}, volume = {72}, number = {}, pages = {101955}, doi = {10.1016/j.bpg.2024.101955}, pmid = {39645282}, issn = {1532-1916}, mesh = {Humans ; *Hematopoietic Stem Cell Transplantation/adverse effects ; *Gastrointestinal Microbiome/physiology ; Child ; Animals ; }, abstract = {Hematopoietic stem cell transplantation (HSCT) is used in children as a treatment for various cancers, e.g. acute lymphoblastic leukemia (ALL), acute myeloid leukemia (AML), or other diseases, e.g. severe congenital immunodeficiency, metabolic disorders, hence the patient population is quite diverse. There is an increasing interest on the role of the microbiome in peri-transplant period. In this review, concepts of HSCT with the focus on the importance of microbiome composition, its changes during treatment and possible microbiota oriented interventions will be discussed. This paper analyzes data in pediatric population, but in view of interesting results and absence of analogous data for pediatric patients, it also looks at studies performed on adult population and pre-clinical trials on animals discussing possible translation to children.}, }
@article {pmid39645281, year = {2024}, author = {Ryan, T and Ling, S and Trinh, A and Segal, JP}, title = {The role of the microbiome in immune checkpoint inhibitor colitis and hepatitis.}, journal = {Best practice &amp; research. Clinical gastroenterology}, volume = {72}, number = {}, pages = {101945}, doi = {10.1016/j.bpg.2024.101945}, pmid = {39645281}, issn = {1532-1916}, mesh = {Humans ; *Immune Checkpoint Inhibitors/adverse effects ; *Gastrointestinal Microbiome/drug effects/immunology ; *Colitis/chemically induced/microbiology/immunology ; Hepatitis/microbiology/immunology ; Chemical and Drug Induced Liver Injury/immunology/microbiology/etiology ; Neoplasms/drug therapy/immunology/microbiology ; }, abstract = {Immune checkpoint inhibitors have revolutionised management for a variety of different types of malignancies. However, gastrointestinal adverse effects, in particular colitis and hepatitis, are relatively common with up to 30 % of patients being affected. The gut microbiome has emerged as a potential contributor to both the effectiveness of immune checkpoint inhibitors and their side effects. This review will attempt to examine the impact the microbiome has on adverse effects as a result of immune checkpoint inhibitors as well as the potential for manipulation of the microbiome as a form of management for immune mediated colitis.}, }
@article {pmid39645279, year = {2024}, author = {Fusco, W and Bricca, L and Kaitsas, F and Tartaglia, MF and Venturini, I and Rugge, M and Gasbarrini, A and Cammarota, G and Ianiro, G}, title = {Gut microbiota in colorectal cancer: From pathogenesis to clinic.}, journal = {Best practice &amp; research. Clinical gastroenterology}, volume = {72}, number = {}, pages = {101941}, doi = {10.1016/j.bpg.2024.101941}, pmid = {39645279}, issn = {1532-1916}, mesh = {Humans ; *Colorectal Neoplasms/microbiology/epidemiology ; *Gastrointestinal Microbiome/physiology ; Early Detection of Cancer/methods ; Biomarkers, Tumor/metabolism/analysis ; Dysbiosis ; }, abstract = {Colorectal cancer is the third most common type of cancer, with a significant burden on healthcare and social systems. Its incidence is constantly rising, due to the spread of unhealthy lifestyle, i.e. Western diet. Increasing evidence suggests that westernization-driven microbiome alterations may play a critical role in colorectal tumorigenesis. The current screening strategies for this neoplasm, mainly fecal immunochemical tests, are burdened by unsatisfactory accuracy. Novel, non-invasive biomarkers are rising as the new frontier of colorectal cancer screening, and the microbiome-based ones are showing positive and optimistic results. This Review describes our current knowledge on the role of gut microbiota in colorectal cancer, from its pathogenetic action to its clinical potential as diagnostic biomarker.}, }
@article {pmid39606443, year = {2024}, author = {Celorrio, M and Shumilov, K and Ni, A and Self, WK and Vitorino, FNL and Rodgers, R and Schriefer, LA and Garcia, B and Layden, BT and Egervari, G and Baldridge, MT and Friess, SH}, title = {Short-chain fatty acids are a key mediator of gut microbial regulation of T cell trafficking and differentiation after traumatic brain injury.}, journal = {Research square}, volume = {}, number = {}, pages = {}, pmid = {39606443}, issn = {2693-5015}, support = {R01 NS097721/NS/NINDS NIH HHS/United States ; }, abstract = {The gut microbiota has emerged as a pivotal regulator of host inflammatory processes after traumatic brain injury (TBI). However, the mechanisms by which the gut microbiota communicates to the brain in TBI are still under investigation. We previously reported that gut microbiota depletion (GMD) using antibiotics after TBI resulted in increased microglial activation, reduced neurogenesis, and reduced T cell infiltration. In the present study, we have demonstrated that intestinal T cells contribute to the pool of cells infiltrating the brain after TBI. Depletion or genetic deletion of T cells before injury reversed GMD induced reductions in post-TBI neurogenesis. Short-chain fatty acid supplementation increased T regulatory and T helper1 cell infiltration to the brain along with restoring neurogenesis and microglia activation after TBI with GMD. These data suggest that T cell subsets are essential cellular mediators by which the gut microbiota modulates TBI pathogenesis, a finding with important therapeutic implications.}, }
@article {pmid39649006, year = {2022}, author = {Demmig-Adams, B and Polutchko, SK and Zenir, MC and Fourounjian, P and Stewart, JJ and López-Pozo, M and Adams, WW}, title = {Intersections: photosynthesis, abiotic stress, and the plant microbiome.}, journal = {Photosynthetica}, volume = {60}, number = {1}, pages = {59-69}, pmid = {39649006}, issn = {1573-9058}, abstract = {Climate change impacts environmental conditions that affect photosynthesis. This review examines the effect of combinations of elevated atmospheric CO2, long photoperiods, and/or unfavorable nitrogen supply. Under moderate stress, perturbed plant source-sink ratio and redox state can be rebalanced but may result in reduced foliar protein content in C3 plants and a higher carbon-to-nitrogen ratio of plant biomass. More severe environmental conditions can trigger pronounced photosynthetic downregulation and impair growth. We comprehensively evaluate available evidence that microbial partners may be able to support plant productivity under challenging environmental conditions by providing (1) nutrients, (2) an additional carbohydrate sink, and (3) regulators of plant metabolism, especially plant redox state. In evaluating the latter mechanism, we note parallels to metabolic control in photosymbioses and microbial regulation of human redox biology.}, }
@article {pmid39645278, year = {2024}, author = {Garcia-Mateo, S and Rondinella, D and Ponziani, FR and Miele, L and Gasbarrini, A and Cammarota, G and Lanas, &#xc1; and Gomollón, F}, title = {Gut microbiome and metabolic dysfunction-associated steatotic liver disease: Pathogenic role and potential for therapeutics.}, journal = {Best practice &amp; research. Clinical gastroenterology}, volume = {72}, number = {}, pages = {101924}, doi = {10.1016/j.bpg.2024.101924}, pmid = {39645278}, issn = {1532-1916}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Fecal Microbiota Transplantation ; *Probiotics/therapeutic use ; *Prebiotics/administration &amp; dosage ; Non-alcoholic Fatty Liver Disease/microbiology/therapy/metabolism ; Dysbiosis ; Diet, Mediterranean ; }, abstract = {Gut microbiota plays key functions in the human body, and its alteration is associated with several human disorders. Moreover, its manipulation is being investigated as a potential therapeutic strategy. In this narrative review we will dissect the involvement of the gut microbiota and of the gut-liver axis on metabolic dysfunction-associated steatotic liver disease (MASLD). Additionally, we will review the effects of lifestyle interventions commonly used for MASLD (i.e. Mediterranean diet and physical exercise) on gut microbiome, to understand if their beneficial effect can be microbially mediated. Finally, we will discuss the role and the available evidence of therapeutic microbiome modulators, including prebiotics, probiotics, symbiotics, and fecal microbiota transplantation (FMT), in the management of MASLD.}, }
@article {pmid39645277, year = {2024}, author = {Severino, A and Tohumcu, E and Tamai, L and Dargenio, P and Porcari, S and Rondinella, D and Venturini, I and Maida, M and Gasbarrini, A and Cammarota, G and Ianiro, G}, title = {The microbiome-driven impact of western diet in the development of noncommunicable chronic disorders.}, journal = {Best practice &amp; research. Clinical gastroenterology}, volume = {72}, number = {}, pages = {101923}, doi = {10.1016/j.bpg.2024.101923}, pmid = {39645277}, issn = {1532-1916}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Noncommunicable Diseases/epidemiology ; *Diet, Western/adverse effects ; Dysbiosis ; Chronic Disease ; Inflammation/immunology/microbiology ; }, abstract = {Noncommunicable chronic disorders (NCDs) are multifactorial disorders that share a state of chronic, low-grade inflammation together with an imbalance of gut microbiota. NCDs are becoming increasingly prevalent worldwide, and mainly in Western countries, with a significant impact on global health. Societal changes, together with the widespread diffusion of modern agricultural methods and food processing, have led to a significant shift in dietary habits over the past century, with an increased diffusion of the Western diet (WD). WD includes foods high in saturated fat, refined sugars, salt, sweeteners, and low in fiber, and is characterized by overeating, frequent snacking, and a prolonged postprandial state. An increasing body of evidence supports the association between the diffusion of WD and the rising prevalence of NCDs. WD also negatively affects both gut microbiota and the immune system by driving to microbial alterations, gut barrier dysfunction, increased intestinal permeability, and leakage of harmful bacterial metabolites into the bloodstream, with consequent contribution to the development of systemic low-grade inflammation. In this review article we aim to dissect the role of gut microbiota imbalance and gut barrier impairment in mediating the detrimental effects of WD on the development of NCDs, and to identify potential therapeutic strategies.}, }
@article {pmid39645225, year = {2024}, author = {Galemmo, M}, title = {Gut Check: Addressing Gaps in Gut Microbiome Research for Infants with Congenital Heart Disease.}, journal = {The Journal of pediatrics}, volume = {}, number = {}, pages = {114429}, doi = {10.1016/j.jpeds.2024.114429}, pmid = {39645225}, issn = {1097-6833}, }
@article {pmid39645224, year = {2024}, author = {Fundora, MP and Calamaro, C and Wu, Y and Brown, AM and St John, A and Keiffer, R and Xiang, Y and Liu, K and Gillespie, S and Denning, PW and Sanders-Lewis, K and Seitter, B and Bai, J}, title = {Reply to Letter "Gut Check: Addressing Gaps in Gut Microbiome Research for Infants with Congenital Heart Disease".}, journal = {The Journal of pediatrics}, volume = {}, number = {}, pages = {114430}, doi = {10.1016/j.jpeds.2024.114430}, pmid = {39645224}, issn = {1097-6833}, }
@article {pmid39645048, year = {2024}, author = {Iriah, SC and Rodriguez, N and Febo, M and Morrissette, M and Strandwitz, P and Kulkarni, P and Ferris, CF}, title = {The Microbiome's Influence on the Neurobiology of Opioid Addiction and Brain Connectivity.}, journal = {Brain research bulletin}, volume = {}, number = {}, pages = {111159}, doi = {10.1016/j.brainresbull.2024.111159}, pmid = {39645048}, issn = {1873-2747}, abstract = {BACKGROUND: Opioids are the most effective and potent analgesics available for acute pain management. With no viable alternative for treating chronic or post operative pain, it is not surprising that over 10 million people misuse opioids. This study explores the developmental influence of the microbiome on resistance to opioid addictive behavior and functional connectivity.<br><br>METHODS: Female germ free reared (GFR) mice were compared to wild-type (WT) mice, before and after conventionalization using conditioned place preference (CPP) with oxycodone (OXY) exposure. Functional connectivity data were collected providing site-specific analysis for over 140 different brain areas.<br><br>RESULTS: GFR mice showed significant reduction in CPP after OXY exposure. When GFR mice are conventionalized CPP reward behavior mirrors WT mice. Functional connectivity data shows significant differences across several brain regions e.g., thalamus, hippocampus, and sensory cortices between GFR and WT before and after conventionalization. Prior to conventionalization GFR mice showed hyperconnectivity that became less organized and more global after conventionalization. Sequencing of the fecal microbiome of the GFR mice before conventionalization showed an absence of normal murine gut microbiome members, but the presence of Corynebacterium, Staphylococcus, Paenibacillus, and Turicibacter.<br><br>CONCLUSION: The implications suggest the microbiome has a direct impact on the development of reward seeking behavior. With the widespread number of opioid receptors found in the gut, studying the interaction between the microbiota and substance use disorder may lead to a better understanding of the mechanisms that lead to the development of addiction as well as potential treatments.}, }
@article {pmid39644773, year = {2024}, author = {Hu, Y and Hu, X and Jiang, L and Luo, J and Huang, J and Sun, Y and Qiao, Y and Wu, H and Zhou, S and Li, H and Li, J and Zhou, L and Zheng, S}, title = {Microbiome and metabolomics reveal the effect of gut microbiota on liver regeneration of fatty liver disease.}, journal = {EBioMedicine}, volume = {111}, number = {}, pages = {105482}, doi = {10.1016/j.ebiom.2024.105482}, pmid = {39644773}, issn = {2352-3964}, abstract = {BACKGROUND: Metabolic dysfunction-associated fatty liver disease (MAFLD) is associated with impaired regenerative capacity and poor postoperative prognosis following hepatectomy. Previous research has highlighted the importance of the gut-liver axis in the physiological and pathological processes of the liver. However, the contribution of gut bacteria to the regeneration of livers with MAFLD and its metabolic regulatory mechanisms remain elusive.<br><br>METHODS: Partial hepatectomy (PHx) was performed on C57Bl/6J mice fed with high-fat diet (HFD) for 12 weeks. Pathological examination, immunohistochemistry, and qRT-PCR analysis were performed to assess the severity of steatosis and proliferative potential. The gut microbiome was examined by 16S rRNA gene sequencing and shotgun metagenomics, whereas liver metabolomics was analysed via untargeted and targeted metabolomics using liquid chromatography-tandem mass spectrometry (LC-MS).<br><br>FINDINGS: HFD-induced hepatic steatosis in mice led to impaired liver regeneration following PHx. The gut microbiota and liver metabolites were altered along with the liver regeneration process. Longitudinal time-series analysis revealed dynamic alterations in these data, whereas correlation analysis screened out bacterial candidates that potentially influence liver regeneration in MAFLD by modulating metabolic pathways. Among these bacteria, the dominant bacterium Akkermansia was selected for subsequent investigation. MAFLD mice gavaged with Akkermansia muciniphila (A.&#xa0;muciniphila) exhibited reduced liver lipid accumulation and accelerated liver regeneration, possibly through the regulation of the tricarboxylic acid (TCA) cycle.<br><br>INTERPRETATION: These data demonstrated the interplay between the gut microbiome, liver metabolomics, and liver regeneration in mice with MAFLD. A.&#xa0;muciniphila has the potential to serve as a clinical intervention agent to accelerate postoperative recovery in MAFLD.<br><br>FUNDING: This work was supported by the Research Project of Jinan Microecological Biomedicine Shandong Laboratory [JNL-2022008B]; the Zhejiang Provincial Natural Science Foundation of China [LZ21H180001]; the Fundamental Research Funds for the Central Universities [No. 2022ZFJH003].}, }
@article {pmid39644740, year = {2024}, author = {Gardiner, B and Wardill, HR and O'Connor, G and Hargrave, D and Lett, AM}, title = {The impact of fibre and prebiotic interventions on outcomes in cancer and haematopoietic stem cell transplantation: A systematic review.}, journal = {Clinical nutrition (Edinburgh, Scotland)}, volume = {44}, number = {}, pages = {86-100}, doi = {10.1016/j.clnu.2024.11.022}, pmid = {39644740}, issn = {1532-1983}, abstract = {BACKGROUND &amp; AIMS: Cancer therapy is associated with a range of toxicities that severely impact patient well-being and a range of clinical outcomes. Dietary fibre/prebiotics characteristically improve the gastrointestinal microenvironment, which consequently elicits beneficial downstream effects that could be relevant to the prevention and management of treatment-related toxicities. Despite the compelling theoretical scientific rationale there has been limited effort to synthesise the available evidence to conclude such scientific underpinning to the clinical use of fibre/prebiotics in cancer patients. Therefore, this systematic review aimed to evaluate the clinical impact of fibre/prebiotic-based interventions on gastrointestinal-side effects; gastrointestinal-microbiome; clinical outcomes; nutrition status and body composition; and quality-of-life in children and adults being treated for cancer or undergoing a haematopoietic stem cell transplant (HSCT).<br><br>METHODS: This study was conducted in adherence to PRISMA guidelines, and the protocol was published prospectively with PROSPERO (CRD42022299428). Three databases (MEDLINE (Ovid), CINHAL, EMBASE) were searched from inception to December 2023. All articles were assessed for bias using the Cochrane risk-of-bias tool RoB 2.0 (for RCTs) and ROBINS-I (for non-RCTs).<br><br>RESULTS: A total of 9989 de-duplicated records were identified, of these, 14 (paediatrics [n&#xa0;=&#xa0;1], adults [n&#xa0;=&#xa0;13]) met the inclusion criteria (randomised controlled trials (RCT) [n&#xa0;=&#xa0;11], observational or non-RCTs [n&#xa0;=&#xa0;3]). The risk-of-bias was graded to be serious/high (n&#xa0;=&#xa0;6); moderate/some concerns (n&#xa0;=&#xa0;7); low (n&#xa0;=&#xa0;1). Interventions included prebiotic supplement (n&#xa0;=&#xa0;8), nutrition supplement/formula with added fibre/prebiotic (n&#xa0;=&#xa0;3) and dietary modification (n&#xa0;=&#xa0;3). The dose of fibre intervention ranged from 2.4g to 30g per day. Substantial heterogeneity of target parameters was identified across a range all outcome categories, precluding definitive conclusions.<br><br>CONCLUSION: The scientific rationale for fibre/prebiotics-based interventions for the prevention or management of cancer treatment-related toxicities is compelling. However, it is clear that the scientific and clinical field remains disconnected in how to effectively translate this approach to improve cancer outcomes. High-quality intervention studies translatable to clinical practice are now evidently crucial to determine if and how fibre/prebiotics should be used to support people undergoing cancer or HSCT therapy.}, }
@article {pmid39644725, year = {2024}, author = {McIntyre, DB and Long, BM and Dawson, BM and Barton, PS}, title = {Effect of insect exclusion and microbial perturbation on piglet mass loss and total body score.}, journal = {Forensic science international}, volume = {367}, number = {}, pages = {112336}, doi = {10.1016/j.forsciint.2024.112336}, pmid = {39644725}, issn = {1872-6283}, abstract = {Recent conceptual and empirical developments in decomposition research have highlighted the intricate dynamics within necrobiome communities and the roles of various decay drivers. Yet the interactions between these factors and their regulatory mechanisms remain relatively unexplored. A comprehensive understanding of this facet of decomposition science is important, given its broad applicability across ecological and forensic disciplines, and current lack of research which investigates the inter-dependencies between two critical components of the necrobiome (the microbiome and insect activity), and the consequences of this interdependency on mass loss and total body score. Here we investigated the relationships among these key aspects of the decay process. We experimentally manipulated these variables by physically excluding insects and chemically perturbing the external microbiome of piglet (Sus scrofa) carcasses and quantified the effects on mass loss and total body score, as well as insect pre-appearance interval and colonisation. We found that piglets in the insect excluded and microbially perturbed treatment groups exhibited a significant delay in reaching 50 + % of mass loss compared with control piglets with insect access and intact microbiome. However, only remains with insects excluded displayed a significantly slower rate of total mass loss throughout the majority of the experiment and remained a significantly higher mass at the endpoint of 11,000 accumulative degree hours. Additionally, all insect excluded and microbially perturbed treatment groups displayed significantly lower total body scores compared to control piglets at corresponding time points. We also observed a significant delay in insect pre-appearance interval and colonisation for piglets with perturbed microbiomes compared to control piglets. Our findings demonstrate the significance of interacting components of the necrobiome, and the power of manipulative experiments in revealing causal relationships between biota and decomposition rates. These considerations are paramount for developing accurate post-mortem interval estimations and a comprehensive understanding of ecological processes during decomposition.}, }
@article {pmid39644691, year = {2024}, author = {Ng, BCK and Lassere, M}, title = {The role of the gastrointestinal microbiome on rheumatoid arthritis, psoriatic arthritis, ankylosing spondylitis and reactive arthritis: A systematic review.}, journal = {Seminars in arthritis and rheumatism}, volume = {70}, number = {}, pages = {152574}, doi = {10.1016/j.semarthrit.2024.152574}, pmid = {39644691}, issn = {1532-866X}, abstract = {BACKGROUND: There is an increasing body of literature observing a state of dysbiosis in the gut microbiome in different autoimmune conditions including inflammatory arthritis. It is unknown whether the microbiome can be a biomarker for prognostication purposes or for stratification of treatment strategies. This review aims to evaluate the existing evidence on the association between the microbiome and inflammatory arthritis, including rheumatoid arthritis (RA), psoriatic arthritis (PsA) and ankylosing spondylitis (AS) and reactive arthritis (ReA) population groups.<br><br>METHODS: This systematic review was performed based on methods from the Cochrane guidelines and reported based on PRISMA criteria. Studies exploring the microbiome of patients with RA, AS, PsA or ReA compared with controls via 16s rRNA or shotgun sequencing were evaluated. The outcomes of interest include alpha and beta diversity, abundance or depletion of organisms and functional analysis. Literature up to August 2024 was retrieved searching the databases PubMed, Medline, ScienceDirect, Scopus, Web of Science, Cochrane, EMBASE and CINAHL. All references were systematically evaluated by two reviewers. Quality of the studies were evaluated by the Newcastle-Ottawa Scale.<br><br>FINDINGS: The review yielded 25,794 search results, of which 53 studies were included for the RA group, 34 studies for the AS group, 6 studies for the PsA group and 2 studies for the ReA group. Reduced diversity has been observed in disease groups and in patients with higher disease activity.<br><br>INTERPRETATION: There are limited longitudinal studies on the role of the microbiome in inflammatory arthritis, in particular PsA. Existing cross-sectional studies suggest altered microbiome in disease states compared with controls. Further studies are required to understand the utility of the microbiome as a biomarker to better understand prognosis and tailor treatments.}, }
@article {pmid39644640, year = {2024}, author = {Li, Q and Chen, Y and Zhang, J and Zhang, S and Li, J}, title = {Specificity of benthic invertebrate gill-associated microbiome contributes to host fitness to localized heterogeneous environment in the cold seep.}, journal = {The Science of the total environment}, volume = {958}, number = {}, pages = {177861}, doi = {10.1016/j.scitotenv.2024.177861}, pmid = {39644640}, issn = {1879-1026}, abstract = {The deep hydrocarbon fluids discharged into the water column at cold seeps create diverse and heterogeneous habitats on the seafloor. Symbiosis is essential for the survival of marine life in extreme deep-sea environments. Although the symbiotic relationship between chemoautotrophic bacteria and invertebrates has been reported, our understanding of these host-microbe interactions under heterogeneous environment remains limited. In this study, we evaluated the bacterial community structures, histological and subcellular localization, and potential functions of the gill microbiomes of six invertebrates in the Haima cold seep, South China Sea. The results showed distinct gill-associated microbiomes in these six invertebrates. Gigantidas haimaensis and Archivesica marissinica exhibit a highly dependent symbiotic relationship with their intracellular gill symbionts, characterized by a simple composition. In contrast, Alvinocaris longirostris, Shinkaia crosnieri, Phymorhynchus buccinoides, and Paraescarpia echinospica display a loosely dependent association with their extracellular gill-associated microbes, which are notably complex in composition. Moreover, gill microbiome specificity was seen among six invertebrates and host selection could be an underlying mechanism. The potential functional components of these six invertebrate gill microbiomes contribute to host fitness in heterogeneous local environments. The results obtained from our study provide insights into the ecology and evolution of host-microbe interactions and the underlying mechanisms in extreme marine environments. This information is critical for predicting the responses of benthic fauna to environmental changes in cold seeps.}, }
@article {pmid39644613, year = {2024}, author = {Mondal, R and Ritu, RB and Kitaoka, K and Azahar, NM and Moniruzzaman, M and Ogata, S and Kiyoshige, E and Tohara, H and Kobayashi, Y and Kashihara, N and Naito, T and Nakashima, N and Tamura, K and Nishimura, K and Viera, AJ and Yano, Y}, title = {Oral microbiome alpha diversity and all-cause, cardiovascular, and non-cardiovascular mortality in US adults: Evidence from the NHANES 2009-2019.}, journal = {Atherosclerosis}, volume = {401}, number = {}, pages = {119074}, doi = {10.1016/j.atherosclerosis.2024.119074}, pmid = {39644613}, issn = {1879-1484}, abstract = {BACKGROUND AND AIMS: Knowledge about the association between oral microbiome diversity within individuals and cardiovascular disease (CVD) and non-CVD mortality is scarce. Besides, variation by sex and racial and ethnic groups, and the potential mediators of these associations remain unclear. We aimed to investigate the associations of oral microbiome alpha diversity with all-cause, CVD, and non-CVD mortality, and the interaction effects of sex and racial and ethnic groups and potential mediators in the associations.<br><br>METHODS: The National Health and Nutrition Examination Survey (NHANES) is a population-based observational study, conducted periodically in Mexican American, Other Hispanic, Non-Hispanic (NH) White, NH Black, and other racial/ethnic participants. We linked 2009-12 survey data of 8199 adults to the mortality data until 2019. By analyzing RNA gene sequences from oral rinse samples, microbiome alpha diversity within individuals was assessed using operational taxonomic unit (OTU) richness. Potential mediators included obesity, diabetes mellitus, dyslipidemia, hypertension, and periodontitis. Multivariable Cox proportional hazards regression and causal mediation analysis were used.<br><br>RESULTS: Baseline mean&#xa0;&#xb1;&#xa0;standard deviation (SD) age was 42.1&#xa0;&#xb1;&#xa0;15.1 years. Over a median follow-up of 9.1 years, 405 all-cause mortality occurred (CVD, 105; non-CVD, 300). Each 1-SD increment in OTU richness was inversely associated with all-cause mortality (hazard ratio [HR] 0.92, 95&#xa0;% confidence interval [CI] 0.90-0.95), CVD mortality (HR, 0.92; 95&#xa0;% CI, 0.90-0.95), and non-CVD mortality (HR, 0.92; 95&#xa0;% CI, 0.90-0.95). With evidence of significant racial and ethnic groups-interaction (p <0.05), these associations were evident in Mexican American, NH White, and others racial/ethnic participants. None of the potential mediators significantly mediated the associations of OTU richness with all-cause, CVD, and non-CVD mortality.<br><br>CONCLUSIONS: Lower oral microbiome alpha diversity is associated with higher risk for all-cause, CVD, and non-CVD mortality, and the associations are varied by racial and ethnic groups.}, }
@article {pmid39644601, year = {2024}, author = {Cai, H and Li, T and Feng, W and Wu, X and Zhao, Y and Wang, T}, title = {Triple probiotics attenuate colitis via inhibiting macrophage glycolysis dependent pro-inflammatory response.}, journal = {Biochemical and biophysical research communications}, volume = {742}, number = {}, pages = {151128}, doi = {10.1016/j.bbrc.2024.151128}, pmid = {39644601}, issn = {1090-2104}, abstract = {Probiotics, a class of live microorganisms, play an important role in anti-inflammation, regulating immunity and optimizing intestinal microecological environment. In this study, we constructed a combination of three strains - Lactobacillus acidophilus, Bacillus bulgaricus, and Bacillus subtilis - to ferment triple probiotics Bornlisy. Our findings indicate that Bornlisy has a significant therapeutic effect in alleviating colitis in mice, further proofing its ability to suppress inflammation in colon, enhance intestinal barrier function and restore imbalanced intestinal microbiome. Then we found Bornlisy could modulate immune response by inhibiting macrophage glycolysis and ultimately attenuated the progression of colitis in mice. Our investigation into the therapeutic efficacy of Bornlisy in colitis revealed that triple probiotics offer a promising approach for the management of intestinal inflammation.}, }
@article {pmid39644546, year = {2024}, author = {Lay, JJ and Huang, YT and Han, CL and Zhong, WZ}, title = {Functional microbiome and phytoremediation enhance soil diesel degradation via enzyme activity.}, journal = {Journal of environmental management}, volume = {373}, number = {}, pages = {123604}, doi = {10.1016/j.jenvman.2024.123604}, pmid = {39644546}, issn = {1095-8630}, abstract = {This study investigates the enhancement of diesel degradation in contaminated soil through the synergistic effects of functional microbiomes and phytoremediation, emphasizing increased enzyme activity. The approach integrates a hydrogen-producing microbiome (HMb) with phytoremediation techniques. Observations revealed changes in soil conditions, including increases in moisture levels from 12.5% to 20% and a shift in pH from 6.9 to an alkaline range of 8.0-8.5 due to the treatment. Organic matter content also improved, supporting microbial activity. These modifications were closely monitored to evaluate their impact on microbial growth and enzyme activity. The findings showed that total petroleum hydrocarbons (TPH) in diesel-contaminated soil decreased by 78.1% using the combined HMb and phytoremediation method. This decrease was markedly higher than the 30.4% achieved through water drenching and the 30.9% with HMb alone. Central to this success were Clostridium sp. and Sporolactobacillus sp., which played essential roles in hydrocarbon degradation. Improved soil conditions supported an increase in microbial populations, with bacterial counts peaking at 6.0 x 10[11] by day 4, enhancing degradation. Additionally, Bermuda grass survival rates increased to 35% by day 35. In the HMb and planting combination, amylase activity peaked at 100% by day 10, significantly aiding degradation, although it later decreased to 1% by day 35. This research presents a robust strategy for diesel-contaminated soil remediation, highlighting significant advancements in microbial growth and degradation efficiency.}, }
@article {pmid39644437, year = {2024}, author = {Esteban, V and Gilabert, P and Ferrer, C and Gálvez, B and Chiner, E and Colom, MF}, title = {Affinity of Malassezia and Other Yeasts for Pulmonary Lipids.}, journal = {Mycopathologia}, volume = {190}, number = {1}, pages = {1}, pmid = {39644437}, issn = {1573-0832}, support = {1134/2020//Sociedad Espa&#xf1;ola de Neumolog&#xed;a y Cirug&#xed;a Tor&#xe1;cica/ ; Young researcher grant 2021//Sociedad Valenciana de Neumolog&#xed;a/ ; }, mesh = {*Culture Media/chemistry ; *Malassezia/growth &amp; development/metabolism ; Lung/microbiology ; Humans ; Pulmonary Surfactants/metabolism ; Animals ; Candida/growth &amp; development/drug effects ; Lipids/analysis ; Cryptococcus/growth &amp; development/metabolism ; 1,2-Dipalmitoylphosphatidylcholine/chemistry ; }, abstract = {Pulmonary surfactant, the primary substance lining the epithelium of the human Lower Respiratory Tract (LRT), is rich in lipids, with dipalmitoyl-phosphatidylcholine (DPPC) being the most abundant. Although surfactants are known to have antifungal activity against some yeast species, the significant presence of species like Malassezia restricta in the lung mycobiome suggests that these yeasts may exhibit some level of lipo-tolerance or even lipo-affinity for pulmonary lipids. This study explored the affinity and tolerance of yeasts, identified as significant members of the lung microbiome, to pulmonary lipids through culture-based methods. Eleven species from the genera Malassezia, Candida (including the new genera Nakaseomyces and Meyerozyma), and Cryptococcus were tested for their growth on media containing pulmonary lipids such as DPPC and commercial porcine surfactant and in other culture medium that contain non-pulmonary lipids such as glycerol monostearate and tweens. The yeasts' lipo-affinity or lipo-tolerance was assessed based on their growth on these lipids compared to standard media, specifically Modified Leeming Notman Agar (MLNA) for Malassezia species and Sabouraud Dextrose Agar (SDA) for the other genera. The addition of DPPC or surfactant to the media enhanced the growth of most Malassezia yeasts and some Cryptococcus species. C. parapsilosis, Meyerozyma guilliermondii and Cryptococcus neoformans s.s. showed similar growth to that on the standard media, while the other yeasts primarily demonstrated lipo-tolerance without lipo-affinity for these compounds. To our knowledge, this is the first report on the influence of pulmonary lipids on the in vitro growth of Malassezia spp. and other yeast members of the lung mycobiome. Some yeasts, such as Malassezia restricta, commonly found in the lower respiratory tract (LRT), exhibit specific affinity for lung lipids like DPPC and commercial porcine surfactant. This finding suggests that lung lipids may play a significant role in shaping the LRT mycobiome.}, }
@article {pmid39644431, year = {2024}, author = {Kara, K and Pi Rci, G and Yılmaz Öztaş, S and Demi R, S and Yılmaz, K}, title = {Effect of milk thistle (Silybum marianum L.) oil on pro-inflammatory cytokines, acute phase proteins, rumen metagenomic profile, rumen fluid variables and performance in calves.}, journal = {Veterinary research communications}, volume = {49}, number = {1}, pages = {48}, pmid = {39644431}, issn = {1573-7446}, support = {TSA-2023-12255//Bilimsel Ara&#x15f;t&#x131;rma Projeleri, Erciyes &#xdc;niversitesi/ ; }, mesh = {Animals ; Cattle ; *Rumen/microbiology ; Female ; Male ; *Cytokines/metabolism/genetics ; *Plant Oils/pharmacology/administration &amp; dosage ; *Acute-Phase Proteins/metabolism ; *Silybum marianum/chemistry ; *Diet/veterinary ; Dietary Supplements/analysis ; Animal Feed/analysis ; }, abstract = {The aim of this study was to determine the effect of milk thistle (Silybum marianum L., SM) oil supplementation on proinflammatory cytokines, acute phase proteins, rumen metagenomic profile, rumen fluid variables and performance during the milk feeding period of Holstein calves. In the present study, 24 calves that consumed quality and sufficient amount of colostrum (≥50 mg/ml IgG) after birth were divided into three groups, with 8 animals in each group (4 males + 4 females). Individually fed calves were given added SM oil as 0 µL/day/calf (Control group, SM0), 100 µL/day/calf (SM100) and 200 µL/day/calf (SM200). The ration containing concentrated feed mix (90%) + wheat straw (10%) was offered to the calves. SM oil did not change the ammonia nitrogen and pH values of the rumen fluid of calf (P>0.05). The molarities of PA, IBA, IVA and BSCFA in the rumen fluid increased linearly with SM oil dose (P<0.05). The relative abundance of Firmicutes linearly increased and the relative abundance of Actinobacteriota decreased with the addition of SM oil (P<0.05). Relative abundances of Erysipelotrichaceae_UCG_002, Eubacterium_coprostanoligenes_group, Clostridia_UCG_014, Lachnospiraceae_Unknown_1, Lachnospiraceae_NK3A20_group, Shuttleworthia, Selenomonadaceae_Uncultured_1, Rikenellaceae_RC9_gut_group and Succinivibrionaceae_UCG_001 linearly increased with SM oil (P<0.05). Relative abundances of Methanobrevibacter, Acetitomaculum, Olsenella and Megasphaera in calf rumen fluid linearly decreased with SM oil (P<0.05). Concentrations of TNF-α, IFN-ɣ, and SAA of calf' serum at weaning stage linearly decreased with SM oil doses (P<0.05). Serum IgA concentration increased with 100 µL SM oil /day (P<0.05). As a result, the addition of SM oil to calves has the potential to reduce the immune suppression of calves during the milk feeding period and at weaning time, has a positive effect on the microbiome involved in starch and protein catabolism in the rumen fluid, and increases the fermentation end products (PA, IVA and BA). Milk thistle oil has an inhibitory effect on methanogenic archaea and can be used as an anti-methanogenic feed additive and will contribute to the effective use of feed energy.}, }
@article {pmid39644414, year = {2024}, author = {Mohammadi, M}, title = {Cutibacterium acnes bacteriophage therapy: exploring a new frontier in acne vulgaris treatment.}, journal = {Archives of dermatological research}, volume = {317}, number = {1}, pages = {84}, pmid = {39644414}, issn = {1432-069X}, mesh = {*Acne Vulgaris/therapy/microbiology/immunology ; Humans ; *Phage Therapy/methods ; Bacteriophages/physiology ; Propionibacterium acnes ; Skin/microbiology/immunology/pathology ; Microbiota/immunology ; Anti-Bacterial Agents/therapeutic use ; Propionibacteriaceae ; Drug Resistance, Bacterial ; Treatment Outcome ; }, abstract = {The skin microbiome, encompassing a variety of microorganisms, plays a critical role in skin health and function. Acne vulgaris, affecting approximately 9.4% of the global population, is a prevalent skin condition primarily targeting pilosebaceous units rich in sebaceous glands. The condition is influenced by factors such as hormonal changes, sebaceous gland dysfunction, and the activity of Cutibacterium acnes, a gram-positive bacterium linked to acne development. The skin's immune system, particularly keratinocytes with pattern recognition receptors like Toll-like receptors (TLRs), plays a crucial role in recognizing and responding to bacterial presence. The onset of acne is often linked to adolescence, marked by significant hormonal fluctuations. Genetics also plays a role, with family history being a notable risk factor. Acne is characterized by distinct alterations in the C. acnes composition, with specific phylotypes associated with either commensal or pathogenic behavior. Traditional treatments include antibiotics, but the rise of antibiotic resistance has led to exploring alternative therapies, such as bacteriophage therapy. Bacteriophages offer a targeted approach to treating acne by targeting C. acnes strains, potentially reducing antibiotic resistance and enhancing treatment efficacy. Phage therapy shows promise, but further research is needed to fully understand its effectiveness and potential in clinical applications. Additionally, combining phages with antibiotics may offer a synergistic approach to overcoming antibiotic resistance and managing acne.}, }
@article {pmid39643908, year = {2024}, author = {Akram, MZ and Everaert, N and Dunisławska, A}, title = {In ovo sodium butyrate administration differentially impacts growth performance, intestinal barrier function, immune response, and gut microbiota characteristics in low and high hatch-weight broilers.}, journal = {Journal of animal science and biotechnology}, volume = {15}, number = {1}, pages = {165}, pmid = {39643908}, issn = {1674-9782}, support = {Grant agreement No. 955374.//H2020 Marie Sk&#x142;odowska-Curie Actions/ ; }, abstract = {BACKGROUND: Hatch weight (HW) affects broiler growth and low HW (LHW) often leads to suboptimal performance. Sodium butyrate (SB) has been shown to promote growth through enhanced intestinal health. This study investigated how broilers with different HW responded to in ovo SB injection and whether SB could enhance gut health and performance in LHW chicks. Ross 308 broiler eggs were injected on incubation d 12 with physiological saline (control) or SB at 0.1% (SB1), 0.3% (SB3), or 0.5% (SB5). Post-hatch, male chicks from each treatment were categorized as high HW (HHW) or LHW and assigned to 8 groups in a 4 × 2 factorial design. Production parameters were recorded periodically. Intestinal weight, length, and gene expression related to gut barrier function and immune response were examined on d 14 and 42. Cecal microbiota dynamics and predicted functionality were analyzed using 16S rRNA gene sequencing.<br><br>RESULTS: SB treatments did not affect hatchability. HHW-control group exhibited consistently better weight gain and FCR than LHW-control group. SB dose-dependently influenced performance and gut health in both HW categories, with greater effects in LHW broilers at 0.3%. LHW-SB3 group attained highest body weight on d 42, exceeding controls but not significantly differing from HHW-SB3 group. LHW-SB3 group showed upregulation of gut-barrier genes CLDN1 in ileum, TJP1 in jejunum and anti-inflammatory cytokine IL-10 in both jejunum and ileum on d 14. Additionally, LHW-SB3 group upregulated mucin-producing MUC6 gene in ileum, while HHW-SB5 group increased pro-inflammatory IL-12p40 cytokine in caecum on d 42. LHW-SB3 group demonstrated shorter relative intestinal lengths, while HHW-SB5 had longer lengths. HHW-control group had higher bacterial diversity and growth-promoting bacteria while LHW-control group harbored the potential pathogen Helicobacter. SB reshaped gut microbiota biodiversity, composition, and predicted metabolic pathways in both HW categories. The LHW-SB3 group exhibited highest alpha diversity on d 14 and most beneficial bacteria at all timepoints. HHW-SB5 group presented increased pathogenic Escherichia-Shigella and Campylobacter on d 42.<br><br>CONCLUSIONS: HW significantly affects subsequent performance and SB has differential effects based on HW. LHW chicks benefited more from 0.3% SB, showing improvements in growth, intestinal development, health, and gut microbiota characteristics.}, }
@article {pmid39643877, year = {2024}, author = {Cui, Z and Wang, S and Niu, J and Ma, J and Yang, H}, title = {Bifidobacterium species serve as key gut microbiome regulators after intervention in gestational diabetes mellitus.}, journal = {BMC microbiology}, volume = {24}, number = {1}, pages = {520}, pmid = {39643877}, issn = {1471-2180}, support = {22cz020401-4811009//National High Level Hospital Clinical Research/ ; 81830044//National Natural Science Foundation of China/ ; 2021YFC2700700//National Key Research and Development Program of China/ ; }, mesh = {Humans ; *Diabetes, Gestational/microbiology/metabolism/blood ; Pregnancy ; *Gastrointestinal Microbiome/genetics ; Female ; *Bifidobacterium/genetics ; Adult ; *Feces/microbiology ; Fatty Acids, Volatile/metabolism ; Dysbiosis/microbiology ; Genome-Wide Association Study ; Metagenome ; }, abstract = {Gut microbiome dysbiosis is associated with gestational diabetes mellitus (GDM), and its modulation represents a promising approach for enhancing glycemic control. In this study, we aimed to discover specific alterations in the gut microbiome through lifestyle management. We performed metagenome sequencing on fecal samples and measured short-chain fatty acid (SCFA) in plasma samples from 27 well-controlled GDM pregnancies before and after glycemic control. At the same time, 38 normal glucose tolerance (NGT) samples served as controls. Additionally, we employed two-sample Mendelian Randomization (MR) to validate our findings against Genome-Wide Association Study (GWAS) database. Our dynamic analysis revealed Bifidobacterium genus increased in GDM patients after intervention. The MR analysis confirmed that the family of Bifidobacteriaceae (OR 0.929, 95% CI, 0.886-0.975; P = 0.003) was the only negatively associated family with GDM. Further analysis indicated the increased abundance of Bifidobacterium species were negatively correlated with glycemic traits (Spearman rho mean - 0.32 ± 0.34) but positively correlated with plasma SCFA levels (Spearman rho mean 0.24 ± 0.19). Functional analysis revealed that the quorum-sensing pathway had the strongest effect on the ability of Bifidobacterium to promote glucose homeostasis (Spearman rho = -0.34), suggesting its role in regulating intestinal microbiota. Finally, the multivariable MR analysis demonstrated that two pathways, COLANSYN PWY and PWY 7323, responsible for cell surface compound synthesis in gram-negative bacteria, mediated 14.83% (P = 0.017) and 16.64% (P = 0.049) of the protective effects of Bifidobacteriaceae against GDM, respectively. In summary, Bifidobacterium is an effective gut microbiota regulator for GDM-related glucose homeostasis.}, }
@article {pmid39643654, year = {2024}, author = {Ticinesi, A and Siniscalchi, C and Meschi, T and Nouvenne, A}, title = {Gut microbiome and bone health: update on mechanisms, clinical correlations, and possible treatment strategies.}, journal = {Osteoporosis international : a journal established as result of cooperation between the European Foundation for Osteoporosis and the National Osteoporosis Foundation of the USA}, volume = {}, number = {}, pages = {}, pmid = {39643654}, issn = {1433-2965}, abstract = {The intestinal microbiome is increasingly regarded as a relevant modulator of the pathophysiology of several age-related conditions, including frailty, sarcopenia, and cognitive decline. Aging is in fact associated with alteration of the equilibrium between symbiotic bacteria and opportunistic pathogens, leading to dysbiosis. The microbiome is able to regulate intestinal permeability and systemic inflammation, has a central role in intestinal amino acid metabolism, and produces a large number of metabolites and byproducts, with either beneficial or detrimental consequences for the host physiology. Recent evidence, from both preclinical animal models and clinical studies, suggests that these microbiome-centered pathways could contribute to bone homeostasis, regulating the balance between osteoblast and osteoclast function. In this systematic review, we provide an overview of the mechanisms involved in the gut-bone axis, with a particular focus on microbiome function and microbiome-derived mediators including short-chain fatty acids. We also review the current evidence linking gut microbiota dysbiosis with osteopenia and osteoporosis, and the results of the intervention studies on pre-, pro-, or post-biotics targeting bone mineral density loss in both animal models and human beings, indicating knowledge gaps and highlighting possible avenues for future research.}, }
@article {pmid39643526, year = {2024}, author = {Yen, TY and Hsu, C and Lee, NC and Wu, CS and Wang, H and Lee, KY and Lin, CR and Lu, CY and Tsai, ML and Liu, TY and Lin, C and Chen, CY and Chang, LY and Lai, F and Huang, LM}, title = {Signatures of lower respiratory tract microbiome in children with severe community-acquired pneumonia using shotgun metagenomic sequencing.}, journal = {Journal of microbiology, immunology, and infection = Wei mian yu gan ran za zhi}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jmii.2024.11.011}, pmid = {39643526}, issn = {1995-9133}, abstract = {BACKGROUND: Severe community-acquired pneumonia was associated with high morbidity and mortality in children. However, species-level microbiome of lower airway was sparse, and we used shotgun metagenomic next-generation sequencing to explore microbial signatures.<br><br>METHODS: We conducted a prospective cohort study to recruit children under 18 who required admission to an intensive care unit for community-acquired pneumonia between December 2019 and February 2022. Lower respiratory specimens were collected on admission for shotgun metagenomic sequencing. The children were divided into two groups. Critical cases were patients with respiratory failure requiring endotracheal ventilator support, and severe cases did not require intubation. Signatures of lower respiratory tract microbiome were compared between groups using an exact k-mer matching metagenomic analysis pipeline (Kraken 2) and a metagenome-assembled genomes pipeline (MetaWRAP).<br><br>RESULTS: Totally 66 children were enrolled, and 27 children were critical cases, and the rest were severe cases. There were significant differences in microbial community structure between different severity groups, and microbial abundance was negatively correlated with disease severity. The results showed that Haemophilus influenzae was more prominent in children who were critical, accompanied with increased expression of intracellular transport, secretion, and vesicle transport genes. Rothia mucilaginosa, Dolosigranulum pigrum, and Prevotella melaninogenica tended to be present in less severe community-acquired pneumonia group.<br><br>CONCLUSION: This study demonstrated that significantly different microbial community was associated with severity of community-acquired pneumonia requiring intensive care admission. Species-level shotgun metagenomic sequencing facilitates the exploration of potentially pathogenic or protective microbes and shed the light of probiotic development in lower respiratory tract.}, }
@article {pmid39643486, year = {2024}, author = {Reyes-Sosa, MB and Valle-Gough, R and Ponce-Caballero, MDC and Arena-Ortiz, ML}, title = {Bacterial richness assessment in water and sediments in the northern coast of the Yucatan Peninsula.}, journal = {Revista Argentina de microbiologia}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.ram.2024.10.009}, pmid = {39643486}, issn = {0325-7541}, abstract = {Given the importance of the coastal environments and the multiple ecological services that they provide, it is important to explore and understand the interactions that occur within them. The microbiome is a key factor for the understanding of the dynamics of these fragile sites. A metagenomic study based on the profiling of the 16S ribosomal gene was carried out in order to assess the bacterial diversity present in the northern coastal zone of the Yucatan Peninsula. The results showed that water and sediment samples share some similarities regarding the bacterial genera found, only differing in the quantitative part. Through a PCO (principal coordinates) analysis clear differences between sediment and water samples could be observed. The highest relative diversity was found in wetland and lagoon sediment samples, respectively. It was observed that 3-8% of the total sequence reads belonged to opportunistic genera such as: Vibrio in the sea samples and Capnocytophaga in the other environments. Salinity and pH were the factors which contributed the most to the differences among the communities in the various environments in the coastal zone. There is an important similarity in the sediments across the different environments within the studied coastal zone. The data presented herein contribute to setting a baseline for research in the coastal region of the Yucatan Peninsula.}, }
@article {pmid39643393, year = {2024}, author = {O'Connor, E and Vieira, FR and Di Tomassi, I and Richardson, R and Hockett, KL and Bull, CT and Pecchia, JA}, title = {Manipulating button mushroom casing affects the disease dynamics of blotch and green mold disease.}, journal = {Fungal biology}, volume = {128}, number = {8 Pt A}, pages = {2266-2273}, doi = {10.1016/j.funbio.2024.11.001}, pmid = {39643393}, issn = {1878-6146}, mesh = {*Agaricus/growth &amp; development ; *Trichoderma ; Pseudomonas ; Plant Diseases/microbiology/prevention &amp; control ; }, abstract = {Productive cultivation of the button mushroom (Agaricus bisporus) relies on the use of selective substrates and effective disease management. In extending our previous work on manipulating the developmental microbiome (devome), this study employs the strategy of substrate passaging to explore its effects on crop outcomes and disease dynamics. Here we subjected the casing substrate to ten cycles of passaging. This manipulated substrate stimulated early pinning (primordia formation) by at least three days. Passaged casing also altered disease dynamics when challenged with two commercially important A. bisporus pathogens, Pseudomonas tolaasii (causing bacterial blotch) and Trichoderma aggressivum f. aggressivum (responsible for green mold). Passaged casing had a suppressive effect on blotch disease and a conducive effect on green mold disease. Blotch suppression resulted in a significantly higher yield of asymptomatic mushrooms in all three mushroom harvests (flushes) and in the overall crop yield. Blotch severity was also significantly reduced in passaged casing compared to standard casing due to a lower yield of mushrooms with the highest degree of blotch disease expression. Green mold disease expression was markedly higher in passaged casing, leading to lower numbers of asymptomatic mushrooms. Zones where no growth of hyphae or mushrooms were also observed in passaged casing due to green mold disease pressure. The stimulating effect of passaged casing on mushroom development and the dynamic outcomes for disease challenge from two distinct, commercially damaging diseases, demonstrates the potential for passaged casing to be used as material to study more sustainable mushroom production and disease management practices.}, }
@article {pmid39643348, year = {2024}, author = {Ma, X and Fan, M and Hannachi, K and Qian, H and Li, Y and Wang, L}, title = {Unveiling the microbiota-mediated impact of different dietary proteins on post-digestive processes: A simulated in vitro approach.}, journal = {Food research international (Ottawa, Ont.)}, volume = {198}, number = {}, pages = {115381}, doi = {10.1016/j.foodres.2024.115381}, pmid = {39643348}, issn = {1873-7145}, mesh = {*Digestion ; *Gastrointestinal Microbiome/physiology ; Animals ; *Fermentation ; Dietary Proteins/metabolism ; Cattle ; Swine ; Chickens ; Fatty Acids, Volatile/metabolism ; Plant Proteins, Dietary/metabolism ; Animal Proteins, Dietary ; }, abstract = {Protein digestion and microbial metabolism play crucial roles in overall health. However, the mechanisms that differentiate the digestion and metabolism of dietary proteins from different sources in the organism remain poorly understood. This study investigated the digestive properties and microbial fermentation of various animal proteins (chicken, pork, beef, and casein) and plant proteins (soy bean, mung bean, kidney bean, rice, and wheat) in an in vitro simulation. The results indicated that animal-derived proteins had higher essential amino acid content (33.97-37.12 g/100 g) and digestibility levels (49.15-60.94 %), and provided more small molecule peptides upon digestion. Nevertheless, soy bean and wheat proteins also exhibited higher digestibility (54.70 % and 60.94 %), probably due to the extraction process. The fermentation results showed that distinct metabolic profiles that emerged for different protein sources. Plant-derived proteins (especially kidney bean, rice and wheat) promoted the proliferation of beneficial bacteria and microbial diversification and stimulated short-chain fatty acids (SCFA) production. Conversely, meat proteins (pork, chicken, beef) had significantly lower microbial diversity and SCFA than these plant proteins. These findings provide valuable insights into the effects of dietary protein sources on digestion and gut microbiome, and offer scientific guidance for optimizing dietary choices to improve health.}, }
@article {pmid39643213, year = {2024}, author = {Chen, W and Yan, X and Song, X and Yang, Y and Wang, X and Xu, G and Wang, T and Liu, Y and Fan, Z and Song, G}, title = {Effects of Fzd6 on intestinal flora and neuroinflammation in lipopolysaccharide-induced depression-like mice.}, journal = {Journal of affective disorders}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jad.2024.12.011}, pmid = {39643213}, issn = {1573-2517}, abstract = {BACKGROUND: The gut microbiome is critical for the pathophysiology of depression, and inflammation is one of the factors contributing to depression. Fzd6 has been implicated in depression. This study aimed to elucidate the effects of the Fzd6 mutation on gut microbiota structure and the possible regulatory mechanisms involved in depression-associated neuroinflammation.<br><br>METHODS: Wild-type (Fzd6[WT]) and Fzd6 mutant (Fzd6[Q152E]) male mice were treated with lipopolysaccharide (LPS) for 7&#x202f;days. Behavioral experiments were used to detect the behavioral changes of mice in each group, and the composition of intestinal flora and systemic inflammation levels of mice were further detected.<br><br>RESULTS: In LPS mice, the Fzd6 mutation enhanced depression-like behavior symptoms, increased the release of pro-inflammatory cytokines, decreased the release of anti-inflammatory cytokines, and caused intestinal flora disturbance. Subsequently, 16SrRNA sequencing revealed significant changes in the relative abundance of the inflammation-associated bacterial groups Ruminococcaceae and Lachnospiraceae in Fzd6[Q152E] mice. In mice with depression, the levels of G protein-coupled receptors, GPR41 and GPR43, and glucagon-like peptide-1 (GLP-1) in the small intestine were down-regulated, and the expression of GLP-1 receptor (GLP-1R), peroxisome proliferators activated receptors gamma (PPAR-&#x3b3;), and nuclear factor kappa-B inhibitor alpha (I&#x3ba;B&#x3b1;) in the hippocampus was also down-regulated, while the expression of nuclear factor kappa-B p65 (NF-&#x3ba;B p65) was up-regulated.<br><br>LIMITATIONS: The size of the spleen was not studied in this model, and the Fzd6 mutation itself does not cause systemic inflammation such as IL-6.<br><br>CONCLUSION: These results demonstrate that mutations in Fzd6 regulate the composition of the gut flora, which contributes to depression-associated inflammation.}, }
@article {pmid39643125, year = {2024}, author = {Alfahl, Z and Einarsson, GG and Elborn, JS and Gilpin, DF and O'Neill, K and Ferguson, K and Hill, AT and Loebinger, MR and Carroll, M and Gatheral, T and De Soyza, A and Chalmers, JD and Johnson, C and Hurst, JR and Brown, JS and Bradley, JM and Tunney, MM}, title = {Airway total bacterial density, microbiota community composition and relationship with clinical parameters in bronchiectasis.}, journal = {Respiratory medicine}, volume = {}, number = {}, pages = {107906}, doi = {10.1016/j.rmed.2024.107906}, pmid = {39643125}, issn = {1532-3064}, abstract = {BACKGROUND AND OBJECTIVE: This study explored the relationship between total bacterial density, airway microbiota composition and clinical parameters in bronchiectasis. We determined changes with time during clinical stability and following antibiotic treatment of a pulmonary exacerbation.<br><br>METHODS: We conducted a multicentre longitudinal cohort study of UK participants with CT confirmed bronchiectasis. Sputum samples and clinical parameters [FEV1% predicted, lung clearance index, C-reactive protein, white cell count and Quality of Life] were collected when participants were clinically stable and pre/post-antibiotic treatment of an exacerbation. Total bacterial density and microbiota community composition was measured by quantitative polymerase chain reaction and sequencing of the V4 region of bacterial 16S rRNA, respectively.<br><br>RESULTS: Among 105 participants at baseline, 65 (62%) were female with a mean age of 65 years and FEV1 at 69% predicted. In participants who remained clinically stable (n=15), no significant changes were observed in bacterial density, microbiota diversity, richness, evenness, and dominance (p=0.30, 0.45, 0.54, 0.23 and 0.43; respectively) across four time points over a 1-year period. Similarly, for participants with paired pre/post-antibiotic treatment samples (n=19), no significant changes were observed (p=0.30, 0.46, 0.44, 0.71 and 0.58; respectively). However, considerable fluctuation in community composition between samples was apparent for most patients. Total bacterial density and microbiota composition did not correlate with clinical parameters at baseline (n=75).<br><br>CONCLUSIONS: Stability in bacterial density and microbiota diversity, richness, evenness and dominance was observed over time at a population level but considerable fluctuation was apparent in samples from individual patients.}, }
@article {pmid39643107, year = {2024}, author = {Khedpande, N and Barve, K}, title = {Role of gut dysbiosis in drug-resistant epilepsy: Pathogenesis and available therapeutic strategies.}, journal = {Brain research}, volume = {}, number = {}, pages = {149385}, doi = {10.1016/j.brainres.2024.149385}, pmid = {39643107}, issn = {1872-6240}, abstract = {Over 70 million people worldwide suffer from epilepsy, a persistent brain disorder. Although there are more than 20 antiseizure drugs available for the symptomatic treatment of epilepsy, about one-third of patients with epilepsy experience seizures that show resistance to pharmacotherapy. Since patients with drug-resistant epilepsy are more prone to physical injuries, psychosocial dysfunction, early death, and deteriorated life quality, the development of safer and more effective treatments is a crucial clinical need. The gut-brain axis and microbiome research advances have provided new insights into the pathophysiology of epilepsy, the resistance to anti-seizure medicine, and potential treatment targets. Inflammation, disturbance of the blood-brain barrier, and altered neurotransmitters are key pathways linked to gut dysbiosis. The characterization of microbial species and functional pathways has advanced thanks to metagenomic sequencing and high-throughput analysis. In this review, we elaborate on the gut-mediated molecular pathways involved in drug-resistant epilepsy, the gut- modulatory therapeutic options, and their combination with antiseizure medications for drug-resistant epilepsy.}, }
@article {pmid39643017, year = {2024}, author = {Ouwehand, J and Peijnenburg, WJGM and Vijver, MG}, title = {Microbial function matters: Microbiome-aware nano-ecotoxicology needs functional endpoints besides compositional data.}, journal = {Chemosphere}, volume = {369}, number = {}, pages = {143905}, doi = {10.1016/j.chemosphere.2024.143905}, pmid = {39643017}, issn = {1879-1298}, abstract = {The microbiome provides an active barrier to the external environment and aids in the metabolism of the host. Nanomaterials are known to interact with this microbiome host plane. Given the recent advances in techniques to study the microbiome, there has been a vast increase in studies trying to find causality in host response via the microbiome in nano-ecotoxicology. Our review integrates the latest advancements in understanding the microbiome's role in elucidating host health related to nanomaterial exposure, thereby explicitly emphasizing the gap between compositional and functional studies. Both the techniques used to interfere and the current understanding of microbiome-host relationships in nano-ecotoxicology are discussed. To further highlight the functional side of the microbiome, we performed an explorative meta-analysis to bridge the gap between top-down and bottom-up studies. This review gives a perspective on generalising microbiome-aware nano-ecotoxicology and discusses methodologies to enhance the interpretation of nanomaterial or chemical exposure to host-microbiome interactions. The current study discloses that correlations built on compositional data are not a good proxy for host outcome and more in-depth analysis coupled with functional analysis should be explored more in microbiome-aware nano-ecotoxicology.}, }
@article {pmid39642943, year = {2024}, author = {Baskaran, K and Moshkovich, M and Hart, L and Shah, N and Chowdhury, F and Shanmuganathan, M and Britz-McKibbin, P and Pai, N}, title = {The role of urine metabolomics in the diagnosis and management of adult and pediatric Crohn's disease and ulcerative colitis.}, journal = {Biomarkers : biochemical indicators of exposure, response, and susceptibility to chemicals}, volume = {}, number = {}, pages = {1-15}, doi = {10.1080/1354750X.2024.2438734}, pmid = {39642943}, issn = {1366-5804}, abstract = {INTRODUCTION: Urine metabolomics offers a non-invasive approach to diagnose and manage inflammatory bowel disease (IBD), including Crohn's disease (CD) and ulcerative colitis (UC), by identifying distinct metabolic signatures.<br><br>OBJECTIVES: This narrative review summarizes current findings on urinary metabolites in IBD, evaluating their roles in disease differentiation, assessment of activity, and monitoring therapeutic response.<br><br>METHODS: A comprehensive literature search of PubMed and MEDLINE up to October 2023 was conducted using keywords such as "urine metabolomics," "inflammatory bowel disease," "Crohn's disease," "ulcerative colitis," and "urinary biomarkers." Studies were included that described alterations to metabolic pathways, including those related to the urea cycle, central energy metabolism (Krebs cycle), amino acid metabolism, and neurotransmitters.<br><br>RESULTS: Specific urinary metabolites differentiate IBD patients from healthy controls and between CD and UC. Decreased urinary levels of hippurate, acetate, methanol, formate, and methylamine are observed in IBD, indicating altered gut microbiota. In CD patients, urea cycle alterations include reduced urinary urea and ornithine with increased arginine. Changes in Krebs cycle intermediates show decreased citrate and succinate in adults, but increased fumarate and isocitrate in pediatric patients, reflecting energy metabolism differences. Amino acid metabolism differs by age: adults exhibit decreased urinary asparagine, lysine, and histidine, while pediatric patients show increased methionine, proline, aspartic acid, and isoleucine. Elevated urinary neurotransmitters like dopamine are noted in pediatric IBD patients. Urine metabolomics also can monitor treatment efficacy by distinguishing responders from non-responders to therapies and differentiating active disease from remission.<br><br>CONCLUSION: Urine metabolomics provides promising, non-invasive biomarkers to enhance IBD diagnostics by distinguishing CD from UC and offering insights into underlying metabolic disturbances, paving the way for more precise, accessible patient care.}, }
@article {pmid39642880, year = {2024}, author = {Jeong, H and Lee, B and Cho, SY and Lee, Y and Kim, J and Hur, S and Cho, K and Kim, KH and Kim, SH and Taek Nam, K}, title = {Microbiota-derived short-chain fatty acids determine stem cell characteristics of gastric chief cells.}, journal = {Developmental cell}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.devcel.2024.11.007}, pmid = {39642880}, issn = {1878-1551}, abstract = {The gastric mucosa is a highly dynamic tissue that undergoes constant self-renewal through stem cell differentiation. Chief cells maintain a quiescent state in homeostasis but are responsible for regeneration after injury. Although the role of microbiome-host interactions in the intestine is well studied, less is known about these interactions in the stomach. Using the mouse organoid and germ-free mouse models, we show that microbiota-derived short-chain fatty acids (SCFAs) suppress the proliferation of chief cells in mice. This effect is mediated by activation of G-protein-coupled receptor 43. Most importantly, through metabolomics and transplantation studies, we show butyrate-producing Lactobacillus intestinalis modulates the proliferation of chief cells in mice. Our findings identify a mechanism by which the microbiota regulates the cell characteristics of chief cells, providing insight into the complex interplay between the host and its microbial environment and the mechanisms underlying gastric homeostasis, with potential therapeutic implications for gastric diseases.}, }
@article {pmid39642873, year = {2024}, author = {Kristensen, M and de Steenhuijsen Piters, WAA and Wildenbeest, J and van Houten, MA and Zuurbier, RP and Hasrat, R and Arp, K and Chu, MLJN and Billard, M and Heikkinen, T and Cunningham, S and Snape, M and Drysdale, SB and Thwaites, RS and Martinon-Torres, F and Pollard, AJ and Openshaw, PJM and Aerssen, J and Binkowska, J and Bont, L and Bogaert, D and , }, title = {The respiratory microbiome is linked to the severity of RSV infections and the persistence of symptoms in children.}, journal = {Cell reports. Medicine}, volume = {}, number = {}, pages = {101836}, doi = {10.1016/j.xcrm.2024.101836}, pmid = {39642873}, issn = {2666-3791}, abstract = {Respiratory syncytial virus (RSV) is the leading cause of infant respiratory infections and hospitalizations. To investigate the relationship between the respiratory microbiome and RSV infection, we sequence nasopharyngeal samples from a birth cohort and a pediatric case-control study (Respiratory Syncytial virus Consortium in Europe [RESCEU]). 1,537 samples are collected shortly after birth ("baseline"), during RSV infection and convalescence, and from healthy controls. We find a modest association between baseline microbiota and the severity of consecutive RSV infections. The respiratory microbiota during infection clearly differs between infants with RSV and controls. Haemophilus, Streptococcus, and Moraxella abundance are associated with severe disease and persistence of symptoms, whereas stepwise increasing abundance of Dolosigranulum and Corynebacterium is associated with milder disease and health. We conclude that the neonatal respiratory microbiota is only modestly associated with RSV severity during the first year of life. However, the respiratory microbiota at the time of infection is strongly associated with disease severity and residual symptoms.}, }
@article {pmid39642737, year = {2024}, author = {Medriano, CA and Kim, S and Kim, LH and Bae, S}, title = {Chronic Exposure of Adult Zebrafish to Polyethylene and Polyester-based Microplastics: Metabolomic and Gut Microbiome Alterations Reflecting Dysbiosis and Resilience.}, journal = {Journal of hazardous materials}, volume = {484}, number = {}, pages = {136691}, doi = {10.1016/j.jhazmat.2024.136691}, pmid = {39642737}, issn = {1873-3336}, abstract = {The study explored the ecotoxicological effects of chronic exposure to microplastic (MP) on adult zebrafish, focusing on environmentally relevant concentrations of polyethylene (PE) beads and polyester (PES). High-throughput untargeted metabolomics via UPLC-QToF-MS and 16S metagenomics for gut microbiota analysis were used to assess ecotoxicity in zebrafish exposed to varying concentrations of PE and PES. The VIP (Variable Importance in Projection) scores indicated PE exposure primarily impacted phospholipids, ceramides, and nucleotide-related compounds, while PES exposure led to alterations in lipid-related compounds, chitin, and amino acid derivatives. From MSEA (Metabolite Set Enrichment Analysis) and Mummichog analyses, PE and PES significantly disrupted key metabolomic pathways associated with inflammation, immune responses, and apoptosis, including leukotriene and arachidonic acid metabolism and the formation of putative anti-inflammatory metabolites from EPA. PE caused physical disruption and inflammation of the epithelial barrier, whereas PES affected gut microbiota interactions, impairing digestion and metabolism. Although alpha diversity within the gut microbiome remained stable, beta diversity analysis revealed significant shifts in microbial composition and structure, suggesting a disruption of functional balance and an increased susceptibility to pathogens. Chronic PE and PES exposures induced shifts in the gut microbial community and interaction network with potential increases in pathogenic bacteria and alteration in commensal bacteria, demonstrating the microbiome's resilience and adaptability to stressors of MPs exposure. High-throughput metabolomics and 16S metagenomics revealed potential chronic diseases associated with inflammation, immune system disorders, metabolic dysfunction, and gut dysbiosis, highlighting the complex relationship between gut microbiome resilience and metabolic disruption under MP-induced stress, with significant ecological implications.}, }
@article {pmid39642696, year = {2024}, author = {Koshida, T and Gohda, T and Kaga, N and Taka, H and Shimozawa, K and Murakoshi, M and Yamashiro, Y and Suzuki, Y}, title = {Inappropriate diet and hygiene status affect the progression of diabetic kidney disease by causing dysbiosis.}, journal = {Nutrition (Burbank, Los Angeles County, Calif.)}, volume = {131}, number = {}, pages = {112633}, doi = {10.1016/j.nut.2024.112633}, pmid = {39642696}, issn = {1873-1244}, abstract = {OBJECTIVE: Although the effects of an unhealthy diet on the risks of diabetes and its renal complications are well understood, the effects of hygiene status have not been fully elucidated.<br><br>We created four groups of mice according to the diet fed (standard [SD] or high-fat [HFD]) and their living environment (conventional [CV] or specific pathogen-free [SPF]), and characterized the extent of their kidney pathology, their gut microbiota, and their fecal short-chain fatty acid (SCFA) concentrations.<br><br>RESULTS: The body masses and glycated hemoglobin levels of the HFD and CV groups were significantly higher than those of the SD and SPF groups, respectively. The renal mRNA expression of markers of inflammation and fibrosis and the protein level of CD31 were higher in the HFD and CV groups than in the SD and SPF groups, respectively. Although the alpha diversities and total SCFA concentrations of the HFD and CV groups were significantly lower than those of the SD and SPF groups, respectively, the mRNA expression of genes involved in inflammation, innate immunity, tight junctions, and glucose transporters in the gut was only affected by HFD.<br><br>CONCLUSIONS: Gut microbial dysbiosis, owing to the combined effects of inappropriate diet and excessive hygiene, accompanied by lower intestinal SCFA production, may contribute to the development and/or progression of diabetes and diabetic kidney disease through the induction of inflammation and fibrosis.}, }
@article {pmid39642431, year = {2024}, author = {Bertini, F and Catania, V and Scirè Calabrisotto, L and Dara, M and Bisanti, L and La Corte, C and Staropoli, M and Piazzese, D and Parisi, MG and Parrinello, D and Cammarata, M}, title = {A multi-comprehensive approach to assess the responses of the Mediterranean mussel Mytilus galloprovincialis (Lamarck, 1919) to a simulation of a diesel-oil mixture spill.}, journal = {Aquatic toxicology (Amsterdam, Netherlands)}, volume = {279}, number = {}, pages = {107188}, doi = {10.1016/j.aquatox.2024.107188}, pmid = {39642431}, issn = {1879-1514}, abstract = {Oil spills are a major cause of pollution impacting marine ecosystems. In this work, the effects of short-term exposure to three different concentrations of a hydrocarbon mixture (HC), that simulated the action of such an event, were investigated on Mytilus galloprovincialis specimens. Physiological effects were measured using a battery of biomarkers consisting of cellular activity (phagocytosis), immune-related enzymes, chaperonins (HSP70 and HSC70), and histomorphological alterations. Different concentrations of HC led to a significant decrease in phagocytosis, especially following high concentrations. Immune-related enzymes evaluated in hemolymph and digestive gland extract showed up-regulation, suggesting the activation of antioxidant, detoxicant, and inflammatory responses. Morphological alterations of digestive gland tubules were observed after exposure to the HC. HSP70 and HSC70 activity was up regulated following the treatments, indicating their involvement in maintaining organism homeostasis. In addition, the diversity and composition of hemolymph and digestive gland microbiota exposed to HC were analyzed by automated ribosomal intergenic spacer analysis (ARISA) and a Next Generation Sequencing (NGS) approach to evaluate the connection with hydrocarbon contamination. Metagenomic analysis revealed significant differences in the hemolymph and digestive gland microbiota composition between mussels exposed and unexposed to HC. Exposure to increasing HC concentrations had a positive effect on microbial diversity with clear adaptative responses, and an increase in the relative abundance of several known degrading bacterial genera, including Alcanivorax, Roseovarius, Pseudomonas, Vibrio, Oleibacter. These results show the utility of a multi-comprehensive approach to evaluating functional adaptation in terms of immunological dysfunctions and microbiota alteration in the sentinel organism M. galloprovincialis.}, }
@article {pmid39642324, year = {2024}, author = {Yao, H and Xu, J and Zhou, A and Shen, D and Dong, Q and Yang, X and Li, M and Mi, X and Lu, Y and Zhong, R and Shi, X and Tai, Q and Chen, G and Shi, B and Sun, L and Zhou, D and Yao, Y and He, S}, title = {Gut microbiota-mediated hsa_circ_0126925 targets BCAA metabolic enzyme BCAT2 to exacerbate colorectal cancer progression.}, journal = {Molecular cancer research : MCR}, volume = {}, number = {}, pages = {}, doi = {10.1158/1541-7786.MCR-24-0434}, pmid = {39642324}, issn = {1557-3125}, abstract = {Recent evidence indicates that a high-fat diet (HFD) can promote tumor development, especially colorectal cancer (CRC), by influencing the microbiota. Regulatory circular RNAs (circRNAs) play an important role in modulating host-microbe interactions; however, the specific mechanisms by which circRNAs influence cancer progression by regulating these interactions remain unclear. Here, we report that consumption of a HFD modulates the microbiota by specifically upregulating the expression of the noncoding RNA hsa_circ_0126925 (herein referred to as circ_0126925) in CRC. Acting as a scaffold, circ_0126925 hinders the recruitment of the E3 ubiquitin ligase tripartite motif-containing protein 21 (TRIM21) to branched-chain amino acid transaminase 2 (BCAT2), leading to reduced degradation of BCAT2. This reduction in targeted degradation of BCAT2 can protect tumours from limited branched-chain amino acids (BCAAs) interference by improving the metabolism of BCAAs in CRC. Taken together, these data demonstrate that circ_0126925 plays a critical role in promoting the progression of CRC by maintaining BCAA metabolism and provide insight into the functions and crosstalk of circ_0126925 in host-microbe interactions in CRC. Implications: This study preliminarily confirms that circRNAs do indeed respond to microbiota/microbial metabolites, providing further evidence for the potential development of circRNAs as diagnostic tools and/or therapeutic agents to alleviate microbiome related pathology in humans.}, }
@article {pmid39642194, year = {2024}, author = {Liu, Y and Hu, J and Gore, J}, title = {Ecosystem stability relies on diversity difference between trophic levels.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {121}, number = {50}, pages = {e2416740121}, doi = {10.1073/pnas.2416740121}, pmid = {39642194}, issn = {1091-6490}, mesh = {*Biodiversity ; Animals ; *Food Chain ; *Ecosystem ; Models, Biological ; Predatory Behavior/physiology ; }, abstract = {The stability of ecological communities has a profound impact on humans, ranging from individual health influenced by the microbiome to ecosystem services provided by fisheries. A long-standing goal of ecology is the elucidation of the interplay between biodiversity and ecosystem stability, with some ecologists warning of instability due to loss of species diversity while others arguing that greater diversity will instead lead to instability. Here, by considering a minimal two-level ecosystem with multiple predator and prey species, we show that stability does not depend on absolute diversity but rather on diversity differences between levels. We found that increasing diversity in either level first destabilizes but then stabilizes the community (i.e., a reentrant stability transition). We therefore find that it is the diversity difference between levels that is the key to stability, with the least stable communities having similar diversities in different levels. An analytical stability criterion is derived, demonstrating quantitatively that the critical diversity difference is determined by the correlation between how one level affects another and how it is affected in turn. Our stability criterion also applies to consumer-resource models with other forms of interaction such as cross-feeding. Finally, we show that stability depends on diversity differences in ecosystems with three trophic levels. Our finding of a nonmonotonic dependence of stability on diversity provides a natural explanation for the variety of diversity-stability relationships reported in the literature, and emphasizes the significance of level structure in predicting complex community behaviors.}, }
@article {pmid39642168, year = {2024}, author = {Champion, C and Momal, R and Le Chatelier, E and Sola, M and Mariadassou, M and Berland, M}, title = {OneNet-One network to rule them all: Consensus network inference from microbiome data.}, journal = {PLoS computational biology}, volume = {20}, number = {12}, pages = {e1012627}, doi = {10.1371/journal.pcbi.1012627}, pmid = {39642168}, issn = {1553-7358}, abstract = {Modeling microbial interactions as sparse and reproducible networks is a major challenge in microbial ecology. Direct interactions between the microbial species of a biome can help to understand the mechanisms through which microbial communities influence the system. Most state-of-the art methods reconstruct networks from abundance data using Gaussian Graphical Models, for which several statistically grounded and computationnally efficient inference approaches are available. However, the multiplicity of existing methods, when applied to the same dataset, generates very different networks. In this article, we present OneNet, a consensus network inference method that combines seven methods based on stability selection. This resampling procedure is used to tune a regularization parameter by computing how often edges are selected in the networks. We modified the stability selection framework to use edge selection frequencies directly and combine them in the inferred network to ensure that only reproducible edges are included in the consensus. We demonstrated on synthetic data that our method generally led to slightly sparser networks while achieving much higher precision than any single method. We further applied the method to gut microbiome data from liver-cirrothic patients and demonstrated that the resulting network exhibited a microbial guild that was meaningful in terms of human health.}, }
@article {pmid39641864, year = {2024}, author = {Hoogendijk, R and van den Broek, TJM and Lee, H and Mueller, S and Kline, C and Bianco, J and Top, J and de Zoete, MR and Kester, L and Calkoen, F and van der Lugt, J}, title = {Omnigene-Gut[tm] ensures fecal microbiome stability in the pediatric population.}, journal = {AMB Express}, volume = {14}, number = {1}, pages = {132}, pmid = {39641864}, issn = {2191-0855}, abstract = {Increasing evidence exists that the gut microbiome influences toxicity as well as outcomes in a variety of cancers. To investigate the role of the gut microbiome in pediatric neuro-oncology, microbiome analysis has been included in multiple prospective pediatric neuro-oncology clinical trials (NCT05009992, NCT04732065, NCT04775485). In these trials, the OMNIgene-GUT[tm] preservation tubes are used for the collection of the feces. OMNIgene-GUT[tm] has demonstrated reliability in preserving the composition of the gut microbiome in adults; however, its validation for use in the pediatric population remains limited. Therefore, we compared the quality of the DNA by 16S rRNA gene sequencing after various methods of stabilizing fecal samples in pediatric populations, from the direct freeze method at - 80 °C to preserving samples with OMNIgene-GUT[tm] at room temperature for various durations. Our results showed that there were no statistically significant differences between the alpha-diversity, and beta-diversity. However, pairwise differential abundance analyses demonstrated that OMNIgene-GUT™ is superior in maintaining microbial community structure compared to storing samples without any preservation method. With the OMNIgene-GUT[tm]'s stabilization of the fecal samples being superior and its ease-of-use benefits, it proves to be a valid and ideal method of stabilizing fecal samples for current and future pediatric clinical trials.}, }
@article {pmid39641605, year = {2024}, author = {Bao, Z and Chen, B and Yu, K and Wei, Y and Liang, X and Yao, H and Liao, X and Xie, W and Yin, K}, title = {Microbiome dynamics and functional profiles in deep-sea wood-fall micro-ecosystem: insights into drive pattern of community assembly, biogeochemical processes, and lignocellulose degradation.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0216524}, doi = {10.1128/aem.02165-24}, pmid = {39641605}, issn = {1098-5336}, abstract = {Wood-fall micro-ecosystems contribute to biogeochemical processes in the oligotrophic deep ocean. However, the community assembly processes and biogeochemical functions of microbiomes in wood fall remain unclear. This study investigated the diversity, community structure, assembly processes, and functional profiles of bacteria and fungi in a deep-sea wood fall from the South China Sea using physicochemical indices, amplicon sequencing, and metagenomics. The results showed that distinct wood-fall contact surfaces exhibit habitat heterogeneity. The bacterial community of all contact surfaces and the fungal community of seawater contact surface (SWCS) were affected by homogeneous selection. In SWCS and transition region (TR), bacterial communities were influenced by dispersal limitation, whereas fungal communities were affected by homogenizing dispersal. The Venn diagram visualization revealed that the shared fungal community between SWCS and TR was dominated by Aspergillaceae. Additionally, the bacterial community demonstrated a higher genetic potential for sulfur, nitrogen, and methane metabolism than fungi. The sediment contact surface enriched modules were associated with dissimilatory sulfate reduction and methanogenesis, whereas the modules related to nitrate reduction exhibited enrichment characteristics in TR. Moreover, fungi showed a stronger potential for lignocellulase production compared to bacteria, with Microascaceae and Nectriaceae identified as potential contributors to lignocellulose degradation. These results indicate that environmental filtering and organism exchange levels regulated the microbial community assembly of wood fall. The biogeochemical cycling of sulfur, nitrogen, and methane was mainly driven by the bacterial community. Nevertheless, the terrestrial fungi Microascaceae and Nectriaceae might degrade lignocellulose via the combined action of multiple lignocellulases.IMPORTANCEThe presence and activity of microbial communities may play a crucial role in the biogeochemical cycle of deep-sea wood-fall micro-ecosystems. Previous studies on wood falls have focused on the microbiome diversity, community composition, and environmental impact, while few have investigated wood-fall micro-ecosystems by distinguishing among distinct contact surfaces. Our study investigated the microbiome dynamics and functional profiles of bacteria and fungi among distinct wood-fall contact surfaces. We found that the microbiome community assembly was regulated by environmental filtering and organism exchange levels. Bacteria drive the biogeochemical cycling of sulfur, nitrogen, and methane in wood fall through diverse metabolic pathways, whereas fungi are crucial for lignocellulose degradation. Ultimately, this study provides new insights into the driving pattern of community assembly, biogeochemical processes, and lignocellulose degradation in the microbiomes of deep-sea wood-fall micro-ecosystems, enhancing our comprehension of the ecological impacts of organic falls on deep-sea oligotrophic environments.}, }
@article {pmid39641544, year = {2024}, author = {Madaan, T and Doan, K and Hartman, A and Gherardini, D and Ventrola, A and Zhang, Y and Kotagiri, N}, title = {Advances in Microbiome-Based Therapeutics for Dermatological Disorders: Current Insights and Future Directions.}, journal = {Experimental dermatology}, volume = {33}, number = {12}, pages = {e70019}, doi = {10.1111/exd.70019}, pmid = {39641544}, issn = {1600-0625}, support = {CDMRP ME200246//Congressionally Directed Medical Research Programs/ ; R01HL168588//Office of Extramural Research, National Institutes of Health/ ; R01CA279962//Office of Extramural Research, National Institutes of Health/ ; }, mesh = {Humans ; *Microbiota ; *Skin Diseases/therapy/microbiology ; *Skin/microbiology ; Dermatitis, Atopic/therapy/microbiology ; Psoriasis/therapy/microbiology ; Hidradenitis Suppurativa/therapy/microbiology/drug therapy ; Skin Neoplasms/therapy/microbiology ; Probiotics/therapeutic use ; Diabetic Foot/therapy/microbiology ; }, abstract = {The human skin hosts an estimated 1000 bacterial species that are essential for maintaining skin health. Extensive clinical and preclinical studies have established the significant role of the skin microbiome in dermatological disorders such as atopic dermatitis, psoriasis, diabetic foot ulcers, hidradenitis suppurativa and skin cancers. In these conditions, the skin microbiome is not only altered but, in some cases, implicated in disease pathophysiology. Microbiome-based therapies (MBTs) represent an emerging category of live biotherapeutic products with tremendous potential as a novel intervention platform for skin diseases. Beyond using established wild-type strains native to the skin, these therapies can be enhanced to express targeted therapeutic molecules, offering more tailored treatment approaches. This review explores the role of the skin microbiome in various common skin disorders, with a particular focus on the development and therapeutic potential of MBTs for treating these conditions.}, }
@article {pmid39640900, year = {2024}, author = {Pahirah, N and Narkwichean, A and Taweechotipatr, M and Wannaiampikul, S and Duang-Udom, C and Laosooksathit, W}, title = {Comparison of Gut Microbiomes Between Neonates Born by Cesarean Section and Vaginal Delivery: Prospective Observational Study.}, journal = {BioMed research international}, volume = {2024}, number = {}, pages = {8302361}, pmid = {39640900}, issn = {2314-6141}, mesh = {Humans ; *Cesarean Section ; *Gastrointestinal Microbiome ; Infant, Newborn ; Female ; Prospective Studies ; *Delivery, Obstetric ; Pregnancy ; *RNA, Ribosomal, 16S/genetics ; Male ; Feces/microbiology ; Thailand ; Bifidobacterium ; }, abstract = {Background: Balanced diversity and abundance of gut microbiome play important roles in human health, including neonatal health. Though not established, there is evidence that the delivery route could alter the diversity of neonatal gut microbiomes. Objective: The objective of the study was to investigate the differences in the gut microbiomes of neonates delivered via cesarean section compared to those born by vaginal delivery and to identify the predominant microbial taxa present in each group. Study Design: A prospective observational study of 281 healthy neonates born between February 2021 and April 2023 at Her Royal Highness Maha Chakri Sirindhorn Medical Center, Srinakharinwirot University, Thailand, was performed. The study population was divided into two groups: 139 neonates born via vaginal delivery and 141 neonates born via cesarean section. The microbiota composition of each neonate's fecal sample was identified by using 16S ribosomal ribonucleic acid metagenomic sequencing. Results: Neonates delivered vaginally exhibited a gut microbiome with higher abundance and diversity than those delivered by cesarean delivery. Bifidobacterium was the dominant genus in both groups. Bifidobacterium breve was the dominant species and was significantly higher in cesarean-delivered neonates compared to those delivered vaginally (24.0% and 9.2%, respectively) (p < 0.001). However, the taxonomy of only 89 (64.0%) and 44 (31.43%) fecal samples could be identified from the vaginal and cesarean delivery groups, respectively. Conclusion: Route of delivery is associated with neonatal gut microbiome abundance and diversity. Neonates delivered via vaginal delivery exhibited higher diversity but lower abundance of the dominant species in the gut microbiome. Trial Registration: Thai Clinical Trials Registry identifier: TCTR20221024003.}, }
@article {pmid39640850, year = {2024}, author = {Alattas, H and Glick, BR and Murphy, DV and Scott, C}, title = {Harnessing Pseudomonas spp. for sustainable plant crop protection.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1485197}, pmid = {39640850}, issn = {1664-302X}, abstract = {This review examines the role of Pseudomonas spp. bacteria as biocontrol agents against crop diseases, focusing on their mechanisms of action, efficacy, and potential applications in sustainable agriculture. Pseudomonas spp., ubiquitous in soil ecosystems and root microbiomes, have attracted attention for their ability to suppress phytopathogens and enhance plant health through various mechanisms. These include direct competition for nutrients, production of antimicrobial compounds and volatile organic compounds, competition using type VI secretion systems, and indirect induction of systemic resistance. Our review shows that Pseudomonas strains effectively control a wide range of diseases across diverse plant species, with some strains demonstrating efficacy comparable to chemical fungicides. However, the review also highlights challenges in achieving consistent performance when using Pseudomonas inoculants under field conditions due to various biotic and abiotic factors. Strategies to optimize biocontrol potential, such as formulation techniques, application methods, and integration with other management practices, are discussed. The advantages of Pseudomonas-based biocontrol for sustainable agriculture include reduced reliance on chemical pesticides, enhanced crop productivity, and improved environmental sustainability. Future research directions should focus on understanding the complex interactions within the plant microbiome, optimizing delivery systems, and addressing regulatory hurdles for commercial deployment. This review underscores the significant potential of Pseudomonas spp. in sustainable crop protection while acknowledging the need for further research to fully harness their capabilities in agricultural systems.}, }
@article {pmid39640827, year = {2024}, author = {Liu, J and Xiang, K and He, H and Chen, W}, title = {Endoscopic brush sampling identifies mucosa associated microbiota in colorectal adenomas.}, journal = {Heliyon}, volume = {10}, number = {20}, pages = {e38901}, pmid = {39640827}, issn = {2405-8440}, abstract = {The intestinal microbiome plays a crucial role in colorectal adenomas and the mucosa associated microbiota are thought to play a more critical role in interactions with the host immune system. Current omics approaches, offer a holistic assessment of the gut microbiome and the human host interaction. To enhance the value of data from these sequencing methods, appropriate sample collection is vital. We evaluated the potential use of endoscopic brush samples for mucosal microbiota analysis in colorectal adenomas and compared it with direct adenoma tissue sequencing in terms of microbial gene sequencing. The results showed a significant increase in microbial diversity in samples collected by the endoscopic brush, which did not interfere with pathological biopsy. This study found that utilizing endoscopic brush sampling for the microbiome analysis of colorectal adenomas offers several advantages over the direct examination of microbiomes within tumor tissues, including the capacity to accurately collect gut microbiome from different locations in the intestine, circumventing interference from tissue genes, providing more abundant microbial data and enabling inclusion of small adenomas without disrupting pathological biopsies.}, }
@article {pmid39640678, year = {2024}, author = {Kato, Y and Takamura, M and Wada, K and Usuda, H and Abe, S and Mitaki, S and Nagai, A}, title = {Fusobacterium in oral bacterial flora relates with asymptomatic brain lesions.}, journal = {Heliyon}, volume = {10}, number = {20}, pages = {e39277}, pmid = {39640678}, issn = {2405-8440}, abstract = {BACKGROUND: Specific bacterial species in the oral cavity contribute to cerebral hemorrhage and microbleeds. The relationship between oral bacterial flora and asymptomatic brain lesions (ABL) remains unclear. This study aimed to investigate this relationship in a healthy Japanese cohort.<br><br>METHODS: This cross-sectional study included participants who underwent health examinations at our Brain Dock facility between October 2020 and March 2021. The oral microbiomes of participants with and without ABL were compared using magnetic resonance imaging. To extensively assess the oral bacterial flora, the differences in genes and species compositions between the ABL and noBL (without brain lesions) groups were statistically evaluated via extensive analysis using 16S rRNA gene-based cloning.<br><br>RESULTS: Among 143 patients, 48.3&#xa0;% had ABL. In the univariate analyses, Fusobacterium and Leptotrichia were associated with ABL (P&#xa0;=&#xa0;0.017 and P&#xa0;<&#xa0;0.001, respectively). In the adjusted models, Fusobacterium was associated with ABL (P&#xa0;=&#xa0;0.006). In an intergroup comparison of seven Fusobacterium species, F. nucleatum, F. naviforme, and F. canifelinum were associated with ABL (P&#xa0;<&#xa0;0.001, P&#xa0;=&#xa0;0.002, P&#xa0;<&#xa0;0.001).<br><br>CONCLUSIONS: The elevation of Fusobacterium in the ABL indicates the importance of the microbiome in the oral cavity as a factor in inducing cerebral small-vessel disease in healthy individuals, whose preventive approach might have an impact on therapeutic applications.}, }
@article {pmid39640675, year = {2024}, author = {Chiba, N and Suzuki, S and Enriquez-Vera, D and Utsunomiya, A and Kubuki, Y and Hidaka, T and Shimoda, K and Nakahata, S and Yamada, T and Morishita, K}, title = {Succinic semialdehyde derived from the gut microbiota can promote the proliferation of adult T-cell leukemia/lymphoma cells.}, journal = {Heliyon}, volume = {10}, number = {20}, pages = {e38507}, pmid = {39640675}, issn = {2405-8440}, abstract = {Adult T-cell leukemia/lymphoma (ATLL) is a refractory blood cancer with severe immunodeficiency resulting from retroviral infection. ATLL develops in only 5 % of HTLV-1-infected individuals, but the entire mechanism of ATLL progression remains unknown. Since recent studies have reported that the gut microbiome influences the progression of various diseases, we hypothesized that ATLL is also related to the gut microbiome and aimed to investigate this relationship. We analyzed the taxonomic and functional profiles of the gut microbiota of ATLL patients (n = 28) and HTLV-1-infected individuals (n = 37). We found that the succinic semialdehyde (SSA) synthesis pathway was significantly enriched in the gut microbiome of ATLL patients (P = 0.000682), and Klebsiella, whose abundance was significantly greater in ATLL patients and high-risk HTLV-1-infected individuals (P = 0.0326), was the main contributor to this pathway. Administration of SSAs to ATLL cell lines resulted in significant cell proliferation. Herein, we propose that the gut microbiome can regulate ATLL progression via metabolites.}, }
@article {pmid39640645, year = {2024}, author = {Ali, A and Ullah, Z and Ullah, R and Kazi, M}, title = {Barley a nutritional powerhouse for gut health and chronic disease defense.}, journal = {Heliyon}, volume = {10}, number = {20}, pages = {e38669}, pmid = {39640645}, issn = {2405-8440}, abstract = {BACKGROUND: Digestive issues are recognized as significant contributors to various chronic diseases, including obesity, diabetes, and cardiovascular disease. Barley, a traditional grain, offers considerable promise in addressing these health challenges due to unique nutritional and bioactive compounds.<br><br>OBJECTIVE: This review examines the therapeutic potential of various parts of barley, underutilized resource, for chronic disease prevention and management.<br><br>METHOD: ology: A comprehensive literature search was conducted across multiple databases like Google Scholar, PubMed, and ISI Web of Science, to identify nutritional components and functional ingredients in barley that contribute to gut health and chronic disease mitigation.<br><br>RESULTS: The finding suggests that humans digest barley starch more slowly than wheat and rice, which benefits chronic disease management. Barley's high-molecular-weight &#x3b2;-glucan high content acts as a prebiotic, promotes gut health through microbiome modulation and short-chain fatty acid production, potentially preventing colon cancer and boosting immunity. Recent studies on exploring barley grass of high land showed functional ingredients such as flavonoids, saponarin lutonarin, superoxide dismutase, gamma-aminobutyric acid, polyphenols K, Ca, Se, tryptophan chlorophyll, and vitamins, suggesting potential for enhanced antioxidant activity and improved management of chronic conditions like diabetes, cholesterol, hypertension, cardiovascular health, liver protection, and even boosted immunity.<br><br>CONCLUSION: This review underscores the therapeutic potential of barley and its components in chronic disease management, highlighting the need for well-designed clinical trials to translate these findings into effective interventions.}, }
@article {pmid39640590, year = {2024}, author = {Midya, V and Nagdeo, K and Lane, JM and Torres-Olascoaga, LA and Martínez, GG and Horton, MK and McRae, N and Lopez, I and Landero, J and Gennings, C and Téllez-Rojo, MM and Wright, RO and Arora, M and Eggers, S}, title = {Akkermansia muciniphila attenuates association between specific metal exposures during pregnancy and depressive symptoms in late childhood.}, journal = {iScience}, volume = {27}, number = {12}, pages = {111335}, pmid = {39640590}, issn = {2589-0042}, abstract = {Emerging research suggests that exposures to metals during pregnancy and consequent disruptions in gut microbiome (GM) are associated with depressive disorders in childhood. Akkermansia muciniphila, a GM bacteria, has been studied for its potential antidepressant effects. However, its role in influencing the association between prenatal metal exposures and depressive symptoms during childhood is unknown. Leveraging a well-characterized pediatric birth cohort and its microbiome substudy (n = 112), we investigated whether a certain subgroup of children at 9-11-year-of-age (characterized by a specific pattern of prenatal exposure to groups of metals or metal-clique) had worsened depressive symptoms and if the presence of A.muciniphila in GM modifies this association. A subgroup of children characterized by the prenatal metal-clique signature of zinc-chromium-cobalt had significantly increased depression scores; however, within that subgroup, children with A.muciniphila had much lower depression scores than those without A.muciniphila in the GM. Our analysis provides exploratory evidence hypothesizing A.muciniphila as an intervention attenuating the effect of prenatal metal-exposures-associated depressive disorders in late childhood.}, }
@article {pmid39640576, year = {2024}, author = {Starikova, EV and Galeeva, YS and Fedorov, DE and Korneenko, EV and Speranskaya, AS and Selezneva, OV and Zoruk, PY and Klimina, KM and Veselovsky, VA and Morozov, MD and Boldyreva, DI and Olekhnovich, EI and Manolov, AI and Pavlenko, AV and Kozlov, IE and Yanushevich, OO and Krikheli, NI and Levchenko, OV and Andreev, DN and Sokolov, FS and Fomenko, AK and Devkota, MK and Andreev, NG and Zaborovsky, AV and Tsaregorodtsev, SV and Evdokimov, VV and Bely, PA and Maev, IV and Govorun, VM and Ilina, EN}, title = {Oropharyngeal resistome remains stable during COVID-19 therapy, while fecal resistome shifts toward a less diverse resistotype.}, journal = {iScience}, volume = {27}, number = {12}, pages = {111319}, pmid = {39640576}, issn = {2589-0042}, abstract = {Antimicrobial resistance poses a serious threat to global public health. The COVID-19 pandemic underscored the need to monitor the dissemination of antimicrobial resistance genes and understand the mechanisms driving this process. In this study, we analyzed changes to the oropharyngeal and fecal resistomes of patients with COVID-19 undergoing therapy in a hospital setting. A targeted sequencing panel of 4,937 resistance genes was used to comprehensively characterize resistomes. Our results demonstrated that the oropharyngeal resistome is homogeneous, showing low variability over time. In contrast, fecal samples clustered into two distinct resistotypes that were only partially related to enterotypes. Approximately half of the patients changed their resistotype within a week of therapy, with the majority transitioning to a less diverse and ermB-dominated resistotype 2. Common macrolide resistance genes were identified in over 80% of both oropharyngeal and fecal samples, likely originating from streptococci. Our findings suggest that the fecal resistome is a dynamic system that can exist in certain "states" and is capable of transitioning from one state to another. To date, this is the first study to comprehensively describe the oropharyngeal resistome and its variability over time, and one of the first studies to demonstrate the temporal dynamics of the fecal resistotypes.}, }
@article {pmid39640572, year = {2024}, author = {Guan, X and Bu, F and Fu, Y and Zhang, H and Xiang, H and Chen, X and Chen, T and Wu, X and Wu, K and Liu, L and Dong, X}, title = {Immunogenic peptides putatively from intratumor microbes: Opportunities for colorectal cancer treatment.}, journal = {iScience}, volume = {27}, number = {12}, pages = {111338}, pmid = {39640572}, issn = {2589-0042}, abstract = {Recent evidence has confirmed the presence of intratumor microbes, yet their impact on the immunopeptidome remains largely unexplored. Here we introduced an integrated strategy to identify the immunopeptidome originated from intratumor microbes. Analyzing 10 colorectal cancer (CRC) patients, we identified 154 putative microbe-derived human leukocyte antigen (HLA)-I ligands. Predominantly bacterial in origin, these peptides were notably abundant in Fusobacterium nucleatum, the most prevalent bacterium differentiating between normal and tumor tissues. We discovered 20 peptides originating from F. nucleatum, thirteen of which, including two peptides shared across multiple patients, were tumor specific. Validation experiments confirmed that the putative microbe-derived peptide could activate CD8[+] T cell responses. Our findings indicate that HLA-I molecules are capable of presenting intratumor microbe-derived peptides in CRC, potentially contributing to CD8[+] T cell-mediated immunity and suggesting potential strategies for cancer immunotherapy.}, }
@article {pmid39640544, year = {2024}, author = {Müller, CBM and Tümmler, LM and Reyer, H and Viergutz, T and Kuhla, B}, title = {Interactions between rumen epithelium-associated microbiota and host immunological and metabolic adaptations in response to different milk replacer feeding intensities in dairy calves.}, journal = {Animal nutrition (Zhongguo xu mu shou yi xue hui)}, volume = {19}, number = {}, pages = {287-300}, pmid = {39640544}, issn = {2405-6383}, abstract = {The milk replacer feeding regime in dairy calves has a great impact on metabolic and immunological functioning and affects animal welfare and lifetime performance. The feeding regime influences the rumen microbial composition, and epithelium-associated microbes may interact with the immune system of the host. We examined the correlations between blood leukocyte counts and the rumen epithelium-associated microbiome in dairy calves fed 2 different milk replacer feeding intensities and if these factors related to metabolic traits. Fourteen newborn female dairy calves were allocated to a group receiving either 10% (n = 7) or 20% (n = 7) milk replacer of their body weight (on average 41 kg) and provided ad libitum access to grass hay and concentrate pellets. At 3 weeks of life, all calves were fitted with a rumen cannula. Calves were weaned at 12 weeks of life and received a total mixed ration for ad libitum intake. Pre- (8-10 weeks of life) and post-weaning (21-23 weeks of life), methane production was measured in respiration chambers, and rumen epithelium and blood were sampled for 16S rRNA sequencing and leukocyte analyses, respectively. Pre-weaning, the reduced milk replacer feeding intensity was accompanied with higher concentrate intake but lower growth performance (P < 0.001), a higher abundance of amylolytic and lower abundance of cellulolytic epimural microbes. The group fed a low milk replacer intensity had also greater portions of monocytes (P = 0.031), CD8[+] (P < 0.001), and CD14[+] (P = 0.044) leukocytes, suggesting elevated inflammatory conditions. Correlations between CD8[+] T cells and rumen methanogens, Ruminococcaceae, and Lachnospiraceae were recorded, but these were not consistent throughout maturation. Post-weaning, differences in feed intake and rumen microbial composition converged among milk replacer groups, while differences in growth performance (P = 0.040) and CD8[+] cells (P < 0.001) were still present. In conclusion, a reduced milk replacer feeding intensity in dairy calves compromised growth performance and immunity and this effect persisted in the long-term. Significant correlations between the proportion of leukocytes and distinct epimural microbe taxa indicated an interplay between rumen epimural colonization and immune functioning of the host. However, further research is required addressing this interplay between rumen epimural microbes and immune functioning in dairy calves.}, }
@article {pmid39640487, year = {2024}, author = {Gao, M and Li, J and Han, X and Zhang, B and Chen, J and Lang, J and Zhang, Q}, title = {Effect of melatonin on gut microbiome and metabolomics in diabetic cognitive impairment.}, journal = {Frontiers in pharmacology}, volume = {15}, number = {}, pages = {1489834}, pmid = {39640487}, issn = {1663-9812}, abstract = {INTRODUCTION: Diabetic cognitive impairment(DCI) presents as a central nervous complication of diabetes especially among aging population. Melatonin (MEL) is known for its antioxidant and anti-inflammation effects in neuroprotective aspects. Recent evidence has demonstrated that the gut microbiome plays a key role in DCI by modulating cognitive function through the gut-brain crosstalk. MEL has been shown to modulate gut microbiota composition in diabetic model. However, the underlying mechanism through which the gut microbiome contributes to DCI remains unclear. This study aims to investigate the effect and mechanism of MEL in attenuating DCI in relation to regulating the gut microbiome and metabolomics.<br><br>METHODS: Cognitive and memory function were assessed by the Morris water maze test, histopathological assessment of brain tissues, and immunoblotting of neuroinflammation and apoptosis. The levels of serum tumor necrosis factor-&#x3b1; (TNF-&#x3b1;) and Interleukin-18 (IL-18) were measured by enzyme-linked immunoassays to reflect the circulatory inflammation level.16S rRNA microbiome sequencing analysis was performed on control mice(db-m group), diabetic mice(db-db group) and MEL-treated diabetic mice(db-dbMEL group). Gut metabolites changes were characterized using liquid chromatography tandem mass spectrometry (LC-MS/MS).<br><br>RESULTS: Our study confirmed that MEL alleviated diabetes-induced cognition and memory dysfunction. MEL protected against neuroinflammation and apoptosis in hippocampus of db-db mice. MEL corrected the increased abundance of Bacteroides and Dorea and the reduced abundance of Prevotella in db-db mice. The vast majority of differential metabolites among the three groups were lipids and lipid-like molecules. MEL significantly restored the reduced levels of pyruvate and lactic acid.<br><br>DISCUSSION: Our results supported the use of MEL as a promising therapeutic agent for DCI, in which the underlying mechanism may be associated with gut microbiome and metabolomics regulation.}, }
@article {pmid39640432, year = {2024}, author = {Retzinger, AC and Retzinger, GS}, title = {The Acari Hypothesis, VI: human sebum and the cutaneous microbiome in allergy and in lipid homeostasis.}, journal = {Frontiers in allergy}, volume = {5}, number = {}, pages = {1478279}, pmid = {39640432}, issn = {2673-6101}, abstract = {The Acari Hypothesis posits that acarians, i.e., mites and ticks, are causative agents of IgE-mediated conditions. This report further develops The Hypothesis, providing rationale for the childhood predilection of allergy. In short, Malassezia, a fungus native to human skin and utterly dependent on sebaceous lipids, prevents allergy by deterring acarians. Because sebum output is limited before puberty, children are more prone to allergy than are adults. Competition for sebaceous lipids by Staphylococcus aureus influences not only Malassezia number-and, consequently, allergic predisposition-but also lipid homeostasis. The latter, in turn, contributes to dyslipidemia and associated conditions, e.g., the metabolic syndrome.}, }
@article {pmid39640399, year = {2024}, author = {Krause, SMB and Wang, R and Dohrmann, AB and Walz, M and Loewen, A and Tebbe, CC}, title = {Abundance and composition data of microbiomes in agricultural biogas plants of Lower Saxony, Germany, with variation in organic substrates, process parameters and nutrients.}, journal = {Data in brief}, volume = {57}, number = {}, pages = {111095}, pmid = {39640399}, issn = {2352-3409}, abstract = {This article presents high-throughput DNA sequencing, quantitative PCR data of microbial communities, and process parameters as recovered from eight biogas plants (BPs) located in Lower Saxony, Germany. Samples were collected from both the main (MD) and secondary digesters (SD). Additionally, for 4 BPs, samples were also obtained from the residue digester storage (RDS). Different BPs employed various types of substrates originating from cattle manure, chicken manure, pig manure, or renewable resources. Information on physico-chemical process parameters and concentrations of macro- and micro-nutrients in the BPs is provided. Total DNA from all samples were extracted using a phenol-chloroform-based method. To determine the abundance of bacteria and archaea, their 16S rRNA genes were quantified by real-time PCR (qPCR), and to characterize their community composition, paired-end DNA sequence reads were generated from PCR amplicons with Illumina MiSeq. All statistical analyses were performed in R to explore the microbial diversity, abundance, and community structure among different BPs and digesters (MD, SD, RDS). The presence and distribution of the major bacterial and archaeal phyla indicated for each BP unique and diverse microbial communities with typically higher bacterial than archaeal abundances.}, }
@article {pmid39640398, year = {2024}, author = {Kim, J and Nam, KH and Lee, JW and Chun, SJ}, title = {Whole genome sequence data of Galbitalea sp. strain isolated from gut of Spodoptera litura (Lepidoptera: Noctuidae) in South Korea.}, journal = {Data in brief}, volume = {57}, number = {}, pages = {111127}, pmid = {39640398}, issn = {2352-3409}, abstract = {Spodoptera litura (Lepidoptera: Noctuidae), commonly referred to as the cotton leafworm, is a widespread herbivorous pest found in both tropical and temperate regions. We isolated a novel bacterium, Galbitalea sp. and performed whole genome sequencing using the Illumina HiSeq X. Strain SE-J8 is a novel GC-rich bacterium isolated from the gut of S. litura in South Korea. The genome consists of 53 contigs with a total size of 3,332,109 bp, an N50 of 117,772 bp, and a GC% of 71.5 %. The annotation predicted a total of 3144 protein-coding genes and 55 RNA genes, which were classified under 230 subsystems. One third of the subsystems was predominantly associated with the metabolism of proteins, amino acids, and their derivatives. The strain has been deposited in the Korean Culture Center of Microorganisms (KCCM) under the accession number KCCM 43469, and the Japan Collection of Microorganisms (JCM) under the accession number JCM 36272. The draft genome sequence data have been submitted to the National Center for Biotechnology Information (NCBI) (Bioproject ID Accession Number: PRJNA983434; Biosample ID Accession Number: SAMN35725676; GenBank: GCA_030345695.1; https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_030345695.1/).}, }
@article {pmid39640340, year = {2024}, author = {Ma, BDY and Chan, TYH and Lo, BWY}, title = {Unveiling the hidden culprit: How the brain-gut axis fuels neuroinflammation in ischemic stroke.}, journal = {Surgical neurology international}, volume = {15}, number = {}, pages = {394}, pmid = {39640340}, issn = {2229-5097}, abstract = {BACKGROUND: The brain-gut axis represents a bidirectional communication network between the gut microbiome and the central nervous system that plays an important role in homeostasis. Compelling evidence now confirms that ischemic stroke disrupts this delicate balance by inducing gut dysbiosis.<br><br>METHODS: A comprehensive literature search was performed in PubMed, Web of Science, and Google Scholar for articles published between January 2000 and January 2023 using relevant keywords. Studies were limited to English and included original studies, literature, and systematic reviewers from peer-reviewed journals which discussed gut microbiota composition in models/subjects with ischemic stroke or assessed stroke impact on gut microbiota. Comments, meeting abstracts, and case reports were excluded. From the 80 relevant articles, we summarized key findings related to gut microbiota changes after stroke and their association with stroke outcomes.<br><br>RESULTS: Emerging preclinical evidence underscores the pivotal role of the gut microbiome in glial cell development and function. Germ-free models exhibit compromised microglial activation and impaired cellular debris clearance, exacerbating tissue damage following ischemic stroke. Targeted interventions, including prebiotics, probiotics, and fecal microbiota transplantation, have demonstrated efficacy in rescuing glial phenotypes in preclinical stroke models. Beyond its local effects, the gut microbiome significantly influences systemic immunity. Ischemic stroke polarizes pro-inflammatory phenotypes of neutrophils and T cells, amplifying neurovascular inflammation. Microbiota manipulation modulates leukocyte trafficking and metabolic signaling, offering potential avenues to mitigate infarct pathology.<br><br>CONCLUSION: Our review demonstrates that in preclinical stroke models, modulating the lipopolysaccharide, short-chain fatty acid, and trimethylamine N-oxide pathways through the gut-brain axis reduces infarct sizes and edema and improves functional recovery after ischemic stroke. Further exploration of this important axis may unveil additional adjunctive stroke therapies by elucidating the complex interplay between the microbiome and the brain. Rigorously controlled clinical studies are now warranted to translate these promising preclinical findings and investigate whether manipulating the microbiome-brain relationship can help improve outcomes for stroke patients. Overall, continued research on the gut-brain axis holds exciting possibilities for developing novel treatment strategies that may enhance recovery after stroke.}, }
@article {pmid39639864, year = {2024}, author = {Huang, L and Jiang, C and Yan, M and Wan, W and Li, S and Xiang, Z and Wu, J}, title = {The oral-gut microbiome axis in breast cancer: from basic research to therapeutic applications.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1413266}, pmid = {39639864}, issn = {2235-2988}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Breast Neoplasms/microbiology/therapy ; Female ; *Mouth/microbiology ; Carcinogenesis ; Animals ; }, abstract = {As a complicated and heterogeneous condition, breast cancer (BC) has posed a tremendous public health challenge across the world. Recent studies have uncovered the crucial effect of human microbiota on various perspectives of health and disease, which include cancer. The oral-gut microbiome axis, particularly, have been implicated in the occurrence and development of colorectal cancer through their intricate interactions with host immune system and modulation of systemic inflammation. However, the research concerning the impact of oral-gut microbiome axis on BC remains scarce. This study focused on comprehensively reviewing and summarizing the latest ideas about the potential bidirectional relation of the gut with oral microbiota in BC, emphasizing their potential impact on tumorigenesis, treatment response, and overall patient outcomes. This review can reveal the prospect of tumor microecology and propose a novel viewpoint that the oral-gut microbiome axis can be a breakthrough point in future BC studies.}, }
@article {pmid39639405, year = {2024}, author = {Nechalová, L and Bielik, V and Hric, I and Babicová, M and Baranovičová, E and Grendár, M and Koška, J and Penesová, A}, title = {Gut microbiota and metabolic responses to a 12-week caloric restriction combined with strength and HIIT training in patients with obesity: a randomized trial.}, journal = {BMC sports science, medicine &amp; rehabilitation}, volume = {16}, number = {1}, pages = {239}, pmid = {39639405}, issn = {2052-1847}, support = {UK/213/2022//Grant mlad&#xfd;ch UK/ ; APVV-17-0099//Agent&#xfa;ra na Podporu V&#xfd;skumu a V&#xfd;voja/ ; VEGA 1/0260/21//Vedeck&#xe1; Grantov&#xe1; Agent&#xfa;ra M&#x160;VVa&#x160; SR a SAV/ ; VEGA 2/0129/20//Vedeck&#xe1; Grantov&#xe1; Agent&#xfa;ra M&#x160;VVa&#x160; SR a SAV/ ; }, abstract = {BACKGROUND: Nowadays, obesity has become a major health issue. In addition to negatively affecting body composition and metabolic health, recent evidence shows unfavorable shifts in gut microbiota in individuals with obesity. However, the effects of weight loss on gut microbes and metabolites remain controversial. Therefore, the purpose of this study was to investigate the effects of a 12-week program on gut microbiota and metabolic health in patients with obesity.<br><br>METHODS: We conducted a controlled trial in 23 male and female patients with obesity. Twelve participants completed a 12-week program of caloric restriction combined with strength and HIIT training (INT, pre-BMI 37.33&#x2009;&#xb1;&#x2009;6.57&#xa0;kg/m[2]), and eleven participants were designated as non-intervention controls (pre-BMI 38.65&#x2009;&#xb1;&#x2009;8.07&#xa0;kg/m[2]). Metagenomic sequencing of the V3-V4 region of the 16S rDNA gene from fecal samples allowed for gut microbiota classification. Nuclear magnetic resonance spectroscopy characterized selected serum and fecal metabolite concentrations.<br><br>RESULTS: Within INT, we observed a significant improvement in body composition; a significant decrease in liver enzymes (AST, ALT, and GMT); a significant increase in the relative abundance of the commensal bacteria (e.g., Akkermansia muciniphila,&#xa0;Parabacteroides merdae, and Phocaeicola vulgatus); and a significant decrease in the relative abundance of SCFA-producing bacteria (e.g., the genera Butyrivibrio, Coprococcus, and Blautia). In addition, significant correlations were found between gut microbes, body composition, metabolic health biomarkers, and SCFAs. Notably, the Random Forest Machine Learning analysis identified predictors (Butyrivibrio fibrisolvens, Blautia caecimuris, Coprococcus comes, and waist circumference) with a moderate ability to discriminate between INT subjects pre- and post-intervention.<br><br>CONCLUSIONS: Our results indicate that a 12-week caloric restriction combined with strength and HIIT training positively influences body composition, metabolic health biomarkers, gut microbiota, and microbial metabolites, demonstrating significant correlations among these variables. We observed a significant increase in the relative abundance of bacteria linked to obesity, e.g., Akkermansia muciniphila. Additionally, our study contributes to the ongoing debate about the role of SCFAs in obesity, as we observed a significant decrease in SCFA producers after a 12-week program.<br><br>TRIAL REGISTRATION: The trial was registered on [05/12/2014] with ClinicalTrials.gov (No: NCT02325804).}, }
@article {pmid39639386, year = {2024}, author = {Griffin, TM and Lopes, EBP and Cortassa, D and Batushansky, A and Jeffries, MA and Makosa, D and Jopkiewicz, A and Mehta-D'souza, P and Komaravolu, RK and Kinter, MT}, title = {Sexually dimorphic metabolic effects of a high fat diet on knee osteoarthritis in mice.}, journal = {Biology of sex differences}, volume = {15}, number = {1}, pages = {103}, pmid = {39639386}, issn = {2042-6410}, support = {3R01AG049058-03S1//NIH Office of Research on Women's Health/ ; R24GM137786, P20GM103447, P30GM114731/GM/NIGMS NIH HHS/United States ; I01BX004666, I01BX004882, BX006046, CX002494//U.S. Department of Veterans Affairs/ ; n/a//Oklahoma Medical Research Foundation/ ; R33AR078075, R01AR076440/AR/NIAMS NIH HHS/United States ; }, mesh = {Animals ; *Diet, High-Fat/adverse effects ; Male ; Female ; *Osteoarthritis, Knee/metabolism/pathology/etiology ; *Sex Characteristics ; *Mice, Inbred C57BL ; Obesity/metabolism ; Mice ; Insulin Resistance ; Cartilage, Articular/metabolism/pathology ; }, abstract = {BACKGROUND: Women have a higher risk of developing osteoarthritis (OA) than men, including with obesity. To better understand this disparity, we investigated sex differences in metabolic and inflammatory factors associated with OA using a diet-induced mouse model of obesity. We hypothesized that 20 weeks of high-fat diet (HFD) would induce sexually dimorphic changes in both systemic and local risk factors of knee OA.<br><br>METHODS: Male and female C57BL/6J mice were fed Chow or HFD from 6 to 26 weeks of age (n&#x2009;=&#x2009;12 per diet and sex). We performed broad metabolic phenotyping, 16&#xa0;S gut microbiome analysis, targeted gene expression analysis of synovium-infrapatellar fat tissue, targeted gene expression and proteomic analysis of articular cartilage, chondrocyte metabolic profiling, and OA histopathology. Two-way ANOVA statistics were utilized to determine the contribution of sex and diet and their interaction on outcomes.<br><br>RESULTS: Mice fed HFD weighed 1.76-fold (p&#x2009;<&#x2009;0.0001) and 1.60-fold (p&#x2009;<&#x2009;0.0001) more than male and female Chow cohorts, respectively, with both sexes reaching similar body fat levels (male: 43.9 &#xb1; 2.2%; female: 44.1 &#xb1; 3.8%). HFD caused greater cartilage pathology (p&#x2009;<&#x2009;0.024) and synovial hyperplasia (p&#x2009;<&#x2009;0.038) versus Chow in both sexes. Cartilage pathology was greater in male versus female mice (p&#x2009;=&#x2009;0.048), and only male mice developed osteophytes with HFD (p&#x2009;=&#x2009;0.044). Both sexes exhibited metabolic inflexibility on HFD, but only male mice developed glucose intolerance (p&#x2009;<&#x2009;0.0001), fatty liver (p&#x2009;<&#x2009;0.0001), and elevated serum amylase (p&#x2009;<&#x2009;0.0001) with HFD versus Chow. HFD treatment caused sex-dependent differences in gut microbiota beta diversity (p&#x2009;=&#x2009;0.01) and alteration in specific microbiome clades, such as a HFD-dependent reduction in abundance of Bifidobacterium only in male mice. In knee synovium and infrapatellar fat tissue, HFD upregulated the expression of pro-inflammatory and pro-fibrotic genes predominantly in female mice. In cartilage, lipid metabolism proteins were more abundant with HFD in male mice, whereas proteins involved in glycolysis/gluconeogenesis and biosynthesis of amino acids were greater in cartilage of female mice. Sex-dependent metabolic differences were observed in cartilage from young, healthy mice prior to pubertal maturation, but not in primary juvenile chondrocytes studied in vitro.<br><br>CONCLUSIONS: HFD induced numerous sex differences in metabolic and inflammatory outcomes, especially in joint tissues, suggesting that sex-specific cellular processes are involved during development of early-stage OA with obesity.}, }
@article {pmid39639355, year = {2024}, author = {Benga, L and Rehm, A and Gougoula, C and Westhoff, P and Wachtmeister, T and Benten, WPM and Engelhardt, E and Weber, APM and Köhrer, K and Sager, M and Janssen, S}, title = {The host genotype actively shapes its microbiome across generations in laboratory mice.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {256}, pmid = {39639355}, issn = {2049-2618}, mesh = {Animals ; Mice ; Female ; *Genotype ; *Mice, Inbred BALB C ; *Mice, Inbred C57BL ; *Microbiota ; Male ; Maternal Inheritance ; Embryo, Mammalian/microbiology ; Host Microbial Interactions ; Pregnancy ; }, abstract = {BACKGROUND: The microbiome greatly affects health and wellbeing. Evolutionarily, it is doubtful that a host would rely on chance alone to pass on microbial colonization to its offspring. However, the literature currently offers only limited evidence regarding two alternative hypotheses: active microbial shaping by host genetic factors or transmission of a microbial maternal legacy.<br><br>RESULTS: To further dissect the influence of host genetics and maternal inheritance, we collected two-cell stage embryos from two representative wild types, C57BL6/J and BALB/c, and transferred a mixture of both genotype embryos into hybrid recipient mice to be inoculated by an identical microbiome at birth.<br><br>CONCLUSIONS: Observing the offspring for six generations unequivocally emphasizes the impact of host genetic factors over maternal legacy in constant environments, akin to murine laboratory experiments. Interestingly, maternal legacy solely controlled the microbiome in the first offspring generation. However, current evidence supporting maternal legacy has not extended beyond this initial generation, resolving the aforementioned debate. Video Abstract.}, }
@article {pmid39639333, year = {2024}, author = {Granato, A and Renwick, S and Yau, C and Kong, T and Daigneault, MC and Knip, M and ,  and Allen-Vercoe, E and Danska, JS}, title = {Analysis of early childhood intestinal microbial dynamics in a continuous-flow bioreactor.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {255}, pmid = {39639333}, issn = {2049-2618}, mesh = {Humans ; *Gastrointestinal Microbiome ; Infant ; *Feces/microbiology ; *Bioreactors/microbiology ; *Bacteria/classification/isolation &amp; purification/genetics ; Child, Preschool ; RNA, Ribosomal, 16S/genetics ; Female ; Male ; }, abstract = {BACKGROUND: The human gut microbiota is inoculated at birth and undergoes a process of assembly and diversification during the first few years of life. Studies in mice and humans have revealed associations between the early-life gut microbiome and future susceptibility to immune and metabolic diseases. To resolve microbe and host contributing factors to early-life development and to disease states requires experimental platforms that support reproducible, longitudinal, and high-content analyses.<br><br>RESULTS: Here, we deployed a continuous single-stage chemostat culture model of the human distal gut to study gut microbiota from 18- to 24-month-old children integrating both culture-dependent and -independent methods. Chemostat cultures recapitulated multiple aspects of the fecal microbial ecosystem enabling investigation of relationships between bacterial strains and metabolic function, as well as a resource from which we isolated and curated a diverse library of early life bacterial strains.<br><br>CONCLUSIONS: We report the reproducible, longitudinal dynamics of early-life bacterial communities cultured in an advanced model of the human gut providing an experimental approach and a characterized bacterial resource to support future investigations of the human gut microbiota in early childhood.}, }
@article {pmid39639304, year = {2024}, author = {Ma, ZS}, title = {Species specificity and specificity diversity (SSD) framework: a novel method for detecting the unique and enriched species associated with disease by leveraging the microbiome heterogeneity.}, journal = {BMC biology}, volume = {22}, number = {1}, pages = {283}, pmid = {39639304}, issn = {1741-7007}, mesh = {*Species Specificity ; *Microbiota ; Humans ; Biodiversity ; }, abstract = {BACKGROUND: Differentiating the microbiome changes associated with diseases is challenging but critically important. Majority of existing efforts have been focused on a community level, but the discerning power of community or holistic metrics such as diversity analysis seems limited. This prompts many researchers to believe that the promise should be downward to species or even strain level-effectively and efficiently identifying unique or enriched species in diseased microbiomes with statistical rigor. Nevertheless, virtually, all species-level approaches such as differential abundance and differential network analysis methods exclusively rely on species abundances without considering species distribution information, while it can be said that distribution is equally, if not more, important than abundance in shaping the spatiotemporal heterogeneity of community compositions.<br><br>RESULTS: Here, we fill the gap by developing a novel framework-species specificity and specificity diversity (SSD)-that synthesizes both abundance and distribution information to differentiate microbiomes, at both species and community scales, under different environmental gradients such as the healthy and diseased treatments. The proposed SSD framework consists of three essential elements. The first is species specificity (SS), a concept that reincarnates the traditional specialist-generalist continuum and is defined by Mariadassou et al. (Ecol Lett 18:974-82, 2015). The SS synthesizes a species' local prevalence (distribution) and global abundance information and attaches specificity measure to each species in a specific habitat (e.g., healthy or diseased treatment). The second element is a new concept to introduce here, the (species) specificity diversity (SD), which is inspired by traditional species (abundance) diversity in community ecology and measures the diversity of specificity (a proxy for metacommunity heterogeneity, essentially) with Renyi's entropy. The third element is a pair of statistical tests based on the principle of permutation tests.<br><br>CONCLUSIONS: The SSD framework can (i) identify and catalogue lists of unique species (US), significantly enriched species (ES) in each treatment based on SS and specificity permutation (SP) test and (ii) measure the holistic differences between assemblages (or treatments) based on SD and specificity diversity permutation (SDP) test. Both capacities can be enabling technologies for general comparative microbiome research including risk assessment, diagnosis, and treatment of microbiome-associated diseases.}, }
@article {pmid39639265, year = {2024}, author = {Ma, ZS}, title = {Revisiting microgenderome: detecting and cataloguing sexually unique and enriched species in human microbiomes.}, journal = {BMC biology}, volume = {22}, number = {1}, pages = {284}, pmid = {39639265}, issn = {1741-7007}, mesh = {Humans ; Female ; Male ; *Microbiota ; *Sex Characteristics ; Species Specificity ; }, abstract = {BACKGROUND: Microgenderome or arguably more accurately microsexome refers to studies on sexual dimorphism of human microbiomes aimed at investigating bidirectional interactions between human microbiomes, sex hormones, and immune systems. It is important because of its implications to disease susceptibility and therapy, in which men and women demonstrate divergence in many diseases especially autoimmune diseases. In a previous report [1], we presented analyses of several key ecological aspects of microgenderome by leveraging the large datasets of the HMP (human microbiome project) but failed to offer species-level composition differences such as sexually unique species (US) and enriched species (ES). Existing approaches, for such tasks, including differential species relative abundance analysis and differential network analysis, possess certain limitations given that virtually all rely on species abundance alone or are univariate, while ignoring species distribution information across samples. Obviously, it is both species abundance and distribution that shape/drive the structure and dynamics of human microbiomes, and both should be equally responsible for the universal heterogeneity of microbiomes including the sexual dimorphism.<br><br>RESULTS: Here, we fill the gap by taking advantages of a recently developed computational algorithm, species specificity, and specificity diversity (SSD) framework (refer to the companion article) to reanalyze the HMP and complementary seminovaginal microbiome datasets. The SSD framework can randomly search and catalogue the sexually specific unique/enriched species with statistical rigor, guided by species specificity (a synthetic metric of abundance and distribution) and specificity diversity (SD). The SSD framework reveals that men seem to have more unique species than women in their gut and reproductive system microbiomes, but women seem to have more unique species than men in the airway, oral, and skin microbiomes, which is likely due to sexual dimorphism in the hormone and immune systems. We further investigate co-dependency and heterogeneity of those sexually unique/enriched species across 15 body sites, with core/periphery network analyses.<br><br>CONCLUSIONS: This study not only produced sexually unique/enriched species in the human microbiomes and analyzed their codependency and heterogeneity but also further validated the robustness of the SSD framework presented in the companion article, by performing all negative control tests based on the HMP gut microbiome samples.}, }
@article {pmid39639142, year = {2024}, author = {Jones, S}, title = {Microbiome interventions for children raise the ethical stakes.}, journal = {Nature}, volume = {}, number = {}, pages = {}, pmid = {39639142}, issn = {1476-4687}, }
@article {pmid39639122, year = {2024}, author = {Kozma Kim, Z and Park, YS and Yang, TJ and Kim, H and Lee, YH}, title = {Root microbiome of Panax ginseng in comparison with three other medicinal plants in the families of Araliaceae and Apiaceae.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {30381}, pmid = {39639122}, issn = {2045-2322}, support = {2018R1A5A1023599, 2021M3H9A1096935, and RS-2023-00275965, and 2022R1C1C2002739//National Research Foundation of Korea/ ; 2018R1A5A1023599, 2021M3H9A1096935, and RS-2023-00275965, and 2022R1C1C2002739//National Research Foundation of Korea/ ; 2018R1A5A1023599, 2021M3H9A1096935, and RS-2023-00275965, and 2022R1C1C2002739//National Research Foundation of Korea/ ; 2018R1A5A1023599, 2021M3H9A1096935, and RS-2023-00275965, and 2022R1C1C2002739//National Research Foundation of Korea/ ; 2018R1A5A1023599, 2021M3H9A1096935, and RS-2023-00275965, and 2022R1C1C2002739//National Research Foundation of Korea/ ; }, mesh = {*Plant Roots/microbiology ; *Plants, Medicinal/microbiology ; *Panax/microbiology ; *Microbiota/genetics ; Apiaceae/microbiology ; Phylogeny ; Bacteria/genetics/classification ; Fungi/genetics/classification ; Endophytes/genetics ; Biodiversity ; }, abstract = {The intricate interplay between endophytic microorganisms and plants in the upkeep of biodiversity, the stability of communities, and the operation of ecosystems needs to be more adequately extensive. Although root-associated microbial communities of plants have been revealed for the last decade, the understanding of bacterial and fungal communities associated with the roots of medicinal plants remains elusive. To highlight the importance of Panax ginseng Meyer (PG) in our research, we investigated the root endophytic bacterial and fungal communities of Panax ginseng Meyer (PG), alongside Aralia cordata (AC), Angelica gigas (AG), and Peucedanum japonicum (PJ), utilizing amplicon-based community profiling and advanced bioinformatic methodologies. The study aimed to investigate the root-endophytic microbiota of ginseng and three other medicinal plants and identify similarities in microbiome composition across different plant species and families. Results revealed that root-endophytic bacterial and fungal communities were influenced by plant species and phylogenetic differences at the family level. Differential abundance tests and random forest models showed microbial features within the same plant family. PG had a distinctive microbial profile with significant B1653_o_Enterobacterales and F8_o_Helotiales. PG had a core microbiome, B10_Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium, and a more evenly distributed microbial network compared to AG, PJ, and AC. Our research reveals the intricate endophytic microbial communities within the roots of medicinal plants, pinpointing specific taxa that may be pivotal to their medicinal qualities and overall plant health. These insights carry notable implications for future studies, particularly those focused on the endophytes of PG and their secondary metabolites, as they deepen our understanding of plant-microbe interactions and their role in enhancing the plants' therapeutic potential.}, }
@article {pmid39638782, year = {2024}, author = {Rosario, SR and Long, MD and Chilakapati, S and Gomez, EC and Battaglia, S and Singh, PK and Wang, J and Wang, K and Attwood, K and Hess, SM and McGray, AJR and Odunsi, K and Segal, BH and Paragh, G and Liu, S and Wargo, JA and Zsiros, E}, title = {Integrative multi-omics analysis uncovers tumor-immune-gut axis influencing immunotherapy outcomes in ovarian cancer.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {10609}, pmid = {39638782}, issn = {2041-1723}, support = {U24 CA232979-01S5//U.S. Department of Health &amp; Human Services | NIH | National Cancer Institute (NCI)/ ; R25 CA203650/CA/NCI NIH HHS/United States ; }, mesh = {Humans ; Female ; *Ovarian Neoplasms/immunology/therapy/drug therapy ; *Immunotherapy/methods ; *Gastrointestinal Microbiome/drug effects ; *Bevacizumab/therapeutic use ; Middle Aged ; *Antibodies, Monoclonal, Humanized/therapeutic use ; Aged ; Cyclophosphamide/therapeutic use ; Progression-Free Survival ; Adult ; Antineoplastic Combined Chemotherapy Protocols/therapeutic use ; Neoplasm Recurrence, Local/immunology ; Quality of Life ; Treatment Outcome ; Multiomics ; }, abstract = {Recurrent ovarian cancer patients, especially those resistant to platinum, lack effective curative treatments. To address this, we conducted a phase 2 clinical trial (NCT02853318) combining pembrolizumab with bevacizumab, to increase T cell infiltration into the tumor, and oral cyclophosphamide, to reduce the number of regulatory T cells. The trial accrued 40 heavily pretreated recurrent ovarian cancer patients. The primary endpoint, progression free survival, was extended to a median of 10.2 months. The secondary endpoints demonstrated an objective response rate of 47.5%, and disease control in 30% of patients for over a year while maintaining a good quality of life. We performed comprehensive molecular, immune, microbiome, and metabolic profiling on samples of trial patients. Here, we show increased T and B cell clusters and distinct microbial patterns with amino acid and lipid metabolism are linked to exceptional clinical responses. This study suggests the immune milieu and host-microbiome can be leveraged to improve antitumor response in future immunotherapy trials.}, }
@article {pmid39638178, year = {2024}, author = {Gong, JZ and Huang, JJ and Pan, M and Jin, QW and Fan, YM and Shi, WQ and Huang, SY}, title = {Cathepsin L of Fasciola hepatica meliorates colitis by altering the gut microbiome and inflammatory macrophages.}, journal = {International journal of biological macromolecules}, volume = {}, number = {}, pages = {138270}, doi = {10.1016/j.ijbiomac.2024.138270}, pmid = {39638178}, issn = {1879-0003}, abstract = {Helminths can relieve the development of autoimmune diseases and inflammatory diseases, by inducing anti-inflammatory innate immune responses. Here, we report that CL7, a Cathepsin L protein secreted by Fasciola hepatica, inhibited the activation of the NF-κB and MAPK signaling resulting in reduced secretion of inflammatory mediators in macrophages. Furthermore，we found that CL7 could prevent dextran sulfate sodium (DSS) induced ulcerative colitis (UC). CL7 and ESP administration restored DSS-induced body weight loss, colon shortening, and injury, significantly decreased the disease activity index (DAI) and alleviated colonic epithelial injury. CL7 noticeably suppressed the DSS-triggered M1 polarization upregulation and inhibited IL-17 and other inflammatory mediator production in UC mice. Additionally, CL7 ameliorated DSS-induced microbiota dysbiosis. Results of Antibiotic treatment (ABX) and fecal microbial transplants (FMT) suggested that the gut microbiota played an important role in CL7 treating UC. These findings propose that CL7 could be a promising strategy for UC therapy.}, }
@article {pmid39638096, year = {2024}, author = {Costa, CM and Pedrosa, SS and Kirkland, JL and Reis, F and Madureira, R}, title = {The senotherapeutic potential of phytochemicals for age-related intestinal disease.}, journal = {Ageing research reviews}, volume = {}, number = {}, pages = {102619}, doi = {10.1016/j.arr.2024.102619}, pmid = {39638096}, issn = {1872-9649}, abstract = {During the last few decades, life expectancy has increased worldwide along with the prevalence of several age-related diseases. Among aging pathways, cellular senescence and chronic inflammation (or "inflammaging") appear to be connected to gut homeostasis and dysbiosis of the microbiome. Cellular senescence is a state of essentially irreversible cell cycle arrest that occurs in response to stress. Although senescent cells (SC) remain metabolically active, they do not proliferate and can secrete inflammatory and other factors comprising the senescence-associated secretory phenotype (SASP). Accumulation of SCs has been linked to onset of several age-related diseases, in the brain, bones, the gastrointestinal tract, and other organs and tissues. The gut microbiome undergoes substantial changes with aging and is tightly interconnected with either successful (healthy) aging or disease. Senotherapeutic drugs are compounds that can clear senescent cells or modulate the release of SASP and hence attenuate the impact of the senescence-associated pro-inflammatory state. Phytochemicals, phenolic compounds and terpenes, which have antioxidant and anti-inflammatory activities, could also be senotherapeutic given their ability to act upon senescence-linked cellular pathways. The aim of this review is to dissect links among the gut microbiome, cellular senescence, inflammaging, and disease, as well as to explore phytochemicals as potential senotherapeutics, focusing on their interactions with gut microbiota. Coordinated targeting of these inter-related processes might unveil new strategies for promoting healthy aging.}, }
@article {pmid39637989, year = {2024}, author = {Raval, H and Bhattacharya, S and Bhirud, D and Sangave, PC and Gupta, GL and Paraskar, G and Jha, M and Sharma, S and Belemkar, S and Kumar, D and Maheshwari, R}, title = {Fabrication of lactoferrin-chitosan-etoposide nanoparticles with melatonin via carbodiimide coupling: In-vitro &amp; in-vivo evaluation for colon cancer.}, journal = {Journal of controlled release : official journal of the Controlled Release Society}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jconrel.2024.11.077}, pmid = {39637989}, issn = {1873-4995}, abstract = {This study presents the development of melatonin-coated lactoferrin-chitosan nanoparticles (ETP-CS-LF-MLT-NPs) using ionic gelation and carbodiimide coupling for colorectal cancer treatment. The nanoparticles were characterized by an average size of 208.7 ± 1.25 nm, a zeta potential of 30.77 ± 1.21 mV, and 82.45 % drug encapsulation efficiency. In vitro drug release studies showed sustained, pH-responsive release, with 98.68 ± 4.12 % released at pH 5.5 over 24 h. The nanoparticles exhibited significant cytotoxicity in HCT116 cells (IC50 = 15.32 μg/mL), inducing ROS generation, apoptosis, and G2/M cell cycle arrest, with notable downregulation of BCL2 gene expression. Enhanced cellular uptake due to lactoferrin targeting improved therapeutic efficacy. In In vivo studies, the nanoparticles demonstrated significant tumor reduction and selective colon accumulation in a DMH-induced colorectal cancer rat model, along with improved pharmacokinetics, showing extended plasma circulation and bioavailability compared to free etoposide. Biocompatibility assays, including hemolysis (<1 %), platelet aggregation, and HET-CAM tests, confirmed the safety profiling of the prepared nanoparticles. The nanoparticles also inhibited Proteus mirabilis (ZOI = 1.9 cm) and exhibited promising effects on the gut microbiome of treated animals. Altogether, ETP-CS-LF-MLT-NPs hold great potential for targeted colorectal cancer therapy, improving drug delivery, tumor targeting, bioavailability, and reducing systemic toxicity.}, }
@article {pmid39637857, year = {2024}, author = {Vaher, K and Cabez, MB and Parga, PL and Binkowska, J and van Beveren, GJ and Odendaal, ML and Sullivan, G and Stoye, DQ and Corrigan, A and Quigley, AJ and Thrippleton, MJ and Bastin, ME and Bogaert, D and Boardman, JP}, title = {The neonatal gut microbiota: A role in the encephalopathy of prematurity.}, journal = {Cell reports. Medicine}, volume = {}, number = {}, pages = {101845}, doi = {10.1016/j.xcrm.2024.101845}, pmid = {39637857}, issn = {2666-3791}, abstract = {Preterm birth correlates with brain dysmaturation and neurocognitive impairment. The gut microbiome associates with behavioral outcomes in typical development, but its relationship with neurodevelopment in preterm infants is unknown. We characterize fecal microbiome in a cohort of 147 neonates enriched for very preterm birth using 16S-based and shotgun metagenomic sequencing. Delivery mode strongly correlates with the preterm microbiome shortly after birth. Low birth gestational age, infant sex assigned at birth, and antibiotics associate with microbiome composition at neonatal intensive care unit discharge. We integrate these data with term-equivalent structural and diffusion brain MRI. Bacterial community composition associates with MRI features of encephalopathy of prematurity. Particularly, abundances of Escherichia coli and Klebsiella spp. correlate with microstructural parameters in deep and cortical gray matter. Metagenome functional capacity analyses suggest that these bacteria may interact with brain microstructure via tryptophan and propionate metabolism. This study indicates that the gut microbiome associates with brain development following preterm birth.}, }
@article {pmid39637856, year = {2024}, author = {Caty, SN and Alvarez-Buylla, A and Vasek, C and Tapia, EE and Martin, NA and McLaughlin, T and Golde, CL and Weber, PK and Mayali, X and Coloma, LA and Morris, MM and O'Connell, LA}, title = {Alkaloids are associated with increased microbial diversity and metabolic function in poison frogs.}, journal = {Current biology : CB}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cub.2024.10.069}, pmid = {39637856}, issn = {1879-0445}, abstract = {Shifts in host-associated microbiomes can impact both host and microbes.[1][,][2][,][3][,][4][,][5][,][6] It is of interest to understand how perturbations, like the introduction of exogenous chemicals,[7][,][8][,][9][,][10][,][11][,][12][,][13] impact microbiomes. In poison frogs (family Dendrobatidae), the skin microbiome is exposed to alkaloids that the frogs sequester for defense.[14][,][15][,][16][,][17][,][18][,][19] These alkaloids are antimicrobial[20][,][21][,][22]; however, their effect on the frogs' skin microbiome is unknown. To test this, we characterized microbial communities from field-collected dendrobatid frogs. Then, we conducted a laboratory experiment to monitor the effect of the alkaloid decahydroquinoline (DHQ) on the microbiome of two frog species with contrasting alkaloid loads in nature. In both datasets, we found that alkaloid-exposed microbiomes were more phylogenetically diverse, with an increase in diversity among rare taxa. To better understand the isolate-specific response to alkaloids, we cultured microbial isolates from poison frog skin and found that many isolates exhibited enhanced growth or were not impacted by the addition of DHQ. To further explore the microbial response to alkaloids, we sequenced the metagenomes from high- and low-alkaloid frogs and observed a greater diversity of genes associated with nitrogen and carbon metabolism in high-alkaloid frogs. From these data, we hypothesized that some strains may metabolize the alkaloids. We used stable isotope tracing coupled to nanoSIMS (nanoscale secondary ion mass spectrometry), which supported the idea that some of these isolates are able to metabolize DHQ. Together, these data suggest that poison frog alkaloids open new niches for skin-associated microbes with specific adaptations, such as alkaloid metabolism, that enable survival in this environment.}, }
@article {pmid39637140, year = {2024}, author = {Cheibchalard, T and Leelahavanichkul, A and Chatthanathon, P and Klankeo, P and Hirankarn, N and Somboonna, N}, title = {Fungal microbiome in gut of systemic lupus erythematosus (SLE)-prone mice (pristane and FCGRIIb deficiency), a possible impact of fungi in lupus.}, journal = {PloS one}, volume = {19}, number = {12}, pages = {e0314662}, doi = {10.1371/journal.pone.0314662}, pmid = {39637140}, issn = {1932-6203}, mesh = {Animals ; *Lupus Erythematosus, Systemic/microbiology/immunology ; Mice ; *Gastrointestinal Microbiome ; *Receptors, IgG/genetics/deficiency ; Mycobiome ; Disease Models, Animal ; Terpenes ; Fungi/genetics/isolation &amp; purification ; Female ; Feces/microbiology ; Mice, Inbred C57BL ; }, abstract = {The gut mycobiota (fungal microbiota) plays a crucial role in the immune system, potentially impacting autoimmune diseases such as systemic lupus erythematosus (SLE). Despite growing interest, data on intestinal fungi in SLE remain limited. This study thereby investigated the human-mimicked (mice) gut mycobiome and quantitative gut mycobiome analyses using universal fungal internal transcribed spacer 2 (ITS2) DNA next generation sequencing and real-time PCR, tracking time-series dynamics from preclinical to established SLE conditions in two SLE-prone mouse models. These models included pristane -induced mice, representing an environmental cause of SLE, and Fc gamma receptor RIIb (FcgRIIb) deficiency mice, representing a genetic factor. Fecal samples and different intestinal sections from mice aged 2-10 months were analyzed, including samples from 4-month-old and 11-month-old mice, which represented preclinical lupus (negative for anti-dsDNA) and established SLE conditions (positive for anti-dsDNA with proteinuria), respectively, alongside age-matched healthy controls. Results showed increased fungal diversity, specific changes in gut fungal species (i.e. increased Candida spp.), and an elevated Basidiomycota-to-Ascomycota (Basidiomycota/Ascomycota) ratio, which correlated with lupus activity in both lupus models. Linear discriminant analysis Effect Size (LEfSe; a possible representative organism) helped identify specific fungal difference between the lupus models. Our findings revealed that active lupus states may elevate gut fungal populations and alter fungal components in both the pristane and genetically susceptible SLE-prone mice, as indicated by mycobiota and quantitative mycobiota analyses. These changes could, in turn, influence disease activity. This research is essential for a deeper understand of the SLE-gut microbiome association, as the gut microbiome comprises both bacterial and fungal symbiosis. Manipulating fungal communities could present a potential therapeutic avenue for influencing disease outcomes in lupus. Further studies are crucial to clarify the direct role of gut fungi in lupus disease progression.}, }
@article {pmid39637086, year = {2024}, author = {Arellano-Hernández, HD and Montes-Carreto, LM and Guerrero, JA and Martinez-Romero, E}, title = {The fecal microbiota of the mouse-eared bat (Myotis velifer) with new records of microbial taxa for bats.}, journal = {PloS one}, volume = {19}, number = {12}, pages = {e0314847}, doi = {10.1371/journal.pone.0314847}, pmid = {39637086}, issn = {1932-6203}, mesh = {Animals ; *Chiroptera/microbiology ; *Feces/microbiology ; Female ; Male ; *RNA, Ribosomal, 16S/genetics ; Bacteria/classification/genetics/isolation &amp; purification ; Microbiota/genetics ; Mexico ; Phylogeny ; Gastrointestinal Microbiome/genetics ; }, abstract = {Studies on the fecal microbiome of wild animals reveal valuable information on the feeding habits of the host and the possible roles of bacteria in digestion. In this work we characterized the fecal microbiota of seven male and seven female Myotis velifer bats using the V3-V4 regions of the 16S rRNA gene. Fecal samples were collected at the El Salitre cave in Mexico. We obtained 81 amplicon sequence variants, identifying four phyla, 12 families and 14 genera for females and seven phyla, 21 families and 26 genera for males. The phylum Synergistota is reported for the first time in bats. The most abundant phyla were Pseudomonadota and Fusobacteriota. Male feces showed a greater taxonomic richness than those from females. This study revealed that the fecal microbiota of M. velifer had a unique and more diverse composition compared to the microbiota reported for other bats. We identified 24 families and two abundant genera Cetobacterium and Haematospirillum in both males and females. Cetobacterium may produce vitamin B12 that is not produced by animals and Haematospirillum, which has been reported as an emerging human pathogen, may produce non-volatile organic acids. These genera had not been previously reported in the bat microbiota.}, }
@article {pmid39637059, year = {2024}, author = {Richardson, EA and Garshong, R and Chen, K and Crossley, D and Mclean, BS and Wasserberg, G and Apperson, CS and Roe, RM and Ponnusamy, L}, title = {Orientia, Rickettsia, and the microbiome in rodent attached chiggers in North Carolina, USA.}, journal = {PloS one}, volume = {19}, number = {12}, pages = {e0311698}, doi = {10.1371/journal.pone.0311698}, pmid = {39637059}, issn = {1932-6203}, mesh = {Animals ; North Carolina ; *Microbiota/genetics ; *Rickettsia/genetics/isolation &amp; purification/classification ; *RNA, Ribosomal, 16S/genetics ; Trombiculidae/microbiology ; Rodentia/microbiology ; Phylogeny ; }, abstract = {Chiggers are larval mites that pose a significant health risk globally via the spread of scrub typhus. However, fundamental studies into the bacterial microbiome in North America have never been considered. In this investigation, chiggers were collected in the wild from two locally common rodent host species (i.e., Sigmodon hispidus and Peromyscus leucopus) in three different ecoregions of North Carolina (NC), United States to investigate the composition of their bacterial communities, including potential pathogens. DNA was extracted from the chiggers, and the V3-V4 regions of the bacterial 16S rRNA gene were sequenced using next-generation sequencing (NGS). Alpha diversity metrics revealed significant differences in bacterial diversity among different collection counties. Beta diversity metrics also revealed that bacterial communities across counties were significantly different, suggesting changes in the microbiome as the environment changed. Specifically, we saw that the two western NC collection counties had similar bacterial composition as did the two eastern collection counties. In addition, we found that the chigger microbiome bacterial diversity and composition differed between rodent host species. The 16S rRNA sequence reads were assigned to 64 phyla, 106 orders, 199 families, and 359 genera. The major bacterial phylum was Actinobacteria. The most abundant species were in the genera Corynebacterium, Propionibacterium, class ZB2, and Methylobacterium. Sequences derived from potential pathogens within the genera Orientia and Rickettsia were also detected. Our findings provide the first insights into the ecology of chigger microbiomes in the US. Further research is required to determine if the potential pathogens found detected in chiggers are a threat to humans and wildlife.}, }
@article {pmid39636804, year = {2024}, author = {Calderon, MS and Bustamante, DE and Perez, J and Fernandez-Güimac, SLJ and Mendoza, JE and Barboza, JI and Ayala, RY and Carrion, JV}, title = {Diversity and functional role of bacterial microbiota in spontaneous coffee fermentation in northern Peru using shotgun metagenomics.}, journal = {Journal of food science}, volume = {}, number = {}, pages = {}, doi = {10.1111/1750-3841.17583}, pmid = {39636804}, issn = {1750-3841}, support = {//Consejo Nacional de Ciencia, Tecnolog&#xed;a e Innovaci&#xf3;n Tecnol&#xf3;gica/ ; N&#xb0; 030-2018-FONDECYT-BM-IADT-MU//Peruvian CONCYTEC under the projects Metacaf&#xe9;/ ; N&#xb0; PE501081184-2022-PROCIENCIA//Metacaf&#xe9; 2.0/ ; //Vicerrectorado de Investigaci&#xf3;n (VRIN) de la UNTRM/ ; }, abstract = {Peru is the ninth-largest coffee producer and the largest organic coffee exporter worldwide. Specific modifications in the microbial consortia during fermentation control the flavor of coffee. It is still unclear how fermentation duration affects microbial communities. This study aimed to provide insights into the diversity and functional behavior of the bacterial microbiome during coffee fermentation in northern Peru using shotgun metagenomics. Accordingly, metagenomic DNA was extracted and sequenced from samples of the liquid fraction during the short fermentation process (SFP) in Amazonas (6 and 12 h) and long fermentation process (LFP) in Cajamarca (6, 12, 18, 24, and 36 h). Our findings indicate that common (e.g., Acetobacter, Lactobacillus, Leuconostoc, and Weissella) and unique (e.g., Acidiphilium and Methylobacterium) acid-tolerant bacteria from the SFP and LFP play crucial roles and have a positive impact on the sensory qualities of coffee. Specifically, the LFP from San Ignacio might be associated with the high sensory quality of coffee based on the release of catalytic, hydrolase, oxidoreductase, transferase, and transporter enzymes in the InterPro and KEGG profiles. Additionally, these bacterial microorganisms metabolize several compounds (e.g., isoleucine, betaine, galactose, tryptophan, arginine, and cobalamin) into volatile compounds, mainly in the LFP, enhancing the flavor and aroma of coffees. This characteristic suggests that the LFP has a stronger effect on coffee quality than does the SFP on the basis of bacterial diversity and functional prediction. These findings provide new perspectives on the potential biotechnological uses of autochthonous microorganisms to produce superior-quality coffee beans from northern Peru.}, }
@article {pmid39636749, year = {2024}, author = {Liu, L and Yin, T and Zhang, X and Sun, L and Yin, Y}, title = {Temporal and Spatial Variation of the Human Placental Microbiota During Pregnancy.}, journal = {American journal of reproductive immunology (New York, N.Y. : 1989)}, volume = {92}, number = {6}, pages = {e70023}, doi = {10.1111/aji.70023}, pmid = {39636749}, issn = {1600-0897}, support = {BK20231370//2023 Jiangsu Provincial Natural Science Foundation/ ; FYRC 202010//Jiangsu Maternal and Child Health Hospital/ ; PY2022044//Young Scholars Fostering Fund of the First Affiliated Hospital of Nanjing Medical University/ ; }, mesh = {Humans ; Pregnancy ; Female ; *Placenta/microbiology ; *Microbiota ; Adult ; Case-Control Studies ; Premature Birth/microbiology ; Bacteria/classification/genetics/isolation &amp; purification ; Streptococcus agalactiae/isolation &amp; purification ; }, abstract = {PROBLEM: Previously believed sterile, the placenta hosts distinct microbial species across various locations. This study aims to elucidate the temporal and spatial variations of placental microbiota throughout gestation, addressing gaps in current understanding.<br><br>METHOD OF STUDY: A case-control study at a single-center compared microbial profiles in pregnant women delivering preterm (<37&#xa0;weeks) or at term (>37&#xa0;weeks) across placental sites: basal plate, fetal membranes, and placental villous. Microbial abundance and diversity were evaluated using QIIME and the R package "Phyloseq," while Q-PCR with specific primers validated absolute abundance in samples.<br><br>RESULTS: We found no alteration in bacterial communities based on delivery mode across all samples. Q-PCR detected low-abundance bacteria, notably enriched in preterm samples, especially in early preterm cases. Throughout gestation, bacterial composition varied, with increasing levels of Proteobacteria and Firmicutes observed in the placenta. Significant differences in bacterial profiles were noted across locations and gestational stages, with Ralstonia insidiosa consistently present in the basal plate throughout gestation. Species-specific Q-PCR confirmed the presence of Ralstonia and revealed an inverse relationship between Streptococcus agalactiae and pregnancy progression.<br><br>CONCLUSIONS: The placenta hosts its own microbiome, with distinct profiles observed between term and preterm samples. Further research is needed to clarify the impact of bacterial dysbiosis on preterm birth and develop methods to distinguish pathological bacteria from the natural microbiome.}, }
@article {pmid39636254, year = {2024}, author = {Clare, C and Rutter, JW and Fedorec, AJH and Frank, S and Barnes, CP}, title = {Bacterial microcompartment utilization in the human commensal Escherichia coli Nissle 1917.}, journal = {Journal of bacteriology}, volume = {}, number = {}, pages = {e0026924}, doi = {10.1128/jb.00269-24}, pmid = {39636254}, issn = {1098-5530}, abstract = {UNLABELLED: Bacterial microcompartments (BMCs) are self-assembled protein structures often utilized by bacteria as a modular metabolic unit, enabling the catalysis and utilization of less common carbon and nitrogen sources within a self-contained compartment. The ethanolamine (EA) utilization (eut) BMC has been widely demonstrated in enteropathogens, such as Salmonella enterica, and current research is exploring its activity in the commensal species that populate the human gut. Escherichia coli Nissle 1917 (EcN) is a strong colonizer and probiotic in gut microbial communities and has been used extensively for microbiome engineering. In this study, the utilization of ethanolamine as a sole carbon source and the formation of the eut BMC in EcN were demonstrated through growth assays and visualization with transmission electron microscopy. Subsequently, flux balance analysis was used to further investigate the metabolic activity of this pathway. It was found that not only is the utilization of the eut BMC for the degradation of EA as a carbon source in EcN comparable with that of Salmonella enterica but also that ammonium is released into solution as a byproduct in EcN but not in S. enterica. Control of EA-dependent growth was demonstrated using different concentrations of the operon inducer, vitamin B12. We show that vitamin B12-dependent EA utilization as the sole carbon source enables growth in EcN, and demonstrate the concurrent formation of the BMC shell and inducible control of the eut operon.<br><br>IMPORTANCE: The human gut is a complex environment of different bacterial species, nutrient sources, and changing conditions that are essential for human health. An imbalance can allow for the emergence of opportunistic pathogens. Bacterial microcompartments (BMCs) are utilized by bacteria to metabolize less common nutrients, conferring a growth advantage. Although widely studied in enteropathogens, there is limited research on BMC activity in commensal species. We demonstrate the formation of the eut BMC and utilization of ethanolamine as a carbon source in the human gut commensal Escherichia coli Nissle 1917 (EcN). Additionally, we found increased ammonium production when EcN utilized ethanolamine but did not see the same in Salmonella enterica, highlighting potential differences in how these species affect the wider microbial community.}, }
@article {pmid39636074, year = {2025}, author = {Graf, MD and Murgueitio, N and Vogel, SC and Hicks, L and Carlson, AL and Propper, CB and Kimmel, M}, title = {Maternal Prenatal Stress and the Offspring Gut Microbiome: A Cross-Species Systematic Review.}, journal = {Developmental psychobiology}, volume = {67}, number = {1}, pages = {e70005}, doi = {10.1002/dev.70005}, pmid = {39636074}, issn = {1098-2302}, support = {//National&#xa0;Institute of Health/ ; /NR/NINR NIH HHS/United States ; }, mesh = {*Gastrointestinal Microbiome/physiology ; Pregnancy ; Female ; *Prenatal Exposure Delayed Effects/microbiology ; Animals ; Humans ; *Stress, Psychological/microbiology ; }, abstract = {The prenatal period is a critical developmental juncture with enduring effects on offspring health trajectories. An individual's gut microbiome is associated with health and developmental outcomes across the lifespan. Prenatal stress can disrupt an infant's microbiome, thereby increasing susceptibility to adverse outcomes. This cross-species systematic review investigates whether maternal prenatal stress affects the offspring's gut microbiome. The study analyzes 19 empirical, peer-reviewed research articles, including humans, rodents, and non-human primates, that included prenatal stress as a primary independent variable and offspring gut microbiome characteristics as an outcome variable. Prenatal stress appeared to correlate with differences in beta diversity and specific microbial taxa, but not alpha diversity. Prenatal stress is positively correlated with Proteobacteria, Bacteroidaceae, Lachnospiraceae, Prevotellaceae, Bacteroides, and Serratia. Negative correlations were observed for Actinobacteria, Enterobacteriaceae, Streptococcaceae, Bifidobacteria, Eggerthella, Parabacteroides, and Streptococcus. Evidence for the direction of association between prenatal stress and Lactobacillus was mixed. The synthesis of findings was limited by differences in study design, operationalization and timing of prenatal stress, timing of infant microbiome sampling, and microbiome analysis methods.}, }
@article {pmid39635985, year = {2024}, author = {Mulders, MCF and van Koetsveld, PM and Feelders, RA and Hofland, LJ and de Herder, WW and Kraaij, R and Hofland, J}, title = {Gut microbial and functional alterations lead to metagenomic signatures for midgut neuroendocrine tumor patients and for carcinoid syndrome.}, journal = {Endocrine-related cancer}, volume = {}, number = {}, pages = {}, doi = {10.1530/ERC-24-0145}, pmid = {39635985}, issn = {1479-6821}, abstract = {Midgut neuroendocrine tumors (NET) derive from enterochromaffin cells, which have an close interrelationship with intestinal microbiota. Recently, we utilized 16S rRNA sequencing to uncover that midgut NET patients have a depleted gut microbiome and a specific fecal microbial signature. This study aims to validate these findings and to further characterize the role of microbes and microbial metabolic pathways in midgut NET patients with and without carcinoid syndrome (CS). Fecal samples from 60 midgut NET patients and 20 household-matched controls were subjected to whole metagenomics sequencing. We found that the gut microbial community composition of midgut NET patients differed from that of controls, with 2 genera, 17 species and 9 microbial pathways showing differential abundance (p < 0.001). No differences in microbial composition were observed between midgut NET patients with and without CS (p < 0.05). However, we did observe changes in inter-genus correlations of Bacteroides, Odoribacter, Parasutterella, Klebsielle, Ruminococcus and Proteobacteria when comparing these two patient groups. A signature of 16 microbial species (area under the receiver operating characteristic curve (AUROC) 0.892) or 18 microbial pathways (AUROC 0.909) accurately predicted the presence of a midgut NET. Furthermore, a microbial signature consisting of 14 functional microbial pathways distinguished CS patients from non-CS patients (AUROC 0.807). This study confirms that the gut microbiome of midgut NET patients is altered at the metagenomic level, which is not related to the presence of CS. A fecal microbial signature could constitute a novel biomarker for the diagnosis of midgut NET or CS.}, }
@article {pmid39635413, year = {2024}, author = {Xu, Z and Yang, L and Chen, H and Liu, S and Li, X and Li, S and Ying, C and Li, X and Du, R and Liu, D}, title = {Saccharomyces cerevisiae and Kluyveromyces marxianus yeast co-cultures modulate the ruminal microbiome and metabolite availability to enhance rumen barrier function and growth performance in weaned lambs.}, journal = {Animal nutrition (Zhongguo xu mu shou yi xue hui)}, volume = {19}, number = {}, pages = {139-152}, pmid = {39635413}, issn = {2405-6383}, abstract = {In lambs, weaning imposes stress that can contribute to impaired rumen epithelial barrier functionality and immunological dysregulation. In this study, the effects of a yeast co-culture consisting of Saccharomyces cerevisiae and Kluyveromyces marxianus (NM) on rumen health in lambs was evaluated, with a focus on parameters including growth performance, ruminal fermentation, and epithelial barrier integrity, ruminal metabolic function, and the composition of the ruminal bacteria. In total, 24 lambs were grouped into four groups of six lambs including a control (C) group fed a basal diet, and N, M, and NM groups in which lambs were fed the basal diet respectively supplemented with S. cerevisiae yeast cultures (30 g/d per head), K. marxianus yeast cultures (30 g/d per head), and co-cultures of both yeasts (30 g/d per head), the experiment lasted for 42 d. Subsequent analyses revealed that relative to the C group, the average daily gain (ADG) of lambs in the NM group was significantly greater and exhibited significant increases in a range of mRNA relative expression including monocarboxylate transporter 1 (MCT1), (Na[+])/hydrogen (H[+]) exchanger 1 (NHE1), (Na[+])/hydrogen (H[+]) exchanger 3 (NHE3), proton-coupled amino acid transporter 1 (PAT1), vacuolar H[+]-ATPase (vH+ ATPase), claudin-1, occludin in the rumen epithelium (P < 0.05). Compared with the C group, the pH of the rumen contents in the NM group was significantly decreased , and the concentrations of acetate, propionate, and butyrate were significantly increased (P < 0.05). Analysis of the rumen bacteria showed that the NM group exhibited increases in the relative abundance of Prevotella, Treponema, Moryella, Fibrobacter, CF231 and Ruminococcus (P < 0.05). Metabolomics analyses revealed an increase in the relative content of phthalic acid and cinnamaldehyde in the NM group as compared to the C group (P < 0.05), together with the greater relative content of L-tyrosine, L-dopa, rosmarinic acid, and tyrosol generated by the tyrosine metabolic pathway (P < 0.05). Spearman's correlation analyses revealed relative abundance levels of Fibrobacter and Ruminococcus were positively correlated with the mRNA relative expression levels of PAT1, NHE3, and zonula occluden-1 (ZO-1), as well as with tyrosol, phthalic acid, and cinnamaldehyde levels (P < 0.05). Ultimately, these results suggest that dietary supplementation with NM has a wide range of beneficial effects on weaned lambs and is superior to single bacterial fermentation. These effects include improvements in daily gain and rumen epithelial barrier integrity, as well as improvements in the composition of the rumen microbiome, and alterations in tyrosine metabolic pathways.}, }
@article {pmid39635041, year = {2024}, author = {Dora, D and Revisnyei, P and Mihucz, A and Kiraly, P and Szklenarik, G and Dulka, E and Galffy, G and Lohinai, Z}, title = {Metabolic pathways from the gut metatranscriptome are associated with COPD and respiratory function in lung cancer patients.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1381170}, pmid = {39635041}, issn = {2235-2988}, mesh = {Humans ; *Pulmonary Disease, Chronic Obstructive/microbiology/metabolism/physiopathology ; *Gastrointestinal Microbiome/genetics ; *Metabolic Networks and Pathways/genetics ; *Lung Neoplasms/microbiology/genetics ; Male ; *Feces/microbiology ; Female ; Aged ; Middle Aged ; Carcinoma, Non-Small-Cell Lung/genetics/microbiology ; Transcriptome ; Metagenomics/methods ; Bacteria/genetics/classification/isolation &amp; purification/metabolism ; Streptococcus/genetics/isolation &amp; purification/metabolism ; }, abstract = {INTRODUCTION: Changes in the human gut microbiome have been linked to various chronic diseases, including chronic obstructive pulmonary disease (COPD). While substantial knowledge is available on the genomic features of fecal communities, little is known about the microbiome's transcriptional activity. Here, we analyzed the metatranscriptomic (MTR) abundance of MetaCyc pathways, SuperPathways, and protein domain families (PFAM) represented by the gut microbiome in a cohort of non-small cell lung cancer (NSCLC) patients with- or without COPD comorbidity.<br><br>METHODS: Fecal samples of 40 NSCLC patients with- or without COPD comorbidity were collected at the time of diagnosis. Data was preprocessed using the Metaphlan3/Humann3 pipeline and BioCyc[&#xa9;] to identify metabolic SuperPathways. LEfSe analysis was conducted on Pathway- and PFAM abundance data to determine COPD- and non-COPD-related clusters.<br><br>RESULTS: Key genera Streptococcus, Escherichia, Gemella, and Lactobacillus were significantly more active transcriptionally compared to their metagenomic presence. LEfSe analysis identified 11 MetaCyc pathways that were significantly overrepresented in patients with- and without COPD comorbidity. According to Spearman's rank correlation, Smoking PY showed a significant negative correlation with Glycolysis IV, Purine Ribonucleoside Degradation and Glycogen Biosynthesis I, and a significant positive correlation with Superpathway of Ac-CoA Biosynthesis and Glyoxylate cycle, whereas forced expiratory volume in the first second (FEV1) showed a significant negative correlation with Glycolysis IV and a significant positive correlation with Glycogen Biosynthesis I. Furthermore, COPD patients showed a significantly increased MTR abundance in ~60% of SuperPathways, indicating a universally increased MTR activity in this condition. FEV1 showed a significant correlation with SuperPathways Carbohydrate degradation, Glycan biosynthesis, and Glycolysis. Taxonomic analysis suggested a more prominent MTR activity from multiple Streptococcus species, Enterococcus (E.) faecalis, E. faecium and Escherichia (E.) coli than expected from their metagenomic abundance. Multiple protein domain families (PFAMs) were identified as more associated with COPD, E. faecium, E.coli, and Streptococcus salivarius, contributing the most to these PFAMs.<br><br>CONCLUSION: Metatranscriptome analysis identified COPD-related subsets of lung cancer with potential therapeutic relevance.}, }
@article {pmid39635024, year = {2024}, author = {Skladany, L and Kubanek, N and Adamcova Selcanova, S and Zilincanova, D and Havaj, D and Sulejova, K and Soltys, K and Messingerova, L and Lichvar, M and Laffers, L and Zilincan, M and Honsova, E and Liptak, P and Banovcin, P and Bures, J and Koller, T and Golubnitschaja, O and Arab, JP}, title = {3PM-guided innovation in treatments of severe alcohol-associated hepatitis utilizing fecal microbiota transplantation.}, journal = {The EPMA journal}, volume = {15}, number = {4}, pages = {677-692}, pmid = {39635024}, issn = {1878-5077}, abstract = {RATIONALE: Severe alcohol-associated hepatitis (SAH) is the most critical, acute, inflammatory phenotype within the alcohol-associated liver disease (ALD) spectrum, characterized by high 30- and 90-day mortality. Since several decades, corticosteroids (CS) are the only approved pharmacotherapy offering highly limited survival benefits. Contextually, there is an evident demand for 3PM innovation in the area meeting patients' needs and improving individual outcomes. Fecal microbiota transplantation (FMT) has emerged as one of the new potential therapeutic options. In this study, we aimed to address the crucial 3PM domains in order to assess (i) the impact of FMT on mortality in SAH patients beyond CS, (ii) to identify factors associated with the outcome to be improved (iii) the prediction of futility, (iv) prevention of suboptimal individual outcomes linked to increased mortality, and (v) personalized allocation of therapy.<br><br>METHODS: We conducted a prospective study (NCT04758806) in adult patients with SAH who were non-responders (NR) to or non-eligible (NE) for CS between January 2018 and August 2022. The intervention consisted of five 100&#xa0;ml of FMT, prepared from 30&#xa0;g stool from an unrelated healthy donor and frozen at&#x2009;-&#x2009;80 &#xb0;C, administered daily to the upper gastrointestinal (GI) tract. We evaluated the impact of FMT on 30- and 90-day mortality which we compared to the control group selected by the propensity score matching and treated by the standard of care; the control group was derived from the RH7 registry of patients hospitalized at the liver unit (NCT04767945). We have also scrutinized the FMT outcome against established and potential&#xa0;prognostic factors for SAH - such as the model for end-stage liver disease (MELD), Maddrey Discriminant Function (MDF), acute-on-chronic liver failure (ACLF), Liver Frailty Index (LFI), hepatic venous-portal pressure gradient (HVPG) and Alcoholic Hepatitis Histologic Score (AHHS) - to see if the 3PM method assigns them a new dimension in predicting response to therapy, prevention of suboptimal individual outcomes, and personalized patient management.<br><br>RESULTS: We enrolled 44 patients with SAH (NR or NE) on an intention-to-treat basis; we analyzed 33 patients per protocol for associated factors (after an additional 11 being excluded for receiving less than 5 doses of FMT), and 31 patients by propensity score matching for corresponding individual outcomes, respectively. The mean age was 49.6&#xa0;years, 11 patients (33.3%) were females. The median MELD score was 29, and ACLF of any degree had 27 patients (81.8%). FMT improved 30-day mortality (p&#x2009;=&#x2009;0.0204) and non-significantly improved 90-day mortality (p&#x2009;=&#x2009;0.4386). Univariate analysis identified MELD&#x2009;&#x2265;&#x2009;30, MDF&#x2009;&#x2265;&#x2009;90, and ACLF grade&#x2009;>&#x2009;1 as significant predictors of 30-day mortality, (p&#x2009;=&#x2009;0.031; p&#x2009;=&#x2009;0.014; p&#x2009;=&#x2009;0.034). Survival was not associated with baseline LFI, HVPG, or AHHS.<br><br>In the most difficult-to-treat sub-cohort of patients with SAH (i.e., NR/NE), FMT improved 30-day mortality. Factors associated with benefit included MELD&#x2009;&#x2264;&#x2009;30, MDF&#x2009;&#x2264;&#x2009;90, and ACLF&#x2009;<&#x2009;2. These results support the potential of gut microbiome as a therapeutic target in the context of 3PM research and vice versa - to use 3PM methodology as the expedient unifying template for microbiome research. The results allow for immediate impact on the innovative concepts of (i) personalized phenotyping and stratification of the disease for the clinical research and practice, (ii) multilevel predictive diagnosis related to personalized/precise treatment allocation including evidence-based (ii) prevention of futile and sub-optimally effective therapy, as well as (iii) targeted prevention of poor individual outcomes in patients with SAH. Moreover, our results add to the existing evidence with the potential to generate new research along the SAH's pathogenetic pathways such as diverse individual susceptibility to alcohol toxicity, host-specific mitochondrial function and systemic inflammation, and the role of gut dysbiosis thereof.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13167-024-00381-5.}, }
@article {pmid39635020, year = {2024}, author = {Mi, Y and Chen, K and Lin, S and Tong, L and Zhou, J and Wan, M}, title = {Lactobacillaceae-mediated eye-brain-gut axis regulates high myopia-related anxiety: from the perspective of predictive, preventive, and personalized medicine.}, journal = {The EPMA journal}, volume = {15}, number = {4}, pages = {573-585}, pmid = {39635020}, issn = {1878-5077}, abstract = {BACKGROUND: High myopia has become a major cause of blindness worldwide and can contribute to emotional deficits through its impact on the central nervous system. The potential crosstalk with gut microbiome positions high myopia as a valuable model for studying the eye-brain-gut axis, highlighting the intricate interplay between visual health, neurological function, and the gut microbiome. Understanding these connections is crucial from a predictive, preventive, and personalized medicine (PPPM) perspective, as it may reveal novel intervention targets for managing both visual and mental health.<br><br>In our study, we hypothesized that visual stimuli associated with high myopia may lead to gut microecological dysregulation, potentially triggering mood disorders such as anxiety and depression. To test this hypothesis, we assessed genetic associations between high myopia (N&#x2009;=&#x2009;50,372) and depression (N&#x2009;=&#x2009;674,452) as well as anxiety (N&#x2009;=&#x2009;21,761) using inverse variance weighted as the primary analytical method. We also investigated the potential mediating role of the gut microbiome (N&#x2009;=&#x2009;18,340). The findings were validated in an independent cohort and summarized through meta-analysis.<br><br>RESULTS: A genetic causal relationship between high myopia and anxiety was found (odds ratio [OR]&#x2009;=&#x2009;8.76; 95% confidence interval [CI], 2.69-28.54; p&#x2009;=&#x2009;3.16&#x2009;&#xd7;&#x2009;10[-4]), with 20.3% of the effect mediated by the gut microbiome family Lactobacillaceae (&#x3b2;&#x2009;=&#x2009;0.517; 95% CI, 0.104-1.090; p&#x2009;=&#x2009;0.037). The analysis also showed a suggestive causal relationship between high myopia and depression (OR&#x2009;=&#x2009;1.25; 95% CI, 1.00-1.57; p&#x2009;=&#x2009;0.048).<br><br>CONCLUSIONS: Our study shows that high myopia causes anxiety via the Lactobacillaceae family of the gut microbiome, supporting the eye-brain-gut axis concept. This underscores the need to shift from reactive to predictive, preventive, and personalized medicine (PPPM). Targeting Lactobacillaceae offers novel insights for early intervention and personalized treatment of high myopia-related anxiety and sheds light on interventions for other vision-related brain disorders.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13167-024-00387-z.}, }
@article {pmid39635016, year = {2024}, author = {Zhao, W and Li, S and Li, Q and Li, Q and Zheng, Y and Lu, H}, title = {Mendelian randomization reveals predictive, preventive, and personalized insights into inflammatory bowel disease: the role of gut microbiome and circulating inflammatory proteins.}, journal = {The EPMA journal}, volume = {15}, number = {4}, pages = {693-709}, pmid = {39635016}, issn = {1878-5077}, abstract = {BACKGROUND: A chronic illness with increasing global frequency, inflammatory bowel disease (IBD), which includes ulcerative colitis (UC) and Crohn's disease (CD), profoundly affects patients' quality of life and healthcare systems. IBD pathogenesis consists of changes in gut microbiota, immune system dysregulation, and genetic predisposition. Although emerging data suggests that gut microbiota and circulating inflammatory proteins play critical roles in IBD, their utility as biomarkers for predictive, preventive, and personalized medicine (PPPM) remains incompletely understood.<br><br>We hypothesized that specific gut microbiota and inflammatory proteins causally influence IBD risk and mediate pathways between gut microbiota and IBD development. We employed Mendelian randomization (MR) using genome-wide association studies (GWAS) to explore these causal relationships, including further analyses on UC and CD subtypes.<br><br>RESULTS: We identified eight gut microbiota species linked to IBD, with four protective and four increasing risk. Nine inflammatory proteins were also associated, six increasing risk and three protective. MMP-10 and IL-10R&#x3b1; mediated the effects of Clostridiaceae1 on IBD risk. For UC, five microbiota species were protective, five were risk factors, and two proteins increased risk while three were protective. IL-10R&#x3b1; mediated the effects of Clostridiaceae1 on UC risk. For CD, eight microbiota species were protective, four increased risk, and nine proteins were implicated. However, no mediation pathways were supported by multivariable MR.<br><br>CONCLUSIONS: This study highlights specific gut microbiota and inflammatory proteins that may serve as therapeutic targets for PPPM in IBD, UC, and CD. These findings offer new insights into IBD pathogenesis and suggest potential avenues for improved prevention, early detection, and personalized treatment strategies.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13167-024-00384-2.}, }
@article {pmid39143813, year = {2024}, author = {Perkins, EM and Mundt, CC}, title = {Associations Among Cultivar Cropping Sequence, 2,4-Diacetlyphloroglucinol-Producing Pseudomonad Populations, and Take-All Disease of Winter Wheat in Oregon.}, journal = {Plant disease}, volume = {}, number = {}, pages = {PDIS02240372RE}, doi = {10.1094/PDIS-02-24-0372-RE}, pmid = {39143813}, issn = {0191-2917}, abstract = {Take-all of wheat (Triticum aestivum L.), caused by Gaeumannomyces tritici (syn. G. graminis var. tritici), is perhaps the most important soilborne disease of wheat globally and can cause substantial yield losses under several cropping scenarios in Oregon. Although resistance to take-all has not been identified in hexaploid wheat, continuous cropping of wheat for several years can reduce take-all severity through the development of suppressive soils, a process called "take-all decline" (TAD). Extensive work has shown that TAD is driven primarily by members of the Pseudomonas fluorescens complex that produce 2,4-diacetlyphloroglucinol (DAPG), an antibiotic that is associated with antagonism and induced host resistance against multiple pathogens. Field experiments were conducted to determine the influence of agronomically relevant first-year wheat cultivars on take-all levels and ability to accumulate DAPG-producing pseudomonads within their rhizospheres in second-year field trials and in greenhouse trials. One first-year wheat cultivar consistently resulted in less take-all in second-year wheat and accumulated significantly more DAPG-producing pseudomonads than other cultivars, suggesting a potential mechanism for take-all reduction associated with that cultivar. An intermediate level of take-all suppression in other cultivars was not clearly associated with population size of DAPG-producing pseudomonads, however. The first-year cultivar effect on take-all dominated in subsequent plantings, and its impact was not specific to the first-year cultivar. Our results confirm that wheat cultivars may be used to suppress take-all when deployed appropriately over cropping seasons, an approach that is cost-effective, sustainable, and currently being used by some wheat growers in Oregon to reduce take-all.}, }
@article {pmid39634564, year = {2024}, author = {Lee, D and Maaskant, A and Ngo, H and Montijn, RC and Bakker, J and Langermans, JAM and Levin, E}, title = {A rapid, affordable, and reliable method for profiling microbiome biomarkers from fecal images.}, journal = {iScience}, volume = {27}, number = {12}, pages = {111310}, pmid = {39634564}, issn = {2589-0042}, abstract = {Human and veterinary healthcare professionals are interested in utilizing the gut-microbiome as a target to diagnose, treat, and prevent (gastrointestinal) diseases. However, the current microbiome analysis techniques are expensive and time-consuming, and data interpretation requires the expertise of specialists. Therefore, we explored the development and application of artificial intelligence technology for rapid, affordable, and reliable microbiome profiling in rhesus macaques (Macaca mulatta). Tailor-made learning algorithms were created by integrating digital images of fecal samples with corresponding whole-genome sequenced microbial profiles. These algorithms were trained to identify alpha-diversity (Shannon index), key microbial markers, and fecal consistency from the digital images of fecal smears. A binary classification strategy was applied to distinguish between samples with high and low diversity and presence or absence of selected bacterial genera. Our results revealed a successful proof of concept for "high and low" prediction of diversity, fecal consistency, and "present or absent" for selected bacterial genera.}, }
@article {pmid39634557, year = {2024}, author = {Huang, G and Li, W and Liu, Y and Zhou, J and Wei, F}, title = {Evidences from gut microbiome and habitat landscape indicate continued threat of extinction for the Hainan gibbon.}, journal = {iScience}, volume = {27}, number = {12}, pages = {111352}, pmid = {39634557}, issn = {2589-0042}, abstract = {Little is known about the population health status of the world's rarest primate, the Hainan gibbon. Here, the largest gut microbiome dataset yet constructed was generated from all five extant breeding groups of the Hainan gibbons, with 42 samples from individuals spanning all ages and sexes, in addition to dry and wet seasons. Groups A and B exhibited higher diversity of gut microbiota and food resources, in contrast to the subsequently established Groups C, D, and E. Significantly, Group C demonstrated the lowest gut microbial diversity and higher abundance of vector-related Pestivirus, which may be attributed to their proximity to the primary forest edge and the village. We also inferred the origin and possible dispersal paths of the newly established Group E. These findings indicate that Hainan gibbons are still facing viral zoonosis and the threat of extinction, as illuminated by an understanding of the gut microbiome and habitat landscape ecology.}, }
@article {pmid39634324, year = {2024}, author = {Shao, L and Zhang, B and Song, Y and Lyu, Z and Zhang, W and Yang, W and Fu, J and Li, J and Shi, J}, title = {Mucosal Hub Bacteria as Potential Targets for Improving High-Fat Diet-Related Intestinal Barrier Injury.}, journal = {The Canadian journal of infectious diseases &amp; medical microbiology = Journal canadien des maladies infectieuses et de la microbiologie medicale}, volume = {2024}, number = {}, pages = {3652740}, pmid = {39634324}, issn = {1712-9532}, abstract = {Background: Intestinal barrier injury contributes to multiple diseases such as obesity and diabetes, whereas no treatment options are available. Methods: Due to close interactions between mucosal microbiome and intestinal barrier, we evaluated the potential of mucosal bacteria in providing targets for high-fat diet (HFD)-related intestinal barrier injury. Whole-genome metagenomics was used to evaluate mucosal microbiome, while intestinal barrier injury was estimated using serum LPS, FITC-dextran intensity, and ZO-1 protein. Results: We found that HFD induced significant fat accumulation in epididymal tissue at weeks 4 and 12, while ALT, LDL, and TC increased at week 12. Intestinal barrier injury was confirmed by elevated serum LPS at both weeks, upregulated FITC-dextran intensity, and decreased ZO-1 protein at week 12. Fourteen species such as Phocaeicola vulgatus differed in HFD-fed mice. The co-occurrence network of mucosal microbiome shifted from scale-free graph in controls to nearly random graph in HFD-fed mice. Besides, 10 hub bacteria especially Bacteroides ovatus decreased drastically in both mucosal and fecal samples of HFD-fed mice, correlated with intestinal permeability, ALT, and KEGG pathways such as "Mitochondrial biogenesis" and "metabolism". Moreover, Bacteroides ovatus has been confirmed to improve intestinal barrier function in a recent study. Conclusion: Mucosal hub bacteria can provide potential targets for improving HFD-related intestinal barrier function.}, }
@article {pmid39634265, year = {2024}, author = {Turco, L and Della Monica, R and Giordano, P and Cuomo, M and Biazzo, M and Mateu, B and Di Liello, R and Daniele, B and Normanno, N and De Luca, A and Rachiglio, AM and Chiaramonte, C and Giugliano, FM and Chiariotti, L and Catapano, G and Coretti, L and Lembo, F}, title = {Case report: Tracing in parallel the salivary and gut microbiota profiles to assist Larotrectinib anticancer treatment for NTRK fusion-positive glioblastoma.}, journal = {Frontiers in oncology}, volume = {14}, number = {}, pages = {1458990}, pmid = {39634265}, issn = {2234-943X}, abstract = {Oncotherapy can shape intestinal microbiota, which, in turn, may influence therapy effectiveness. Furthermore, microbiome signatures during treatments can be leveraged for the development of personalised therapeutic protocols in cancer treatment based on the identification of microbiota profiles as prognostic tools. Here, for the first time, the trajectory of gut and salivary microbiota in a patient treated with Larotrectinib, a targeted therapy approved for diagnosed glioblastoma multiforme neurotrophic tyrosine receptor kinase (NTRK) gene fusion-positive, has been accurately investigated. We based our analyses on histological diagnosis, genomic and epigenomic profiling of tumour DNA, and faecal and salivary full-length 16S rRNA gene sequencing. The study clearly evidenced a remodelling of the bacterial communities following 1 month of the NTRK-inhibitor treatment, at both gut and oral levels. We reported a boosting of specific bacteria also described in response to other chemotherapeutic approaches, such as Enterococcus faecium, E. hirae, Akkermansia muciniphila, Barnesiella intestinihominis, and Bacteroides fragilis. Moreover, several bacterial species were similarly modulated upon Larotrectinib in faecal and saliva samples. Our results suggest a parallel dynamism of microbiota profiles in both body matrices possibly useful to identify microbial biomarkers as contributors to precision medicine in cancer therapies.}, }
@article {pmid39634064, year = {2024}, author = {Hu, D and Hu, L and Xiao, O and Chen, J and Dai, X and Sun, Y and Kong, Z}, title = {Bibliometric analysis of research trends and advancements in medicinal plant microbiome.}, journal = {Frontiers in plant science}, volume = {15}, number = {}, pages = {1495198}, pmid = {39634064}, issn = {1664-462X}, abstract = {Medicinal plants and microorganisms are closely linked, with microorganisms boosting plant growth, offering pest control, and enhancing secondary compound production. However, there's a lack of systematic research, detailed molecular studies, and standardized methods for effectively using microorganisms in developing products from medicinal plants. To enhance understanding of the present research progress, emerging patterns, and key areas pertaining to microorganisms found in medicinal plants, CiteSpace bibliometric software was employed to visualize and analyze 1269 English publications sourced from the Science Net Core Collection database. Through the utilization of keyword co-occurrence analysis and cluster analysis methods, this study seeks to explore collaborative networks among countries, institutions, and scholars involved in the study of microorganisms in medicinal plants. This review highlights key research areas in microbiology, focusing on evaluating natural compounds for antibacterial properties and the impact of secondary metabolites on microbial communities, aiming to highlight significant research domains and primary focuses for researchers and professionals engaged in the field of microbiology concerning medicinal plants.}, }
@article {pmid39633815, year = {2024}, author = {Khan, IM and Nassar, N and Chang, H and Khan, S and Cheng, M and Wang, Z and Xiang, X}, title = {The microbiota: a key regulator of health, productivity, and reproductive success in mammals.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1480811}, pmid = {39633815}, issn = {1664-302X}, abstract = {The microbiota, intensely intertwined with mammalian physiology, significantly impacts health, productivity, and reproductive functions. The normal microbiota interacts with the host through the following key mechanisms: acting as a protective barrier against pathogens, maintain mucosal barrier integrity, assisting in nutrient metabolism, and modulating of the immune response. Therefore, supporting growth and development of host, and providing protection against pathogens and toxic substances. The microbiota significantly influences brain development and behavior, as demonstrated by comprehensive findings from controlled laboratory experiments and human clinical studies. The prospects suggested that gut microbiome influence neurodevelopmental processes, modulate stress responses, and affect cognitive function through the gut-brain axis. Microbiota in the gastrointestinal tract of farm animals break down and ferment the ingested feed into nutrients, utilize to produce meat and milk. Among the beneficial by-products of gut microbiota, short-chain fatty acids (SCFAs) are particularly noteworthy for their substantial role in disease prevention and the promotion of various productive aspects in mammals. The microbiota plays a pivotal role in the reproductive hormonal systems of mammals, boosting reproductive performance in both sexes and fostering the maternal-infant connection, thereby becoming a crucial factor in sustaining mammalian existence. The microbiota is a critical factor influencing reproductive success and production traits in mammals. A well-balanced microbiome improves nutrient absorption and metabolic efficiency, leading to better growth rates, increased milk production, and enhanced overall health. Additionally, it regulates key reproductive hormones like estrogen and progesterone, which are essential for successful conception and pregnancy. Understanding the role of gut microbiota offers valuable insights for optimizing breeding and improving production outcomes, contributing to advancements in agriculture and veterinary medicine. This study emphasizes the critical ecological roles of mammalian microbiota, highlighting their essential contributions to health, productivity, and reproductive success. By integrating human and veterinary perspectives, it demonstrates how microbial communities enhance immune function, metabolic processes, and hormonal regulation across species, offering insights that benefit both clinical and agricultural advancements.}, }
@article {pmid39633813, year = {2024}, author = {Yang, R and Shi, Z and Li, Y and Huang, X and Li, Y and Li, X and Chen, Q and Hu, Y and Li, X}, title = {Research focus and emerging trends of the gut microbiome and infant: a bibliometric analysis from 2004 to 2024.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1459867}, pmid = {39633813}, issn = {1664-302X}, abstract = {BACKGROUND: Over the past two decades, gut microbiota has demonstrated unprecedented potential in human diseases and health. The gut microbiota in early life is crucial for later health outcomes. This study aims to reveal the knowledge collaboration network, research hotspots, and explore the emerging trends in the fields of infant and gut microbiome using bibliometric analysis.<br><br>METHOD: We searched the literature on infant and gut microbiome in the Web of Science Core Collection (WOSCC) database from 2004 to 2024. CiteSpace V (version: 6.3.R1) and VOSview (version: 1.6.20) were used to display the top authors, journals, institutions, countries, authors, keywords, co-cited articles, and potential trends.<br><br>RESULTS: A total of 9,899 documents were retrieved from the Web of Science Core Collection. The United States, China, and Italy were the three most productive countries with 3,163, 1,510, and 660 publications. The University of California System was the most prolific institution (524 publications). Van Sinderen, Douwe from University College Cork of Ireland was the most impactful author. Many studies have focused on atopic dermatitis (AD), necrotizing enterocolitis (NEC), as well as the immune mechanisms and microbial treatments for these diseases, such as probiotic strains mixtures and human milk oligosaccharides (HMOs). The mother-to-infant microbiome transmission, chain fatty acids, and butyrate maybe the emerging trends.<br><br>CONCLUSION: This study provided an overview of the knowledge structure of infant and gut microbiome, as well as a reference for future research.}, }
@article {pmid39633812, year = {2024}, author = {Bauchinger, F and Seki, D and Berry, D}, title = {Characteristics of putative keystones in the healthy adult human gut microbiota as determined by correlation network analysis.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1454634}, pmid = {39633812}, issn = {1664-302X}, abstract = {Keystone species are thought to play a critical role in determining the structure and function of microbial communities. As they are important candidates for microbiome-targeted interventions, the identification and characterization of keystones is a pressing research goal. Both empirical as well as computational approaches to identify keystones have been proposed, and in particular correlation network analysis is frequently utilized to interrogate sequencing-based microbiome data. Here, we apply an established method for identifying putative keystone taxa in correlation networks. We develop a robust workflow for network construction and systematically evaluate the effects of taxonomic resolution on network properties and the identification of keystone taxa. We are able to identify correlation network keystone species and genera, but could not detect taxa with high keystone potential at lower taxonomic resolution. Based on the correlation patterns observed, we hypothesize that the identified putative keystone taxa have a stabilizing effect that is exerted on correlated taxa. Correlation network analysis further revealed subcommunities present in the dataset that are remarkably similar to previously described patterns. The interrogation of available metatranscriptomes also revealed distinct transcriptional states present in all putative keystone taxa. These results suggest that keystone taxa may have stabilizing properties in a subset of community members rather than global effects. The work presented here contributes to the understanding of correlation network keystone taxa and sheds light on their potential ecological significance.}, }
@article {pmid39633808, year = {2024}, author = {Guo, Y and Feng, H and Du, L and Yu, Z}, title = {Patterns of antibiotic resistance genes and virulence factor genes in the gut microbiome of patients with osteoarthritis and rheumatoid arthritis.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1427313}, pmid = {39633808}, issn = {1664-302X}, abstract = {BACKGROUND: The gut microbiome compositions of osteoarthritis (OA) and rheumatoid arthritis (RA) patients have been revealed; however, the functional genomics, particularly antibiotic resistance genes (ARGs) and virulence factor genes (VFGs), have not yet been explored.<br><br>METHODS: We used gut metagenomic data to elucidate the distribution of ARGs and VFGs. Building on these differences in gut microbiome, we developed a diagnostic model using a random forest classifier based on ARG and VFG abundances.<br><br>RESULTS: Our results indicated that both OA and RA patients exhibit significantly higher alpha diversity in ARGs, as measured by observed genes, the Shannon index, and the Simpson index, compared to healthy controls. However, this increased diversity is not significantly different between OA and RA patients. In contrast, VFGs showed higher diversity in RA patients than in healthy individuals, which was not as pronounced in OA patients. An analysis of the top 20 ARGs and VFGs revealed a largely similar composition between the three groups, with notable exceptions of certain genes that were uniquely enriched in either OA or RA patients. This suggests unique microbial patterns associated with each condition. Our beta diversity analysis further demonstrated distinct distributions of ARG and VFG profiles across the three groups, with several genes significantly enriched in both OA and RA patients, indicating potential markers for these diseases. The model achieved high accuracy (74.7-83.6%) when distinguishing both OA and RA from healthy controls using ARG profiles and substantial accuracy using VFG profiles.<br><br>CONCLUSION: These results support the potential of ARGs and VFGs as reliable biomarkers for diagnosing OA and RA.}, }
@article {pmid39633804, year = {2024}, author = {Sharma, N and Das, BK and Bhattacharjya, BK and Chaudhari, A and Behera, BK and Kumar, AP and Chakraborty, HJ}, title = {Metagenomic insights into microbial community, functional annotation, and antibiotic resistance genes in Himalayan Brahmaputra River sediment, India.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1426463}, pmid = {39633804}, issn = {1664-302X}, abstract = {INTRODUCTION: The Brahmaputra, a major transboundary river of the Himalayas flowing predominantly through Northeast India, particularly Assam, is increasingly endangered by contamination due to rapid urbanization and anthropogenic pressures. These environmental changes pose significant risks at the microbial level, affecting nutrient cycling and productivity, and thereby impacting river ecosystem health. The next-generation sequencing technology using a metagenomics approach has revolutionized our understanding of the microbiome and its critical role in various aquatic environments.<br><br>METHODS: The present study aimed to investigate the structure of the bacterial community and its functional potentials within the sediments of the Brahmaputra River, India, using high-throughput shotgun metagenomics. Additionally, this study sought to explore the presence of antimicrobial resistance genes in the river's sediment.<br><br>RESULTS AND DISCUSSION: Shotgun metagenomics revealed a diverse bacterial community comprising 31 phyla, 52 classes, 291 families, 1,016 genera, and 3,630 species. Dominant phyla included Pseudomonadota (62.47-83.48%), Actinobacteria (11.10-24.89%), Bacteroidetes (0.97-3.82%), Firmicutes (0.54-3.94%), Cyanobacteria (0.14-1.70%), and Planctomycetes (0.30-0.78%). Functional profiling highlighted significant involvement in energy metabolism, amino acid and central carbon metabolism, stress response, and degradation pathways, emphasizing the microbial community's role in ecosystem functioning and resilience. Notably, 50 types of antibiotic resistance genes (ARGs) were detected, with resistance profiles spanning multidrug, aminoglycoside, &#x3b2;-lactam, fluoroquinolone, rifampicin, sulfonamide, and tetracycline classes. Network analysis underscored the intricate relationships among ARG subtypes, suggesting potential mechanisms of resistance propagation. Furthermore, plasmid-related genes and 185 virulence factor genes (VFGs) were identified, indicating additional layers of microbial adaptation and potential pathogenicity within the river sediments. This comprehensive microbial and functional profiling of the Brahmaputra's sediment metagenome provides crucial insights into microbial diversity, resistance potential, and ecological functions, offering a foundation for informed management and mitigation strategies to preserve river health and mitigate pollution impacts.}, }
@article {pmid39633586, year = {2025}, author = {Moura, IB and Buckley, AM}, title = {Using nutrition to help recovery from infections.}, journal = {Current opinion in gastroenterology}, volume = {41}, number = {1}, pages = {54-58}, doi = {10.1097/MOG.0000000000001068}, pmid = {39633586}, issn = {1531-7056}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Dysbiosis ; *Anti-Bacterial Agents/therapeutic use ; Clostridium Infections ; Dietary Fiber/administration &amp; dosage ; Clostridioides difficile ; }, abstract = {PURPOSE OF REVIEW: Antibiotics are a cornerstone of modern medicine, but antibiotic consumption can have depleting effects on the gut microbiota, potentially leading to gastrointestinal symptoms and other diseases, namely Clostridioides difficile infection. Because nutrition is a major driver of gut microbiota diversity and function, here we explore the current evidence on the potential of diets in alleviate the deleterious effects of antibiotics consumed during infections.<br><br>RECENT FINDINGS: Beneficial nutrients can enhance the symbiotic effect of the gut microbiota with the host, supporting anti-inflammatory responses and maintaining tight junction integrity. Short-chain fatty acids have been shown to positively affect the immune response, reducing the severity of C. difficile infection, whereas high-fibre diets have been shown to promote faster recovery of the gut microbiota after antibiotic therapy.<br><br>SUMMARY: The role of nutrition during infection is gaining momentum, with key findings exploring the effect of some nutrients in limiting the severity of infections and helping the microbiota recover from antibiotic-induced dysbiosis. Although this field is in its infancy, these findings open the possibility of personalised nutrition as a way of restoring microbiome diversity. But more work is needed to identify the most effective types and combinations of nutrients to achieve this.}, }
@article {pmid39633476, year = {2024}, author = {Manrique-de-la-Cuba, MF and Parada-Pozo, G and Rodríguez-Marconi, S and López-Rodríguez, MR and Abades, S and Trefault, N}, title = {Evidence of habitat specificity in sponge microbiomes from Antarctica.}, journal = {Environmental microbiome}, volume = {19}, number = {1}, pages = {100}, pmid = {39633476}, issn = {2524-6372}, support = {Fondecyt N&#xb0; 1230758//Agencia Nacional de Investigaci&#xf3;n y Desarrollo/ ; Fondecyt N&#xb0; 1230758//Agencia Nacional de Investigaci&#xf3;n y Desarrollo/ ; Fondecyt N&#xb0; 1230758//Agencia Nacional de Investigaci&#xf3;n y Desarrollo/ ; Fondecyt N&#xb0; 1230758//Agencia Nacional de Investigaci&#xf3;n y Desarrollo/ ; Fondecyt N&#xb0; 1230758//Agencia Nacional de Investigaci&#xf3;n y Desarrollo/ ; DG_02-22//Instituo Antartico Chileno- INACH/ ; Doctoral fellowship N&#xb0; 21211164//Agencia Nacional de Investigaci&#xf3;n e Innovaci&#xf3;n/ ; }, abstract = {BACKGROUND: Marine sponges and their microbiomes are ecosystem engineers distributed across the globe. However, most research has focused on tropical and temperate sponges, while polar regions like Antarctica have been largely neglected. Despite its harsh conditions and geographical isolation, Antarctica is densely populated by sponges. In this study, we explored the extent of habitat specificity in the diversity, community composition, and microbial co-occurrence within Antarctic sponge microbiomes, in comparison to those from other marine environments. We used massive sequencing of 16S rRNA genes and integrated multiple databases to incorporate Antarctic sponges as a habitat in global microbiome analyses.<br><br>RESULTS: Our study revealed significant differences in microbial diversity and community composition between Antarctic and non-Antarctic sponges. We found that most microorganisms present in Antarctic sponges are unique to the South Shetland Islands. Nitrosomonas oligotropha, Candidatus Nitrosopumilus, Polaribacter, SAR116 clade, and Low Salinity Nitrite-Oxidizing Bacteria (LS-NOB) are microbial members characterizing the Antarctic sponge microbiomes. Based on their exclusivity and presence across different sponges worldwide, we identified habitat-specific and habitat-generalist bacteria associated with each habitat. They are particularly abundant and connected within all the Antarctic sponges, suggesting that they may play a crucial role as keystone species within these sponge ecosystems.<br><br>CONCLUSIONS: This study provides significant insights into the microbial diversity and community composition of sponges in Antarctica and non-Antarctic ecoregions. Our findings provide evidence for habitat-specific patterns that differentiate the microbiomes of Antarctic sponges from elsewhere, indicating the strong influence of environmental selection and dispersal limitation wrapped into the Antarctic ecoregions to shape more similar microbial communities in distantly related sponges. This study contributes to understanding signatures of microbial community assembly in the Antarctic sponges and has important implications for the ecology and evolution of these unique marine environments.}, }
@article {pmid39633419, year = {2024}, author = {Alghamdi, AK and Parween, S and Hirt, H and Saad, MM}, title = {Unveiling the bacterial diversity and potential of the Avicennia marina ecosystem for enhancing plant resilience to saline conditions.}, journal = {Environmental microbiome}, volume = {19}, number = {1}, pages = {101}, pmid = {39633419}, issn = {2524-6372}, abstract = {BACKGROUND: Avicennia marina ecosystems are critical for coastal protection, water quality enhancement, and biodiversity support. These unique ecosystems thrive in extreme saline conditions and host a diverse microbiome that significantly contributes to plant resilience and growth. Global food security is increasingly threatened by crop yield losses due to abiotic stresses, including saline soils. Traditional plant breeding for salt tolerance is both costly and time-consuming. This study explores the potential of bacteria from A. marina to enhance plant growth under saline conditions, emphasizing their ecological significance.<br><br>RESULTS: We analyzed the microbiome of A. marina from the Red Sea coast using high-throughput Illumina sequencing and culture-dependent methods across various compartments (bulk soil, rhizosphere, rhizoplane, roots, and leaves). Our findings revealed distinct compartment-specific microbial communities, with Proteobacteria being the dominant phylum. Functional predictions indicated diverse microbial roles in metal uptake and plant growth promotion (PGP). Remarkably, our culture-dependent methods allowed us to recover 56% of the bacterial diversity present in the microbiome, resulting in the isolation and characterization of 256 bacterial strains. These isolates were screened for PGP traits, including salt and heat tolerance, siderophore production, and pectinase activity. Out of the 77 bacterial isolates tested, 11 demonstrated a significant ability to enhance Arabidopsis growth under salt stress.<br><br>CONCLUSIONS: Our study highlights the ecological significance of mangrove microbiomes and the potential of culture collections in offering innovative solutions for ecological restoration and crop production in saline conditions. The unique collection of mangrove bacteria, particularly from the rhizosphere and endophytes, showcases significant PGP traits and stress tolerance capabilities. These findings emphasize the importance of functional traits, such as salt tolerance, in the recruitment of endophytic bacteria by plants over taxonomic affiliation. The identified bacterial strains hold potential not only for developing biofertilizers to improve crop productivity but also for ecological restoration projects aimed at rehabilitating saline-degraded lands, thereby contributing to overall ecosystem health and sustainability.}, }
@article {pmid39633321, year = {2024}, author = {Farias, RM and Jiang, Y and Levy, EJ and Hwang, C and Wang, J and Burton, EM and Cohen, L and Ajami, N and Wargo, JA and Daniel, CR and McQuade, JL}, title = {Diet and Immune Effects Trial (DIET)- a randomized, double-blinded dietary intervention study in patients with melanoma receiving immunotherapy.}, journal = {BMC cancer}, volume = {24}, number = {1}, pages = {1493}, pmid = {39633321}, issn = {1471-2407}, mesh = {Humans ; *Melanoma/therapy/immunology/diet therapy ; Double-Blind Method ; *Gastrointestinal Microbiome/immunology ; Female ; Male ; Immunotherapy/methods ; Dietary Fiber/administration &amp; dosage ; Adult ; Middle Aged ; Immune Checkpoint Inhibitors/therapeutic use ; Quality of Life ; Aged ; Diet ; Skin Neoplasms/diet therapy/immunology/therapy ; }, abstract = {BACKGROUND: Gut microbiome modulation is a promising strategy for enhancing the response to immune checkpoint blockade (ICB). Fecal microbiota transplant studies have shown positive signals of improved outcomes in both ICB-naïve and refractory melanoma patients; however, this strategy is challenging to scale. Diet is a key determinant of the gut microbiota, and we have previously shown that (a) habitual high dietary fiber intake is associated with an improved response to ICB and (b) fiber manipulation in mice impacts antitumor immunity. We recently demonstrated the feasibility of a controlled high-fiber dietary intervention (HFDI) conducted in melanoma survivors with excellent compliance and tolerance. Building on this, we are now conducting a phase II randomized trial of HFDI versus a healthy control diet in melanoma patients receiving ICB.<br><br>METHODS: This is a randomized, double-blind, fully controlled feeding study that will enroll 45 melanoma patients starting standard-of-care (SOC) ICB in three settings: adjuvant, neoadjuvant, and unresectable. Patients are randomized 2:1 to the HFDI (target fiber 50&#xa0;g/day from whole foods) or healthy control diet (target fiber 20&#xa0;g/day) stratified by BMI and cohort. All meals are prepared by the MD Anderson Bionutrition Core and are isocaloric and macronutrient-controlled. The intervention includes a 1-week equilibration period and then up to 11 weeks of diet intervention. Longitudinal blood, stool and tumor tissue (if available) are collected throughout the trial and at 12 weeks post intervention.<br><br>DISCUSSION: This DIET study is the first fully controlled feeding study among cancer patients who are actively receiving immunotherapy. The goal of the current study is to establish the effects of dietary intervention on the structure and function of the gut microbiome in patients with melanoma treated with SOC immunotherapies. The secondary endpoints include changes in systemic and tumor immunity, changes in the metabolic profile, quality of life, symptoms, disease response and immunotherapy toxicity.<br><br>TRIAL REGISTRATION: This protocol is registered with the U.S. National Institutes of Health trial registry, ClinicalTrials.gov, under the identifier NCT04645680. First posted 2020-11-27; last verified 2024-06.}, }
@article {pmid39633292, year = {2024}, author = {Ma, X and Li, T and Liu, C and Ge, H and Zheng, D and Ma, J and Guo, Y and Zhang, X and Liu, J and Liu, Y and Li, Y and Shen, W and Ma, Y and Liu, Y and Su, R and Wang, T and Zhang, X and Ma, J and Wang, H}, title = {Alterations of gut microbiota and metabolome are associated with primary nephrotic syndrome in children.}, journal = {BMC microbiology}, volume = {24}, number = {1}, pages = {519}, pmid = {39633292}, issn = {1471-2180}, support = {2023AAC03550//the Ningxia Natural Science Foundation, China/ ; 2023-NWKYP-043//the Scientifc Research Project on Health System in Ningxia Autonomous Region, China/ ; XM2022046//the Research Project of Ningxia Medical University, China/ ; 2022BSB03112//the Ningxia Gut Homeostasis and Chronic Disease Prevention and Treatment Scientifc and Technological Innovation Team, China/ ; 2023BEG02011//the Key Research and Development Program of Ningxia, China/ ; 2023GKLRLX17//Program of Ningxia Science and Technology Leading Talent/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; *Nephrotic Syndrome/microbiology/metabolism ; *Metabolome ; Child ; Male ; Female ; *Feces/microbiology ; *Dysbiosis/microbiology ; Child, Preschool ; T-Lymphocytes, Regulatory/immunology ; Th17 Cells/immunology/metabolism ; Faecalibacterium ; Bacteria/classification/isolation &amp; purification/metabolism/genetics ; }, abstract = {BACKGROUND: Primary nephrotic syndrome (PNS) is a common glomerular disease in children. Dysbiosis of gut microbiota acts as a cause of Treg abnormalities. However, the intestinal metabolic impact of PNS with children remains poorly understood. This study aims to investigate the dynamic changes of gut microbiota and it's metabolism in children with PNS.<br><br>METHODS: Fecal and peripheral blood samples were separately collected from patients with initial diagnosis of PNS (PNS_In group), recurrence of PNS (PNS_Re group), and healthy controls (HCs group). The fecal samples were subjected to the microbiome and metabolome by the multi-omics analysis. Additionally, the peripheral blood samples were collected and associated inflammatory indicators were determined.<br><br>RESULTS: We found that in PNS_In group, lipopolysaccharide (LPS), pro-inflammatory interleukin (IL)-6, IL-17A, IL-23p19, and IL-1&#x3b2; were significantly increased compared with those in HCs group. However, these abnormalities were dramatically reversed in PNS_Re group treated with prednisone acetate. Moreover, the crucial Treg/Th17 axis in PNS inflammation was also proved to be discriminated between PNS and HCs. Gut microbial dysbiosis was identified in PNS_In and PNS_Re patients. At the genus level, compared to HCs group, the abundance of Faecalibacterium notably changed in PNS_In and PNS_Re groups, showing negatively correlated with inflammatory factors. Moreover, the fecal metabolome of PNS_In and PNS_Re remarkably altered with the major impacts in the metabolism of phenylalanine, ABC transporters, arginine and proline.<br><br>CONCLUSION: The dynamic changes of gut microbiota and associated metabolites are closely correlated with initial period and recurrence of PNS in children via probably regulating inflammatory Th17/Treg axis, which may potentially provide novel targets for the control of the disease.<br><br>CLINICAL TRIAL NUMBER: Not applicable.}, }
@article {pmid39633134, year = {2024}, author = {Han, GH and Yu, J and Kang, MJ and Park, MJ and Noh, CH and Kim, YJ and Kwon, KK}, title = {Phylosymbiosis in Seven Wild Fish Species Collected Off the Southern Coast of Korea: Skin Microbiome Most Strongly Reflects Evolutionary Pressures.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {153}, pmid = {39633134}, issn = {1432-184X}, support = {20210469//Ministry of Oceans and Fisheries/ ; }, mesh = {Animals ; Republic of Korea ; *Microbiota ; *Skin/microbiology ; *Phylogeny ; *RNA, Ribosomal, 16S/genetics ; *Fishes/microbiology ; *Symbiosis ; *Bacteria/classification/genetics/isolation &amp; purification ; Gills/microbiology ; Biological Evolution ; Species Specificity ; }, abstract = {Phylosymbiosis is defined as the relationship in which the microbiome recapitulates the phylogeny of the host and has been demonstrated in a variety of terrestrial organisms, although it has been understudied in fish, the most phylogenetically diverse vertebrate. Given that the species-specificity of fish microbiomes was detected in multiple body parts and differed by body parts, we assumed that the phylogenetic reflection of the microbiome would differ across body parts. Thus, we analyze the difference of phylosymbiotic relationships in the microbial communities found in three body parts (skin, gills, and intestine) of seven wild fish species from four families (Labridae, Sebastidae, Sparidae, and Rajidae) via 16S rRNA gene amplicon sequencing. Fishes were purchased at Docheon port market in Tongyeong City, Korea and were transported to nearby research institutes for aliveness. Mantel tests using dissimilarity values of microbiomes and hosts' divergence times showed that the differences in microbial communities in all three body parts were related to the hosts' divergence time. This pattern was the most pronounced in the skin. Furthermore, fishes from the same family showed similar bacterial compositions on their skins and gills, with clear differences depending on the family, with the exception of Labridae. These results suggest that the skin microbiome is particularly vulnerable to evolutionary pressures. We hypothesized that the evolution of the fish immune system and the difference in feeding habits induced the stronger phylosymbiotic signal in the skin. Collectively, this dataset will be useful for understanding the fish microbiome and give insights into phylosymbiosis of aquatic animals across body parts.}, }
@article {pmid39633131, year = {2024}, author = {Petrić Howe, N and Bates, E}, title = {Why breast cancer treatments might work best just after your period.}, journal = {Nature}, volume = {}, number = {}, pages = {}, doi = {10.1038/d41586-024-03986-y}, pmid = {39633131}, issn = {1476-4687}, }
@article {pmid39633061, year = {2024}, author = {Paduano, S and Marchesi, I and Valeriani, F and Frezza, G and Facchini, MC and Romano Spica, V and Bargellini, A}, title = {Characterization by 16S Amplicon Sequencing of Bacterial Communities Overall and During the Maturation Process of Peloids in Two Spas of an Italian Thermal Complex.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {152}, pmid = {39633061}, issn = {1432-184X}, mesh = {*Bacteria/genetics/classification/isolation &amp; purification ; Italy ; *RNA, Ribosomal, 16S/genetics ; *Microbiota ; *Clay/chemistry ; Biodiversity ; High-Throughput Nucleotide Sequencing ; DNA, Bacterial/genetics ; Mineral Waters/microbiology ; Phylogeny ; }, abstract = {Peloids are made by mixing clay materials with thermo-mineral waters, enriched with organic substances from microorganisms during maturation. Their beneficial properties may depend on clay minerals, water characteristics, and microbial components, although strong evidence is lacking. Next Generation Sequencing (NGS) allows a comprehensive approach to studying the entire microbial community, including cultivable and uncultivable bacteria. Our study aims to characterize, by NGS, the bacterial community overall and during the maturation process of thermal muds in two spas (A-B) of an Italian thermal complex. Peloids were produced from sulfurous-bromine-iodine thermal water and clay material: natural mud for spa A and sterile clay for spa B. Thermal waters and peloids at different maturation stages (2/4/6 months) were analyzed for microbiome characterization by 16S amplicon sequencing. Biodiversity profiles showed a low level of similarity between peloids and water used for their maturation. Peloids from spa A showed greater microbial richness than those from spa B, suggesting that natural mud with an existing bacterial community leads to greater biodiversity than sterile clay. Genera involved in sulfur metabolism were prevalent in both spas, as expected considering peloids matured in sulfide-rich water. For all three maturation stages, the prevalent genera were Thiobacillus and Pelobacter in spa A and Thiobacillus, Thauera, Pelobacter, and Desulfuromonas in spa B. Richness and diversity indices showed that the community seemed to stabilize after 2-4 months. The 16S amplicon sequencing to study bacterial communities enables the identification of a biological signature that characterizes a specific thermal matrix, defining its therapeutic and cosmetic properties. The bacterial composition of peloids is affected by the thermal water and the type of clay material used in their formulation and maturation.}, }
@article {pmid39632843, year = {2024}, author = {Zhang, Z and Fang, Y and He, Y and Farag, MA and Zeng, M and Sun, Y and Peng, S and Jiang, S and Zhang, X and Chen, K and Xu, M and Han, Z and Zhang, J}, title = {Bifidobacterium animalis Probio-M8 improves sarcopenia physical performance by mitigating creatine restrictions imposed by microbial metabolites.}, journal = {NPJ biofilms and microbiomes}, volume = {10}, number = {1}, pages = {144}, pmid = {39632843}, issn = {2055-5008}, support = {32160545//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32222066//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {*Sarcopenia/metabolism ; *Gastrointestinal Microbiome ; Animals ; *Creatine ; *Probiotics/administration &amp; dosage ; Mice ; Humans ; *Bifidobacterium animalis ; Male ; *Feces/microbiology/chemistry ; Metabolome ; Aged ; Female ; Physical Functional Performance ; Mice, Inbred C57BL ; Indoles ; }, abstract = {Sarcopenia is a major health challenge due to an aging population. Probiotics may improve muscle function through gut-muscle axis, but their efficacy and mechanisms in treating sarcopenia remain unclear. This study investigated the impact of Bifidobacterium animalis subsp. lactis Probio-M8 (Probio-M8) on old mice and sarcopenia patients. We analyzed 43 subjects, including gut microbiome, fecal metabolome, and serum metabolome, using a multi-omics approach to assess whether Probio-M8 can improve sarcopenia by modulating gut microbial metabolites. Probio-M8 significantly improved muscle function in aged mice and enhanced physical performance in sarcopenia patients. It reduced pathogenic gut species and increased beneficial metabolites such as indole-3-lactic acid, acetoacetic acid, and creatine. Mediating effect analyses revealed that Probio-M8 effectively reduced n-dodecanoyl-L-homoserine lactone level in gut concurrent with increased creatine circulation, to significantly enhance host physical properties. These findings provide new insights into probiotics as a potential treatment for sarcopenia by modulating gut microbiota metabolism.}, }
@article {pmid39632543, year = {2024}, author = {Taherkhani, S and Ahmadi, P and Nasiraie, LR and Janzadeh, A and Honardoost, M and Sedghi Esfahani, S}, title = {Flavonoids and the gut microbiome: a powerful duo for brain health.}, journal = {Critical reviews in food science and nutrition}, volume = {}, number = {}, pages = {1-16}, doi = {10.1080/10408398.2024.2435593}, pmid = {39632543}, issn = {1549-7852}, abstract = {Flavonoids, a class of polyphenolic compounds, are widely distributed in plant-based foods and have been recognized for their potential to promote overall health and well-being. Flavonoids in fruits and vegetables offer various beneficial effects such as anti-aging, anticancer, and anti-inflammatory properties. Flavonoids have been extensively studied for their neuroprotective properties, which are attributed to their ability to cross the blood-brain barrier and interact with neural cells. Factors like gut microbiota composition, age, genetics, and diet can impact how well flavonoids are absorbed in the gut. The gut microbiota can enhance the absorption of flavonoids through enzymatic processes, making microbiota composition a key factor influenced by age, genetics, and diet. Flavonoids can modulate the gut microbiota through prebiotic and antimicrobial effects, affecting the production of beneficial microbial metabolites like short-chain fatty acids (SCFAs) such as butyrate, which play a role in brain function and health. The gut microbiome also modulates the immune system, which is critical for preventing neuroinflammation. Additionally, flavonoids can benefit mental and psychological health by influencing anti-inflammatory signaling pathways in brain cells and increasing the absorption of tyrosine and tryptophan, precursors to neurotransmitters like serotonin, dopamine, norepinephrine, adrenaline, and gamma-aminobutyric acid (GABA). The flavonoid-gut microbiome axis is a complex and multifaceted relationship that has significant implications for neurological health. This review will explore how genetic and environmental factors can impact flavonoid absorption and the positive effects of flavonoids on brain health and the gut microbiota network.}, }
@article {pmid39632512, year = {2024}, author = {Sinha, A and Griffith, L and Acharjee, A}, title = {Systematic Review and Meta-Analysis: Taurine and Its Association With Colorectal Carcinoma.}, journal = {Cancer medicine}, volume = {13}, number = {23}, pages = {e70424}, doi = {10.1002/cam4.70424}, pmid = {39632512}, issn = {2045-7634}, support = {//Health Data Research UK/ ; //NIHR Birmingham SRMRC/ ; }, mesh = {*Taurine ; Humans ; *Colorectal Neoplasms/metabolism/pathology ; Biomarkers, Tumor/metabolism ; Prognosis ; }, abstract = {BACKGROUND: Colorectal cancer (CRC) is one of the most common cancers. Various options are available for treatment, but prognosis is still poor in the more advanced stages. Current screening methods are not as accurate for distinguishing between benign and malignant growths, resulting in unnecessary invasive procedures. Recently a focus has been placed on identifying metabolites. Of these, taurine has frequently been detected, and this particular compound has a multifactorial role in human physiology.<br><br>METHODS: We conducted a systematic review of studies up till November 2023. Searches were done in three databases- MEDLINE, CINAHL-Ebsco, and PubMed. Three independent reviewers filter titles, abstracts, and full-texts according to selection criteria. Ten studies (samples&#x2009;=&#x2009;1714) were identified showing a differential level of taurine in CRC patient samples. Quality assessment accounted for the risk of bias of each study using the 'robvis' tool. Where meaningful comparisons could be made, meta-analyses were carried out using the 'R' program for precalculated effect sizes with 'metagen' in R. The 'meta' package was utilised for creation of forest plots.<br><br>FINDINGS: Taurine was shown to significantly increase odds of CRC. It was also significantly associated with being a discriminator for CRC as a diagnostic metabolite. This was maintained at various stages of CRC. Taurine had increased expression in CRC patients, especially when the matrix utilised was blood. Nevertheless, there was significant heterogeneity for some outcomes.<br><br>INTERPRETATION: In conclusion, these findings highlight the potential of using taurine as well as other bile acid metabolites (lithocholic and ursodeoxycholic acid) to diagnose CRC and illustrate the link with microbiome interactions. Overall increased taurine concentration are associated with significantly increased odds for CRC. There was mostly an increase in relative expression of taurine in CRC samples, excluding results from Wang et&#xa0;al.}, }
@article {pmid39632378, year = {2024}, author = {Li, Y and Hu, W and Lin, B and Ma, T and Zhang, Z and Hu, W and Zhou, R and Kwok, LY and Sun, Z and Zhu, C and Zhang, H}, title = {Omic characterizing and targeting gut dysbiosis in children with autism spectrum disorder: symptom alleviation through combined probiotic and medium-carbohydrate diet intervention - a pilot study.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2434675}, doi = {10.1080/19490976.2024.2434675}, pmid = {39632378}, issn = {1949-0984}, mesh = {Humans ; *Autism Spectrum Disorder/diet therapy/microbiology ; Pilot Projects ; *Probiotics/administration &amp; dosage ; *Gastrointestinal Microbiome ; *Dysbiosis/microbiology/diet therapy/therapy ; Male ; Child ; Female ; *Feces/microbiology/chemistry ; Child, Preschool ; Bacteria/classification/isolation &amp; purification/genetics/metabolism ; Dietary Carbohydrates/metabolism/administration &amp; dosage ; Bifidobacterium animalis ; }, abstract = {Autism spectrum disorder (ASD) currently lacks effective diagnostic and therapeutic approaches. Disruptions in the gut ecosystem have been observed in individuals with ASD, suggesting that targeting gut microbiota through probiotic and dietary supplementation may serve as a potential treatment strategy. This two-phase study aimed to characterize the fecal metagenome of children with ASD and investigate the beneficial effects of a combined probiotic and medium-carbohydrate intervention in ASD. Fecal metagenomes of children with ASD were compared to those of typically developing children, revealing intestinal dysbiosis in ASD, characterized by reduced levels of Prevotella sp. Dialister invisus, and Bacteroides sp. along with increased predicted abundances of inosine, glutamate, xanthine, and methylxanthine. The gut bacteriome and phageome exhibited high cooperativity. In a 3-month pilot study, Bifidobacterium animalis subsp. lactis Probio-M8 (Probio-M8) was administered alongside a medium-carbohydrate diet to Chinese children with ASD. The primary endpoint was the Childhood Autism Rating Scale (CARS), while the secondary endpoint was the Gastrointestinal Symptom Rating Scale (GSRS). A total of 72 autistic children were initially recruited for the intervention study, but only 53 completed the intervention. Probio-M8, in combination with dietary intervention, significantly improved CARS and GSRS scores, increased fecal levels of Bifidobacterium animalis, Akkermansia muciniphila, Fusicatenibacter saccharivorans, and Sutterella sp. while also reducing Blautia obeum (Benjamini-Hochberg corrected p ≤ 0.05 for all cases). The intervention also modulated fecal metabolites associated with the metabolism of amino acids (lysine), neurotransmitters (glutamate, γ-aminobutyric acid), polyunsaturated fatty acids (arachidonate, myristic acid), and vitamin B3. In conclusion, Probio-M8 combined with medium-carbohydrate diet effectively improved ASD symptoms, with associated changes in the gut microbiome and metabolome, supporting its potential as an adjunctive therapy for ASD.}, }
@article {pmid39631929, year = {2024}, author = {Sandhu, KK and Scott, A and Tatler, AL and Belchamber, KBR and Cox, MJ}, title = {Macrophages and the microbiome in chronic obstructive pulmonary disease.}, journal = {European respiratory review : an official journal of the European Respiratory Society}, volume = {33}, number = {174}, pages = {}, pmid = {39631929}, issn = {1600-0617}, mesh = {*Pulmonary Disease, Chronic Obstructive/microbiology/immunology/physiopathology ; Humans ; *Microbiota ; *Lung/microbiology/immunology/physiopathology ; *Host-Pathogen Interactions ; *Macrophages, Alveolar/microbiology/immunology ; Animals ; *Phagocytosis ; Bacteria/immunology ; Macrophages/microbiology/immunology ; Dysbiosis ; }, abstract = {COPD is a heterogeneous disease of the lungs characterised by restricted airflow. Chronic inflammation and recurrent bacterial infections are known to be important driving factors in exacerbations of this disease. Despite a marked increase in the number of alveolar macrophages present in the lungs of COPD patients, there is evidence of reduced clearance of pathogenic bacteria, leading to recurrent infection, exacerbation and subsequent lung function decline. This is thought to be attributed to a defect in the phagocytic capability of both alveolar and monocyte-derived macrophages in COPD. In addition to this defect, there is apparent selectivity in bacterial uptake by COPD macrophages because certain pathogenic genera, such as Haemophilus, Moraxella and Streptococcus, are taken up more readily than others. The respiratory microbiome plays a key role in regulating the host immune response both in health and during chronic inflammation. In patients with COPD, there are distinct changes in the composition of the respiratory microbiome, particularly the lower respiratory tract, where dominance of clinically relevant pathogenic species is commonly observed. Whether there are links between these changes in the microbiome and dysfunctional macrophage phagocytosis has not yet been widely studied. This review aims to discuss what is currently known about these phenomena and to explore interactions between macrophages and the respiratory microbiome.}, }
@article {pmid39631927, year = {2024}, author = {Milczewska, J and Syunyaeva, Z and Żabińska-Jaroń, A and Sands, D and Thee, S}, title = {Changing profile of bacterial infection and microbiome in cystic fibrosis: when to use antibiotics in the era of CFTR-modulator therapy.}, journal = {European respiratory review : an official journal of the European Respiratory Society}, volume = {33}, number = {174}, pages = {}, pmid = {39631927}, issn = {1600-0617}, mesh = {*Cystic Fibrosis/microbiology/drug therapy ; Humans ; *Cystic Fibrosis Transmembrane Conductance Regulator/genetics/metabolism ; *Anti-Bacterial Agents/therapeutic use/adverse effects ; *Quinolones/therapeutic use/adverse effects ; *Microbiota/drug effects ; Treatment Outcome ; *Aminophenols/therapeutic use ; *Bacterial Infections/drug therapy/microbiology/diagnosis ; Respiratory Tract Infections/microbiology/drug therapy/diagnosis ; Chloride Channel Agonists/therapeutic use ; Drug Combinations ; Lung/microbiology/drug effects/physiopathology ; Bacteria/drug effects/metabolism ; Clinical Decision-Making ; Host-Pathogen Interactions ; Risk Factors ; Indoles/therapeutic use/adverse effects ; Benzodioxoles/therapeutic use/adverse effects ; }, abstract = {The advent of cystic fibrosis transmembrane conductance regulator (CFTR) modulator therapy, especially the triple therapy combining the drugs elexacaftor, tezacaftor, ivacaftor (ETI), has significantly changed the course of the disease in people with cystic fibrosis (pwCF). ETI, which is approved for the majority (80-90%) of pwCF, partially restores CFTR channel function, resulting in improved mucociliary clearance and, consequently, improved lung function, respiratory symptoms and pulmonary exacerbations. The bacterial burden of classical CF pathogens such as Pseudomonas aeruginosa and Staphylococcus aureus is reduced without reaching eradication in the majority of infected patients. Limited data is available on less common or emerging bacterial pathogens. ETI has a positive effect on the lung microbiome but does not fully restore it to a healthy state. Due to the significant reduction in sputum production under ETI, respiratory samples such as deep-throat swabs are commonly taken, despite their inadequate representation of lower respiratory tract pathogens. Currently, there are still unanswered questions related to this new therapy, such as the clinical impact of infection with cystic fibrosis (CF) pathogens, the value of molecular diagnostic tests, the durability of the effects on respiratory infection and the role of fungal and viral infections. This article reviews the changes in bacterial lung infections and the microbiome in CF to provide evidence for the use of antibiotics in the era of ETI.}, }
@article {pmid39631783, year = {2024}, author = {Liu, J and Yu, M and Wang, X and Qi, M and Wu, M}, title = {Dynamic Changes in Microbiome and Metabolome during Sun-Drying of Oysters (Crassostrea gigas), a Traditional Procedure in South China.}, journal = {Journal of microbiology and biotechnology}, volume = {34}, number = {12}, pages = {2558-2567}, doi = {10.4014/jmb.2312.12033}, pmid = {39631783}, issn = {1738-8872}, abstract = {Sun-drying constitutes a traditional method employed in the preparation of dried oysters within the coastal regions of South China. However, its ramifications on nutritional attributes and the genesis of flavor-contributory compounds in the resultant dried oysters remain significantly unexplored. This research endeavors to scrutinize the repercussions of the production process on the microbiota and metabolites within dried oysters. Utilizing 16s rRNA amplicon sequencing, the identification of 409 operational taxonomic units (OTUs) ensued, wherein Proteobacteria, Bacteroidetes, Firmicutes, Tenericutes, and Actinobacteria surfaced as the primary pathogenic bacteria present in oyster samples. Analysis of the dried oyster sample metabolomes via LC-MS unveiled a discernible augmentation in compounds associated with steroid hormone biosynthesis, arachidonic acid metabolism, biosynthesis of unsaturated fatty acids, and linoleic acid metabolism throughout the entirety of the drying process. Subsequent exploration into the association between metabolites and bacterial communities highlighted the prevailing coexistence of Mycoplasma, Psychrilyobacter, and Vibrio demonstrating negative correlations with a substantial number of metabolites across categories including organic acid and its derivatives, nucleotide and its metabolites, free fatty acids, and amino acids. Conversely, Shewanella and Arcobacter exhibited positive correlations with these metabolite categories. This exhaustive investigation offers invaluable insights into the dynamic alterations within the microbiota and metabolites of dried oysters across diverse drying periods. These findings are anticipated to significantly contribute to the advancement of production techniques and the formulation of enhanced safety measures for the processing of dried oysters.}, }
@article {pmid39631576, year = {2024}, author = {Puja, BK and Mallick, S and Dey, T and Chanda, S and Ghosh, S}, title = {Xylooligosaccharide recovery from sugarcane bagasse using β-xylosidase-less xylanase, BsXln1, produced by Bacillus stercoris DWS1: Characterization, antioxidant potential and influence on probiotics growth under anaerobic conditions.}, journal = {International journal of biological macromolecules}, volume = {}, number = {}, pages = {138307}, doi = {10.1016/j.ijbiomac.2024.138307}, pmid = {39631576}, issn = {1879-0003}, abstract = {Xylooligosaccharides (XOS) are excellent prebiotic which improve health through selective modulation of beneficial gut microbiome. Its production from agroresidues using microbial xylanase is considered as sustainable and economic approach. In this study a xylanase producing bacterium isolated from decaying wood soil was phylogenetically identified and designated as Bacillus stercoris DWS1. Xylanase (BsXln1) purified from the bacterium had pH and temperature optima of 7 and 37-60 °C, respectively, and it retained 85 % activity upon preincubation at 60 °C for 40 min. Indicating its moderate thermostability. Zymogram analysis of partially purified BsXln1 revealed its molecular weight of ~35 kDa. B. stercoris DWS1 produced 200 U mL[-1] of BsXln1 in presence of 1.5 % sugarcane bagasse (SCB) as carbon source; which was enhanced to 591 U mL[-1] through optimization of cultural conditions. Xylan extracted from SCB was morphologically and structurally characterized, and then depolymerized by BsXln1 to yield XOS (400 mg g[-1]). Analysis of purified XOS by TLC, followed by ESI-MS showed predominance of xylobiose and xylotriose. XOS exhibited in vitro antioxidant activities against DPPH and ABTS free radicals, however, it had limited prebiotic activity on Lactobacillus plantarum and Lactobacillus fermentum under anaerobic condition. In conclusion, the xylanase, BsXln1, produced by B. stercoris DWS1 can be used in food industries for efficient production of bioactive XOS from agroresidues.}, }
@article {pmid39631567, year = {2024}, author = {Hamada, K and Nakanishi, Y and Muta, Y and Omatsu, M and Iwane, K and Ikeda, M and Chen, J and Masui, Y and Aoyama, N and Agatsuma, N and Yamakawa, G and Utsumi, T and Kitamoto, H and Okabe, M and Itatani, Y and Adachi, T and Yasuda, K and Yamamoto, S and Fukuda, A and Kuroda, E and Ohmuraya, M and Obama, K and Hirota, S and Ikeuchi, H and Nakanishi, K and Seno, H}, title = {Retinoblastoma-Binding Protein 9 Suppresses Intestinal Inflammation and Inflammation-Induced Tumorigenesis in Mice.}, journal = {Cellular and molecular gastroenterology and hepatology}, volume = {}, number = {}, pages = {101435}, doi = {10.1016/j.jcmgh.2024.101435}, pmid = {39631567}, issn = {2352-345X}, abstract = {BACKGROUND &amp; AIMS: Retinoblastoma-binding protein 9 (RBBP9) was initially reported as cell cycle regulator via RB/E2F. Accumulating evidence has revealed the importance of RBBP9 in physiological and pathological states including inflammatory disease. However, the functional role of RBBP9 in ulcerative colitis (UC) and colitis-associated cancer (CAC) remains elusive.<br><br>METHODS: Human samples of UC and CAC were examined by immunohistochemical and bioinformatics analyses. We established dextran sodium sulfate (DSS)-induced colitis, azoxymethane (AOM)/DSS-induced CAC model, and Apc[Min/+] sporadic tumor model using wild-type and Rbbp9[-/-] mice. RNA sequencing was analyzed to identify the phenotype alternation upon Rbbp9 deletion. In addition, genetic and pharmacological inhibition of the Janus kinase (JAK)/signal transducer and activator of transcription 1 (STAT1) pathway was performed.<br><br>RESULTS: The expression of RBBP9 was reduced in human UC and CAC samples. The loss of RBBP9 enhanced the activation of interferon (IFN)/JAK/STAT1 signaling, resulting in susceptibility to DSS-induced colitis and AOM/DSS-induced CAC tumors by increasing epithelial cell apoptosis and immune activation. An in vitro kinase assay revealed that RBBP9 directly regulated JAK/STAT1 signaling by suppressing STAT1 phosphorylation. A positive feedback loop involving epithelial cell apoptosis, commensal microbiome invasion, and activation of submucosal immune activity was identified in Rbbp9[-/-] mouse intestines through enhanced JAK/STAT1 signaling in RBBP9-deficient epithelial cells and macrophages. The genetic inhibition of STAT1 or treatment with the JAK/STAT inhibitor reversed epithelial cell apoptosis and mitigated the enhanced susceptibility to DSS-induced colitis in Rbbp9[-/-] mice.<br><br>CONCLUSIONS: RBBP9 suppresses the intestinal inflammation by negatively regulating JAK/STAT1 signaling pathway.}, }
@article {pmid39631408, year = {2024}, author = {Risk, BD and Graham, EL and Zhang, M and Wei, Y and Stark, GC and Brown, GD and Gentile, CL and Weir, TL}, title = {Bacillus subtilis DE111 partially reverses endothelial dysfunction in western-diet fed mice.}, journal = {Beneficial microbes}, volume = {}, number = {}, pages = {1-17}, doi = {10.1163/18762891-bja00052}, pmid = {39631408}, issn = {1876-2891}, abstract = {Imbalances in the gut microbiome have emerged as an important factor in endothelial dysfunction, a significant risk factor for cardiovascular disease. Thus, interventions targeting the microbiome may prove helpful in preventing or reversing this impairment. We previously reported that spore-forming Bacillus subtilis DE111 improved endothelial function in a cohort of healthy, non-obese humans after a four-week intervention. Building on these promising results, the present study sought to investigate whether administering B. subtilis DE111 could reverse endothelial dysfunction in mice with diet-induced obesity. Male C57BL/6J mice were fed a Western diet (WD; n = 24) or standard diet (SD; n = 24) for ten weeks to induce endothelial dysfunction, after which half of the animals in each group (n = 12) were allocated to receive B. subtilis DE111 (hereafter, PB) formulated into the diet for an additional eight weeks. Outcomes included endothelial-dependent arterial dilation, glucose tolerance, body weight changes, microbiota profiles, and assessments of intestinal permeability and mucosal immunity markers. Furthermore, a cell culture model of gut barrier function was used to assess the effects of PB on gut barrier integrity. PB treatment significantly attenuated WD-induced mesenteric endothelial-dependent arterial dilation, independent of changes in other cardiometabolic parameters or changes in gut barrier function. In vitro trans-epithelial electrical resistance of the Caco-2 cell culture confirmed that neither PB-conditioned media nor faecal waters from B. subtilis-treated human stool resulted in gut barrier improvements, nor did they protect against inflammation-associated barrier disruptions. Unsurprisingly, microbiota analysis revealed significant differences in Shannon's alpha diversity of WD-fed animals compared to SD. These data suggest that PB consumption significantly attenuated WD diet-induced endothelial dysfunction; however, the underlying mechanisms of this protection were not determined. Improvement in endothelial function was independent of PB-mediated changes to body weight or gut barrier function. Further studies should explore B. subtilis-mediated immune responses or metabolite production as mechanisms underlying these endothelial protective effects.}, }
@article {pmid39631339, year = {2024}, author = {Feng, T and Meng, Z and Li, H and Chen, G and Liu, C and Tang, K and Chen, J}, title = {Industrial hemp (Cannabis sativa L.) adapts to cadmium stress by reshaping rhizosphere fungal community.}, journal = {The Science of the total environment}, volume = {957}, number = {}, pages = {177851}, doi = {10.1016/j.scitotenv.2024.177851}, pmid = {39631339}, issn = {1879-1026}, abstract = {Increasing evidence indicates that plants under environmental stress can actively seek the help of microbes ('cry-for-help' hypothesis). However, empirical evidence underlying this strategy is limited under metal-stress conditions. Here, we employed integrated microbial community profiling in cadmium (Cd) polluted soil and culture-based methods to investigate the three-way interactions between the industrial hemp (Cannabis Sativa L.), rhizospheric microbes, and Cd stress. Results from the pot and three cycles of the successful hemp planting experiments showed that Cd stress significantly affected the composition of rhizosphere fungi in industrial hemp and induced enrichment of the fungal operational taxonomic unit (OTU)3 (Cladosporium). A representative of OTU3 (strain DM-2) was successfully isolated. In a hydroponic experiment, inoculation of DM-2 significantly increased the shoot length (by 25.84 %) and fresh weight (by 92.66 %) of hemp seedlings when compared to the absence of DM-2 under the Cd stress. The findings indicate that DM-2 inoculation could effectively alleviate the Cd stress in hemp seedlings. Metabolomic analysis of spent media with or without DM-2 revealed the association of DM-2 with the transformation of root exudates to melatonin, which may be a key chemical in plant-microbe interactions against abiotic stresses. The findings will inform efforts to manipulate the root microbiome to enhance plant growth in polluted environments.}, }
@article {pmid39631325, year = {2024}, author = {Zhang, Y and Liu, Q and Xie, H and Zhang, W and Lin, X and Zhang, H and Yu, H and Ma, Y and Zhang, C and Geng, H and Shi, N and Cui, L and Li, B and Li, YF}, title = {Fecal microbiota transplantation as an effective way in treating methylmercury-poisoned rats.}, journal = {The Science of the total environment}, volume = {957}, number = {}, pages = {177850}, doi = {10.1016/j.scitotenv.2024.177850}, pmid = {39631325}, issn = {1879-1026}, abstract = {Methylmercury (MeHg) can cause devastating neurotoxicity in animals and human beings. Gut microbiota dysbiosis has been found in MeHg-poisoned animals. Fecal microbiota transplantation (FMT) has been shown to improve clinical outcomes in a variety of diseases such as epilepsy, amyotrophic lateral sclerosis (ALS) and autism. The aim of this study was to investigate the effects of FMT on MeHg-poisoned rats. FMT treatment was applied to MeHg-poisoned rats for 14 days. The neurobehavior, weight changes, dopamine (DA), the total Hg and MeHg level were evaluated. Besides, the gut microbiota and metabolites change in feces were also checked. It was found that FMT helped weight gain, alleviated the neurological disorders, enhanced fecal mercury excretion and MeHg demethylation, reconstructed gut microbiome and promoted the production of gut-brain axis related-metabolites in MeHg-poisoned rats. This study elaborates on the therapeutic efficacy of FMT in treating of MeHg-poisoned rats, which sheds lights on the treatment of neurological diseases like Minamata Disease and even Parkinson's Disease.}, }
@article {pmid39631282, year = {2024}, author = {Ji, W and Kim, TY and Lee, CW and Kim, ZH and Jung, JY and Ban, BC and Kong, C and Kim, M}, title = {Supplementation of Parachlorella sp. in feed promote the gut microbiome colonization and fecal IgA response of broiler in both early and late period.}, journal = {Poultry science}, volume = {104}, number = {1}, pages = {104572}, doi = {10.1016/j.psj.2024.104572}, pmid = {39631282}, issn = {1525-3171}, abstract = {This study evaluated the effects of Parachlorella sp. KSN1 (PA) supplementation on the gut microbiota and intestinal immunity of broilers of different ages. A total of 180 Ross 308 broiler chicks were weighed and divided into early (1 to 10 days post hatch) and late (11 to 28 days post hatch) periods, with six replicates of 10 chicks per cage assigned to two dietary groups. The experimental diets included a corn-soybean meal-based control diet and a treatment diet supplemented with 0.5% PA, replacing corn or corn starch, and fed ad libitum for the assigned experimental period. On days 10 and 28, two broilers from each of the six replicate cages, with 7 broilers per cage in each group, were selected and euthanized, and cecal feces and intestinal tissue samples were collected. PA supplementation did not significantly affect broilers growth performance during both the early and the late periods. However, PA supplementation altered the cecal microbiome, with Clostridiaceae and Clostridium exhibiting prominent and consistent changes. In terms of intestinal immunity, PA supplementation significantly increased the number of CD3+ and CD4+ T cells when administered only during the early period. Cecal IgA levels were significantly increased by PA supplementation during both the early and late periods. A significant positive correlation was observed between IgA, Clostridiaceae and Clostridium during the early and late periods. Gene expression analysis identified 40 upregulated genes, including polymeric immunoglobulin receptor (pIgR), and 142 downregulated genes, including marginal zone B and B1 cell specific protein and immunoglobulin lambda-like polypeptide 1 that were associated with the IgA response in PA-treated broilers during the early period. This study demonstrated that PA supplementation promotes gut microbial colonization and intestinal immunity development during the early age of broilers. These findings suggest that the early growth period of broilers is the optimal time for dietary immunomodulation to promote gut health in broilers.}, }
@article {pmid39631125, year = {2024}, author = {Zhang, JY and Li, XY and Li, DX and Zhang, ZH and Hu, LQ and Sun, CX and Zhang, XN and Wu, M and Liu, LT}, title = {Endoplasmic reticulum stress in intestinal microecology: A controller of antineoplastic drug-related cardiovascular toxicity.}, journal = {Biomedicine &amp; pharmacotherapy = Biomedecine &amp; pharmacotherapie}, volume = {181}, number = {}, pages = {117720}, doi = {10.1016/j.biopha.2024.117720}, pmid = {39631125}, issn = {1950-6007}, abstract = {Endoplasmic reticulum (ER) stress is extensively studied as a pivotal role in the pathological processes associated with intestinal microecology. In antineoplastic drug treatments, ER stress is implicated in altering the permeability of the mechanical barrier, depleting the chemical barrier, causing dysbiosis, exacerbating immune responses and inflammation in the immune barrier. Enteric dysbiosis and intestinal dysfunction significantly affect the circulatory system in various heart disorders. In antineoplastic drug-related cardiovascular (CV) toxicity, ER stress constitutes a web of relationships in the host-microbiome symbiotic regulatory loop. Therefore, understanding the holobiont perspective will help de-escalate spatial and temporal restrictions. This review investigates the role of ER stress-mediated gut microecological alterations in antineoplastic treatment-induced CV toxicity.}, }
@article {pmid39630952, year = {2024}, author = {Gao, F and Shen, Y and Wu, H and Laue, HE and Lau, FK and Gillet, V and Lai, Y and Shrubsole, MJ and Prada, D and Zhang, W and Liu, Z and Bellenger, JP and Takser, L and Baccarelli, AA}, title = {Associations of Stool Metal Exposures with Childhood Gut Microbiome Multiomics Profiles in a Prospective Birth Cohort Study.}, journal = {Environmental science &amp; technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.4c09642}, pmid = {39630952}, issn = {1520-5851}, abstract = {Metal exposures are closely related to childhood developmental health. However, their effects on the childhood gut microbiome, which also impacts health, are largely unexplored using microbiome multiomics including the metagenome and metatranscriptome. This study examined the associations of fecal profiles of metal/element exposures with gut microbiome species and active functional pathways in 8- to 12-year-old children (N = 116) participating in the GESTation and Environment (GESTE) cohort study. We analyzed 19 stool metal and element concentrations (B, Na, Mg, Al, K, Ca, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, As, Mo, Cd, Ba, and Pb). Covariate-adjusted linear regression models identified several significant microbiome associations with continuous stool metal/element concentrations. For instance, Zn was positively associated with Turicibacter sanguinis (coef = 1.354, q-value = 0.039) and negatively associated with Eubacterium eligens (coef = -0.794, q-value = 0.044). Higher concentrations of Cd were associated with lower Eubacterium eligens (coef = -0.774, q-value = 0.045). Additionally, a total of 490 significant functional pathways such as biosynthesis and degradation/utilization/assimilation were identified, corresponding to different functions, including amino acid synthesis and carbohydrate degradation. Our results suggest links among metal exposures, pediatric gut microbiome multiomics, and potential health implications. Future work will further explore their relation to childhood health.}, }
@article {pmid39630497, year = {2024}, author = {Kundu, S and Dos Santos Correia, G and Lee, YS and Ng, S and Sykes, L and Chan, D and Lewis, H and Brown, RG and Kindinger, L and Dell, A and Feizi, T and Haslam, SM and Liu, Y and Marchesi, JR and MacIntyre, DA and Bennett, PR}, title = {Secretor status is a modifier of vaginal microbiota-associated preterm birth risk.}, journal = {Microbial genomics}, volume = {10}, number = {12}, pages = {}, pmid = {39630497}, issn = {2057-5858}, mesh = {Humans ; Female ; *Vagina/microbiology ; *Premature Birth/microbiology ; Pregnancy ; *Lactobacillus/genetics ; *Microbiota ; Adult ; Galactoside 2-alpha-L-fucosyltransferase ; Fucosyltransferases/genetics ; Lactobacillus gasseri/genetics ; Infant, Newborn ; }, abstract = {Mutations in the FUT2 gene that result in a lack of expression of histo-blood group antigens on secreted glycoproteins may shape the vaginal microbiota with consequences for birth outcome. To test this, we analysed the relationship between secretor status, vaginal microbiota and gestational length in an ethnically diverse cohort of 302 pregnant women, including 82 who delivered preterm. Lactobacillus gasseri and L. jensenii were found to have distinct co-occurrence patterns with other microbial taxa in non-secretors. Moreover, non-secretors with Lactobacillus spp. depleted high diversity vaginal microbiota in early pregnancy had significantly shorter gestational length than Lactobacillus spp. dominated non-secretors (mean of 241.54 days (sd=47.14) versus 266.21 (23.61); P-value=0.0251). Similar gestational length differences were observed between non-secretors with high vaginal diversity and secretors with Lactobacillus spp. dominance (mean of 262.52 days (SD=27.73); p-value=0.0439) or depletion (mean of 266.05 days (SD=20.81); p-value=0.0312). Our data highlight secretor status and blood-group antigen expression as being important mediators of vaginal microbiota-host interactions in the context of preterm birth risk.}, }
@article {pmid39629992, year = {2024}, author = {Chen, Y and Lei, L and Xia, M and Cheng, R and Cai, H and Hu, T}, title = {The association between oral microbiome and gastric precancerous lesions.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0132224}, doi = {10.1128/msystems.01322-24}, pmid = {39629992}, issn = {2379-5077}, abstract = {Gastric precancerous lesions are thought to be precursors in the occurrence and development of gastric cancer through Correa's cascade. Recent studies have investigated the association between the oral microbiome and gastric precancerous lesions. However, there has yet to be a comprehensive synthesis review of the existing literature on the relationship between oral microbiome and gastric precancerous lesions. A systematic review was conducted to characterize the literature on the association between oral microbiome and gastric precancerous lesions. The studies show that oral microbiome is dynamic in individuals with gastric precancerous lesions. Oral-derived microorganisms were colonized in the gastric precancerous lesions. Interactions between oral and gastric microbiomes affect the response of the host immunity. The abnormal proliferation of oral-associated microorganisms may be linked to the reduction of gastric acid. The present review supports the potential association between oral microbiome and gastric precancerous lesions. However, the interactions are complex and multifaceted, which require further investigation.}, }
@article {pmid39629949, year = {2024}, author = {Yuan, H and Chlipala, GE and Bangash, HI and Meenakshi, R and Chen, D and Trivedi, HM and DiPietro, LA and Gajendrareddy, P and Chen, L}, title = {Dynamics of Human Palatal Wound Healing and the Associated Microbiome.}, journal = {Journal of dental research}, volume = {}, number = {}, pages = {220345241288761}, doi = {10.1177/00220345241288761}, pmid = {39629949}, issn = {1544-0591}, abstract = {Wound healing in the oral mucosa is superior to that in the skin, with faster wound closure accompanied by reduced inflammation, less angiogenesis, and minimal scar formation. A well-characterized oral wound model is critical to investigating the mechanisms of oral wound closure and the efficacy of various clinical interventions. Currently, there are a few human oral wound models, although none of them are well characterized. In the present study, we describe and characterize a human hard palate wound healing model. A 3.5-mm circular and two 1 × 5-mm rectangular full-thickness wounds were made in the first and second molar region, 5 mm from the gingival margin, on the hard palate of human subjects. The circular wound was used to monitor wound closure and collect swabs for a microbiome analysis via 16s rRNA sequencing. The rectangular wounds were biopsied and the tissue was used to evaluate the gene expression of wound healing-related mediators by real-time polymerase chain reaction. Saliva was also collected to examine the protein levels of similar molecules by enzyme-linked immunosorbent assays. Circular wounds were nearly closed on day 7 after wounding. Significant changes in the gene expression of inflammatory cytokines, growth factors, antimicrobial peptides, and extracellular matrix-related molecules were identified in day 1 and day 3 wound tissue and compared with unwounded tissue on day 0. Changes in the protein levels of various mediators were limited in the saliva. In addition, alpha diversity, beta diversity, and differential microbiome analysis demonstrated significant changes in bacterial colonization of the wound surface over time compared with unwounded mucosa. In summary, we comprehensively characterize a human hard palate wound-healing model that details the dynamic changes of wound closure, levels of wound healing-related mediators in the wound and saliva, and the oral wound microbiome.}, }
@article {pmid39629909, year = {2024}, author = {Sin, HCL and Haifer, C}, title = {Faecal transplantation: the good, the bad and the ugly.}, journal = {Internal medicine journal}, volume = {}, number = {}, pages = {}, doi = {10.1111/imj.16559}, pmid = {39629909}, issn = {1445-5994}, abstract = {There continues to be significant interest from both clinicians and patients in using faecal transplantation, as the integral role of the gut microbiome is increasingly recognised in various disease conditions, both within and beyond the gut. This Clinical Perspectives article provides an overview of existing literature, factors limiting the use of faecal microbial transplantation in clinical practice and exciting new advancements on the horizon.}, }
@article {pmid39629903, year = {2024}, author = {Vallianatou, GN and Douladiris, N and Mageiros, L and Manousakis, E and Zisaki, V and Galani, M and Xepapadaki, P and Taka, S and Papadopoulos, NG}, title = {Duration of food protein-induced allergic proctocolitis (FPIAP) and the role of intestinal microbiota.}, journal = {Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology}, volume = {35}, number = {12}, pages = {e70008}, pmid = {39629903}, issn = {1399-3038}, support = {//Diary Goat Cooperative/ ; }, mesh = {*Proctocolitis/diagnosis/immunology ; Humans ; *Gastrointestinal Microbiome/immunology ; Infant ; Prospective Studies ; Male ; Female ; Animals ; *Milk Hypersensitivity/diagnosis/immunology ; Immune Tolerance ; Food Hypersensitivity/immunology/diagnosis ; Feces/microbiology ; Cattle ; Infant Formula ; Goats ; Allergens/immunology ; }, abstract = {BACKGROUND: Food protein-induced allergic proctocolitis (FPIAP) is the leading cause of rectal bleeding in infants. Tolerance is presumed to develop until the first year of age, although natural history studies are scarce, making the determination of the ideal duration for any intervention, challenging. Intestinal microbiota (IM) is crucial in food allergy development; however, data for FPIAP remain limited. This study aimed to assess FPIAP remission after 3 months of milk avoidance and its correlation with IM longitudinal changes.<br><br>METHODS: A prospective observational study of infants aged &#x2264;6&#x2009;months with a diagnosis of FPIAP. After 3&#x2009;months of management according to a clinical algorithm, infants were subjected to a milk challenge using either a cow (CM) or a goat (GM) milk formula in a random order. Stool samples were collected longitudinally for microbiome analysis.<br><br>RESULTS: Out of 61 infants, 57 were challenged (29 with CM, 28 with GM). Of these, 55 (96.5%) achieved tolerance, with no difference in tolerance rates between CM (28/29) and GM (27/28). The average age of tolerance development was 6.3&#x2009;months. Enterobacteriaceae clusters (Klebsiella- and Shigella-dominated) were most often represented in samples from symptomatic infants. In contrast, Bacteroides and Bifidobacteria clusters emerged later, in apparently healthy infants.<br><br>CONCLUSION: A 3-month intervention was sufficient for almost all infants to achieve tolerance. GM was tolerated equally well to CM. Symptomatic FPIAP is associated with immature enterotypes, while disease remission coincides with microbiome changes in time.}, }
@article {pmid39629792, year = {2024}, author = {González-García, S and Hamdan-Partida, A and Pérez-Ramos, J and Aguirre-Garrido, JF and Bustos-Hamdan, A and Bustos-Martínez, J}, title = {Comparison of the bacterial microbiome in the pharynx and nasal cavity of persistent, intermittent carriers and non-carriers of Staphylococcus aureus.}, journal = {Journal of medical microbiology}, volume = {73}, number = {12}, pages = {}, pmid = {39629792}, issn = {1473-5644}, mesh = {Humans ; *Pharynx/microbiology ; *Staphylococcus aureus/isolation &amp; purification/genetics ; *Carrier State/microbiology ; *Nasal Cavity/microbiology ; *Microbiota ; *Staphylococcal Infections/microbiology ; Male ; Female ; Adult ; Young Adult ; RNA, Ribosomal, 16S/genetics ; DNA, Bacterial/genetics ; }, abstract = {Introduction. Staphylococcus aureus is a bacterium that colonizes various human sites. The pharynx has been considered as a site of little clinical relevance and little studied. Recently, it has been reported that S. aureus can colonize more the pharynx than the nose. In addition, S. aureus can persist in these sites for prolonged periods of time.Hypothesis. The composition of the pharyngeal and nasal microbiome will differ between persistent, intermittent carriers and non-carriers of S. aureus.Aim. Determine whether the pharyngeal and nasal microbiome is different between carriers and non-carriers of S. aureus.Methodology. S. aureus carriers were monitored by means of pharyngeal and nasal exudates of apparently healthy adult university students for 3 months. Samples from individuals of the same carrier type were pooled, and DNA was extracted and the 16S rRNA was sequenced. The sequences were analysed in MOTHUR v.1.48.0 software, by analysing the percentages of relative abundance in the STAMP 2.1.3 program, in addition to the predictive analysis of metabolic pathways in PICRUSt2.Results. A greater colonization of S. aureus was found in the pharynx than in the nose. The microbiomes of S. aureus carriers and non-carriers do not show significant differences. The main microbiome difference found was between pharyngeal and nasal microbiomes. No significant differences were found in the abundance of the genus Staphylococcus in pharyngeal and nasal S. aureus carriers and non-carriers. The nasal microbiome was found to have more variation compared to the pharyngeal microbiome, which appears to be more stable between individuals and pools. Predictive analysis of metabolic pathways showed a greater presence of Staphylococcus-associated pathways in the nose than in the pharynx.Conclusion. S. aureus can colonize and persist in the pharynx in equal or greater proportion than in the nose. No statistically significant differences were found in the microbiome of the pharyngeal and nasal carriers and non-carriers of S. aureus, but the pharyngeal and nasal microbiomes are different independent of the type of S. aureus carrier or non-carrier. Therefore, the microbiome apparently does not influence the persistence of S. aureus.}, }
@article {pmid39629478, year = {2024}, author = {Kumar, S and Das, S and Jiya, N and Sharma, A and Saha, C and Sharma, P and Tamang, S and Thakur, N}, title = {Bacterial diversity along the geothermal gradients: insights from the high-altitude Himalayan hot spring habitats of Sikkim.}, journal = {Current research in microbial sciences}, volume = {7}, number = {}, pages = {100310}, pmid = {39629478}, issn = {2666-5174}, abstract = {Geothermal habitats present a unique opportunity to study microbial adaptation to varying temperature conditions. In such environments, distinct temperature gradients foster diverse microbial communities, each adapted to its optimal niche. However, the complex dynamics of bacterial populations in across these gradients high-altitude hot springs remain largely unexplored. We hypothesize that temperature is a primary driver of microbial diversity, and bacterial richness peaks at intermediate temperatures. To investigate this, we analysed bacterial diversity using 16S rRNA amplicon sequencing across three temperature regions: hot region of 56-65 °C (hot spring), warm region of 35-37 °C (path carrying hot spring water to the river), and cold region of 4-7 °C (river basin). Our findings showed that Bacillota was the most abundant phylum (45.51 %), followed by Pseudomonadota (32.81 %) and Actinomycetota (7.2 %). Bacillota and Chloroflexota flourished in the hot and warm regions, while Pseudomonadota thrived in cooler areas. Core microbiome analysis indicated that species richness was highest in the warm region, declining in both cold and hot regions. Interestingly, an anomaly was observed with Staphylococcus, which was more abundant in cases where ponds were used for bathing and recreation. In contrast, Clostridium was mostly found in cold regions, likely due to its viability in soil and ability to remain dormant as a spore-forming bacterium. The warm region showed the highest bacterial diversity, while richness decreased in both cold and hot regions. This highlights the temperature-dependent nature of microbial communities, with optimal diversity in moderate thermal conditions. The study offers new insights into microbial dynamics in high-altitude geothermal systems.}, }
@article {pmid39629213, year = {2024}, author = {Ramos, S and Júnior, E and Alegria, O and Vieira, E and Patroca, S and Cecília, A and Moreira, F and Nunes, A}, title = {Metagenomics insights into bacterial diversity and antibiotic resistome of the sewage in the city of Belém, Pará, Brazil.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1466353}, pmid = {39629213}, issn = {1664-302X}, abstract = {INTRODUCTION: The advancement of antimicrobial resistance is a significant public health issue today. With the spread of resistant bacterial strains in water resources, especially in urban sewage, metagenomic studies enable the investigation of the microbial composition and resistance genes present in these locations. This study characterized the bacterial community and antibiotic resistance genes in a sewage system that receives effluents from various sources through metagenomics.<br><br>METHODS: One liter of surface water was collected at four points of a sewage channel, and after filtration, the total DNA was extracted and then sequenced on an NGS platform (Illumina&#xae; NextSeq). The sequenced data were trimmed, and the microbiome was predicted using the Kraken software, while the resistome was analyzed on the CARD webserver. All ecological and statistical analyses were performed using the. RStudio tool.<br><br>RESULTS AND DISCUSSION: The complete metagenome results showed a community with high diversity at the beginning and more restricted diversity at the end of the sampling, with a predominance of the phyla Bacteroidetes, Actinobacteria, Firmicutes, and Proteobacteria. Most species were considered pathogenic, with an emphasis on those belonging to the Enterobacteriaceae family. It was possible to identify bacterial groups of different threat levels to human health according to a report by the U.S. Centers for Disease Control and Prevention. The resistome analysis predominantly revealed genes that confer resistance to multiple drugs, followed by aminoglycosides and macrolides, with efflux pumps and drug inactivation being the most prevalent resistance mechanisms. This work was pioneering in characterizing resistance in a sanitary environment in the Amazon region and reinforces that sanitation measures for urban sewage are necessary to prevent the advancement of antibiotic resistance and the contamination of water resources, as evidenced by the process of eutrophication.}, }
@article {pmid39629207, year = {2024}, author = {Martinez-Fernandez, G and Kinley, RD and Smith, WJM and Simington, J and Joseph, S and Tahery, S and Durmic, Z and Vercoe, P}, title = {Effect of fit-for-purpose biochars on rumen fermentation, microbial communities, and methane production in cattle.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1463817}, pmid = {39629207}, issn = {1664-302X}, abstract = {INTRODUCTION: Biochar has gained significant attention as a possible anti-methanogenic supplement for ruminants due to its potential to reduce methane (CH4) emissions from enteric fermentation. However, its effects on rumen methanogenesis have been inconsistent and, in some cases, contradictory. These variations are likely influenced by factors such as the type of biochar used, its source material, and how it is administered, including the form in which it is provided and the dosage needed to achieve desired outcomes. This study aimed to examine the effects of two fit-for-purpose biochars on rumen fermentation, CH4 emissions, and the rumen microbiome of cattle-fed roughage-based diets. Two experiments were conducted to assess the potential of biochar in mitigating CH4 emissions.<br><br>EXPERIMENT 1: This was a controlled pen trial conducted over 56&#x2009;days, involving 12 steers that were fed Rhodes grass hay ad libitum. The animals were assigned to one of four treatment groups: control (no biochar, only molasses), low dose (50&#x2009;g biochar/animal/day), mid dose (100&#x2009;g biochar/animal/day), or high dose (200&#x2009;g biochar/animal/day). Two types of biochar, Biochar 1 and Biochar 2, were administered with molasses (200&#x2009;mL per animal/day). Methane emissions were measured using open-circuit respiration chambers, and rumen fluid samples were collected for analysis of the rumen microbial community and fermentation metabolite.<br><br>EXPERIMENT 2: In this trial, 45 heifers were selected and grazed together in a single paddock for 60&#x2009;days to assess the effects of biochar on productivity and CH4 emissions under grazing conditions. The animals were allocated to one of three treatment groups (15 animals per group): control (no biochar, only molasses), Biochar 1, or Biochar 2. Each group was administered biochar at an estimated single dose of 100&#x2009;g per animal/day mixed with molasses. Methane emissions were measured using GreenFeed systems in the field to monitor CH&#x2084; production from individual animals.<br><br>RESULTS: In the controlled pen trial (Experiment 1), biochar supplementation resulted in a reduction of CH&#x2084; emissions by 8.8-12.9% without any negative effects on rumen fermentation or dry matter intake (DMI). Minor changes were observed in the rumen bacterial community, particularly in the Christensenellaceae and Prevotellaceae families. However, in the grazing trial (Experiment 2), no significant differences in CH&#x2084; emissions or productivity were detected with biochar supplementation.<br><br>CONCLUSION: While the results from controlled feeding conditions suggest that biochar has the potential to reduce enteric CH&#x2084; emissions, the lack of significant findings under grazing conditions highlights the need for further research. Future studies should focus on identifying biochar types, doses, and delivery methods that are effective in reducing CH&#x2084; emissions in grazing systems without compromising cattle productivity.}, }
@article {pmid39629175, year = {2024}, author = {Leasi, F and Eckert, EM and Norenburg, JL and Thomas, WK and Sevigny, JL and Hall, JA and Wirshing, HH and Fontaneto, D}, title = {Microbiota Associated With Ototyphlonemertes Species (Nemertea, Hoplonemertea, Monostilifera, Ototyphlonemertidae) Reveal Evidence of Phylosymbiosis.}, journal = {Ecology and evolution}, volume = {14}, number = {12}, pages = {e70471}, pmid = {39629175}, issn = {2045-7758}, abstract = {Phylosymbiosis, the association between the phylogenetic relatedness of hosts and the composition of their microbial communities, is a widespread phenomenon in diverse animal taxa. However, the generality of the existence of such a pattern has been questioned in many animals across the tree of life, including small-sized aquatic invertebrates. This study aims to investigate the microbial communities associated with poorly known marine interstitial nemerteans to uncover their microbiota diversity and assess the occurrence of phylosymbiosis. Specimens from various Central American sites were analyzed using morphology-based taxonomy and molecular techniques targeting the host 18S rRNA gene whereas their microbial association was analyzed by targeting the prokaryotic 16S rRNA gene. Phylogenetic and statistical analyses were conducted to examine the potential effects of host nemertean taxa and sampling locations on the host-associated microbial communities. The results provide compelling evidence of phylosymbiosis in meiofaunal nemertean species, highlighting the significant impact of host genetic relatedness on microbiome diversity in small-sized animals. This finding supports previous studies that demonstrate how certain nemertean species harbor distinct microbial communities with functional and ecological implications. Given the remarkable diversity of meiofaunal animals-spanning numerous phyla with varying lifestyles and co-existing in the same habitat-combined with advancements in multi-omics approaches, there is a promising opportunity to deepen our understanding of the evolutionary and ecological interactions between hosts and their microbiota throughout the animal tree of life.}, }
@article {pmid39628997, year = {2024}, author = {Lian, M and Sun, M and Han, B and Baranova, A and Cao, H and Zhang, F}, title = {Gut microbiome's causal role in head and neck cancer: findings from mendelian randomization.}, journal = {Frontiers in oncology}, volume = {14}, number = {}, pages = {1453202}, pmid = {39628997}, issn = {2234-943X}, abstract = {INTRODUCTION: The gut microbiome (GM) has been implicated in cancer pathogenesis and treatment, including head and neck cancers (HNC). However, the specific microbial compositions influencing HNC and the underlying mechanisms remain largely unknown.<br><br>METHODS: This study utilized published genome-wide association studies (GWAS) summary data-based two-sample Mendelian randomization (MR) to uncover the GM compositions that exert significant causal effects on HNC. Functional annotation and enrichment analysis were conducted to better understand the significant genetic variables and their connection with HNC. The HNC dataset included 2,281 cases and 314,193 controls. The GM GWAS data of 211 gut taxa (35 families, 20 orders, 16 classes, 9 phyla, and 131 genera) were obtained from the MibioGen consortium, involving 18,340 participants.<br><br>RESULTS: MR analysis revealed four GM compositions exerting causal effects on HNC. Specifically, family Peptococcaceae.id.2024 was significantly associated with a 35% reduced risk of HNC (OR=0.65; 95%CI=0.48-0.90; P=0.0080). In contrast, genus DefluviitaleaceaeUCG-011.id.11287 (OR=1.54; 95%CI=1.13-2.09; P=0.0060), genus Gordonibacter.id.821 (OR=1.23; 95%CI=1.05-1.45; P=0.012), and genus Methanobrevibacter.id.123 (OR=1.28; 95%CI=1.01-1.62; P=0.040) showed a significant association with an increased risk of HNC. These GMs interact with genes and genetic variants involved in signaling pathways, such as GTPase regulation, influencing tumor progression and disease prognosis.<br><br>CONCLUSIONS: Our study demonstrates, for the first time, the causal influence of specific gut microbiome compositions on HNC, offering significant insights for advancing clinical research and personalized treatments. The identified GMs may serve as potential biomarkers or therapeutic targets, paving the way for innovative approaches in HNC diagnosis, prevention, and therapy.}, }
@article {pmid39628929, year = {2023}, author = {Wang, M and Lei, M and He, H}, title = {Catalog of operational taxonomic units and unified amplicon sequencing data for the microbiomes of medicinal plant roots.}, journal = {Engineering microbiology}, volume = {3}, number = {3}, pages = {100087}, pmid = {39628929}, issn = {2667-3703}, abstract = {China has a rich history of cultivating medicinal plants, whose root microbial communities closely interact with the medicinal plants, thereby influencing their growth, health, and medicinal properties. Currently, researchers widely use 16S rRNA gene amplicon sequencing to study these root microbial communities. However, publicly available sequence datasets often lack essential sample information or contain errors, impeding the reuse of the datasets in the future. In this study, we aimed to create a united, reliable, and readily usable source of 16S rRNA gene sequences for medicinal plant root microbiomes. We compiled a catalog of 1392 microbiome samples for 58 medicinal plants from 58 studies, and manually provided essential sample information based on the experimental setup described in the associated papers. We then processed the sequences using a custom pipeline, generating a united catalog of operational taxonomic units (OTUs) and conducting taxonomic classification. We also predicted the ecological functions of the communities for each sample. Finally, we used this dataset, to compare the rhizosphere bacterial communities of Pseudostellaria heterophylla from Fujian and Guizhou Provinces, revealing significant differences in the community composition of the same plant from different geographic locations. By providing a comprehensive and united catalog of amplicon sequences and OTUs for medicinal plant root bacterial communities, this study offers an invaluable resource for future comparative studies and data mining.}, }
@article {pmid39628868, year = {2024}, author = {Yue, Y and Luasiri, P and Li, J and Laosam, P and Sangsawad, P}, title = {Research advancements on the diversity and host interaction of gut microbiota in chickens.}, journal = {Frontiers in veterinary science}, volume = {11}, number = {}, pages = {1492545}, pmid = {39628868}, issn = {2297-1769}, abstract = {The maintenance of host health and immune function is heavily dependent on the gut microbiota. However, the precise contribution of individual microbial taxa to regulating the overall functionality of the gut microbiome remains inadequately investigated. Chickens are commonly used as models for studying poultry gut microbiota, with high-throughput 16S rRNA sequencing has emerged as a valuable tool for assessing both its composition and functionality. The interactions between the gut's microbial community and its host significantly influence health outcomes, disease susceptibility, and various mechanisms affecting gastrointestinal function. Despite substantial research efforts, the dynamic nature of this microbial ecosystem has led to inconsistencies in findings related to chicken gut microbiota, which is largely attributed to variations in rearing conditions. Consequently, the interaction between the chickens' gut microflora and its host remains inadequately explored. This review highlights recent advances in understanding these relationships, with a specific focus on microbial composition, diversity, functional mechanisms, and their potential implications for improving poultry production.}, }
@article {pmid39628590, year = {2024}, author = {Zhang, ZF and Li, M}, title = {The way to uncovering and utilizing marine microbial resources.}, journal = {Engineering microbiology}, volume = {4}, number = {4}, pages = {100175}, pmid = {39628590}, issn = {2667-3703}, abstract = {Recently, Chen et al. published their breakthrough results on a marine microbial genomic catalog and genetic potentials in bioprospecting in Nature, providing unprecedented opportunities for development and utilization of genetic resources of marine microorganisms. To highlight this article, we summarized and highlighted their breakthroughs seriatim.}, }
@article {pmid39628558, year = {2024}, author = {Turner, M and Van Hulzen, L and Guse, K and Agany, D and Pietri, JE}, title = {The gut microbiota confers resistance against Salmonella Typhimurium in cockroaches by modulating innate immunity.}, journal = {iScience}, volume = {27}, number = {12}, pages = {111293}, pmid = {39628558}, issn = {2589-0042}, abstract = {Cockroaches exhibit unexplained intra- and interpopulation variation in susceptibility to Salmonella enterica serovar Typhimurium (S. Typhimurium) infection. Here, we show that the gut microbiota has a protective effect against colonization by ingested S. Typhimurium in cockroaches. We further examine two potential mechanisms for this effect, showing that commensal bacteria present in the gut do not compete with S. Typhimurium during growth in cockroach feces, but rather prime expression of host antimicrobial peptide genes that suppress S. Typhimurium infection. Lastly, we determine that neither absolute abundance of the microbiota nor its overall diversity is linked to infection susceptibility. Instead, we identify several minority bacterial taxa that exhibit interindividual variation in abundance as key indicators of infection susceptibility among genetically similar individuals. These findings illuminate the potential of cockroaches as an invertebrate model for interspecies microbial interactions and provide insight into vector-borne Salmonella transmission, suggesting that the microbiota of cockroaches could be targeted to reduce pathogen transmission.}, }
@article {pmid39628527, year = {2024}, author = {Lengrand, S and Dubois, B and Pesenti, L and Debode, F and Legrève, A}, title = {Humic substances increase tomato tolerance to osmotic stress while modulating vertically transmitted endophytic bacterial communities.}, journal = {Frontiers in plant science}, volume = {15}, number = {}, pages = {1488671}, pmid = {39628527}, issn = {1664-462X}, abstract = {While humic substances (HS) are recognized for their role in enhancing plant growth under abiotic stress by modulating hormonal and redox metabolisms, a key question remains: how do HS influence the microbiota associated with plants? This study hypothesizes that the effects of HS extend beyond plant physiology, impacting the plant-associated bacterial community. To explore this, we investigated the combined and individual impacts of HS and osmotic stress on tomato plant physiology and root endophytic communities. Tomatoes were grown within a sterile hydroponic system, which allowed the experiment to focus on seed-transmitted endophytic bacteria. Moreover, sequencing the 16S-ITS-23S region of the rrn operon (~4,500 bp) in a metabarcoding assay using the PNA-chr11 clamp nearly eliminated the reads assigned to Solanum lycopersicum and allowed the species-level identification of these communities. Our findings revealed that HS, osmotic stress, and their combined application induce changes in bacterial endophytic communities. Osmotic stress led to reduced plant growth and a decrease in Bradyrhizobium sp., while the application of HS under osmotic stress resulted in increased tomato growth, accompanied by an increase in Frigoribacterium sp., Roseateles sp., and Hymenobacter sp., along with a decrease in Sphingomonas sp. Finally, HS application under non-stress conditions did not affect plant growth but did alter the endophytic community, increasing Hymenobacter sp. and decreasing Sphingomonas sp. This study enhances the understanding of plant-endophyte interactions under stress and HS application, highlighting the significance of the vertically transmitted core microbiome in tomato roots and suggesting new insights into the mode of action of HS that was used as a biostimulant.}, }
@article {pmid39628343, year = {2024}, author = {Staudacher, HM and Teasdale, S and Cowan, C and Opie, R and Jacka, FN and Rocks, T}, title = {Diet interventions for depression: Review and recommendations for practice.}, journal = {The Australian and New Zealand journal of psychiatry}, volume = {}, number = {}, pages = {48674241289010}, doi = {10.1177/00048674241289010}, pmid = {39628343}, issn = {1440-1614}, abstract = {OBJECTIVE: this paper aims to present the evidence for the role of diet in the prevention and treatment of depression, review the potential underlying mechanisms and provide practice recommendations for mental health clinicians.<br><br>METHODS: A literature review was conducted through searches of PubMed with the search terms 'depression', 'diet', 'prevention', 'treatment' and 'mechanisms' and combinations thereof. Additional articles were identified through hand searching.<br><br>RESULTS: Greater adherence to several healthy dietary patterns, traditional diets such as the Mediterranean diet and other diets such as the DASH diet are associated with or can treat symptoms of depression. Several limitations of the research were noted, many of which relate to inherent challenges of studying diet. Mechanisms by which dietary intervention can influence mood include the gut microbiome, modulation of inflammatory processes, reduction in oxidative stress and modulation of hypothalamic-pituitary-adrenal axis function. Recommendations for mental health clinicians to enable translation of the evidence into practice are provided.<br><br>CONCLUSION: Diet can play an important role in preventing and treating depression. Mental health clinicians are well placed to provide dietary counselling and to use clinical judgement in choosing the specific approach that reflects the needs of the patient but are encouraged to refer to a specialist dietitian where necessary.}, }
@article {pmid39627922, year = {2024}, author = {Shimizu, H and Kamada, A and Akao, T and Kanno, Y and Koyama, K and Iwashita, K and Goto-Yamamoto, N}, title = {Yeast diversity during the spontaneous fermentation of wine in a winery and in a laboratory using sterilized equipment.}, journal = {Journal of bioscience and bioengineering}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jbiosc.2024.11.001}, pmid = {39627922}, issn = {1347-4421}, abstract = {A recent trend in some wineries is the return to using spontaneous fermentation, but it is not clear whether winery flora or vineyard microorganisms drive fermentation. We compared fungal communities during the spontaneous fermentation of wine produced in a winery and in a laboratory with sterilized equipment using three grape cultivars (Chardonnay, Merlot, and Muscat Bailey A) obtained from the same harvest. High-throughput sequencing analysis based on the ITS1 region showed that Saccharomyces cerevisiae was the dominant species in winery batches at the end of fermentation, but it was not always dominant in laboratory batches. The number of laboratory batches where S. cerevisiae reached more than 50% at the end of fermentation was only 10 of 26. Consistent with this, in the grape juice/must before fermentation, S. cerevisiae accounted for 1.71% of fungal species identified in winery batches and 0.04% in laboratory batches. In addition, in laboratory-based winemaking, juice clarification of Chardonnay and cold maceration of Merlot influenced the microbial communities observed during fermentation. Our findings suggest that S. cerevisiae present in the winery environment participates at an early stage of fermentation, leading to its dominance at the end in wine produced by spontaneous fermentation in a winery.}, }
@article {pmid39627882, year = {2024}, author = {Chen, L and Bao, H and Yang, J and Huo, Y and Zhang, J and Fang, R and Zhang, L}, title = {Dynamics of rice seed-borne bacteria from acquisition to seedling colonization.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {253}, pmid = {39627882}, issn = {2049-2618}, mesh = {*Oryza/microbiology/growth &amp; development ; *Seeds/microbiology/growth &amp; development ; *Seedlings/microbiology/growth &amp; development ; *Bacteria/classification/genetics/isolation &amp; purification ; *RNA, Ribosomal, 16S/genetics ; *Microbiota ; Plant Roots/microbiology ; Germination ; Soil Microbiology ; }, abstract = {BACKGROUND: Rice cultivation relies on planting grains harboring beneficial microbiota. However, the origination, distribution, and transmission dynamics of grain-borne bacteria remain unclear.<br><br>RESULTS: Using rice grain as a model system, this study investigates the primary sources, major niches in seeds, and the dynamics of community acquisition, maintenance, and transmission between generations of grain-borne bacteria. Quantitative PCR and 16S rRNA gene sequencing demonstrate rice grains acquiring bacteria primarily from the external environment during panicle heading and flowering. These bacteria concentrate between the caryopsis and glumes, establishing sizable communities in developing seeds. The dominant taxa included Pantoea, Pseudomonas, and Sphingomonas. Throughout seed development and storage, community structure remains consistent while abundance fluctuates within one order of magnitude. Upon germination under axenic conditions, seed bacteria successfully colonize shoots and roots of offspring seedlings. However, bacteria transmitted solely through internal routes fail to form comparably large communities. Analysis of taxonomic composition uncovers dramatic reshaping from seeds to seedlings, potentially reflecting functional adaptation.<br><br>CONCLUSIONS: We clarify seed-borne bacterial origination, acquisition timing, seed colonization, intergenerational transmission, and seedling diversification. Our findings provide novel insights into rice seed bacterial dynamics critical for microbiome management. Video Abstract.}, }
@article {pmid39627869, year = {2024}, author = {Richy, E and Thiago Dobbler, P and Tláskal, V and López-Mondéjar, R and Baldrian, P and Kyselková, M}, title = {Long-read sequencing sheds light on key bacteria contributing to deadwood decomposition processes.}, journal = {Environmental microbiome}, volume = {19}, number = {1}, pages = {99}, pmid = {39627869}, issn = {2524-6372}, support = {CZ.02.01.01/00/22_008/0004635//Ministry of Education, Youth and Sports of the Czech Republic/ ; }, abstract = {BACKGROUND: Deadwood decomposition is an essential ecological process in forest ecosystems, playing a key role in nutrient cycling and carbon sequestration by enriching soils with organic matter. This process is driven by diverse microbial communities encompassing specialized functions in breaking down organic matter, but the specific roles of individual microorganisms in this process are still not fully understood.<br><br>RESULTS: Here, we characterized the deadwood microbiome in a natural mixed temperate forest in Central Europe using PacBio HiFi long-read sequencing and a genome-resolved transcriptomics approach in order to uncover key microbial contributors to wood decomposition. We obtained high quality assemblies, which allowed attribution of complex microbial functions such as nitrogen fixation to individual microbial taxa and enabled the recovery of metagenome-assembled genomes (MAGs) from both abundant and rare deadwood bacteria. We successfully assembled 69 MAGs (including 14 high-quality and 7 single-contig genomes) from 4 samples, representing most of the abundant bacterial phyla in deadwood. The MAGs exhibited a rich diversity of carbohydrate-active enzymes (CAZymes), with Myxococcota encoding the highest number of CAZymes and the full complement of enzymes required for cellulose decomposition. For the first time we observed active nitrogen fixation by Steroidobacteraceae, as well as hemicellulose degradation and chitin recycling by Patescibacteria. Furthermore, PacBio HiFi sequencing identified over 1000 biosynthetic gene clusters, highlighting a vast potential for secondary metabolite production in deadwood, particularly in Pseudomonadota and Myxococcota.<br><br>CONCLUSIONS: PacBio HiFi long-read sequencing offers comprehensive insights into deadwood decomposition processes by advancing the identification of functional features involving multiple genes. It represents a robust tool for unraveling novel microbial genomes in complex ecosystems and allows the identification of key microorganisms contributing to deadwood decomposition.}, }
@article {pmid39627860, year = {2024}, author = {Swanson, EC and Basting, CM and Klatt, NR}, title = {The role of pharmacomicrobiomics in HIV prevention, treatment, and women's health.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {254}, pmid = {39627860}, issn = {2049-2618}, mesh = {Humans ; *HIV Infections/prevention &amp; control ; Female ; *Pre-Exposure Prophylaxis ; *Anti-HIV Agents/therapeutic use ; *Women's Health ; Microbiota/drug effects ; }, abstract = {In the absence of an effective vaccine or curative treatment for HIV, the global HIV/AIDS epidemic continues despite significant advances in treatment and prevention. Antiretroviral therapy (ART) drugs have transformed HIV from a terminal illness to a manageable chronic condition. Likewise, pre-exposure prophylaxis treatment (PrEP) has dramatically reduced transmission in some of the highest risk populations. However, quality of life and life expectancy in people living with HIV (PWH) still lag significantly behind the general population. The mechanisms that reduce the efficacy of PrEP and ART are multifaceted, but one factor that warrants additional attention is the impact of the microbiome on ART and PrEP efficacy, as well as pharmacokinetics more broadly. In this review, we assess the current state of research on the HIV-associated microbiome, how this impacts treatment efficacy, and how microbiome states can alter HIV susceptibility. We also explore how the mechanisms we propose could extend to the efficacy of other drugs and identify promising areas of research that remain understudied. Video Abstract.}, }
@article {pmid39627693, year = {2024}, author = {Hafsi, A and Moquet, L and Hendrycks, W and De Meyer, M and Virgilio, M and Delatte, H}, title = {Evidence for a gut microbial community conferring adaptability to diet quality and temperature stressors in phytophagous insects: the melon fruit fly Zeugodacus cucurbitae (Diptera: Tephritidae) as a case study.}, journal = {BMC microbiology}, volume = {24}, number = {1}, pages = {514}, pmid = {39627693}, issn = {1471-2180}, mesh = {Animals ; Female ; *Gastrointestinal Microbiome/drug effects ; *RNA, Ribosomal, 16S/genetics ; *Temperature ; *Diet ; *Tephritidae/microbiology/physiology ; *Symbiosis ; Fertility ; Longevity/drug effects ; Bacteria/classification/genetics/isolation &amp; purification/drug effects ; Adaptation, Physiological ; Anti-Bacterial Agents/pharmacology ; Stress, Physiological ; }, abstract = {BACKGROUND: The high invasiveness of phytophagous insects is related to their adaptability to various environments, that can be influenced by their associated microbial community. Microbial symbionts are known to play a key role in the biology, ecology, and evolution of phytophagous insects, but their abundance and diversity are suggested to be influenced by environmental stressors. In this work, using 16 S rRNA metabarcoding we aim to verify (1) if laboratory rearing affects microbial symbiont communities of Zeugodacus cucurbitae females, a cosmopolitan pest of cucurbitaceous crops (2) if temperature, diet quality, and antibiotic treatments affect microbial symbiont communities of both laboratory and wild populations, and (3) if changes in microbial symbiont communities due to temperature, diet and antibiotic affect longevity and fecundity of Z. cucurbitae.<br><br>RESULTS: The results showed that microbial diversity, particularly the &#x3b2;-diversity was significantly affected by insect origin, temperature, diet quality, and antibiotic treatment. The alteration of gut microbial symbionts, specifically Enterobacteriaceae, was associated with low fecundity and longevity of Z. cucurbitae females feeding on optimal diet only. Fecundity reduction in antibiotic treated females was more pronounced when flies were fed on a poor diet without protein.<br><br>CONCLUSIONS: our study proves the relationship between gut microbiome and host fitness under thermal and diet fluctuation highlighting the importance of microbial community in the adaptation of Z. cucurbitae to environmental stress.<br><br>CLINICAL TRIAL NUMBER: Not applicable.}, }
@article {pmid39627462, year = {2024}, author = {Arora, S and Mittal, A and Duari, S and Chauhan, S and Dixit, NK and Mohanty, SK and Sharma, A and Solanki, S and Sharma, AK and Gautam, V and Gahlot, PS and Satija, S and Nanshi, J and Kapoor, N and Cb, L and Sengupta, D and Mehrotra, P and Ghosh, TS and Ahuja, G}, title = {Discovering geroprotectors through the explainable artificial intelligence-based platform AgeXtend.}, journal = {Nature aging}, volume = {}, number = {}, pages = {}, pmid = {39627462}, issn = {2662-8465}, support = {BT/HRD/35/02/2006//Department of Biotechnology, Ministry of Science and Technology (DBT)/ ; SRG/2020/000232//DST | Science and Engineering Research Board (SERB)/ ; }, abstract = {Aging involves metabolic changes that lead to reduced cellular fitness, yet the role of many metabolites in aging is unclear. Understanding the mechanisms of known geroprotective molecules reveals insights into metabolic networks regulating aging and aids in identifying additional geroprotectors. Here we present AgeXtend, an artificial intelligence (AI)-based multimodal geroprotector prediction platform that leverages bioactivity data of known geroprotectors. AgeXtend encompasses modules that predict geroprotective potential, assess toxicity and identify target proteins and potential mechanisms. We found that AgeXtend accurately identified the pro-longevity effects of known geroprotectors excluded from training data, such as metformin and taurine. Using AgeXtend, we screened ~1.1 billion compounds and identified numerous potential geroprotectors, which we validated using yeast and Caenorhabditis elegans lifespan assays, as well as exploring microbiome-derived metabolites. Finally, we evaluated endogenous metabolites predicted as senomodulators using senescence assays in human fibroblasts, highlighting AgeXtend's potential to reveal unidentified geroprotectors and provide insights into aging mechanisms.}, }
@article {pmid39627368, year = {2024}, author = {Keppler, A and Roulier, M and Pfeilmeier, S and Petti, GC and Sintsova, A and Maier, BA and Bortfeld-Miller, M and Sunagawa, S and Zipfel, C and Vorholt, JA}, title = {Plant microbiota feedbacks through dose-responsive expression of general non-self response genes.}, journal = {Nature plants}, volume = {}, number = {}, pages = {}, pmid = {39627368}, issn = {2055-0278}, support = {51NF40_180575//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; }, abstract = {The ability of plants to perceive and react to biotic and abiotic stresses is critical for their health. We recently identified a core set of genes consistently induced by members of the leaf microbiota, termed general non-self response (GNSR) genes. Here we show that GNSR components conversely impact leaf microbiota composition. Specific strains that benefited from this altered assembly triggered strong plant responses, suggesting that the GNSR is a dynamic system that modulates colonization by certain strains. Examination of the GNSR to live and inactivated bacteria revealed that bacterial abundance, cellular composition and exposure time collectively determine the extent of the host response. We link the GNSR to pattern-triggered immunity, as diverse microbe- or danger-associated molecular patterns cause dynamic GNSR gene expression. Our findings suggest that the GNSR is the result of a dose-responsive perception and signalling system that feeds back to the leaf microbiota and contributes to the intricate balance of plant-microbiome interactions.}, }
@article {pmid39627340, year = {2024}, author = {Molina, FJ and Botero, LE and Isaza, JP and Cano, LE and López, L and Valdés, L and Arévalo Arbeláez, AJ and Moreno, I and Pérez Restrepo, LS and Usuga, J and Ciuoderis, K and Hernandez, JP and López-Aladid, R and Fernández, L and Torres, A}, title = {Deciphering the lung microbiota in COVID-19 patients: insights from culture analysis, FilmArray pneumonia panel, ventilation impact, and mortality trends.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {30035}, pmid = {39627340}, issn = {2045-2322}, support = {121084468048//Minciencias, Colombia./ ; }, mesh = {Humans ; *COVID-19/mortality/microbiology/virology ; *Microbiota/genetics ; Male ; Female ; Middle Aged ; *Lung/microbiology ; Aged ; *RNA, Ribosomal, 16S/genetics ; *Respiration, Artificial ; SARS-CoV-2/isolation &amp; purification/genetics ; Bronchoalveolar Lavage Fluid/microbiology ; Coinfection/microbiology/mortality ; Bacteria/genetics/classification/isolation &amp; purification ; Intensive Care Units ; }, abstract = {Few studies have analyzed the role of the lung microbiome in the diagnosis of pulmonary coinfection in ventilated ICU COVID-19 patients. We characterized the lung microbiota in COVID-19 patients with severe pneumonia on invasive mechanical ventilation using full-length 16S rRNA gene sequencing and established its relationship with coinfections, mortality, and the need for mechanical ventilation for more than 7 days. This study included 67 COVID-19 ICU patients. DNA extracted from mini-bronchoalveolar lavage fluid and endotracheal aspirates was amplified by PCR with specific 16S primers (27F and 1492R). General and relative bacterial abundance analysis was also conducted. Alpha diversity was measured by the Shannon and Simpson indices, and differences in the microbiota were established using beta diversity. A linear discriminant analysis (LDA) effect size algorithm was implemented to describe biomarkers. Streptococcus spp. represented 51% of the overall microbial abundance. There were no differences in alpha diversity between the analyzed variables. There was variation in bacterial composition between samples that had positive and negative cultures. The genera Veillonella sp., Granulicatella sp., Enterococcus sp. and Lactiplantibacillus sp., with LDA scores > 2, were biomarkers associated with negative cultures. Rothia sp., with an LDA score > 2, was a biomarker associated with mortality.}, }
@article {pmid39627243, year = {2024}, author = {Jaber, Y and Sarusi-Portuguez, A and Netanely, Y and Naamneh, R and Yacoub, S and Saar, O and Drawshave, N and Eli-Berchoer, L and Shapiro, H and Elinav, E and Wilensky, A and Hovav, AH}, title = {Gingival spatial analysis reveals geographic immunological variation in a microbiota-dependent and -independent manner.}, journal = {NPJ biofilms and microbiomes}, volume = {10}, number = {1}, pages = {142}, pmid = {39627243}, issn = {2055-5008}, support = {2272/20//Israel Science Foundation (ISF)/ ; }, mesh = {Animals ; *Gingiva/microbiology/immunology ; Mice ; *Microbiota ; Spatial Analysis ; Biofilms/growth &amp; development ; Gene Expression Profiling ; Alveolar Bone Loss/microbiology ; Bacteria/classification/genetics ; Mice, Inbred C57BL ; Mouth Mucosa/immunology/microbiology ; Host Microbial Interactions/immunology ; }, abstract = {In mucosal barriers, tissue cells and leukocytes collaborate to form specialized niches that support host-microbiome symbiosis. Understanding the spatial organization of these barriers is crucial for elucidating the mechanisms underlying health and disease. The gingiva, a unique mucosal barrier with significant health implications, exhibits intricate tissue architecture and likely contains specialized immunological regions. Through spatial transcriptomic analysis, this study reveals distinct immunological characteristics between the buccal and palate regions of the murine gingiva, impacting natural alveolar bone loss. The microbiota primarily affects gingival immunity in the buccal region. Additionally, a significant influence of the microbiota on the junctional epithelium facing the oral biofilm offers new insights into neutrophil recruitment. The microbiota also regulates the proliferation and barrier-sealing function of the gingival epithelium. This underscores the presence of immunological niches in the gingiva, with the microbiota differentially influencing them, highlighting the high complexity of this oral mucosal barrier.}, }
@article {pmid39627139, year = {2024}, author = {Cheong, SC and Selvam, B and Ho, GF and Muhamad Nor, I and Tan, CK and Wong, YF and Teo, SH and Lim, KP and Chai, AWY and Yahya, A and Wan Ishak, WZ}, title = {Pembrolizumab (MK-3475) plus platinum and gemcitabine as first-line treatment of recurrent/metastatic head and neck squamous cell carcinoma (PIPER): a phase 2, multicentre, single-arm protocol study in Malaysia.}, journal = {BMJ open}, volume = {14}, number = {12}, pages = {e076898}, doi = {10.1136/bmjopen-2023-076898}, pmid = {39627139}, issn = {2044-6055}, mesh = {Humans ; *Gemcitabine ; *Deoxycytidine/analogs &amp; derivatives/administration &amp; dosage/therapeutic use ; *Antibodies, Monoclonal, Humanized/therapeutic use/administration &amp; dosage ; *Antineoplastic Combined Chemotherapy Protocols/therapeutic use ; *Squamous Cell Carcinoma of Head and Neck/drug therapy ; Malaysia ; *Neoplasm Recurrence, Local/drug therapy ; *Head and Neck Neoplasms/drug therapy/pathology ; Male ; Clinical Trials, Phase II as Topic ; Female ; Multicenter Studies as Topic ; Middle Aged ; Adult ; Cisplatin/administration &amp; dosage/therapeutic use ; }, abstract = {INTRODUCTION: Treatment combination of pembrolizumab plus platinum and 5-fluorouracil (PF) has increased the survival of recurrent or metastatic (R/M) head and neck squamous cell carcinoma (HNSCC). The combination of platinum and gemcitabine (PG) has been shown to be superior to PF in the treatment of R/M nasopharyngeal carcinoma patients. Therefore, we hypothesise that the combination of pembrolizumab with PG would be comparable to pembrolizumab with PF as a first-line treatment in R/M HNSCC.<br><br>METHODS AND ANALYSIS: This is an open-label, multicentre, single-arm, phase 2 study of pembrolizumab plus PG for first-line treatment in subjects with R/M HNSCC in Malaysia. The study is conducted using the Optional Simon optimal 2-stage design. At the initial stage, 26 subjects will be enrolled and if seven or more patients achieve an objective response rate (ORR), then 63 patients will be enrolled. Subjects will be given pembrolizumab 200 mg[3] every 3 weeks up to 35 cycles in combination with chemotherapy for up to six cycles of platinum (either cisplatin at 35 mg/m[2] intravenous on day 1 and day 8 or carboplatin at area under the curve 5 intravenous on day 1 of each 3-week cycle) and gemcitabine at 1250 mg/m[2] intravenous on days 1 and 8 of a 3-week cycle. The primary end point is the ORR as per Response Evaluation Criteria in Solid Tumors 1.1. Secondary end points include the overall survival, progression free survival, response duration and safety. The exploratory objectives include relationships of microbiome profiles, prognostic and predictive biomarkers with the clinical responses.<br><br>ETHICS AND DISSEMINATION: The study was approved by the ethics committee of the University Malaya Medical Centre (202213-10884). Findings will be disseminated through conference presentations and peer review publications.<br><br>TRIAL REGISTRATION NUMBER: ClinicalTrials.gov (www.<br><br>CLINICALTRIAL: gov); NCT05286619.}, }
@article {pmid39626993, year = {2024}, author = {Nielsen, VW and Thomsen, SF and Naik, HB}, title = {Hidradenitis suppurativa pathogenesis: Extrinsic factors.}, journal = {Journal of the American Academy of Dermatology}, volume = {91}, number = {6S}, pages = {S17-S21}, doi = {10.1016/j.jaad.2024.07.1524}, pmid = {39626993}, issn = {1097-6787}, mesh = {*Hidradenitis Suppurativa/immunology/etiology ; Humans ; *Gastrointestinal Microbiome/immunology ; Skin/pathology/immunology/microbiology ; Diet/adverse effects ; Disease Progression ; Tobacco Smoking/adverse effects/epidemiology ; }, abstract = {While genetic predisposition and immune dysregulation are recognized as key contributors to the development of hidradenitis suppurativa, accumulating research points to the influence of extrinsic factors in the pathogenesis of this condition. This review explores the roles of mechanical stress, altered skin and gut microbiome, tobacco smoking, diet, and paradoxical drug reactions as drivers of hidradenitis suppurativa onset and progression. A holistic management approach addressing these factors may be encouraged to improve disease outcomes. Further research is needed to fully determine the causal role of these extrinsic factors and their impact on treatment strategies.}, }
@article {pmid39626992, year = {2024}, author = {Frew, JW}, title = {Intrinsic factors in the pathogenesis of hidradenitis suppurativa: Genetics, hormones, and the microbiome.}, journal = {Journal of the American Academy of Dermatology}, volume = {91}, number = {6S}, pages = {S12-S16}, doi = {10.1016/j.jaad.2024.08.052}, pmid = {39626992}, issn = {1097-6787}, mesh = {*Hidradenitis Suppurativa/microbiology/immunology/genetics ; Humans ; Gonadal Steroid Hormones/physiology/metabolism ; Hair Follicle/microbiology/immunology ; Gastrointestinal Microbiome/immunology/physiology ; Genome-Wide Association Study ; Microbiota/immunology ; Immunity, Innate/genetics ; Insulin Resistance/immunology/genetics ; Metabolic Syndrome/microbiology/immunology ; Adipose Tissue/immunology/microbiology ; Inflammation/microbiology/immunology ; }, abstract = {The pathogenesis of hidradenitis suppurativa is complex and multifaceted. Our understanding of disease mechanisms is in constant flux with new genetic, inflammatory, and microbiological insights upending previous paradigms and enlightening us as to the complex connections between different drivers of disease. This updated review integrates novel genetic insights from genome wide association studies, along with novel basic science data from single cell transcriptomic studies and recent interventional translational work to inform our evolving understanding of the disease. The overarching premise is that hidradenitis suppurativa is a chronic autoinflammatory disorder characterized by inflammatory dysregulation in a background of stem cell fate aberrations highly responsive to hormonal and metabolic changes. Genetic drivers are linked to both hair follicle stem cell fate and cellular response to androgen signaling. The complex mixed inflammatory circuits involve both innate and adaptive immunity, with activation of inflammatory fibroblast subsets and tertiary lymphoid organs in chronic disease. Interplay between inflammation, the cutaneous and gut microbiomes are observed both pre- and posttherapy, however causality remain unclear. Metabolic syndrome, sex hormones and insulin resistance are all interlinked, with adipose tissue being a hormonally active organ able to modulate endogenous sources of sex hormones. Future enquiry regarding factors contributing to disease progression and the identification of novel therapeutic targets will aid in more effective therapeutic strategies for management of this burdensome disease.}, }
@article {pmid39626858, year = {2024}, author = {Williams, EG and Smith, OM and Alsugoor, MH and Albakri, GS and Marber, M}, title = {Integrative Approaches to Atrial Fibrillation Prevention and Management: Leveraging Gut Health for Improved Cardiovascular Outcomes in the Aging Population.}, journal = {Current problems in cardiology}, volume = {}, number = {}, pages = {102952}, doi = {10.1016/j.cpcardiol.2024.102952}, pmid = {39626858}, issn = {1535-6280}, abstract = {Atrial fibrillation (AF) is a prevalent clinical arrhythmia associated with a high incidence and severe complications such as cerebral embolism and heart failure. While the etiology and pathogenesis of AF involve numerous factors, recent research emphasizes the significant role of intestinal microbiota imbalance in the emergence and progression of AF, particularly among older adults. This review investigates the mechanisms by which intestinal flora and their metabolites contribute to the onset of AF in the elderly, highlighting novel interactions between gut health and cardiac function. Current literature often overlooks these critical connections, indicating a substantial research gap in understanding how dysbiosis may exacerbate AF and hinder recovery. Furthermore, exploring the bidirectional relationship between the gut microbiome and systemic inflammation in the context of AF provides a unique perspective that has yet to be thoroughly investigated. Future research should focus on longitudinal studies assessing gut microbiota composition and function in AF patients and consider probiotics or prebiotics as potential adjunctive therapies for mitigating AF. This comprehensive approach may pave the way for innovative treatments integrating cardiology with gastroenterology, enhancing patient outcomes through a holistic understanding of health.}, }
@article {pmid39626841, year = {2024}, author = {Wang, W and Qu, Y and Chen, H and Huang, L and Gu, L}, title = {The Microbial Co-infection Interaction Network in Apical Periodontitis with Sinus Tracts.}, journal = {Journal of dentistry}, volume = {}, number = {}, pages = {105496}, doi = {10.1016/j.jdent.2024.105496}, pmid = {39626841}, issn = {1879-176X}, abstract = {OBJECTIVES: This study aims to characterize the bacterial co-occurrence features and potential interactions associated with the presence of sinus tracts in apical periodontitis in a Chinese population by using 16S rRNA next-generation sequencing (NGS).<br><br>METHODS: Thirty-one samples from twenty-six patients were collected from root canals. Following the extraction of the bacterial DNA, the V3-V4 hypervariable regions of the 16S rRNA gene were sequenced. Compositional diversity, prominent taxa and co-occurrence network analysis were compared according to the presence or absence of sinus tracts.<br><br>RESULTS: The overall microbiota in two groups exhibited distinguished patterns. Actinomyces dominated in samples with sinus tracts while Prevotella was the most abundant in samples without sinus tracts. The major pathogens in sinus tracts exhibited a complex co-occurrence network, in which Pseudomonas formed a distinctive cluster with enriched abundance, and the extensive correlations centered on Desulfovibrio and Pseudoramibacter may suggest novel dependencies. In the network without sinus tracts, the Bacteroidetes and Firmicutes taxa presented close internal associations.<br><br>CONCLUSIONS: The sequencing results confirmed the complexity of the microbiota in AP. The presence of sinus tracts was associated with distinctive infective patterns and complicated microbial co-infection interaction networks. Further investigations should be adopted to elucidate the relationship between the novel interactions and disease progression.<br><br>CLINICAL SIGNIFICANCE: Exploring the microbial interactions leads to a better understanding of etiology of apical periodontitis. Utilizing next generation sequencing techniques, our research uncovered the bacterial community structure and observed co-infection networks associated with sinus tracts, providing potential insights for prognosis prediction and targeted therapeutics of persistent inflammation.}, }
@article {pmid39628703, year = {2022}, author = {Liu, D and Siguenza, NE and Zarrinpar, A and Ding, Y}, title = {Methods of DNA introduction for the engineering of commensal microbes.}, journal = {Engineering microbiology}, volume = {2}, number = {4}, pages = {100048}, pmid = {39628703}, issn = {2667-3703}, abstract = {The microbiome is an essential component of ecological systems and is comprised of a diverse array of microbes. Over the past decades, the accumulated observational evidence reveals a close correlation between the microbiome and human health and disease. Many groups are now manipulating individual microbial strains, species and the community as a whole to gain a mechanistic understanding of the functions of the microbiome. Here, we discuss three major approaches for introducing DNA to engineer model bacteria and isolated undomesticated bacteria, including transformation, transduction, and conjugation. We provide an overview of these approaches and describe the advantages and limitations of each method. In addition, we highlight examples of human microbiome engineering using these approaches. Finally, we provide perspectives for the future of microbiome engineering.}, }
@article {pmid39626831, year = {2024}, author = {Yuwattana, R and Suparan, K and Kerdpoo, S and Arunsak, B and Sanguansermsri, C and Katanyuwong, K and Chattipakorn, N and Wiwattanadittakul, N and Chattipakorn, SC}, title = {Altered gut microbiome profiles in epileptic children are associated with spectrum of anti-seizure medication responsiveness.}, journal = {Brain research}, volume = {}, number = {}, pages = {149367}, doi = {10.1016/j.brainres.2024.149367}, pmid = {39626831}, issn = {1872-6240}, abstract = {Gut microbiota plays a role in epilepsy. However, current knowledge of how gut dysbiosis is associated with a response to anti-seizure medications (ASMs) in epileptic children is still limited. We aimed to characterize the gut microbiota profiles in epileptic children based on response to ASMs. Eighty-six children aged 3-18 years old with a regular oral diet were enrolled onto the study and divided into three groups in accordance with ILAE definitions: 26 healthy controls, 31 drug-sensitive epilepsy (DSE) patients, and 29 drug-resistant epilepsy (DRE) patients. Based on ASM responsiveness, defined as a reduction in seizure frequency of at least 75 % over one year, DRE individuals were subclassified into 13 drug responsive (DRE-DR) and 16 drug non-responsive (DRE-DNR) patients. Feces were collected at the time of enrollment for gut microbiota analysis using 16S rRNA sequencing. Epileptic patients exhibited distinctive gut dysbiotic profiles. Differential abundance investigation revealed that CAG-56 was significantly increased in epileptic patients compared to controls. Saccharimonadales and Peptoclostridium significantly increased in the DSE group, compared to the DRE group. Vibrionaceae, especially Grimontia, Rhodobacteraceae, and Enterobacter were significantly abundant in the DRE-DNR group, followed by abundance in the DRE-DR and DSE groups. Outcomes from PICRUSt2 analysis predicted that epileptic patients, especially those in the DRE group, had increased metabolic pathways responsible for vanillin and taurine degradation, compared to controls. These findings suggest that gut dysbiosis could play roles in epileptogenesis and ASM resistance. Notably, the identified gut microbes could serve as predictive biomarkers for the DRE condition.}, }
@article {pmid39626605, year = {2024}, author = {van der Klein, SAS and Bernardeau, M and Wang, Q and Gibbs, K}, title = {A cross-study analysis of the effect of a dual-strain probiotic applied via the waterline on the growth performance and gut health of broilers under a mild necrotic enteritis challenge.}, journal = {Poultry science}, volume = {104}, number = {1}, pages = {104550}, doi = {10.1016/j.psj.2024.104550}, pmid = {39626605}, issn = {1525-3171}, abstract = {Probiotics offer potential as an approach for the prevention and control of poultry intestinal diseases, but external factors can influence the birds' response. Combining data from multiple trials provides greater confidence around efficacy under varying production conditions. Therefore, this study combined data from three separate trials analyzing the effect of a dual-strain probiotic comprising Lactobacillus acidophilus AG01 and Bifidobacterium animalis subspecies lactis AG02 on broilers during a mild necrotic enteritis (NE) challenge. In each, 1,440 broilers were assigned to floor-pens (40 birds/pen, 12 pens/treatment) in a completely randomized design. Treatments in each trial were a non-challenged control (C); challenged control (10 x dose of Eimeria/bird on d 14 and 1.0 x ∼10[9] colony forming units (CFU)/bird of C. perfringens on d 16-20; CC); and CC supplemented daily via the waterline with 1 × 10[9] CFU/bird of probiotic (CC+Probiotic). Birds were fed corn-soybean mealbased diets by phase (starter: 0 to 14, grower: 15 to 28, finisher: 29 to 42 d of age) ad libitum. Growth performance was monitored over 42 d, NE lesion scoring performed on d 21 and 28 in all trials, and, in Trial 3 only, cecal microbiota composition was analyzed on d 28. From d 1 to 42, CC birds exhibited reduced BW, BW gain (BWG), and feed intake (FI) (-9.2 %, -9.5 %, -5.0 %, respectively; P < 0.05), increased FCR and mortality (+8.5 points and 1.3 % points, respectively; P < 0.05) compared to C, and increased NE induction on d 28 (67.8 vs. 9.4 %, P <0.05). Compared to CC, CC+Probiotic birds exhibited increased BW, BWG and FI (d 42: +6.9 %, +7.1 %, +4.0 %; P < 0.05) and reduced FCR, mortality and d 28 NE lesion scores (-0.5 points, -1.4 % points and -57.1 %, respectively; P < 0.05). The composition of the cecal microbiota of CC+Probiotic birds at 28 d of age exhibited higher abundance of butyrogenic bacterial genera in Trial 3, which may have contributed to the beneficial effects of the probiotic. The results demonstrate that the probiotic ameliorated the negative effects of a mild NE-challenge on growth performance and intestinal symptoms over three trials incorporating variation in season and bird breed.}, }
@article {pmid39626551, year = {2024}, author = {Xu, C and Han, A and Tian, Y and Sun, S}, title = {Based on computer simulation and experimental verification: mining and characterizing novel antimicrobial peptides from soil microbiome.}, journal = {Food chemistry}, volume = {467}, number = {}, pages = {142275}, doi = {10.1016/j.foodchem.2024.142275}, pmid = {39626551}, issn = {1873-7072}, abstract = {Antimicrobial peptides (AMPs) show great promise for enhancing food safety and extending shelf life, but traditional screening methods are complex and costly. To address these issues, we developed a deep learning-based prediction pipeline to identify potential AMPs from soil metagenomic data, achieving high accuracy (92.71 %) and precision (91.29 %). Based on model scoring, surface charge, and Hemopred and ToxinPred screenings, we identified nine candidate peptides. Peptide P4 (GTAWRWHYRARS) showed the best binding affinity to MrkH in molecular docking studies and was validated through molecular dynamics simulations. The chemically synthesized P4 demonstrated significant antimicrobial activity against Klebsiella pneumoniae, Escherichia coli, and Staphylococcus aureus, indicating its potential as an effective alternative to traditional food antimicrobial agents. This study highlights the effectiveness of our integrated prediction pipeline for discovering new AMPs.}, }
@article {pmid39626398, year = {2024}, author = {Song, A and Si, Z and Xu, D and Wei, B and Wang, E and Chong, F and Fan, F}, title = {Lanthanum and cerium added to soil influence microbial carbon and nitrogen cycling genes.}, journal = {Journal of environmental management}, volume = {373}, number = {}, pages = {123509}, doi = {10.1016/j.jenvman.2024.123509}, pmid = {39626398}, issn = {1095-8630}, abstract = {The soil microbiome plays an important role in carbon (C) and nitrogen (N) processing and storage and is influenced by rare earth elements (REEs), which can have both direct and indirect effects on plant metabolic processes. Using conventional physicochemical methods and metagenomic-based analyses, we investigated REEs effects on soil respiration, soil mineral N, soil microbial community structure and functional genes related to C and N metabolism. High doses of cerium (0.16 and 0.32 mmol kg[-1] soil) increased CO2 net production rate by 59 and 42%, and N2O net production rate by 255 and 609%, respectively, compared to no REEs. Similarly, high doses of lanthanum (0.16 and 0.32 mmol kg[-1] soil) increased CO2 net production rate by 47 and 39%, and N2O net production rate by 105 and 187%, respectively. Increased soil respiration from altered relative abundances of key soil microorganisms associated with soil N cycling and organic matter degradation and functional genes encoding enzymes involved in C and N metabolism, accelerated N mineralization. Elevated REEs levels substantially increased the relative abundances of functional genes related to cellulose, chitin, glucans, hemicellulose, lignin, and peptidoglycan degradation. REEs also influenced multiple functional genes associated with the N cycle. The abundance of genes responsible for organic N degradation and synthesis, such as asnB, gdh_K15371, glsA, and gs, increased with elevated cerium and lanthanum concentrations. Similarly, the abundances of denitrification genes, including narl, narJ, narZ, and nosZ, also rose with increasing amounts of cerium and lanthanum. However, the decrease in narB and nirB gene abundance with increasing REE concentrations was attributed to the reduction of nitrate to amino groups. Our findings highlight the influence of REEs on key soil microorganisms associated with soil N cycling and organic matter degradation and key functional genes in soil C and N metabolism, with implications for agriculture, environmental protection, and human health.}, }
@article {pmid39626377, year = {2024}, author = {Hewady, S and Manuel, CR and Pasquali, C and Koya, J and Reznik, SE}, title = {OM-85 attenuates high-fat diet-induced obesity, insulin resistance, gut dysbiosis and nonalcoholic steatohepatitis in a murine model.}, journal = {Biomedicine &amp; pharmacotherapy = Biomedecine &amp; pharmacotherapie}, volume = {181}, number = {}, pages = {117710}, doi = {10.1016/j.biopha.2024.117710}, pmid = {39626377}, issn = {1950-6007}, abstract = {BACKGROUND: Obesity is a global epidemic that is tied to a wide range of human disorders. Chronic consumption of a high-fat diet is linked to disruption of the intestinal microbiome, which drives obesity-related pathophysiology. Broncho-Vaxom® (OM-85), a bacterial lysate used for prophylaxis of recurrent respiratory tract infections, has both immunostimulatory and immunomodulatory functions.<br><br>METHODS: Male C57Bl/6 mice were maintained on normal control vs. high-fat diets for 8 weeks and treated or untreated with OM-85 or with the probiotic Lactobacillus plantarum, as a positive control. Mice were evaluated for weight gain, glucose tolerance, insulin tolerance, gut microbiome composition and non-alcoholic steatohepatitis (NASH).<br><br>RESULTS: High-fat diet mice developed obesity, insulin resistance, NASH and gut dysbiosis with a shift from the Bacteroidetes phylum, such as Bacteroidales order and Muribaculaceae family organisms to Firmicutes groups, such as the Clostridium and Blautia genuses. Treatment with OM-85 led to 1) prevention of obesity, 2) prevention of insulin resistance, 3) attenuation of NASH and 4) attenuation of gut dysbiosis, with decreased levels of the organisms mentioned above and increases in Verrucomicrobiae phylum organisms such as Akkermansia family microbes as well as Muribaculaceae organisms. These shifts in the gut microbiome predict favorable effects on the short chain fatty acid profile in the gut and increased integrity of the intestinal barrier. Pathway analysis showed that OM-85 decreases rates of carbohydrate metabolism, providing an additional mechanism whereby OM-85 prevents obesity.<br><br>CONCLUSION: Immune modulators such as OM-85 should be investigated for their potential therapeutic effects on metabolism.}, }
@article {pmid39626197, year = {2024}, author = {Jéglot, A and Sanchez-Cid, C and Sørensen, SR and Schnorr, KM and Plauborg, F and Vogel, TM and Elsgaard, L}, title = {Bacterial bioaugmentation of woodchip bioreactors to increase nitrate removal in cold agricultural drainage water.}, journal = {Environmental technology}, volume = {}, number = {}, pages = {1-12}, doi = {10.1080/09593330.2024.2432483}, pmid = {39626197}, issn = {1479-487X}, abstract = {Woodchip bioreactors (WBRs) are biological systems designed to prevent excess nitrate (NO3[-]) leaching from agricultural fields to aquatic ecosystems. Nitrate is removed by microbial denitrification, but the enzyme-mediated process slows down at cold temperatures (<10°C), where NO3[-] removal in WBRs can be less than 20%. We studied the use of bacterial bioaugmentation in replicated test-scale WBRs (∼0.1 m[3]) as an environmental technology to increase NO3[-] removal at cold temperatures. Nitrate removal rates increased following injection of a nitrate-reducing inoculum (Pseudomonas proteolytica and Klebsiella sp.), but the effect disappeared within a week and was reproduced in control WBRs by injection of sterile medium (phosphate buffer saline). Metagenome analyses showed a shift in the bacterial community composition after bioaugmentation in the planktonic phase of the woodchip reactors, but not in the solid phase (woodchip matrix). Only in the planktonic phase, Pseudomonas and Klebsiella increased their relative abundance as monitored by 16S rRNA gene sequences. In addition, an increased abundance of genes related to NO3[-] transformation after bacterial inoculation was observed in the metagenomic sequences. After one week, bacterial community composition became similar to its initial state, indicating resilience of the WBR microbial communities. We conclude that improved inoculation methods are needed to unlock the potential of bioaugmentation to increase NO3[-] removal at cold temperatures and make it a relevant technology for practical use at field-scale.}, }
@article {pmid39626068, year = {2024}, author = {Sun, Y and Wang, Y and Yang, Z and Han, X and Zhang, Y and Chen, L and Huo, J and Wu, R and Wang, W and Wang, N}, title = {Neutral Polysaccharide from Platycodonis Radix-Ameliorated PM2.5-Induced Lung Injury by Inhibiting the TLR4/NF-κB p65 Pathway and Regulating the Lung and Gut Microbiome.}, journal = {Journal of agricultural and food chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.jafc.4c07319}, pmid = {39626068}, issn = {1520-5118}, abstract = {Platycodonis radix (PR) has been reported to play a protective role in lung injury. However, much less is known about the protective effect and mechanism of its main component PR polysaccharides (PRPs) in particulate matter (PM2.5)-induced lung injury. Here, a neutral polysaccharide (MW: 244.56 kDa) was isolated from PR, mainly composed of Rha, Ara, Gal, Glc, Xyl, and Man. PRPs significantly improved PM2.5-induced pulmonary edema, oxidative damage, and cell apoptosis and downregulated inflammatory factor levels in bronchoalveolar lavage fluid. Mechanistically, PRPs reduced intestinal mucosal barrier damage, thereby lowering serum lipopolysaccharide levels and inhibiting the overactivation of the TLR4/NF-κB signaling pathway in the lung tissue. Notably, PRPs could optimize the composition of pulmonary and intestinal microbiota. Oral administration of PRPs resulted in enrichment of short-chain fatty acid (SCFA)-producing bacteria, thereby upregulating the levels of acetate, butyrate, and isovalerate. Taken together, PRPs have great potential in preventing and repairing the lung injury caused by PM2.5.}, }
@article {pmid39625754, year = {2024}, author = {Melin, AD}, title = {Baboons, bacteria, and biological clocks address an age-old question.}, journal = {eLife}, volume = {13}, number = {}, pages = {}, doi = {10.7554/eLife.104715}, pmid = {39625754}, issn = {2050-084X}, mesh = {Animals ; *Papio ; *Feces/microbiology ; *Aging/physiology ; Biological Clocks/physiology ; Bacteria/genetics/classification/metabolism ; Gastrointestinal Microbiome/physiology ; }, abstract = {Studying the fecal microbiota of wild baboons helps provide new insight into the factors that influence biological aging.}, }
@article {pmid39625740, year = {2024}, author = {Ebrahimi, F and Subbiah, V and Agar, OT and Legione, AR and Suleria, HAR}, title = {Site-specific impact of polyphenols on the gastrointestinal microbiome.}, journal = {Critical reviews in food science and nutrition}, volume = {}, number = {}, pages = {1-24}, doi = {10.1080/10408398.2024.2434961}, pmid = {39625740}, issn = {1549-7852}, abstract = {The gastrointestinal (GI) tract hosts a diverse microbiota composed of trillions of microorganisms that play crucial roles in maintaining human homeostasis, health, and overall well-being. Dietary polyphenols, primarily found in edible plants, exhibit intricate interactions with the GI microbiota. These polyphenols undergo biotransformation by microbial activity and can modulate the growth of microorganisms, either promoting or inhibiting their proliferation. The composition of microbes in different segments of the GI tract is highly variable and directly influences polyphenols' metabolism. Consequently, it is essential to examine the transformation of the microbiota by dietary polyphenols. Despite their significance, the collective impact of dietary polyphenols, GI site, and GI microbiota remains an underexplored area of study, warranting further investigation. This review aims to address the existing research gap by focusing on the site-specific effects of polyphenols on the oral, esophageal, gastric, small intestinal (duodenum, jejunum, ilium), and large intestinal microbiota.}, }
@article {pmid39625614, year = {2024}, author = {Saeng-Kla, K and Mhuantong, W and Termsaithong, T and Pinyakong, O and Sonthiphand, P}, title = {Biodegradation of Di-2-Ethylhexyl Phthalate by Mangrove Sediment Microbiome Impacted by Chronic Plastic Waste.}, journal = {Marine biotechnology (New York, N.Y.)}, volume = {27}, number = {1}, pages = {19}, pmid = {39625614}, issn = {1436-2236}, support = {FF-072/2567//Mahidol University (Fundamental Fund: fiscal year 2024 by National Science Research and Innovation Fund (NSRF)/ ; }, mesh = {*Diethylhexyl Phthalate/metabolism ; *Geologic Sediments/microbiology ; *Biodegradation, Environmental ; *Microbiota ; Water Pollutants, Chemical/metabolism ; Plastics/metabolism ; Gordonia Bacterium/metabolism/genetics ; Plasticizers/metabolism ; Wetlands ; Bacteria/metabolism/classification/genetics/isolation &amp; purification ; }, abstract = {Plastic pollution through the leaching of di(2-ethylhexyl) phthalate (DEHP), a widely used plasticizer, has led to the emergence of mangrove pollution. This study aimed to assess the DEHP removal efficiency of indigenous mangrove sediment microbiomes and identify key DEHP degraders using microcosm construction and metagenomic analysis. During the 35-day incubation period, the indigenous mangrove sediment microbiome, affected by chronic plastic pollution, demonstrated a 99% degradation efficiency of 200 mg/kg DEHP. Spearman's correlation analysis suggested that Myxococcales, Methyloligellaceae, Mycobacterium, and Micromonospora were potentially responsible for DEHP degradation. Based on PICRUSt2, the DEHP-degrading pathway in the sediment was predicted to be an anaerobic process involving catechol metabolism through catC, pcaD, pcaI, pcaF, and fadA. Efficient bacterial isolates from the mangrove sediment, identified as Gordonia sp. and Gordonia polyisoprenivorans, were able to degrade DEHP (65-97%) within 7 days and showed the ability to degrade other phthalate esters (PAEs).}, }
@article {pmid39625204, year = {2024}, author = {Jin, MH and Li, Y and Yi, SH}, title = {Research Progress on the Application of Human Body Surface Microbiome to Forensic Individual Identification.}, journal = {Fa yi xue za zhi}, volume = {40}, number = {4}, pages = {379-386}, doi = {10.12116/j.issn.1004-5619.2023.531208}, pmid = {39625204}, issn = {1004-5619}, mesh = {Humans ; *Microbiota ; *Skin/microbiology ; *Hair/microbiology ; Forensic Medicine/methods ; DNA Fingerprinting/methods ; Forensic Sciences/methods ; Polymerase Chain Reaction ; }, abstract = {Skin and hair are the outermost interfaces between the human body and the external environment with many microorganisms distributed. These body surface microorganisms have individual specificity and spatial temporal stability and can be transferred to the surface of other objects through contact, and can be easily found at the crime scene, which helps to construct the connection between the suspect and the crime scene. When the sample is degraded or the DNA quantity is too low to obtain sufficient human DNA evidence, the highly amplified copies of body surface microbiome analysis can be used as an adjunct to human DNA typing without affecting DNA extraction and typing, and provide useful information for narrowing the range of suspects. This paper reviews the forensic characteristics and analytical methods of body surface microbiome, the research progress on the application of body surface microbiome to forensic individual identification, and puts forward the challenges of applying body surface microbiome to forensic practice.}, }
@article {pmid39625134, year = {2024}, author = {Kostrzębska, A and Szczepaniak, G}, title = {Anti-acne preparations containing tetracycline, azelaic acid and azeloglycine: Optimization of stability and physicochemical properties.}, journal = {Polimery w medycynie}, volume = {}, number = {}, pages = {}, doi = {10.17219/pim/196256}, pmid = {39625134}, issn = {0370-0747}, abstract = {BACKGROUND: Acne vulgaris is a common inflammatory skin condition affecting almost 85% of the adolescent and young adult population. The etiopathogenesis of this dermatosis involves an imbalance in the skin microbiome, leading to inflammation of both the skin and hair follicles.<br><br>OBJECTIVES: The aim of this study was to develop topical anti-acne formulations with increased therapeutic efficacy and reduced risk of developing antibiotic resistance. Six hydrogel formulations containing azelaic acid or its derivative, azeloglycine, in combination with tetracycline hydrochloride were prepared as part of the study.<br><br>MATERIAL AND METHODS: The investigated formulations were prepared using an Eprus U500 pharmaceutical mixer and the pH was determined using an ERH-11S electrode designed for dense substances and a CPC-505 Elmetron pH-meter. The formulations were analyzed for tetracycline stability in the presence of additional active ingredients and varying pH over a period of 35 days using high-performance liquid chromatography (HPLC). In addition, the effects of azeloglycine and azelaic acid on the viscosity of the prepared formulations were evaluated using a Brookfield DV2T rotational viscometer.<br><br>RESULTS: Chromatographic analysis showed significant stability of tetracycline in most formulations, with azeloglycine-containing formulations showing less degradation of the antibiotic than azelaic acid-containing preparations. In addition, azeloglycine-containing gels exhibited more favorable rheological properties, which may facilitate better application and be more beneficial to patients.<br><br>CONCLUSION: The results suggest that formulations containing azeloglycine and tetracycline may be a promising strategy for acne therapy, offering increased tetracycline stability and an optimal rheological profile, which may result in prolonged therapeutic effect and more effective drug delivery to the skin.}, }
@article {pmid39624934, year = {2024}, author = {Huo, J and Li, X and Zhang, K and Fu, H and Hu, X and Lv, A}, title = {Alteration of Immune Function and Gut Microbiome Composition in Carassius auratus Challenged With Rahnella aquatilis.}, journal = {Journal of fish diseases}, volume = {}, number = {}, pages = {e14054}, doi = {10.1111/jfd.14054}, pmid = {39624934}, issn = {1365-2761}, support = {//National Natural Science Foundation of China (no. 32273182)/ ; //Key Scientific Research Project Universities and Colleges in Tianjin City of China (no. 2019ZD14)/ ; //Natural Science Foundation of Tianjin City of China (no. 23JCZDJC00240)/ ; }, abstract = {Rahnella aquatilis as an emerging pathogen can cause bacterial enteritis in cyprinid fish such as crucian carp Carassius auratus. Currently, the characterisation of immune function and gut microbiome composition in C. auratus orally challenged by R. aquatilis were yet unknown. In this study, we therefore investigated the changes of histopathology, white blood cells (i.e., LEU, NEU and LYM), serum biochemical indicators (e.g., CRE, CK and CHO) and digestive enzyme activity (e.g., LYS, AST, ALT, GSH-Px and AKP), as well as complements and immune-related genes (e.g., C3, F2, LysC, TLR3, MyD88, TGF-β, TNF-α and IL-15) that were significantly altered after the oral administration of R. aquatilis KCL-5. Moreover, the gut microbiome composition and diversity were analysed by using 16S rRNA gene high-throughput sequencing analysis. The correlation analysis showed that the high abundance of phylum Proteobacteria, Actinobacteria, Firmicutes and Fusobacteria was related to the pathogenesis of enteritis caused by oral infection. KEGG enrichment analysis indicated that fatty acid, carbon and pyruvate metabolism were significantly increased pathways (p < 0.05). To our best knowledge, this is a rare report of physicochemical properties and gut microbiome in C. auratus by R. aquatilis infection, which will provide a scientific reference for the clinical diagnosis and prevention of bacterial enteritis in cyprinid fish.}, }
@article {pmid39624807, year = {2024}, author = {Wood, AC and Lee, DJ and Sheridan, PA and Jensen, ET and Ramesh, G and Bertoni, AG and Rich, SS and Chen, YI and Herrington, DM and Rotter, JI and Goodarzi, MO}, title = {Metabolites Link Intake of a Healthy Diet to Better Insulin and Glucose Homeostasis in the Microbiome and Insulin Longitudinal Evaluation Study (MILES).}, journal = {Current developments in nutrition}, volume = {8}, number = {11}, pages = {104462}, pmid = {39624807}, issn = {2475-2991}, abstract = {BACKGROUND: Dietary quality has been linked to better glycemic control, but the precise molecular mechanisms giving rise to these associations are not fully understood.<br><br>OBJECTIVES: To examine the association of metabolites associated with the intake of a healthy diet with measures of insulin/glucose homeostasis.<br><br>METHODS: Using cross-sectional data from 295 United States adults, the associations between 3 diet pattern scores and metabolome-wide metabolites were estimated via linear regression models, which controlled for demographic factors and health behaviors. Subsequently, the associations between the diet-related metabolites with 6 measures of glucose/insulin homeostasis were examined in similar models. A Bonferroni correction was applied to control the family-wise error rate at 5%.<br><br>RESULTS: Fifty-five metabolites were significantly associated with &#x2265;1 diet score (all P < 1.7&#x2217;10[-5]). When these were summed into each of the 3 diet-specific metabolite summary scores, all 3 aggregate measures showed strong associations with 5 out of 6 measures of glucose/insulin homeostasis (P = 9.7&#x2217;10[-5]-4.1&#x2217;10[-13]).<br><br>CONCLUSIONS: Adherence to a priori-defined "healthy diet" is associated with the plasma metabolites that, in turn, are associated with better glycemia. If the associations between replicated in future studies and examined using large-scale longitudinal data, the identified molecules could yield insights into mechanisms by which diet may support glucose and insulin homeostasis.}, }
@article {pmid39624725, year = {2024}, author = {Liu, G and Zhang, S and Xiang, Z and Shirani, I and Chen, Y and Guo, A}, title = {Effects of vaccination and interventions on nasal microbiome and BRD-associated pathogens in calves.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1467908}, pmid = {39624725}, issn = {1664-302X}, abstract = {Vaccination is a widely adopted measure to prevent diseases, but the process of immunization can induce a substantial stress response. This study aimed to investigate the impact of a combined Mycoplasma bovis-BoHV-1 vaccine on the upper respiratory tract microbiome and BRD-associated pathogens in calves, as well as to evaluate the effects of potential interventions. The results showed that the percentage of Pasteurella species in the upper respiratory tract was elevated in calves after vaccination without intervention, and Pasteurella multocida was activated and proliferated. Interestingly, none of the three interventions (Sodium selenite-vitamin E, Astragalus polysaccharide and Ceftiofur sodium) affected antibody production after immunization. The administration of sodium selenite-vitamin E and astragalus polysaccharide reduced serum levels of cortisol and malondialdehyde, increased glutathione peroxidase (GSH-Px) and superoxide dismutase (SOD), and alleviated the proliferation of Pasteurella multocida. Furthermore, the use of ceftiofur sodium almost completely inhibited the proliferation of Pasteurella multocida induced by immune stress. These findings provide a reference for mitigating the negative impacts associated with vaccination and highlight the potential benefits of using targeted nutritional and antimicrobial interventions to optimize immune responses and maintain a stable respiratory microbiome in calves.}, }
@article {pmid39624721, year = {2024}, author = {Liu, C and Dan, H and Yang, Y and Du, Y and Hao, Z and Chen, L and Zhu, K and Liu, B and Niu, L and Zhao, Y and Wang, Y and Shen, L and Gan, M and Zhu, L}, title = {Enhanced immunity: the gut microbiota changes in high-altitude Tibetan pigs compared to Yorkshire pigs.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1469253}, pmid = {39624721}, issn = {1664-302X}, abstract = {INTRODUCTION: Long-term domestication in high-altitude environments has led to unique changes in the gut microbiota of Tibetan Pigs. This study aims to investigate specific alterations in the intestinal flora of Tibetan Pigs compared to Yorkshire pigs.<br><br>METHODS: We employed 16S rRNA and metagenomic sequencing technologies for comprehensive analysis of the gut microbiota. The data collected allowed us to assess microbial community structures and functional capabilities.<br><br>RESULTS: Our analysis revealed that Tibetan Pigs raised under a "free-range + supplementary feeding" model exhibited increased abundance of microbial communities associated with short-chain fatty acid synthesis and the digestion of cellulose and hemicellulose. Notably, the characteristic bacterium Rhodococcus, commonly found in high-altitude environments, was enriched in the gut microbiota of Tibetan Pigs, facilitating the efficient utilization of natural compounds and degradation of toxic substances. Additionally, the increased abundance of probiotics in these pigs enhances their immunity, which may involve mechanisms such as disrupting the structure of pathogenic bacteria and detoxifying harmful metabolites.<br><br>DISCUSSION: These findings underscore the advantages of Tibetan Pigs over common commercial breeds, highlighting their unique gut microbiota adaptations. Furthermore, they open new avenues for screening potential probiotics and developing genetic breeding strategies for improved livestock varieties.<br><br>CONCLUSION: Understanding the distinct gut microbiota of Tibetan Pigs provides valuable insights into their health benefits and resilience, contributing to future research on breed improvement and microbiome applications in agriculture.}, }
@article {pmid39624715, year = {2024}, author = {Semenzato, G and Fani, R}, title = {Endophytic bacteria: a sustainable strategy for enhancing medicinal plant cultivation and preserving microbial diversity.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1477465}, pmid = {39624715}, issn = {1664-302X}, abstract = {Endophytic bacteria, part of the plant microbiome, hold significant potential for enhancing the cultivation and sustainability of medicinal plants (MPs). These microbes are integral to many plant functions, including growth promotion, nutrient acquisition, and resistance to biotic and abiotic stresses. However, traditional cultivation practices often overlook the importance of these beneficial microbes, leading to reduced crop yields, lower phytochemical quality, and increased susceptibility to diseases. The domestication of MPs and the use of chemical fertilizers disrupt the natural microbial diversity in soils, essential for the health and productivity of plants. This disruption can lead to the loss of beneficial plant-microbe interactions, which are vital for the production of bioactive compounds with therapeutic properties. Recent advances in microbiome research, supported by omics technologies, have expanded our understanding of how endophytic bacteria can be leveraged to enhance MP productivity and quality. Endophytic bacteria can directly boost MP productivity by promoting plant growth and health or indirectly by restoring healthy soil microbiomes. They can also be harnessed as microbial factories to produce valuable natural compounds, either by transforming plant-derived precursors into bioactive substances or by synthesizing unique metabolites that mimic MP secondary metabolites. This offers a sustainable and low-cost alternative to traditional MP cultivation, reducing the carbon footprint and preserving endangered species. In conclusion, integrating microbiome research with traditional agricultural practices could revolutionize MP cultivation. By focusing on the microbial component, particularly endophytes, we can develop more sustainable and productive methods for cultivating these plants, ultimately contributing to biodiversity conservation and the production of high-value natural products.}, }
@article {pmid39624362, year = {2024}, author = {Flory, M and Bravo, P and Alam, A}, title = {Impact of gut microbiota and its metabolites on immunometabolism in colorectal cancer.}, journal = {Immunometabolism (Cobham, Surrey)}, volume = {6}, number = {4}, pages = {e00050}, pmid = {39624362}, issn = {2633-0407}, abstract = {Colorectal cancer (CRC) is highly prevalent, accounting for approximately one-tenth of cancer cases and deaths globally. It stands as the second most deadly and third most common cancer type. Although the gut microbiota has been implicated in CRC carcinogenesis for the last several decades, it remains one of the least understood risk factors for CRC development, as the gut microbiota is highly diverse and variable. Many studies have uncovered unique microbial signatures in CRC patients compared with healthy matched controls, with variations dependent on patient age, disease stage, and location. In addition, mechanistic studies revealed that tumor-associated bacteria produce diverse metabolites, proteins, and macromolecules during tumor development and progression in the colon, which impact both cancer cells and immune cells. Here, we summarize microbiota's role in tumor development and progression, then we discuss how the metabolic alterations in CRC tumor cells, immune cells, and the tumor microenvironment result in the reprogramming of activation, differentiation, functions, and phenotypes of immune cells within the tumor. Tumor-associated microbiota also undergoes metabolic adaptation to survive within the tumor environment, leading to immune evasion, accumulation of mutations, and impairment of immune cells. Finally, we conclude with a discussion on the interplay between gut microbiota, immunometabolism, and CRC, highlighting a complex interaction that influences cancer development, progression, and cancer therapy efficacy.}, }
@article {pmid39624265, year = {2024}, author = {Karim, S and Zenzal, TJ and Beati, L and Sen, R and Adegoke, A and Kumar, D and Downs, LP and Keko, M and Nussbaum, A and Becker, DJ and Moore, FR}, title = {Ticks without borders: microbiome of immature neotropical tick species parasitizing migratory songbirds along northern Gulf of Mexico.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1472598}, pmid = {39624265}, issn = {2235-2988}, mesh = {Animals ; *Microbiota ; Gulf of Mexico ; *Songbirds/parasitology/microbiology ; *Animal Migration ; *RNA, Ribosomal, 16S/genetics ; Rickettsia/genetics/isolation &amp; purification/classification ; Tick Infestations/veterinary/parasitology ; Ticks/microbiology ; Francisella/genetics/isolation &amp; purification/classification ; Spiroplasma/genetics/isolation &amp; purification/classification/physiology ; Phylogeny ; }, abstract = {INTRODUCTION: The long-distance, seasonal migrations of birds make them an effective ecological bridge for the movement of ticks. The introduction of exotic tick species to new geographical regions can cause the emergence of novel tick-borne pathogens. This study examined the prevalence of exotic tick species parasitizing migratory songbirds at stopover sites along the northern Gulf of Mexico using the mitochondrial 12S rRNA gene.<br><br>METHODS: Overall, 421 individual ticks in the genera Amblyomma, Haemaphysalis, and Ixodes were recorded from 28 songbird species, of which Amblyomma and Amblyomma longirostre were the most abundant tick genera and species, respectively. A high throughput 16S ribosomal RNA sequencing approach characterized the microbial communities and identified pathogenic microbes in all tick samples.<br><br>RESULTS AND DISCUSSION: Microbial profiles showed that Proteobacteria was the most abundant phylum. The most abundant pathogens were Rickettsia and endosymbiont Francisella, Candidatus Midichloria, and Spiroplasma. Permutation multivariate analysis of variance revealed that the relative abundance of Francisella and Rickettsia drives microbial patterns across the tick genera. We also noted a higher percentage of positive correlations in microbe-microbe interactions among members of the microbial communities. Network analysis suggested a negative correlation between a) Francisella and Rickettsia and, b) Francisella and Cutibacterium. Lastly, mapping the distributions of bird species parasitized during spring migrations highlighted geographic hotspots where migratory songbirds could disperse ticks and their pathogens at stopover sites or upon arrival to their breeding grounds, the latter showing mean dispersal distances from 421-5003 kilometers. These findings spotlight the potential role of migratory birds in the epidemiology of tick-borne pathogens.}, }
@article {pmid39624165, year = {2024}, author = {Zhang, Y and Schluter, J and Zhang, L and Cao, X and Jenq, RR and Feng, H and Haines, J and Zhang, L}, title = {Review and revamp of compositional data transformation: A new framework combining proportion conversion and contrast transformation.}, journal = {Computational and structural biotechnology journal}, volume = {23}, number = {}, pages = {4088-4107}, pmid = {39624165}, issn = {2001-0370}, abstract = {Due to the development of next-generation sequencing technology and an increased appreciation of their role in modulating host immunity and their potential as therapeutic agents, the human microbiome has emerged as a key area of interest in various biological investigations of human health and disease. However, microbiome data present a number of statistical challenges not addressed by existing methods, such as the varying sequencing depth, the compositionality, and zero inflation. Solutions like scaling and transformation methods help to mitigate heterogeneity and release constraints, but often introduce biases and yield inconsistent results on the same data. To address these issues, we conduct a systematic review of compositional data transformation, with a particular focus on the connection and distinction of existing techniques. Additionally, we create a new framework that enables the development of new transformations by combining proportion conversion with contrast transformations. This framework includes well-known methods such as Additive Log Ratio (ALR) and Centered Log Ratio (CLR) as special cases. Using this framework, we develop two novel transformations-Centered Arcsine Contrast (CAC) and Additive Arcsine Contrast (AAC)-which show enhanced performance in scenarios with high zero-inflation. Moreover, our findings suggest that ALR and CLR transformations are more effective when zero values are less prevalent. This comprehensive review and the innovative framework provide microbiome researchers with a significant direction to enhance data transformation procedures and improve analytical outcomes.}, }
@article {pmid39624158, year = {2024}, author = {Jimenez-Lopez, O and Ray, T and Dean, C and Slizovskiy, I and Deere, J and Wolf, T and Moore, S and Primus, A and Høy-Petersen, J and Finstad, S and Mo, J and Sørum, H and Noyes, N}, title = {The gut microbiome and resistome of yellow perch (Perca flavescens) living in Minnesota lakes under varying anthropogenic pressure.}, journal = {One health (Amsterdam, Netherlands)}, volume = {19}, number = {}, pages = {100933}, pmid = {39624158}, issn = {2352-7714}, abstract = {Anthropogenic activities can significantly impact wildlife in natural water bodies, affecting not only the host's physiology but also its microbiome. This study aimed to analyze the gut microbiome and antimicrobial resistance gene profile (i.e., the resistome) of yellow perch living in lakes subjected to different levels of anthropogenic pressure: wastewater effluent-impacted lakes and undeveloped lakes. Total DNA and RNA from gut content samples were extracted and sequenced for analysis. Results indicate that the gut resistome and microbiome of yellow perch differ between lakes, perhaps due to varying anthropogenic pressure. The resistome was predominated by macrolide resistance genes, particularly the MLS23S group, making up 53 % of resistome sequences from effluent-impacted lakes and 73 % from undeveloped lakes. The colistin resistance gene group (mcr) was detected in numerous samples, including variants associated with Aeromonas and the family Enterobacteriaceae. The gut microbiome across all samples was dominated by the phyla Proteobacteria, Firmicutes, and Actinobacteria, with the opportunistic pathogens Plesiomonas shigelloides and Aeromonas veronii more abundant in effluent-impacted lakes. Metagenomic analysis of wild fish samples offers valuable insights into the effects of anthropogenic pressures on microbial communities, including antimicrobial resistance genes, in water bodies.}, }
@article {pmid39624094, year = {2024}, author = {Liang, Y and Zhao, C and Wen, Y and Sheng, D and Wei, T and Hu, T and Dai, J and Zhao, G and Yang, S and Wang, Q and Zhang, L}, title = {Modulation of local immunity by the vaginal microbiome is associated with triggering spontaneous preterm birth.}, journal = {Frontiers in immunology}, volume = {15}, number = {}, pages = {1481611}, pmid = {39624094}, issn = {1664-3224}, mesh = {Humans ; Female ; *Vagina/microbiology/immunology ; Pregnancy ; *Premature Birth/immunology/microbiology ; *Microbiota/immunology ; Adult ; RNA, Ribosomal, 16S/genetics ; }, abstract = {OBJECTIVE: This study aimed to identify immune states associated with a high risk of preterm birth by immunophenotyping in pregnant populations, and to elucidate the characteristics of immune subtypes and their relationships with preterm birth. Additionally, it sought to uncover the microbial composition and functional characteristics of immune states linked to preterm birth, and to evaluate the impact of bacterial interactions on the initiation of preterm birth.<br><br>METHODS: Utilizing 16S rRNA sequencing data and local immune factor expression data from a publicly available longitudinal pregnancy cohort, we conducted immunophenotyping through unsupervised clustering of the immune factors. We compared the differences in vaginal microbiota richness, diversity, and composition between identified immune subtypes using &#x3b1; and &#x3b2; diversity analysis. Signature microbiotas were identified using LEfSe analysis, and functional pathway enrichment variations were analyzed using PICRUSt2. Bidirectional mediation analysis was employed to construct a network of mediating roles, and preliminary in vitro validation of the Microbial-Cytokine-Preterm Birth pathway was performed to explore the effects of microbial and immune characteristics on vaginal epithelial cell function.<br><br>RESULTS: Pregnant women were categorized into three immune subtypes based on local immune status. Microbial functional analysis identified 31 distinct functional pathways, six of which were downregulated in the preterm birth and excessive inflammatory response group. Significant differences in vaginal microbial diversity and composition were observed among pregnant women with different immune subtypes. Bidirectional mediation analysis revealed multiple intermediary roles in preterm birth, highlighting C3b/iC3b and IL-8 in mid-pregnancy and IgE and IgM in late pregnancy.<br><br>CONCLUSION: This study classified pregnant women into three immune subtypes, with the excessive inflammatory response subtype showing a higher predisposition to preterm birth. Mid-pregnancy immune status emerged as a key indicator of preterm birth risk, associated with the vaginal microbiome composition. Microorganisms affected the occurrence of preterm birth by modulating immune factor levels, with time-specific mediation roles observed. Lactobacillus crispatus demonstrated potential in protecting against preterm birth by modulating vaginal immune status.}, }
@article {pmid39624085, year = {2024}, author = {Niu, X and Lu, D and Jaleel, S and Palmer, SN and Mahendroo, M and Zhan, X and Mirpuri, J}, title = {Maternal high fat diet exposure modifies amniotic fluid metabolites and expands group 3 innate lymphoid cells dependent on the maternal microbiome and MyD88-signaling.}, journal = {Frontiers in immunology}, volume = {15}, number = {}, pages = {1439804}, pmid = {39624085}, issn = {1664-3224}, mesh = {Animals ; Female ; *Myeloid Differentiation Factor 88/metabolism/immunology ; Pregnancy ; *Diet, High-Fat/adverse effects ; *Amniotic Fluid/immunology/metabolism ; *Immunity, Innate ; Mice ; *Lymphocytes/immunology/metabolism ; *Signal Transduction/immunology ; Prenatal Exposure Delayed Effects/immunology ; Mice, Knockout ; Mice, Inbred C57BL ; Microbiota/immunology ; Male ; Interleukin-17/metabolism/immunology ; Animals, Newborn ; Maternal Exposure/adverse effects ; }, abstract = {BACKGROUND: Maternal high fat diet (mHFD) exposure expands IL-17 producing group 3 innate lymphoid cells (IL17[+ve] ILC3) in the small intestine of neonatal murine offspring and increases their susceptibility to intestinal inflammation. How mHFD modulates innate immunity in the fetal offspring remains unclear.<br><br>METHODS: Dams were exposed to 60% high fat diet or maintained on regular diet (RD) prior to and during mating. Amniotic fluid (AF) was collected during mid-pregnancy and metabolites examined by global non-targeted mass spectrometry in conventional wild-type (WT) and germ-free pregnant dams. Offspring were delivered by C-section or vaginally and fecal contents examined for major bacterial phyla and small intestinal lamina propria cells (LP) by flow cytometry. Susceptibility to intestinal inflammation was determined using a lipopolysaccharide and platelet-activating factor model (LPS/PAF) in WT, germ-free and MyD88 deficient offspring. Neonatal germ-free pups were exposed to HFD or RD AF by gavage and LP examined by flow cytometry.<br><br>RESULTS: We identified differentially produced metabolites in mHFD AF when compared to RD AF in conventionally raised mice, with no difference seen in germ-free mice. C-section delivery maintained the mHFD phenotype of expansion of IL17[+ve] ILC3 and increased susceptibility to inflammation in neonatal offspring. In addition, mHFD offspring had expansion of IL17[+ve] ILC3 at birth and 2 weeks of life, which was not seen in germ-free and MyD88 KO mice exposed to mHFD. Germ-free and MyD88 KO mice were protected from mHFD induced LPS/PAF injury and IL17[+ve] ILC3 expansion, demonstrating that the maternal microbiome and MyD88 are prenatally necessary for the expansion of IL17[+ve] ILC3 in mHFD offspring. Furthermore, introduction of mHFD AF to neonatal germ-free pups by gavage was sufficient to expand IL17[+ve] ILC3 in the small intestine.<br><br>CONCLUSION: Our findings indicate that mHFD interacts with the maternal microbiome to modify AF metabolites and signal via MyD88 to expand IL17[+ve] ILC3 in murine neonatal offspring.}, }
@article {pmid39624045, year = {2024}, author = {Niranjan, R and Patil, S and Dubey, A and Lochab, B and Priyadarshini, R}, title = {Small cyclic dipeptide produced by Lactobacillus rhamnosus with anti-biofilm properties against Streptococcus mutans biofilm.}, journal = {Biofilm}, volume = {8}, number = {}, pages = {100237}, pmid = {39624045}, issn = {2590-2075}, abstract = {The human oral cavity harbors many bacterial species collectively termed the oral microbiome and is integral for maintaining oral health. Dysbiosis of oral microbiota leads to common oral diseases, including dental caries, gingivitis, and periodontitis. Streptococcus mutans is the primary causative agent of dental caries. Studies have explored the use of probiotic Lactobacillus spp. to mitigate S. mutans biofilms. In the present study, we have tested the use of Lactobacillus rhamnosus extracts/metabolites for anti-biofilm properties. A small organic compound/metabolite was isolated from the cell-free supernatant of L. rhamnosus, and this metabolite resulted in a dose-dependent inhibition of S. mutans biofilms. Confocal microscopy revealed that the thickness of S. mutans biofilms was severely reduced upon metabolite treatment. With the help of FTIR spectra and mass spectrometry analysis, the molecular formula (C11H19O2N2) was deduced. The inhibitor compound was further identified as a small cyclic peptide, cyclo (-L-Leu-L-Pro). Our data also revealed that isolated metabolite impedes S. mutans biofilms by modulating gene expression of several essential genes involved in biofilm establishment.}, }
@article {pmid39623529, year = {2024}, author = {Ma, J and Sun, S and Cheng, X and Meng, C and Zhao, H and Fu, W and Gao, Y and Ma, L and Yang, Z and Yao, H and Su, J}, title = {Unraveling the role of gut microbiome in predicting adverse events in neoadjuvant therapy for rectal cancer.}, journal = {Human vaccines &amp; immunotherapeutics}, volume = {20}, number = {1}, pages = {2430087}, doi = {10.1080/21645515.2024.2430087}, pmid = {39623529}, issn = {2164-554X}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Neoadjuvant Therapy/adverse effects/methods ; Male ; Female ; Middle Aged ; *Rectal Neoplasms/therapy/microbiology ; Aged ; *Feces/microbiology ; Metabolomics ; Metabolome ; Immunotherapy/methods/adverse effects ; Adult ; Chemoradiotherapy/adverse effects/methods ; Metagenomics/methods ; }, abstract = {Some patients may develop adverse events during neoadjuvant chemoradiotherapy combined with immunotherapy, influencing response rates. The roles of intestinal microbiome and its metabolites in therapeutic adverse events remain unclear. We collected baseline fecal samples from 21 patients with adverse events (AE group) and 11 patients without adverse events (Non-AE group). Their microbiota and metabolome were characterized using metagenomic shotgun sequencing and untargeted metabolomics. At the species level, the gut microbiota in the Non-AE group exhibits significantly higher abundance of Clostridium sp. Alistipes sp. and lower abundance of Lachnoclostridium sp. Weissella cibaria, Weissella confusa, compared to the AE group (p < .05). A total of 58 discriminative metabolites were identified between groups. Beta-alanine metabolism was scattered. Boc-beta-cyano-L-alanine and CoQ9 were significantly increased in patients without adverse events, while linoleic acid increased in patients with adverse events. The increased Alistipes sp. in the Non-AE group was positively correlated with Boc-beta-cyano-L-alanine and negatively correlated with linoleic acid (p < .05). We constructed a combined microbiome-metabolite model to distinguish Non-AE and AE patients with an AUC of 0.963 via the random forest algorithm. Our findings provided a novel insight into the interplay of multispecies microbial cluster and metabolites of rectal patients with adverse events in neoadjuvant chemoradiotherapy combined with immunotherapy. These microbiota and metabolites deserve further investigations to reveal their roles in adverse events, providing clues for better treatment scenarios.Trial registration number: ClinicalTrials.gov identifier: NCT05368051.}, }
@article {pmid39622769, year = {2024}, author = {Ivan, FX and Tiew, PY and Jaggi, TK and Thng, KX and Pang, PH and Ong, TH and Abisheganaden, JA and Koh, MS and Chotirmall, SH}, title = {Sputum metagenomics reveals a multidrug resistant Pseudomonas-dominant severe asthma phenotype in an Asian population.}, journal = {Respirology (Carlton, Vic.)}, volume = {}, number = {}, pages = {}, doi = {10.1111/resp.14863}, pmid = {39622769}, issn = {1440-1843}, support = {AcRF Tier 1 Grant (RT1/22)//Singapore Ministry of Education/ ; MOH-000710//Singapore Ministry of Health's National Medical Research Council/ ; MOH-001275-00//Singapore Ministry of Health's National Medical Research Council/ ; MOH-001356//Singapore Ministry of Health's National Medical Research Council/ ; MOH-001636//Singapore Ministry of Health's National Medical Research Council/ ; }, abstract = {BACKGROUND AND OBJECTIVE: While the lung microbiome in severe asthma has been studied, work has employed targeted amplicon-based sequencing approaches without functional assessment with none focused on multi-ethnic Asian populations. Here we investigate the clinical relevance of microbial phenotypes of severe asthma in Asians using metagenomics.<br><br>METHODS: Prospective assessment of clinical, radiological, and immunological measures were performed in a multi-ethnic Asian severe asthma cohort (N&#x2009;=&#x2009;70) recruited across two centres in Singapore. Sputum was subjected to shotgun metagenomic sequencing and patients followed up for a 2-year period. Metagenomic assessment of sputum microbiomes, resistomes and virulomes were related to clinical outcomes.<br><br>RESULTS: The lung microbiome in a multi-ethnic Asian cohort with severe asthma demonstrates an increased abundance of Pseudomonas species. Unsupervised clustering of sputum metagenomes identified two patient clusters: C1 (n&#x2009;=&#x2009;52) characterized by upper airway commensals and C2 (n&#x2009;=&#x2009;18) dominated by established respiratory pathogens including M. catarrhalis, S. aureus and most significantly P. aeruginosa. C2 patients demonstrated a significantly increased exacerbation frequency on 2-year follow up and an antimicrobial resistome characterized by multidrug resistance. Virulomes appear indistinguishable between severe asthmatics with or without co-existing bronchiectasis, and C2 patients exhibit increased gene expression related to biofilm formation, effector delivery systems and microbial motility. Independent comparison of the C2 cluster to a non-asthmatic bronchiectasis cohort demonstrates analogous airway microbial virulence patterns.<br><br>CONCLUSION: Sputum metagenomics demonstrates a multidrug-resistant Pseudomonas-dominant severe asthma phenotype in Asians, characterized by poor clinical outcome including increased exacerbations which is independent of co-existing bronchiectasis.}, }
@article {pmid39622690, year = {2024}, author = {Kim, S and Suh, DH and Lee, S and Kim, HS and Cho, SH and Woo, YR}, title = {Associations Between Skin Microbiome and Metabolome in the Pathogenesis of Atopic Dermatitis Patients With Scalp Involvement.}, journal = {Allergy, asthma &amp; immunology research}, volume = {16}, number = {6}, pages = {668-681}, doi = {10.4168/aair.2024.16.6.668}, pmid = {39622690}, issn = {2092-7355}, support = {2021R1I1A1A01052146/NRF/National Research Foundation of Korea/Korea ; }, abstract = {PURPOSE: Atopic dermatitis (AD) is a chronic inflammatory skin condition influenced by various factors, such as the skin microbiome and metabolome. However, specific contributions of these factors to scalp involvement in AD still need to be explored. In this study, we aimed to assess the associations between the skin microbiome and metabolome in AD patients with scalp dermatitis and healthy controls (HCs).<br><br>METHODS: A total of 20 AD patients with scalp involvement and 16 HCs were recruited, and their skin samples were collected for analysis. Bioinformatic analysis and 16S rRNA metagenomic sequencing were performed, with gas chromatography time-of-flight mass spectrometry (GC-TOF-MS) conducted for AD-associated skin metabolites. Spearman correlation analysis was used to identify the correlations between AD-associated skin bacteria and metabolites.<br><br>RESULTS: The results revealed significant differences in bacterial taxa and metabolites between the lesional and non-lesional scalp skin samples of AD patients (groups LS and NL, respectively) and those of HCs (group HC). Notably, group LS showed a significantly increased relative abundance of the genus Staphylococcus and a decreased abundance of Cutibacterium compared to group HC. The reduced abundance of Cutibacterium was also observed when comparing LS to NL. The GC-TOF-MS analysis identified 33 significantly decreased metabolites and 17 significantly increased metabolites in groups LS and NL compared with group HC. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed that amino acid-related metabolism was significantly altered in the metabolic pathway between groups LS, NL, and HC. Furthermore, Spearman correlation analysis showed significant correlations of the altered bacteria genera and skin metabolites between the 3 groups.<br><br>CONCLUSIONS: The results of this research provide valuable insights into the associations the skin microbiome and metabolome between groups LS, NL, and HC. Identifying these specific contributions may offer new avenues for understanding the pathogenesis of scalp involvement in AD patients and potentially lead to improving management strategies.}, }
@article {pmid39622653, year = {2024}, author = {Lee, HJ and Ham, DW and Seo, SH and Cha, GH and Shin, EH}, title = {Probiotic-induced changes in intestinal microbiome inhibits Toxoplasma gondii infection.}, journal = {Parasites, hosts and diseases}, volume = {62}, number = {4}, pages = {408-423}, doi = {10.3347/PHD.24068}, pmid = {39622653}, issn = {2982-6799}, mesh = {Animals ; *Probiotics/administration &amp; dosage/pharmacology/therapeutic use ; *Gastrointestinal Microbiome/drug effects ; *Mice, Inbred C57BL ; Mice ; *Toxoplasma/drug effects ; Dysbiosis/microbiology ; Feces/microbiology/parasitology ; Toxoplasmosis/prevention &amp; control ; Brain/parasitology/microbiology ; Toxoplasmosis, Animal ; Female ; Disease Models, Animal ; }, abstract = {Toxoplasma gondii primarily invades the central nervous system, causing latent infections. Cysts persist in the host for life and there is currently no effective treatment. T. gondii infects human hosts through contaminated meat, invading the intestinal tissue and leading to changes in the number and composition of the gut microbiota. Since probiotic ingestion modulates intestinal microbiota changes, we hypothesized that intestinal microbiota dysbiosis caused by T. gondii infection would be restored following probiotic supplementation. To this end, we orally infected C57BL/6 mice with 10 T. gondii cysts and administered supplemental probiotics daily. We analyzed the levels of T. gondii B1 gene DNA, indicative of T. gondii infection, in brain tissue. We investigated alterations in the gut microbiota composition and functional pathways between the probiotic and non-probiotic treatment groups via next-generation sequencing analysis of each fecal sample. The infection level in the probiotic-treated group was significantly reduced after 4 weeks (p<0.05). Probiotic supplementation notably changed the gut microbiota after 2 weeks of infection, increasing the relative abundance of Intestinimonas massiliensis and Lawsonibacter asaccharolyticus. Probiotic supplements appear to modulate the gut microbiota, activating functional pathways involved in intestinal short-chain fatty acid production and strengthening the intestinal barrier, thereby impeding T. gondii infection and subsequent proliferation. Our findings provide valuable insights into T. gondii infection control and future study directions.}, }
@article {pmid39622138, year = {2024}, author = {Lanfranchi, A and Magdalena, JA and Cavinato, C and Trably, E}, title = {Highly selective acetate production from wine lees through acidogenic fermentation.}, journal = {Journal of environmental management}, volume = {373}, number = {}, pages = {123532}, doi = {10.1016/j.jenvman.2024.123532}, pmid = {39622138}, issn = {1095-8630}, abstract = {Among winery wastes wine lees have a high, unexplored potential for the production of carboxylic acids and more particularly acetate. In fact, they have a high ethanol and low carbohydrate content which can make thermodynamically feasible the oxidation of ethanol to acetate. In this study, the potential of wine lees for anaerobic acetate production was assessed in batch conditions, 37 °C and pH 5.5. White wine lees (WWL) and red wine lees (RWL) were fermented with and without inoculum, and RWL were also co-fermented with waste activated sludge at 20, 40, 70 and 100 gCOD/L. Endogenous microbiome had the same fermentation performances than the external inoculum in WWL, while it led to almost no carboxylates production in RWL, where the community was dominated by the H2-producer Klebsiella (81.6%). Overall, acetate always represented the majority of carboxylates (58-72% on COD basis). H2 production was low (0.31-6.97 mL H2/g bCODin), thus enabling anaerobic ethanol oxidation to acetate (ΔG = -26.6/-7.4 kJ/mol). In co-fermentation, at 70 and 100 gCOD/L caproate (10.0-16.0%) and heptanoate (1.6-5.4%) appeared, alongside a microbiome enriched in lactate-producers (up to 24.5%). Overall, the high acetate selectivity obtained is promising for biorefinery process coupling.}, }
@article {pmid39621900, year = {2024}, author = {Nielsen, AN and Triplett, RL and Bernardez, LM and Tooley, UA and Herzberg, MP and Lean, RE and Kaplan, S and Meyer, D and Kenley, JK and Alexopoulos, D and Losielle, D and Latham, A and Smyser, TA and Agrawal, A and Shimony, JS and Jackson, JJ and Miller, JP and Raichle, ME and Warner, BB and Rogers, CE and Sylvester, CM and Barch, DM and Luby, JL and Smyser, CD}, title = {Prenatal social disadvantage is associated with alterations in functional networks at birth.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {121}, number = {50}, pages = {e2405448121}, doi = {10.1073/pnas.2405448121}, pmid = {39621900}, issn = {1091-6490}, support = {R01 MH121877/MH/NIMH NIH HHS/United States ; R01 MH113570/MH/NIMH NIH HHS/United States ; R01 MH113883/MH/NIMH NIH HHS/United States ; R01 DA046224/DA/NIDA NIH HHS/United States ; T32 GR0029379//HHS | NIH | National Institute of Mental Health (NIMH)/ ; P50 HD103525/HD/NICHD NIH HHS/United States ; R01 MH090786/MH/NIMH NIH HHS/United States ; }, mesh = {Humans ; Female ; Pregnancy ; *Brain/diagnostic imaging ; *Magnetic Resonance Imaging ; Adult ; Infant, Newborn ; Prenatal Exposure Delayed Effects ; Male ; Nerve Net/diagnostic imaging ; }, abstract = {Childhood exposure to social disadvantage is a major risk factor for psychiatric disorders and poor developmental, educational, and occupational outcomes, presumably because adverse exposures alter the neurodevelopmental processes that contribute to risk trajectories. Yet, given the limited social mobility in the United States and other countries, childhood social disadvantage is frequently preceded by maternal social disadvantage during pregnancy, potentially altering fetal brain development during a period of high neuroplasticity through hormonal, microbiome, epigenetic, and immune factors that cross the placenta and fetal blood-brain barrier. The current study examines prenatal social disadvantage to determine whether these exposures in utero are associated with alterations in functional brain networks as early as birth. As part of the Early Life Adversity and Biological Embedding study, mothers were recruited during pregnancy, prenatal social disadvantage was assessed across trimesters, and their healthy, full-term offspring were imaged using resting-state functional magnetic resonance imaging during the first weeks of life. Multivariate machine learning methods revealed that neonatal functional connectivity (FC) varied as a function of prenatal exposure to social disadvantage (n = 261, R = 0.43, R[2] = 0.18), with validation in an independent sample. Alterations in FC associated with prenatal social disadvantage occurred brain-wide and were most pronounced in association networks (fronto-parietal, ventral attention, dorsal attention) and the somatomotor network. Amygdala FC was altered at birth, with a pattern shared across subcortical structures. These findings provide critical insights into how early in development functional networks begin to diverge in the context of social disadvantage and elucidate the functional networks that are most impacted.}, }
@article {pmid39621633, year = {2024}, author = {Martins, FP and Andrade-Silva, J and Teixeira, BL and Ferrari, A and Christoff, AP and Cruz, GNF and Paladino, FV and de Oliveira, LFV and Hernandes, C}, title = {Oral microbiome test as an alternative diagnostic tool for gastric alterations: A prospective, bicentric cross-sectional study.}, journal = {PloS one}, volume = {19}, number = {12}, pages = {e0314660}, pmid = {39621633}, issn = {1932-6203}, mesh = {Humans ; Cross-Sectional Studies ; Female ; Male ; Middle Aged ; *Mouth/microbiology ; Prospective Studies ; Adult ; *Microbiota ; Brazil ; Aged ; Stomach/microbiology ; Bacteria/genetics/isolation &amp; purification/classification ; Stomach Diseases/microbiology/diagnosis ; }, abstract = {The human microbiome plays a pivotal role in influencing various physiological processes and maintaining overall well-being, including the gastric system. Current diagnostic tests for gastric diseases often involve invasive procedures, sampling limitations, and medication effects, leading to potential diagnostic errors and discomfort to patients. Considering the connection between oral and gastric microbiomes, this cross-sectional study aimed to assess the diagnostic potential of the oral bacterial profile in patients undergoing upper digestive endoscopy. Oral samples from 266 participants across two Brazilian sites (Belterra and Sao Paulo) were sequenced and subjected to bioinformatic analysis to identify microbiome composition across endoscopy outcome groups, exploring alpha and beta-diversity, richness, and differential abundance and prevalence. Prevotella, Haemophilus, Fusobacterium, Neisseria, and Streptococcus were the most abundant genera observed. No significant associations were found between alpha diversity profiles and endoscopy outcomes; beta diversity analyses similarly showed no correlations. Overall, the study did not establish the oral microbiome as a reliable marker for gastric health, underscoring the necessity for broader studies in the development of non-invasive diagnostic tests.}, }
@article {pmid39621295, year = {2024}, author = {Liu, H and Wang, S and Yu, X and Sun, S and Su, Y}, title = {Effect of Resveratrol on the intestinal microbiota in Type2 diabetes Mellitus mice.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {}, number = {}, pages = {}, pmid = {39621295}, issn = {1678-4405}, support = {82060149//the National Natural Science Foundation of China funded project/ ; 202201AT070008//the basic research foundation of Science and Technology Department of Yunnan Province/ ; 202101BA070001-112//the basic research foundation of Science and Technology Department of Yunnan Province/ ; }, abstract = {Some natural products have been found to have a positive effect on the treatment of Type 2 Diabetes Mellitus (T2DM). The effective mechanism by which these natural products work may be attributed to their ability to alter the gut microbiome. In this study, considering the beneficial properties of resveratrol for T2DM, the mechanism of resveratrol in releasing of T2DM, the correlation between the apparent traits of resveratrol in T2DM mice and the changes in intestinal flora structure were explored. The intervention of resveratrol in different dose did effectively improve the apparent T2DM symptoms in mice, including reduced fasting blood glucose, enhance to both the insulin tolerance and glucose tolerance. Simultaneously, resveratrol can effectively ameliorate the pathological condition of the colon and rectum in T2DM mice, leading to a reduction in intestinal villi swelling and fat vacuoles. The intervention of resveratrol led to changes in the gut flora structure of T2DM mice. Erysipelas and Ileibacterium are crucial taxa of resveratrol involved in maintaining the balance of the gut microbiota. The abundance of Erysipelotrichaceae and Ileibacterium was significantly elevated under the treatment of resveratrol, and the compose of the gut microbiota was more inclined to healthy mice. T2DM symptoms could be alleviated by resveratrol through different mechanisms compared to metformin intervention.}, }
@article {pmid39621289, year = {2024}, author = {Salam, LB and Apollos, EE and Obayori, OS and Michael, GI}, title = {Physicochemistry and comparative metagenomics of a tropical estuary persistently inundated with anthropogenic pollutants.}, journal = {Folia microbiologica}, volume = {}, number = {}, pages = {}, pmid = {39621289}, issn = {1874-9356}, abstract = {The physicochemistry, metabolic properties, and microbial community structure of a tropical estuary persistently inundated with anthropogenic pollutants were elucidated using diverse analytical tools and a shotgun metagenomics approach. The physicochemistry of the Awoye estuary surface water (AEW) and sediment (AES) revealed higher values in the sediment for most of the parameters analyzed, while aside from copper and zinc, the concentrations of the detected heavy metals (Cd, Cr, Pb, Fe, As, Ni, Hg, Mn, Se) in the water and sediment were higher than the acceptable thresholds. Hydrocarbon content analysis revealed increasingly high concentrations of high molecular weight polycyclic aromatic hydrocarbons (HMW PAHs) in the sediment. Structurally, the predominant taxa in the AEW metagenome are Proteobacteria (50.35%), Alphaproteobacteria (43.31%), Brevundimonas (49.96%), and Leptolyngbya boryana (14.93%), while in the sediment (AES) metagenome, Proteobacteria (53.03%), Gammaproteobacteria (28.66%), Azospirillum (6.51%), and Acidihalobacter prosperus (7.56%) were preponderant. Statistical analysis of the two microbiomes (AEW, AES) revealed significant statistical differences (P < 0.05) at all the hierarchical levels. Functional characterization of the two metagenomes revealed extensive adaptations of the sediment microbiome to various environmental stressors as evident in the high numbers of putative genes involved in the degradation of diverse classes of aromatic hydrocarbons, efflux, detoxification, and transport of heavy metals, and metabolism of organic/inorganic nutrients. Findings from this study revealed that the estuary sediment is the sink for most of the anthropogenic pollutants and harbors the more adapted microbiome that could serve as a potential bioresource for the bioremediation of the perturbed estuary.}, }
@article {pmid39621160, year = {2024}, author = {Nguyen, L and Shanmugan, S}, title = {A Review Article: The Relationship Between Obesity and Colorectal Cancer.}, journal = {Current diabetes reports}, volume = {25}, number = {1}, pages = {8}, pmid = {39621160}, issn = {1539-0829}, mesh = {Humans ; *Colorectal Neoplasms/etiology/epidemiology ; *Obesity/complications ; Bariatric Surgery ; Risk Factors ; Weight Loss ; Gastrointestinal Microbiome ; }, abstract = {PURPOSE OF REVIEW: This article aims to review the recent literature assessing the relationship between obesity and colorectal carcinogenesis, the effect of obesity on the treatment of colorectal cancer (CRC), tools available to help augment the increased risk, and outcomes for patients who are affected by both obesity and colorectal cancer.<br><br>RECENT FINDINGS: The biochemical mechanisms contributing to CRC carcinogenesis are not well understood but are suspected to be related to adipose tissue leading to a pro-inflammatory state and changes in the gut microbiome. Individuals with obesity are at higher risk for CRC development, worse oncologic outcomes, and increased rates of post-operative complications. Bariatric surgery decreases CRC risk but results with GLP-1 agonists are heterogeneous. Prehabilitation is the only weight loss method that has been demonstrated to decrease risks of post-operative morbidity in this population. Obesity augments CRC risk and outcomes. There are persistent knowledge gaps in etiology and epidemiology for the increased CRC risk in obese patients and more research is required to identify the therapeutic advantage of weight loss on CRC risk.}, }
@article {pmid39620778, year = {2024}, author = {Abramson, SL}, title = {The Skin Microbiome in the First Year of Life and Its Association With Atopic Dermatitis.}, journal = {Pediatrics}, volume = {154}, number = {Suppl 4}, pages = {S8-S9}, doi = {10.1542/peds.2024-069114DC}, pmid = {39620778}, issn = {1098-4275}, }
@article {pmid39620763, year = {2024}, author = {Trotto, N and Hernandez-Trujillo, V}, title = {Longitudinal Dynamics of The Gut Microbiome and Metabolome in Peanut Allergy Development.}, journal = {Pediatrics}, volume = {154}, number = {Suppl 4}, pages = {S12}, doi = {10.1542/peds.2024-069114DI}, pmid = {39620763}, issn = {1098-4275}, }
@article {pmid39620695, year = {2024}, author = {Mallott, EK and Kuthyar, S and Lee, W and Reiman, D and Jiang, H and Chitta, S and Waters, EA and Layden, BT and Sumagin, R and Manzanares, LD and Yang, GY and Sardaro, MLS and Gray, S and Williams, LE and Dai, Y and Curley, JP and Haney, CR and Liechty, ER and Kuzawa, CW and Amato, KR}, title = {The primate gut microbiota contributes to interspecific differences in host metabolism.}, journal = {Microbial genomics}, volume = {10}, number = {12}, pages = {}, doi = {10.1099/mgen.0.001322}, pmid = {39620695}, issn = {2057-5858}, mesh = {Animals ; *Gastrointestinal Microbiome ; Mice ; *Brain/metabolism ; *Primates/microbiology ; Energy Metabolism ; Species Specificity ; Adipose Tissue/metabolism ; Humans ; }, abstract = {Because large brains are energetically expensive, they are associated with metabolic traits that facilitate energy availability across vertebrates. However, the biological underpinnings driving these traits are not known. Given its role in regulating host metabolism in disease studies, we hypothesized that the gut microbiome contributes to variation in normal cross-vertebrate species differences in metabolism, including those associated with the brain's energetic requirements. By inoculating germ-free mice with the gut microbiota (GM) of three primate species - two with relatively larger brains and one with a smaller brain - we demonstrated that the GM of larger-brained primates shifts host metabolism towards energy use and production, while that of smaller-brained primates stimulates energy storage in adipose tissues. Our findings establish a causal role of the GM in normal cross-host species differences in metabolism associated with relative brain size and suggest that the GM may have been an important facilitator of metabolic changes during human evolution that supported encephalization.}, }
@article {pmid39620486, year = {2024}, author = {Luo, Y and Sheikh, TMM and Li, X and Yuan, Y and Yao, F and Wang, M and Guo, X and Wu, J and Shafiq, M and Xie, Q and Jiao, X}, title = {Exploring the dynamics of gut microbiota, antibiotic resistance, and chemotherapy impact in acute leukemia patients: A comprehensive metagenomic analysis.}, journal = {Virulence}, volume = {15}, number = {1}, pages = {2428843}, doi = {10.1080/21505594.2024.2428843}, pmid = {39620486}, issn = {2150-5608}, mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Metagenomics ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; Male ; Female ; Adult ; Middle Aged ; Feces/microbiology ; Bacteria/genetics/drug effects/classification/isolation &amp; purification ; Leukemia/drug therapy/microbiology/complications ; Drug Resistance, Microbial/genetics ; Aged ; Young Adult ; Antineoplastic Agents/adverse effects ; }, abstract = {Leukemia poses significant challenges to its treatment, and understanding its complex pathogenesis is crucial. This study used metagenomic sequencing to investigate the interplay between chemotherapy, gut microbiota, and antibiotic resistance in patients with acute leukemia (AL). Pre- and post-chemotherapy stool samples from patients revealed alterations in microbial richness, taxa, and antibiotic resistance genes (ARGs). The analysis revealed a decreased alpha diversity, increased dispersion in post-chemotherapy samples, and changes in the abundance of specific bacteria. Key bacteria such as Enterococcus, Klebsiella, and Escherichia coli have been identified as prevalent ARG carriers. Correlation analysis between gut microbiota and blood indicators revealed potential links between microbial species and inflammatory biomarkers, including C-reactive protein (CRP) and adenosine deaminase (ADA). This study investigated the impact of antibiotic dosage on microbiota and ARGs, revealing networks connecting co-occurring ARGs with microbial species (179 nodes, 206 edges), and networks associated with ARGs and antibiotic dosages (50 nodes, 50 edges). Antibiotics such as cephamycin and sulfonamide led to multidrug-resistant Klebsiella colonization. Our analyses revealed distinct microbial profiles with Salmonella enterica elevated post-chemotherapy in NF patients and Akkermansia muciniphila elevated pre-chemotherapy. These microbial signatures could inform strategies to modulate the gut microbiome, potentially mitigating the risk of neutropenic fever in patients undergoing chemotherapy. Finally, a comprehensive analysis of KEGG modules shed light on disrupted metabolic pathways after chemotherapy, providing insights into potential targets for managing side effects. Overall, this study revealed intricate relationships between gut microbiota, chemotherapy, and antibiotic resistance, providing new insights into improving therapy and enhancing patient outcomes.}, }
@article {pmid39620359, year = {2024}, author = {López-Agudelo, VA and Falk-Paulsen, M and Bharti, R and Rehman, A and Sommer, F and Wacker, EM and Ellinghaus, D and Luzius, A and Sievers, LK and Liebeke, M and Kaser, A and Rosenstiel, P}, title = {Defective Atg16l1 in intestinal epithelial cells links to altered fecal microbiota and metabolic shifts during pregnancy in mice.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2429267}, doi = {10.1080/19490976.2024.2429267}, pmid = {39620359}, issn = {1949-0984}, mesh = {Animals ; Female ; Pregnancy ; *Gastrointestinal Microbiome ; Mice ; *Feces/microbiology ; *Autophagy-Related Proteins/genetics/metabolism ; Bacteria/classification/genetics/isolation &amp; purification/metabolism ; RNA, Ribosomal, 16S/genetics ; Intestinal Mucosa/microbiology/metabolism ; Epithelial Cells/microbiology/metabolism ; Crohn Disease/microbiology/metabolism ; Mice, Inbred C57BL ; Metagenomics ; Chemokine CXCL1/genetics/metabolism ; }, abstract = {Throughout gestation, the female body undergoes a series of transformations, including profound alterations in intestinal microbial communities. Changes gradually increase toward the end of pregnancy and comprise reduced α-diversity of microbial communities and an increased propensity for energy harvest. Despite the importance of the intestinal microbiota for the pathophysiology of inflammatory bowel diseases, very little is known about the relationship between these microbiota shifts and pregnancy-associated complications of the disease. Here, we explored the longitudinal dynamics of gut microbiota composition and functional potential during pregnancy and after lactation in Atg16l1[∆IEC] mice carrying an intestinal epithelial deletion of the Crohn's disease risk gene Atg16l1. Using 16S rRNA amplicon and shotgun metagenomic sequencing, we demonstrated divergent temporal shifts in microbial composition between Atg16l1 wildtype and Atg16l1[∆IEC] pregnant mice in trimester 3, which was validated in an independent experiment. Observed differences included microbial genera implicated in IBD such as Lachnospiraceae, Roseburia, Ruminococcus, and Turicibacter. Changes partially recovered after lactation. Additionally, metagenomic and metabolomic analyses suggest an increased capacity for chitin degradation, resulting in higher levels of free N-acetyl-glucosamine products in feces, alongside reduced glucose and myo-inositol levels in serum around the time of delivery. On the host side, we found that the immunological response of Atg16l1[∆IEC] mice is characterized by higher colonic mRNA levels of TNFα and CXCL1 in trimester 3 and a lower weight of offspring at birth. Understanding pregnancy-dependent microbiome changes in the context of IBD may constitute the first step in the identification of fecal microbial biomarkers and microbiota-directed therapies that could help improve precision care for managing pregnancies in IBD patients.}, }
@article {pmid39620249, year = {2024}, author = {Kim, LY and Schüssler-Fiorenza Rose, SM and Mengelkoch, S and Moriarity, DP and Gassen, J and Alley, JC and Roos, LG and Jiang, T and Alavi, A and Thota, DD and Zhang, X and Perelman, D and Kodish, T and Krupnick, JL and May, M and Bowman, K and Hua, J and Liao, YJ and Lieberman, AF and Butte, AJ and Lester, P and Thyne, SM and Hilton, JF and Snyder, MP and Slavich, GM}, title = {California Stress, Trauma, and Resilience Study (CalSTARS) protocol: A multiomics-based cross-sectional investigation and randomized controlled trial to elucidate the biology of ACEs and test a precision intervention for reducing stress and enhancing resilience.}, journal = {Stress (Amsterdam, Netherlands)}, volume = {27}, number = {1}, pages = {2401788}, doi = {10.1080/10253890.2024.2401788}, pmid = {39620249}, issn = {1607-8888}, mesh = {Humans ; Cross-Sectional Studies ; *Stress, Psychological ; *Resilience, Psychological ; *Adverse Childhood Experiences ; California ; Adult ; Female ; Male ; Precision Medicine/methods ; Multiomics ; }, abstract = {Adverse Childhood Experiences (ACEs) are very common and presently implicated in 9 out of 10 leading causes of death in the United States. Despite this fact, our mechanistic understanding of how ACEs impact health is limited. Moreover, interventions for reducing stress presently use a one-size-fits-all approach that involves no treatment tailoring or precision. To address these issues, we developed a combined cross-sectional study and randomized controlled trial, called the California Stress, Trauma, and Resilience Study (CalSTARS), to (a) characterize how ACEs influence multisystem biological functioning in adults with all levels of ACE burden and current perceived stress, using multiomics and other complementary approaches, and (b) test the efficacy of our new California Precision Intervention for Stress and Resilience (PRECISE) in adults with elevated perceived stress levels who have experienced the full range of ACEs. The primary trial outcome is perceived stress, and the secondary outcomes span a variety of psychological, emotional, biological, and behavioral variables, as assessed using self-report measures, wearable technologies, and extensive biospecimens (i.e. DNA, saliva, blood, urine, &amp; stool) that will be subjected to genomic, transcriptomic, proteomic, metabolomic, lipidomic, immunomic, and metagenomic/microbiome analysis. In this protocol paper, we describe the scientific gaps motivating this study as well as the sample, study design, procedures, measures, and planned analyses. Ultimately, our goal is to leverage the power of cutting-edge tools from psychology, multiomics, precision medicine, and translational bioinformatics to identify social, molecular, and immunological processes that can be targeted to reduce stress-related disease risk and enhance biopsychosocial resilience in individuals and communities worldwide.}, }
@article {pmid39620150, year = {2024}, author = {Villicaña, C and Moretti, CH and Carbonero, F}, title = {Editorial: Aging and the microbiome.}, journal = {Frontiers in aging}, volume = {5}, number = {}, pages = {1522703}, doi = {10.3389/fragi.2024.1522703}, pmid = {39620150}, issn = {2673-6217}, }
@article {pmid39620114, year = {2024}, author = {An, E and Delgadillo, DR and Yang, J and Agarwal, R and Labus, JS and Pawar, S and Lietman, M and Kilpatrick, LA and Bhatt, RR and Vora, P and Vaughan, A and Dong, TS and Gupta, A}, title = {Stress-Resilience Impacts Psychological Wellbeing: Evidence from Brain-Gut Microbiome Interactions.}, journal = {Nature. Mental health}, volume = {2}, number = {8}, pages = {935-950}, pmid = {39620114}, issn = {2731-6076}, abstract = {The brain-gut-microbiome (BGM) system plays an influential role on mental health. We characterized BGM patterns related to resilience using fecal samples and multimodal MRI. Data integration analysis using latent components showed the high resilience phenotype was associated with lower depression and anxiety symptoms, higher frequency of bacterial transcriptomes (related to environmental adaptation, genetic propagation, energy metabolism, anti-inflammation), increased metabolites (N-acetylglutamate; dimethylglycine), and cortical signatures (increased resting state functional connectivity between reward circuits and sensorimotor networks; decreased grey matter volume and white matter tracts within the emotion regulation network). Our findings support a multi-omic signature involving the BGM system suggesting that resilience impacts psychological symptoms, emotion regulation and cognitive function as reflected by unique neural correlates and microbiome function supporting eubiosis and gut barrier integrity. Bacterial transcriptomes provided the highest classification accuracy suggesting that the microbiome is critical in shaping resilience and highlights that microbiome modifications can optimize mental health.}, }
@article {pmid39620087, year = {2024}, author = {Zhang, X and Xi, T and Wang, Y and Fan, X and Xu, D and Zhang, P and Sun, K and Zhang, Y and Ma, J and Ye, N}, title = {Chemical interactions between kelp Macrocystis pyrifera and symbiotic bacteria under elevated CO2 condition.}, journal = {Marine life science &amp; technology}, volume = {6}, number = {4}, pages = {700-712}, pmid = {39620087}, issn = {2662-1746}, abstract = {UNLABELLED: Kelps are pivotal to temperate coastal ecosystems, providing essential habitat and nutrients for diverse marine life, and significantly enhancing local biodiversity. The impacts of elevated CO2 levels on kelps may induce far-reaching effects throughout the marine food web, with potential consequences for biodiversity and ecosystem functions. This study considers the kelp Macrocystis pyrifera and its symbiotic microorganisms as a holistic functional unit (holobiont) to examine their collective response to heightened CO2 levels. Over a 4 month cultivation from the fertilization of M. pyrifera gametes to the development of juvenile sporophytes, our findings reveal that elevated CO2 levels influence the structure of the M. pyrifera symbiotic microbiome, alter metabolic profiles, and reshape microbe-metabolite interactions using 16S rRNA amplicon sequencing and liquid chromatography coupled to mass spectrometry analysis. Notably, Dinoroseobacter, Sulfitobacter, Methylotenera, Hyphomonas, Milano-WF1B-44 and Methylophaga were selected as microbiome biomarkers, which showed significant increases in comparative abundance with elevated CO2 levels. Stress-response molecules including fatty-acid metabolites, oxylipins, and hormone-like compounds such as methyl jasmonate and prostaglandin F2a emerged as critical metabolomic indicators. We propose that elevated CO2 puts certain stress on the M. pyrifera holobiont, prompting the release of these stress-response molecules. Moreover, these molecules may aid the kelp's adaptation by modulating the microbial community structure, particularly influencing potential pathogenic bacteria, to cope with environmental change. These results will enrich the baseline data related to the chemical interactions between the microbiota and M. pyrifera and provide clues for predicting the resilience of kelps to future climate change.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s42995-024-00259-5.}, }
@article {pmid39620016, year = {2024}, author = {Ertaş Öztürk, Y and Karabudak, E and Eğritaş Gürkan, &#xd6; and Dalgıç, B}, title = {Gut microbiota alterations and associations with nutrients in children with celiac disease.}, journal = {Food science &amp; nutrition}, volume = {12}, number = {11}, pages = {8887-8902}, pmid = {39620016}, issn = {2048-7177}, abstract = {Celiac disease is a chronic inflammatory condition that is not well understood in relation to the microbiome. Our objective was to demonstrate changes in the microbiota and the relationships between nutrients in children with celiac disease (CD) who followed a gluten-free diet (GFD). A group of 11 children who were recently diagnosed with CD, ranging in age from 3 to 12, were monitored for a period of 6 months. GFD is designed based on the individual's specific energy and nutrient needs, with strict control over dietary adherence. Food consumption, blood, and fecal samples were taken. Fecal samples were put through 16s rRNA sequencing. Microbial modifications were demonstrated using alpha diversity, beta diversity, nonmetric multidimensional scaling analysis (NDMS), t-test, and metastats. Mean age was 6.4 ± 2.66 years and 54.5% were male participants. Serological parameters were negative after 6 months. Both unweighted (p = .019) and weighted (p = .021) Unifrac distances were higher before GFD, and differences were reliable according to NDMS analysis (stress = 0.189). The abundance of Bacteroides ovatus was increased (p = .014), whereas unidentified Lachnospiraceae, Paeniclostridium, Paraclostridium Peptostreptococcus, and Dielma were decreased after GFD (p < .001). Associations between nutrients and several genera and species were identified. The presence of genus Bifidobacterium and Bifidobacterium adolescentis was inversely associated with fat intake after GFD (p < .01). Microbiota changes became evident over a period of 6 months. The presence or absence of small bacteria may play a role in the development of CD. Modifying the children's dietary intake can potentially influence the microbial composition.}, }
@article {pmid39619770, year = {2024}, author = {Nwanaforo, E and Obasi, CN and Frazzoli, C and Bede-Ojimadu, O and Orisakwe, OE}, title = {Exposure to Environmental Pollutants and Risk of Diarrhea: A Systematic Review.}, journal = {Environmental health insights}, volume = {18}, number = {}, pages = {11786302241304539}, pmid = {39619770}, issn = {1178-6302}, abstract = {This systematic review investigates the association between environmental pollutants and the risk of diarrhea, a critical public health issue, particularly in low- and middle-income countries. The review synthesizes findings from various studies that highlight the impact of contaminants such as pesticides, heavy metals, polycyclic aromatic hydrocarbons (PAHs), microplastics, and parabens on gastrointestinal health. Following PRISMA guidelines, a comprehensive literature search across databases including PubMed, Scopus, and Google Scholar yielded 496 articles, of which 11 met the inclusion criteria for detailed analysis. The results indicate a significant correlation between exposure to specific pollutants-particularly pesticides like dichlorodiphenyltrichloroethane (DDT), PAHs, arsenic, cadmium, and microplastics-and increased incidences of diarrhea. Notably, studies revealed that prenatal exposure to DDT is linked to higher diarrhea rates among boys in urban settings, while pesticide exposure in childhood correlates with inflammatory bowel disease in adulthood. Mechanistically, these pollutants may disrupt gastrointestinal function through cholinergic effects and endocrine disruption, leading to altered gut motility and microbiome imbalances. Moreover, the review emphasizes the immunosuppressive effects of heavy metals such as mercury and cadmium, which compromise the immune response and increase susceptibility to gastrointestinal infections. Despite the identified associations, there is a notable gap in research regarding geographic distribution and pollutant impacts on health outcomes. The review underscores the necessity for public health interventions aimed at reducing exposure to these environmental pollutants to mitigate their adverse health effects. In conclusion, this systematic review highlights the urgent need for further epidemiological studies in underrepresented areas to enhance our understanding of how environmental pollutants influence public health globally. Recommendations include rigorous monitoring of pollutant levels, public health initiatives to reduce exposure, and policies that restrict emissions of harmful substances. Addressing environmental pollution is crucial for mitigating diarrheal diseases and protecting vulnerable populations from its detrimental effects.}, }
@article {pmid39619727, year = {2024}, author = {Sawan, HM and Shroukh, W and Abutaima, R and Al Omari, SM and Abdel-Qader, DH and Binsuwaidan, R}, title = {Impact of Jordanian Pharmacists' Knowledge of the Human Microbiome: Has the Practice of Antibiotics and Probiotics Dispensing Been Affected? A Cross-Sectional Study.}, journal = {Infection and drug resistance}, volume = {17}, number = {}, pages = {5203-5214}, pmid = {39619727}, issn = {1178-6973}, abstract = {OBJECTIVE: This study aimed to assess Jordanian pharmacists' knowledge of the human microbiome and the impact of their knowledge on their attitudes and practices toward antibiotics and probiotics.<br><br>METHODS: A self-administered survey was designed after reviewing the literature. Participants' demographics were collected, and questions to evaluate pharmacists' knowledge, attitudes, and practices toward antibiotic and probiotic dispensing were asked. The data were analyzed using the Statistical Package for the Social Sciences V.26. Pearson correlations and one-way ANOVA were employed to calculate the significance of knowledge, attitudes, and practices. Statistical significance was considered at p < 0.05.<br><br>RESULTS: Of the 333 respondents, around 75% (n=250) had a high level of general knowledge regarding the human gut microbiome. Almost equal proportions of participants had either intermediate or high levels of knowledge about the role of gut bacteria in health (n=164, 49.2%) (n=166, 49.8%), respectively, while almost two-thirds had an intermediate level of knowledge of the role of gut bacteria in disease (n=197, 59.2%). More than half of the participants had a positive attitude toward antibiotics, probiotics, and the human microbiome (n=179, 53.8%), and the majority (n=239, 71.8%) had an intermediate level of practice with them. There was a significant positive correlation between pharmacists' general knowledge of the human microbiome and their positive attitudes (r=0.306, p < 0.01) and practices (r=0.331, p < 0.01) toward antibiotics and probiotics.<br><br>CONCLUSION: Study results raise the importance of interventional educational measures to promote healthcare professionals' knowledge of the human microbiome and their potential beneficence on pharmacists' attitudes and practices regarding antibiotics and probiotics dispensing. The results also denote the urgent need for probiotics' clinical guidelines to ensure practice uniformity.}, }
@article {pmid39619696, year = {2024}, author = {Kang, P and Bae, GS and Jeon, E and Choi, J and Hwang, EH and Kim, G and Baek, SH and Shim, K and An, YJ and Lim, KS and Kim, Y and Oh, T and Hong, JJ and Lee, WK and Kim, SH and Koo, BS}, title = {Comprehensive effects of fecal microbiota transplantation on cynomolgus macaques across various fecal conditions.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1458923}, pmid = {39619696}, issn = {1664-302X}, abstract = {Fecal microbiota transplantation (FMT) and probiotics therapies represent key clinical options, yet their complex effects on the host are not fully understood. We evaluated the comprehensive effects of FMT using diarrheal or normal feces, as well as probiotic therapies, on multiple anatomical sites in healthy cynomolgus macaques through colonoscopy and surgery. Our research revealed that FMT led to a partial microbiome transplantation without exhibiting the donor's fecal clinical characteristics. Notably, FMT increased insulin and C-peptide levels in each animal according time series, regardless of fecal conditions. Immunologically, a reduction in neutrophil-to-lymphocyte ratio were exclusively observed in femoral veins of FMT group. In blood chemistry analyses, reductions in aspartate aminotransferase, blood urea nitrogen, and creatinine were observed in the femoral veins, while elevated levels of alanine aminotransferase and calcium were exclusively detected in the portal veins. These changes were not observed in the probiotic group. Also, short chain fatty acids were significantly higher increase in portal veins rather than femoral veins. Transcriptome analysis of liver tissues showed that metabolic pathways were primarily affected by both FMT and probiotics therapies. In summary, FMT therapy significantly influenced metabolic, immunologic and transcriptomic responses in normal macaque models, regardless of fecal conditions. Also, these macaque models, which utilize surgery and colonoscopy, serve as a human-like preclinical platform for evaluating long-term effects and anatomically specific responses to gut-targeted interventions, without the need for animal sacrifice.}, }
@article {pmid39619693, year = {2024}, author = {Bai, R and Li, H and Chen, S and Yuan, X and Chen, Y and Huang, Y and Zhou, Q and Guan, H}, title = {Corrigendum: Microbiome and response surface methodology analyses reveal Acetobacter pasteurianus as the core bacteria responsible for aerobic spoilage of corn silage (Zea mays) in hot and humid areas.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1513623}, doi = {10.3389/fmicb.2024.1513623}, pmid = {39619693}, issn = {1664-302X}, abstract = {[This corrects the article DOI: 10.3389/fmicb.2024.1473238.].}, }
@article {pmid39619690, year = {2024}, author = {Wu, X and Liu, X and Xu, W and Chen, W and Zhong, Z and Tan, H and Xiang, T}, title = {A nested case-control study on the association of gut virome in early pregnancy and gestational diabetes mellitus.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1461259}, pmid = {39619690}, issn = {1664-302X}, abstract = {BACKGROUND: Recent studies have increasingly shown the connection between gut microbiome and gestational diabetes mellitus (GDM). However, no studies have explored the relationship between the gut virome and GDM, and the underlying mechanism remains unknown.<br><br>METHODS: We performed a nested case-control study within a follow-up cohort, enrolling 51 patients with GDM and 51 healthy controls. Shotgun metagenomics sequencing was used to explore gut virome profiles during early pregnancy.<br><br>RESULTS: Diversity analysis revealed no difference in the overall gut virome composition between two groups, however, we found greater abundance of Escherichia phage SH2026Stx1 (Q = 0.23), Enterobacteria phage mEp043 c-1 (Q = 0.21), crAssphage cr50_1 (Q = 0.21), Enterobacteria phage phi80 (Q = 0.21), and Escherichia phage HK106 (Q = 0.23) in GDM patients. Cross-kingdom correlation analysis showed the negative correlation between the gut bacterium Eubacterium eligens and three bacteriophages (Escherichia phage SH2026Stx1, Enterobacteria phage mEp043 c-1, and Escherichia phage HK106) in GDM group (r < 0, P < 0.05). Based on gut microbial features and clinical indicators, we constructed a new prediction model using random forest method for GDM with good predictive performance (AUC of 0.893, 95% CI: 0.736 &#x223c; 0.990).<br><br>CONCLUSION: This study is the first to investigate the relationship between the gut virome and GDM as well as the cross-kingdom correlation between gut viruses and bacteria in GDM. Our findings could enhance strategies for preventing and treating GDM from the perspective of gut microbiome, offering valuable insights into its pathogenesis.}, }
@article {pmid39619689, year = {2024}, author = {Wang, C and Wang, D and Li, C and Ge, Z and Hao, L and Albasher, G and Feng, F and Sun, Y and Lyu, Y and Zheng, S}, title = {Microbial communities during the composting process of Agaricus subrufescens and their effects on mushroom agronomic and nutritional qualities.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1471638}, pmid = {39619689}, issn = {1664-302X}, abstract = {INTRODUCTION: Tunnel composting technology for preparing Agaricus subrufescens cultivation media can achieve a higher biological efficiency (BE) and a lower contamination rate (CR). However, this technology lacks in-depth and systematic study.<br><br>METHODS: In the present study, the changes in the microbiome and microbial metabolic functions were surveyed using metagenomic analysis. The physicochemical parameters, agronomic properties and nutritional qualities were also evaluated.<br><br>RESULTS AND DISCUSSION: Results showed that the contents of cellulose, hemicellulose and lignin dropped to 10.18, 11.58, 27.53%, respectively at the end of composting. The tunnel composting technology led to significant increases in crude protein content (32.56%) and crude fiber content (13.68%). Variations of physicochemical characteristics led to different successions of microbial communities. Bacteria manifested significantly higher abundance than fungi. Firmicutes, Actinobacteriota, Chloroffexi and Deinococcota were the predominant bacterial phyla. Ascomycota and Basidiomycota were the dominant fungal phyla in the thermophilic phase. Pseudonocardia, Truepera, and Thermopolyspora were positively correlated with the yield of A. subrufescens. In addition to TN, most of the physicochemical properties were significantly correlated with fungal communities in the thermophilic phase. The metabolisms of carbohydrate, amino acid and energy were the primary enrichment pathways. These findings deepen the understanding of microbial communities composition during the composting of A. subrufescens substrates. Moreover, this study provides a basis for improving tunnel composting technology.}, }
@article {pmid39619675, year = {2024}, author = {Little, A and Deek, RA and Zhang, A and Zhao, N and Ling, W and Wu, MC}, title = {Enhanced visualization of microbiome data in repeated measures designs.}, journal = {Frontiers in genetics}, volume = {15}, number = {}, pages = {1480972}, pmid = {39619675}, issn = {1664-8021}, abstract = {INTRODUCTION: Repeated measures microbiome studies, including longitudinal and clustered designs, offer valuable insights into the dynamics of microbial communities and their associations with various health outcomes. However, visualizing such multivariate data poses significant challenges, particularly in distinguishing meaningful biological patterns from noise introduced by covariates and the complexities of repeated measures.<br><br>METHODS: In this study, we propose a framework to enhance the visualization of repeated measures microbiome data using Principal Coordinates Analysis (PCoA) adjusted for covariates through linear mixed models (LMM). Our method adjusts for confounding variables and accounts for the repeated measures structure of the data, enabling clearer identification of microbial community variations across time points or clusters.<br><br>RESULTS: We demonstrate the utility of our approach through simulated scenarios and real datasets, showing that it effectively mitigates the influence of nuisance covariates and highlights key axes of microbiome variation.<br><br>DISCUSSION: This refined visualization technique provides a robust tool for researchers to explore and understand microbial community dynamics in repeated measures microbiome studies.}, }
@article {pmid39619672, year = {2024}, author = {Li, Y and Chen, J and Yao, H and Xu, X and Zheng, X and Wang, Y and Wang, W}, title = {Gut Microbiota's role in lipoma development: evidence from mendelian randomization.}, journal = {Frontiers in genetics}, volume = {15}, number = {}, pages = {1430671}, pmid = {39619672}, issn = {1664-8021}, abstract = {BACKGROUND: Lipoma, a benign tumor derived from mesenchymal tissue, significantly affects patients' physical and psychological wellbeing. Increasing evidence points to a strong link between the gut microbiome (GM) and lipoma incidence. This study utilizes Mendelian Randomization (MR) to assess the potential causal relationships between the GM and lipoma development.<br><br>METHODS: We conducted a two-sample MR analysis using genome-wide association study (GWAS) data from MiBioGen and FinnGen to explore the causal relationship between GM and lipoma. The GM dataset included 18,340 participants with 14,587 single nucleotide polymorphisms (SNPs), while the lipoma dataset comprised 412,181 participants with 21,306,349 SNPs. We employed 5&#xa0;MR methods: Inverse Variance Weighted (IVW), Weighted Median, Simple Mode, MR-Egger, and Weighted Mode. Additional assessments included Cochran's Q test for result heterogeneity, PRESSO analysis for horizontal pleiotropy, and sensitivity analyses through scatter plots, leave-one-out analyses, funnel plots, and forest plots.<br><br>RESULTS: The IVW method identified 18 gene predictors trans-genus associated with lipoma risk. Protective effects against benign lipoma (BL) were observed in the Eubacterium rectale group, Desulfovibrio, Ruminococcus1, Clostridium sensu stricto1, and Lachnospiraceae UCG001; conversely, Lachnospiraceae UCG008 was linked to increased BL risk. Desulfovibrio provided protection against TS-BL; however, the Family XIII AD3011 group, Eubacterium coprostanoligenes group, Lachnospiraceae NK4A136 group, and Parasutterella were associated with an increased TS-BL risk. The Clostridium innocuum group, Eubacterium rectale group, Anaerotruncus, Ruminiclostridium6, and Lachnospiraceae UCG001 offered protection against LS-BL, while Lachnospiraceae UCG008 was linked to an increased LS-BL risk. The Eubacterium brachy group, Odoribacter, Butyricimonas, Subdoligranulum, and Clostridium sensu stricto1 were protective against HFNS-BL; Ruminococcaceae UCG005 was associated with an increased HFNS-BL risk.<br><br>CONCLUSION: Compared to malignant tumors, research on lipomas has been relatively limited. This study, through MR analysis, provided new evidence of a causal relationship between specific GM and the development of lipomas. Certain gut bacterial species may act as protective or harmful factors in lipoma formation, offering new avenues for future treatment strategies. However, additional research is required to unravel the complexity of how GM influences the pathogenesis of lipomas.}, }
@article {pmid39619660, year = {2024}, author = {Xi, M and Ruan, Q and Zhong, S and Li, J and Qi, W and Xie, C and Wang, X and Abuduxiku, N and Ni, J}, title = {Periodontal bacteria influence systemic diseases through the gut microbiota.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1478362}, pmid = {39619660}, issn = {2235-2988}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Dysbiosis/microbiology ; Diabetes Mellitus/microbiology ; Alzheimer Disease/microbiology ; Bacteria/classification/genetics/pathogenicity ; Cardiovascular Diseases/microbiology ; Mouth/microbiology ; Animals ; }, abstract = {Many systemic diseases, including Alzheimer disease (AD), diabetes mellitus (DM) and cardiovascular disease, are associated with microbiota dysbiosis. The oral and intestinal microbiota are directly connected anatomically, and communicate with each other through the oral-gut microbiome axis to establish and maintain host microbial homeostasis. In addition to directly, periodontal bacteria may also be indirectly involved in the regulation of systemic health and disease through the disturbed gut. This paper provides evidence for the role of periodontal bacteria in systemic diseases via the oral-gut axis and the far-reaching implications of maintaining periodontal health in reducing the risk of many intestinal and parenteral diseases. This may provide insight into the underlying pathogenesis of many systemic diseases and the search for new preventive and therapeutic strategies.}, }
@article {pmid39619641, year = {2024}, author = {Xia, T and Huang, F and Yun, F and Liu, Y and Wang, T and Wang, S and Jin, S and Ma, X and Wang, W and He, J and Teng, K and Zhong, J}, title = {Lacticaseibacillus rhamnosus LRJ-1 alleviates constipation through promoting gut Bacteroides-derived γ-aminobutyric acid production.}, journal = {Current research in food science}, volume = {9}, number = {}, pages = {100924}, pmid = {39619641}, issn = {2665-9271}, abstract = {Multiple gastrointestinal disorders are associated with impaired gut microbiota. Probiotic Lacticaseibacillus rhamnosus can improve bowel disorder, however, the action mechanism is poorly understood. We integrated multi-omics data from the gut metagenome, metabolome, and colon transcriptome of constipated mice underlying L. rhamnosus LRJ-1 treatment to provide insights into host-microbial metabolic pathway. We found that oral administration of L. rhamnosus LRJ-1 alleviated constipation in mice accompanied by the increased abundances of fecal γ-aminobutyric acid (GABA) and intestinal commensal Bacteroides, and the activation of host GABAergic synapses. B. uniformis was the most enriched Bacteroides species in constipated mice treated with L. rhamnosus LRJ-1, and contributed to the increased abundance of GABA in the gut. Administration of either B. uniformis ATCC 8492 or GABA alleviated constipation and increased gastrointestinal motility in constipated mice. Knockout of the GABA biosynthetic gad gene in B. uniformis ATCC 8492 decreased GABA production and blocked its beneficial effects on constipation. These results confirm the therapeutic potential of L. rhamnosus LRJ-1 in alleviating constipation through promoting gut commensal Bacteroides-derived GABA production. Targeting the gut microbiome to regulate GABA production may open new insights for efficient constipation treatment.}, }
@article {pmid39619323, year = {2024}, author = {Mick, GJ and McCormick, KL}, title = {The role of GABA in type 1 diabetes.}, journal = {Frontiers in endocrinology}, volume = {15}, number = {}, pages = {1453396}, pmid = {39619323}, issn = {1664-2392}, mesh = {Humans ; *Diabetes Mellitus, Type 1/metabolism/drug therapy ; *gamma-Aminobutyric Acid/metabolism ; Animals ; Insulin-Secreting Cells/metabolism ; Glutamate Decarboxylase/metabolism ; }, abstract = {Gamma aminobutyric acid (GABA) is synthesized from glutamate by glutamic decarboxylase (GAD). The entero-pancreatic biology of GABA, which is produced by pancreatic islets, GAD-expressing microbiota, enteric immune cells, or ingested through diet, supports an essential physiologic role of GABA in the health and disease. Outside the central nervous system (CNS), GABA is uniquely concentrated in pancreatic β-cells. They express GAD65, which is a type 1 diabetes (T1D) autoantigen. Glutamate constitutes 10% of the amino acids in dietary protein and is preeminently concentrated in human milk. GABA is enriched in many foods, such as tomato and fermented cheese, and is an over-the-counter supplement. Selected microbiota in the midgut have the enzymatic capacity to produce GABA. Intestinal microbiota interact with gut-associated lymphoid tissue to maintain host defenses and immune tolerance, which are implicated in autoimmune disease. Although GABA is a widely known inhibitory neurotransmitter, oral GABA does not cross the blood brain barrier. Three diabetes-related therapeutic actions are ascribed to GABA, namely, increasing pancreatic β-cell content, attenuating excess glucagon and tamping down T-cell immune destruction. These salutary actions have been observed in numerous rodent diabetes models that usually employed high or near-continuous GABA doses. Clinical studies, to date, have identified positive effects of oral GABA on peripheral blood mononuclear cell cytokine release and plasma glucagon. Going forward, it is reassuring that oral GABA therapy has been well-tolerated and devoid of serious adverse effects.}, }
@article {pmid39619284, year = {2024}, author = {Chen, K and Zeng, K and Jin, S and Ma, Y and Cai, L and Xu, P and Nie, Y and Luo, L and Yu, Q and Liu, C}, title = {Lacticaseibacillus rhamnosus LRa05 in the treatment of acute diarrhea in children: a randomized controlled trial.}, journal = {Frontiers in nutrition}, volume = {11}, number = {}, pages = {1479186}, pmid = {39619284}, issn = {2296-861X}, abstract = {INTRODUCTION: The goal of this study is to assess the efficacy and safety of Lacticaseibacillus rhamnosus LRa05, as an adjunct to the treatment of acute watery diarrhea in children.<br><br>METHODS: Eligible diarrheal children were randomized into intervention group (IG, n&#x2009;=&#x2009;57) and control group (CG, n&#x2009;=&#x2009;54), and given probiotics or placebo, respectively.<br><br>RESULTS: The total duration of diarrhea in the IG (121.4&#x2009;&#xb1;&#x2009;13.7&#x2009;h) was significantly shorter than that in the CG (143.9&#x2009;&#xb1;&#x2009;19.8&#x2009;h, p&#x2009;<&#x2009;0.001). More children in the IG showed improvements in diarrhea than those in the CG for both per protocol analysis (70.2 vs. 46.3%, p&#x2009;=&#x2009;0.01) and intention-to-treat analysis (66.7 vs. 41.7%, p&#x2009;=&#x2009;0.003). The LL-37 levels in the IG was markedly higher than that in the CG after the intervention (4349.35&#x2009;&#xb1;&#x2009;1143.86&#x2009;pg./g vs. 3682.49&#x2009;&#xb1;&#x2009;869.21&#x2009;pg./g, p&#x2009;=&#x2009;0.039). The intervention led to higher abundance of Bifidobacterium longum and lower abundance of Enterococcus faecium, Lactobacillus rhamnosus, and Bacteroides fragilis (p&#x2009;<&#x2009;0.05). LRa05 treatment upregulated the functional genes of gut microbiota involving immunity regulation.<br><br>DISCUSSION: Administration of the Lacticaseibacillus rhamnosus LRa05 at a dose of 5&#x2009;&#xd7;&#x2009;10[9]&#x2009;CFU/day to children aged 0-3 years resulted in shorter duration of diarrhea, faster improvement in fecal consistency, and beneficial changes in gut microbiome composition and gene functions.<br><br>CLINICAL TRIAL REGISTRATION: The present study has been approved and registered in the Chinese Clinical Trial Registration Center with the registration number of ChiCTR2100053700 (https://www.chictr.org.cn/showproj.html?proj=141082).}, }
@article {pmid39618884, year = {2024}, author = {He, Z and Naganuma, T and Faluaburu, MS and Nakai, R and Kanda, H and Uchida, M and Imura, S and Hahn, MW}, title = {Bacterial phylotypes associated with rock-dwelling Umbilicaria Lichens from Arctic/Subarctic areas in North America and Northern Europe.}, journal = {Polar biology}, volume = {47}, number = {12}, pages = {1527-1541}, pmid = {39618884}, issn = {0722-4060}, abstract = {UNLABELLED: The diversity of bacteria associated with lichens has received increasing attention. However, studies based on next-generation sequencing of microbiomes have not yet been conducted in the Arctic and Subarctic regions. In this study, rock-dwelling lichens belonging to the Umbilicariaceae family were sampled from the Arctic and Subarctic biological zones. The primary research purpose was to undertake a comparative investigation of the bacterial composition and diversity, identify potential indicators, and explore their potential metabolic pathways. 18S rRNA gene sequences of the fungal partner belonging to the genus Umbilicaria (Ascomycota) and the algal partner affiliated with the lineage Trebouxia (Chlorophyta). Comparing Umbilicaria spp. with a previous study in the Antarctic zone, the fungal partners were more inclined to cluster by sampling region. Operational taxonomic units (OTUs) were established based on a predetermined similarity threshold for V3-V4 sequences, which were ascribed to 19 bacterial phyla, and ten of them were consistently present in all samples. The most distinct zonal indicator genera based on OTU frequencies from Arctic and Subarctic lichens were Capsulimonas (Armatimonadota) and Jatrophihabitans (Actinomycota), respectively. Although the Subarctic zone had higher biodiversity and species richness based on alpha-diversity, the beta-diversity showed that the main species of bacterial communities were not significantly different, and the predictions of metabolic pathways based on the bacterial microbiome in lichen samples from the two zones were similar. These findings provide evidence that the geographical and/or bioclimatic environment and the different lichen-forming fungal species mainly and partially influence bacterial microbiomes and metabolic pathways.<br><br>SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s00300-024-03303-3.}, }
@article {pmid39618850, year = {2024}, author = {Liu, H and Feng, S and Tang, M and Tian, R and Zhang, S}, title = {Gut Commensal Bacteroides thetaiotaomicron Promote Atherothrombosis via Regulating L-Tryptophan Metabolism.}, journal = {Reviews in cardiovascular medicine}, volume = {25}, number = {11}, pages = {395}, pmid = {39618850}, issn = {2153-8174}, abstract = {BACKGROUND: Coronary thrombosis events continue to be the leading cause of morbidity and mortality worldwide. Recently, emerging evidence has highlighted the role of gut microbiota in cardiovascular disease, but few studies have systematically investigated the gut microbiota variation associated with atherothrombosis.<br><br>METHODS: We conducted multi-omics analysis (metagenomics sequencing and serum metabolomics) on 146 subjects from Peking Union Medical College Hospital-Coronary Artery Disease (PUMCH-CAD) cohort. We analyzed the key strains and metabolic pathways related to coronary artery disease (CAD) development, explored the bacterial functional pathway which contributes to atherothrombosis at strain level in depth. Single strain colonization procedures on germ free mice demonstrated the promotion of platelet activation and thrombotic phenotypes of the disordered gut microbiota.<br><br>RESULTS: Gut microbiome and serum metabolome shifts were apparent in cases of CAD progression, Bacteroides spp. disturbed the development of CAD by participating in lipopolysaccharide (LPS), menaquinone and methanogenesis pathways. Particularly, coronary thrombosis is characterized by increased circulatory levels of L-tryptophan, which correlate with Bacteroides thetaiotaomicron that has enriched biosynthetic potential. In germ free mice we demonstrate that Bacteroides thetaiotaomicron colonization could induce thrombosis, aggravate platelet hyperreactivity and augment fecal levels of L-tryptophan.<br><br>CONCLUSIONS: The disordered gut microbiota of CAD contributed to the occurrence and development of atherothrombosis. The key members of the bacterial and metabolic features may become biomarkers for predicting the cardiovascular thrombosis event. Targeting the microbial pathway may have the potential to reduce the incidence of cardiovascular disorders.<br><br>CLINICAL TRIAL REGISTRATION: ChiCTR2000033897, https://www.chictr.org.cn/showproj.html?proj=55023.}, }
@article {pmid39618672, year = {2024}, author = {Dinetz, E and Bocharova, N}, title = {Inflammation in Elite Athletes: A Review of Novel Factors, the Role of Microbiome, and Treatments for Performance Longevity.}, journal = {Cureus}, volume = {16}, number = {10}, pages = {e72720}, pmid = {39618672}, issn = {2168-8184}, abstract = {Inflammation is a prevalent issue among athletes, especially those engaged in high-intensity sports, and can reduce the athlete's long-term potential. Over time, chronic inflammation impedes recovery, performance, and ultimately competitiveness, which is evident among some athletes over others. This article explores more novel concepts contributing to inflammation such as the microbiome and genetic predispositions, which are often overlooked in mainstream management, thereby allowing for more personalized therapies for athletes. Additionally, it introduces ways to address inflammation early to help prolong performance longevity and reduce the risk of serious injury holistically for the overall well-being of professional athletes.}, }
@article {pmid39617896, year = {2024}, author = {Feng, R and Zhu, Q and Wang, A and Wang, H and Wang, J and Chen, P and Zhang, R and Liang, D and Teng, J and Ma, M and Ding, X and Wang, X}, title = {Effect of fecal microbiota transplantation on patients with sporadic amyotrophic lateral sclerosis: a randomized, double-blind, placebo-controlled trial.}, journal = {BMC medicine}, volume = {22}, number = {1}, pages = {566}, pmid = {39617896}, issn = {1741-7015}, mesh = {Humans ; *Amyotrophic Lateral Sclerosis/therapy ; *Fecal Microbiota Transplantation/methods ; Double-Blind Method ; Female ; Male ; Middle Aged ; Aged ; Gastrointestinal Microbiome/physiology ; Treatment Outcome ; Quality of Life ; Adult ; }, abstract = {BACKGROUND: Amyotrophic lateral sclerosis (ALS) is a devastating neurodegenerative disorder marked by the progressive loss of motor neurons. Recent insights into ALS pathogenesis underscore the pivotal role of the gut microbiome, prompting an investigation into the potential therapeutic impact of fecal microbiota transplantation (FMT) on sporadic ALS patients.<br><br>METHODS: Conducted as a double-blind, placebo-controlled, parallel-group, randomized clinical trial, the study enrolled 27 participants from October 2022 to April 2023. The participants were followed up for 6&#xa0;months from February 2023 to October 2023, during in-person visits at baseline, week 15, week 23, and week 35. The participants, evenly randomized, received either healthy donor FMT (FMT, n&#x2009;=&#x2009;14) or a mixture of 0.9% saline and food coloring (E150c) as sham transplantation (placebo, n&#x2009;=&#x2009;13). The primary outcome measured the change in the ALS Functional Rating Scale-Revised (ALSFRS-R) total score from baseline to week 35. Secondary outcomes included changes in gastrointestinal and respiratory functions, muscle strength, autonomic function, cognition, quality of life, intestinal microbiome composition, and plasm neurofilament light chain protein (NFL). Efficacy and safety outcomes were assessed in the intention-to-treat population.<br><br>RESULTS: A total of 27 randomized patients (47% women; mean age, 67.2&#xa0;years), 24 participants completed the entire study. Notably, ALSFRS-R score changes exhibited no significant differences between FMT (6.1 [SD, 3.11]) and placebo (6.41[SD, 2.73]) groups from baseline to week 35. Secondary efficacy outcomes, encompassing respiratory function, muscle strength, autonomic function, cognition, quality of life, and plasm NFL, showed no significant differences. Nevertheless, the FMT group exhibited improvements in constipation, depression, and anxiety symptoms. FMT induced a shift in gut&#xa0;microbiome community composition, marked by increased abundance of Bifidobacterium, which persisted until week 15 (95% CI, 0.04 to 0.28; p&#x2009;=&#x2009;0.01). Gastrointestinal adverse events were the primary manifestations of FMT-related side effects.<br><br>CONCLUSIONS: In this clinical trial involving 27 sporadic ALS patients, FMT did not&#xa0;significantly slow the decline in ALSFRS-R score. Larger multicenter trials&#xa0;are needed to confirm the efficacy of FMT in sporadic ALS patients and to explore the underlying biological mechanisms.<br><br>TRIAL REGISTRATION: Chinese Clinical Trial Registry Identifier: ChiCTR 2200064504.}, }
@article {pmid39617894, year = {2024}, author = {Martínez-Montoro, JI and Martín-Núñez, GM and González-Jiménez, A and Garrido-Sánchez, L and Moreno-Indias, I and Tinahones, FJ}, title = {Interactions between the gut microbiome and DNA methylation patterns in blood and visceral adipose tissue in subjects with different metabolic characteristics.}, journal = {Journal of translational medicine}, volume = {22}, number = {1}, pages = {1089}, pmid = {39617894}, issn = {1479-5876}, support = {CM22/00217//Instituto de Salud Carlos III/ ; }, mesh = {Humans ; *DNA Methylation/genetics ; *Gastrointestinal Microbiome/genetics ; *Intra-Abdominal Fat/metabolism ; Male ; Female ; Middle Aged ; Obesity/microbiology/genetics/blood ; Diabetes Mellitus, Type 2/microbiology/metabolism/genetics/blood ; Case-Control Studies ; Adult ; Insulin Resistance ; }, abstract = {BACKGROUND: The gut microbiome has been reported to induce epigenetic modifications in the host, which may be involved in the pathophysiology of metabolic diseases.<br><br>OBJECTIVE: To evaluate the potential interactions between the gut microbiome and DNA methylome in subjects with different metabolic characteristics.<br><br>METHODS: Sixty-four participants with different metabolic characteristics (i.e., participants without obesity -healthy controls-, and participants with obesity and normal insulin sensitivity/insulin resistance/ type 2 diabetes-T2DM-) were included in this study. A machine learning approach was performed in order to identify distinctive patterns in three omics (gut microbiome, blood DNA methylome, and visceral adipose tissue-VAT- DNA methylome) according to the different study groups.<br><br>RESULTS: Robust distinctive distribution patterns of the three different omics were found between healthy controls and patients with obesity; participants with and without T2DM, and patients with obesity with and without insulin resistance. Importantly, strong correlations between the gut microbiome (including Odoribacteriaceae and Christensenllaceae families) and both blood and VAT DNA methylome were found. Moreover, in the entire study population, three main bacterial genera (Sutterella, Collinsella and Eubacterium) were related to the epigenetic regulation of different genes involved in distinct processes related to cellular metabolism and metabolic diseases, including small ubiquitin-related modifier (SUMO) transferase activity or lipid binding.<br><br>CONCLUSION: We show that distinctive interactions between the gut microbiome and DNA methylome may occur in subjects with different metabolic characteristics. Further research is needed to elucidate the potential role of these interactions in the pathophysiology of obesity and related comorbidities.}, }
@article {pmid39617855, year = {2024}, author = {Tadese, DA and Mwangi, J and Luo, L and Zhang, H and Huang, X and Michira, BB and Zhou, S and Kamau, PM and Lu, Q and Lai, R}, title = {The microbiome's influence on obesity: mechanisms and therapeutic potential.}, journal = {Science China. Life sciences}, volume = {}, number = {}, pages = {}, pmid = {39617855}, issn = {1869-1889}, abstract = {In 2023, the World Obesity Atlas Federation concluded that more than 50% of the world's population would be overweight or obese within the next 12 years. At the heart of this epidemic lies the gut microbiota, a complex ecosystem that profoundly influences obesity-related metabolic health. Its multifaced role encompasses energy harvesting, inflammation, satiety signaling, gut barrier function, gut-brain communication, and adipose tissue homeostasis. Recognizing the complexities of the cross-talk between host physiology and gut microbiota is crucial for developing cutting-edge, microbiome-targeted therapies to address the global obesity crisis and its alarming health and economic repercussions. This narrative review analyzed the current state of knowledge, illuminating emerging research areas and their implications for leveraging gut microbial manipulations as therapeutic strategies to prevent and treat obesity and related disorders in humans. By elucidating the complex relationship between gut microflora and obesity, we aim to contribute to the growing body of knowledge underpinning this critical field, potentially paving the way for novel interventions to combat the worldwide obesity epidemic.}, }
@article {pmid39617812, year = {2024}, author = {He, J and Liu, Y and Xu, H and Wei, X and Chen, M}, title = {Insights into the variations in microbial community structure during the development of periodontitis and its pathogenesis.}, journal = {Clinical oral investigations}, volume = {28}, number = {12}, pages = {675}, pmid = {39617812}, issn = {1436-3771}, mesh = {Humans ; *Periodontitis/microbiology ; Female ; *Microbiota ; Male ; Middle Aged ; Adult ; Disease Progression ; Dental Plaque/microbiology ; Periodontal Index ; }, abstract = {OBJECTIVE: To characterize the subgingival microbiota in subjects with stage I/II periodontitis (moderate periodontitis, MP), stage III/IV periodontitis (severe periodontitis, SP), and periodontal health (PH) at the same probing depth (PD) (shallow ≤ 3 mm, moderate 4-6 mm, or deep ≥ 7 mm), and to investigate the changes associated with probing depth progression.<br><br>MATERIALS AND METHODS: 100 subgingival plaque samples were collected from 50 subjects (16 MP, 17 SP and 17 PH), forming six groups: PHS (PH, shallow), MPS (MP, shallow), MPM (MP, moderate), SPS (SP, shallow), SPM (SP, moderate), and SPD (SP, deep). Samples were analyzed using high-throughput sequencing.<br><br>RESULT: The subgingival microbiome showed significant differences associated with both PD and periodontitis stage (p&#x2009;<&#x2009;0.05). With increasing PD, alpha diversity initially increased and then decreased. Pathogenic genera like Fusobacterium, Filifactor, and Porphyromonas increased, while health-associated genera like Streptococcus and Haemophilus decreased. At shallow sites, the PHS, MPS, and SPS groups showed similar community structure. At moderate and deep sites, the SPM and SPD groups exhibited significant differences in community structure compared to the MPM group, with the SPM and SPD groups showing decreased abundances of Actinomyces and increased abundances of Treponema. The microbial co-networks in the SPD and SPM groups exhibited greater complexity and connectivity and were more resilient to random microbial or node removal.<br><br>CONCLUSIONS: The subgingival microbiome shows strong associations with PD and periodontitis stage.<br><br>CLINICAL RELEVANCE: Once periodontitis progresses to stage III/IV, reconstructing a healthy subgingival microbiome may be challenging, emphasizing the importance of early prevention.}, }
@article {pmid39617703, year = {2024}, author = {Mengting, L and Tao, LI and Fuhao, C and Yan, C and Ni, L and Yuan, Z and Rongqiang, BO and Xia, D}, title = {Weichang' an pill alleviates functional dyspepsia through modulating brain-gut peptides and gut microbiota.}, journal = {Journal of traditional Chinese medicine = Chung i tsa chih ying wen pan}, volume = {44}, number = {6}, pages = {1177-1186}, doi = {10.19852/j.cnki.jtcm.2024.06.006}, pmid = {39617703}, issn = {2589-451X}, support = {2018110031010092//Horizontal Development Foundation of Beijing University of Chinese Medicine: Research and development of Weicang'an pill in the treatment of functional dyspepsia/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; Rats ; *Dyspepsia/drug therapy/microbiology/metabolism ; *Drugs, Chinese Herbal/administration &amp; dosage ; Male ; Humans ; *Gastrointestinal Motility/drug effects ; *Motilin/metabolism ; *Rats, Sprague-Dawley ; *Brain/metabolism/drug effects ; Peptides ; Vasoactive Intestinal Peptide/metabolism/genetics ; Gastrins/metabolism ; Somatostatin/metabolism ; }, abstract = {OBJECTIVE: To evaluate the effect of Weichang'an pill (, WCAP) on functional dyspepsia (FD) and explore its regulation of brain-gut peptides (BGPs) and gut microbiota balance as a potential treatment mechanism.<br><br>METHODS: The "0 &#x2103; saline gavage + irregular feeding and tail clamp" method was used to establish the FD rat model, excluding the normal group. The successfully established FD rat models were randomly divided into the model group and the WCAP1 (WC1), WCAP2 (WC2), WCAP3 (WC3), WCAP4 (WC4), WCAP5 (WC5), and Domperidone (Dom) groups (n = 10 per group). The unhandled rats were designated as the control group. The gastrointestinal motility of the rats was evaluated using the charcoal propulsion test. Histopathology was assessed by hematoxylin and eosin (HE) staining. The enzyme-linked immunosorbnent assay method was used to detect the levels of motilin (MTL), gastrin (GAS), vasoactive intestinal peptide (VIP), and somatostatin (SS) in the serum from each group. In addition, the gut microbiota composition of fecal samples was analyzed using 16S rRNA sequencing.<br><br>RESULTS: Rat models were successfully established according to data from rat state, gastrointestinal motility assessments, and HE staining. WCAP improved FD symptoms by accelerating the gastric emptying and small intestinal transit of FD rats. Mechanistically, WCAP increased the levels of GAS and MTL and reduced the levels of VIP and SS. Moreover, WCAP treatment restored the total relative abundance of Firmicutes and Bacteroidetes, increased the species richness of the gut flora, and modulated the changes in the composition and function of the gut microbiota.<br><br>CONCLUSION: WCAP can effectively promote the recovery of gastrointestinal motility disorders in FD rats. The mechanism may be related to regulating the secretion of BGPs and the composition of the gut microbiota.}, }
@article {pmid39617702, year = {2024}, author = {Yiying, W and Jianjun, L and Yongjian, X and Yongli, Z and Yuqi, W and Mengli, X and Huishu, G and Juanjuan, Q}, title = {Analysis of composition of gut microbial community in a rat model of functional dyspepsia treated with Simo Tang.}, journal = {Journal of traditional Chinese medicine = Chung i tsa chih ying wen pan}, volume = {44}, number = {6}, pages = {1168-1176}, doi = {10.19852/j.cnki.jtcm.20240927.003}, pmid = {39617702}, issn = {2589-451X}, support = {81803896//National Natural Science Foundation of China: Changes of Ras Homolog Gene Family Member A/Rho-associated Coiled-coil Kinase Signaling Pathway in Liver-Stomach Disharmony Functional Dyspepsia Rats and Intervention Mechanism of Simo Tang/ ; 81873156//Role of Gut Microbiota-diaminopimelic Acid Nucleotide-binding and Oligomerization Domain1-receptor-interacting Protein 2 Signal Pathway in Severe Process of Acute Pancreatitis and the Intervention Mechanism of Qingxia Therapy/ ; LZ2020036//Research Project of Liaoning Provincial Department of Education: the Role of Mitochondria-Derived Reactive Oxygen Species Mediated Autophagy Activation in Myocardial Injury in Sepsis/ ; }, mesh = {Animals ; Rats ; *Dyspepsia/drug therapy/microbiology ; *Gastrointestinal Microbiome/drug effects ; Male ; *Bacteria/classification/genetics/isolation &amp; purification/drug effects ; *Drugs, Chinese Herbal/administration &amp; dosage ; *Rats, Sprague-Dawley ; Humans ; Disease Models, Animal ; }, abstract = {OBJECTIVE: To investigate composition of gut microbial community in a rat model of functional dyspepsia (FD) and to explore the interventional effects of Simo Tang (, SMT).<br><br>METHODS: A rat model of FD was established through the tail-clamping stimulation method. The rat model of FD was assessed by the state of rats, their weight, sucrose preference rate, and intestinal propulsion rate. The DNA was extracted from stool samples after treatment with SMT. Amplified polymerase chain reaction (PCR) products of the 16S rDNA were sequenced using NovaseQ6000 after construction of libraries. Composition of gut microbial community in the stool samples was determined and analyzed by cluster analysis, bioinformatic analysis, and analysis of &#x3b1;-diversity and &#x3b2;-diversity.<br><br>RESULTS: The rat model of FD was successfully established using the tail-clamping stimulation method. The statistical results of cluster analysis of operational taxonomic units (OTUs) showed that the relative abundance of OTUs in the FD group was the lowest, while it was the highest in the normal (N) group. The composition of microbiome in the four groups was similar at phyla level. Compared with the FD group, the abundance of Firmicutes was downregulated, and the abundance of Proteobacteria and Bacteroidetes was upregulated in the Simo Tang (SMT) and high-dose Simo Tang (SMT.G) groups. The ratio of Bacteroidetes/ Firmicutes was also elevated. According to the analysis of &#x3b1;-diversity and &#x3b2;-diversity, the abundance of flora in FD rats was significantly reduced. The treatment using SMT appeared beneficial to improve the diversity of flora. SMT could improve the intestinal flora in FD rats. The results showed that FD rats had intestinal flora imbalance, and species diversity increased. The results suggested that SMT could regulate the disorders of intestinal flora caused by FD.<br><br>CONCLUDIONS: SMT could restore gut homeostasis and maintain gut flora diversity by modulating the gut microbiota and its associated metabolites in rats, thereby treating gastrointestinal diseases.}, }
@article {pmid39617567, year = {2025}, author = {Ren, T and Zhang, H and Hu, C}, title = {Molecular biological mechanism of fillers with surface micro-electric field to enhance biodegradation of kitchen-oil wastewater.}, journal = {Journal of environmental sciences (China)}, volume = {152}, number = {}, pages = {453-464}, doi = {10.1016/j.jes.2024.05.051}, pmid = {39617567}, issn = {1001-0742}, mesh = {*Wastewater/chemistry ; *Biodegradation, Environmental ; *Waste Disposal, Fluid/methods ; Water Pollutants, Chemical/metabolism/analysis ; }, abstract = {The kitchen-oil wastewater is characterized by a high concentration of organic matter, complex composition and refractory pollutants, which make wastewater treatment more difficult. Based on the study of using micro-electric field characteristic catalyst HCLL-S8-M to enhance the electron transfer between microorganisms in kitchen-oil wastewater which further improved the COD removal rate, we focus on the microbial community, intracellular metabolism and extracellular respiration, and make an in-depth analysis of the molecular biological mechanisms to microbial treatment in wastewater. It is found that electroactive microorganisms are enriched on the material surface, and the expression levels of cytochrome c and riboflavin genes related to electron transfer are up-regulated, confirming that the surface micro-electric field structure could enhance the electron transfer between microbial species and improve the efficiency of wastewater degradation. This study provides a new idea for the treatment of refractory organic wastewater.}, }
@article {pmid39617313, year = {2024}, author = {Han, XY and Guo, P and Fan, QR and Zhou, QB and Xu, MD and Long, XZ and Cui, LY and Tong, Q}, title = {Synergistic toxicity of cadmium and triadimefon on the microbiota and health of Rana dybowskii tadpoles.}, journal = {Comparative biochemistry and physiology. Toxicology &amp; pharmacology : CBP}, volume = {}, number = {}, pages = {110092}, doi = {10.1016/j.cbpc.2024.110092}, pmid = {39617313}, issn = {1532-0456}, abstract = {The skin and gut microbiota are crucial to amphibians. Triadimefon (TF), a widely used triazole fungicide, controls crop diseases and regulates growth, with uncertain effects on amphibian microbiota. Contamination, typically involving mixed chemicals at low concentrations, including cadmium (Cd) and TF, may detrimentally affect amphibian growth, survival, and microbiota health in both the skin and gut, but few research has examined these consequences. This research examines the impact of Cd and TF on Rana dybowskii tadpoles, focusing on survival, body mass, and microbiome changes over 28 days across four groups: control, Cd, TF, and Cd + TF groups. Results showed significant reductions in survival and body mass in Cd and TF-treated groups, with the combination group being the most affected. Microbiota analysis revealed significant dysbiosis in both gut and skin microbiomes under pollutant stress, with a marked microbiota and a shift in dominant microbial communities. Function prediction analysis based on the microbiome composition highlighted significant differences across various biological pathways, including metabolism, immune system, environmental adaptation, and disease resistance. These alterations suggest that pollutant exposure compromises the tadpoles' ability to maintain homeostasis and resist pathogens. In conclusion, this study reveals the detrimental effects of Cd and TF on the survival, growth, and microbiomes of R. dybowskii tadpoles, indicating significant environmental and health risks.}, }
@article {pmid39617138, year = {2024}, author = {Sanal, MG and George, J}, title = {Do not leave any ambiguity: alcohol in any amount is harmful.}, journal = {Journal of hepatology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jhep.2024.11.039}, pmid = {39617138}, issn = {1600-0641}, }
@article {pmid39617137, year = {2024}, author = {Xing, H and Huang, D and Xue, C}, title = {A Comprehensive Framework for Investigating Oral-Gut Microbiome Dynamics: From Normal Variation to Pathological Changes.}, journal = {Journal of hepatology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jhep.2024.11.036}, pmid = {39617137}, issn = {1600-0641}, }
@article {pmid39617136, year = {2024}, author = {Oommen, TT and Ahamed, R and Philips, CA}, title = {Missing the forest for the trees: time to address stool microbial load and everything else that realistically matters in microbiome studies.}, journal = {Journal of hepatology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jhep.2024.11.037}, pmid = {39617136}, issn = {1600-0641}, }
@article {pmid39617084, year = {2024}, author = {Yang, J and Chen, C and Zhang, H and Chen, B and Xiao, K and Tang, Y and Meng, K and Qin, L and Chen, P}, title = {Serum metabolomics and 16S rRNA amplicon sequencing reveal the role of Puerarin in alleviating bone loss aggravated by antidiabetic agent pioglitazone in type 2 diabetic mice.}, journal = {Journal of ethnopharmacology}, volume = {}, number = {}, pages = {119128}, doi = {10.1016/j.jep.2024.119128}, pmid = {39617084}, issn = {1872-7573}, abstract = {Pioglitazone (PIO) was an anti type 2 diabetes (T2D) agent but caused bone loss and bone marrow fat accumulation. Puerarin (PUE) was a natural component of herbal medicine extracted from Pueraria lobata (Willd.) Ohwi and reduced glycemia and improved bone mass as a supplementary drug. A combination of PIO and PUE might be good for maintaining bone mass and blood glucose.<br><br>AIM OF THE STUDY: We aimed to elucidate the potential correlation and underlying mechanisms of dietary supplement PUE in reducing side effects caused by PIO.<br><br>MATERIALS AND METHODS: In vitro, alkaline phosphatase (ALP) staining, alizarin S (ARS) staining and qRT-PCR were performed to detect the osteogenesis activity in MC3T3-E1 cells. In vivo, we established the T2D model by treating C57BL6/J mice with high-fat diets and streptozotocin (STZ). Micro-CT, hematoxylin and eosin (H&amp;E) staining and tartrate-resistant acid phosphatase (TRAcP) staining were performed to observe the difference in skeletal phenotype. Serum metabolomics and 16S rRNA amplicon sequencing were applied to analyze the potential effect of the combination of PIO and PUE.<br><br>RESULTS: We showed that the PUE could increase ALP activity and mineralization nodes of MC3T3-E1 with PIO. PIO could aggravate bone loss but PUE alleviated the effect caused by PIO in T2D mice. PUE promoted alpha-linolenic acid metabolism and glycerophospholipid metabolism, and affected the alpha diversity of the gut microbiome by regulating the genera of Alloprevotella, Fusobacterium, Rodentibacter, etc. Correlation analysis indicated that sphingosine-1-phosphate, nonadecylic acid, and margaric acid were associated with the effect of PUE.<br><br>CONCLUSIONS: Taken together, we demonstrated that PIO combined with PUE was able to lower blood sugar levels without causing bone loss. The effect of PUE mainly correlated with the genua of Alloprevotella, Fusobacterium, Rodentibacter, and Alistipes. Also, alpha-linolenic acid metabolism and glycerophospholipid metabolism were major targets of PUE.}, }
@article {pmid39617011, year = {2024}, author = {Berzack, S and Galor, A}, title = {Microbiome-based therapeutics for ocular diseases.}, journal = {Clinical &amp; experimental optometry}, volume = {}, number = {}, pages = {1-8}, doi = {10.1080/08164622.2024.2422479}, pmid = {39617011}, issn = {1444-0938}, abstract = {The relationship between the gut microbiome and ocular health has garnered increasing attention within the scientific community. Recent research has focused on the gut-eye axis, examining whether imbalances within the gut microbiome can influence the development, progression and severity of ocular diseases, including dry eye disease, uveitis, and glaucoma. Dysbiosis within the gut microbiome is linked to immune dysregulation, chronic inflammation, and epithelial barrier dysfunction, all of which contribute to ocular pathology. This review synthesises current evidence on these associations, exploring how gut microbiome alterations drive disease mechanisms. Furthermore, it examines the therapeutic potential of microbiome-targeted interventions, including antibiotics, prebiotics, probiotics, and faecal microbiota transplantation, all of which aim to restore microbial balance and modulate immune responses. As the prevalence of these conditions continues to rise, a deeper understanding of the gut-eye axis may facilitate the development of novel, targeted therapies to address unmet needs in the management of ocular diseases.}, }
@article {pmid39616914, year = {2024}, author = {Vandecasteele, B and Viaene, J and Castejón-Del Pino, R and Lataf, A and Cuypers, A and Vandamme, D}, title = {S-enhanced microbial activation of biochars and processed grass fibers for circular horticulture.}, journal = {The Science of the total environment}, volume = {957}, number = {}, pages = {177760}, doi = {10.1016/j.scitotenv.2024.177760}, pmid = {39616914}, issn = {1879-1026}, abstract = {Sulfur-enhanced microbiologically activated biochar and processed grass fibers were tested for suitability as bulk material for horticultural substrates. The potential for use as bulk material was improved when grass fibers with lower biological stability were acidified with elemental sulfur (S). Acidification of the fibers with S was obtained within 2 weeks and resulted in a higher biological stability due to improved decomposition during incubation with S, a change in the microbiome, or inhibition due to high sulfate concentrations, which reduced the decomposition activity. The application of wood-based biochars as bulk or stand-alone material for horticultural substrates is restricted by their high pH and high acid-buffering capacity. Acidification of biochar through microbial activation occurred slowly. The dynamics of lowering pH after S treatment were determined by the acid-buffering capacity of the biochar. In the long term a strong drop in pH was observed in biochars with a low acid-buffering capacity. For the biochars with a high acid-buffering capacity, pH drop was moderate despite a clear decrease in acid-buffering capacity. The microbial activation of biochar was accelerated by adding mineral fertilizer or chitin. Microbial activation of the biochars was confirmed by S mineralization after application of elemental S and by N mineralization from chitin. The acidification of biochars produced from bark or straw-like fiber with elemental S resulted in only small changes in surface properties.}, }
@article {pmid39616662, year = {2024}, author = {Sun, L and Cheng, Z and Wang, M and Wei, C and Liu, H and Yang, Y}, title = {A multi-levels analysis to evaluate the toxicity of microplastics on aquatic insects: A case study with damselfly larvae (Ischnura elegans).}, journal = {Ecotoxicology and environmental safety}, volume = {289}, number = {}, pages = {117447}, doi = {10.1016/j.ecoenv.2024.117447}, pmid = {39616662}, issn = {1090-2414}, abstract = {Microplastic (MP) pollution prevalent in freshwater environments and jeopardizes the organisms living there. Dozens of studies have been conducted to investigate the harmful effects of microplastics on organisms. However, the most diverse and sensitive aquatic insects are often overlooked, also there is a lack of a comprehensive research exploring the toxicity of microplastics. Here, taking the damselfly larvae (Ischnura elegans) as the subject, we investigated the effects of different concentration levels of polystyrene microplastics (PS MPs) on their physiological characters, behavioristics, metabolomics and transcriptomics, as well as gut microbiome. The results showed that the PS MPs had no significant effects on the body weight and survival rate, but led to behavioral inhibition. Furthermore, expression levels of some metabolites altered, such as nicotinic acid, fumaric acid, and stearic acid. Meanwhile, the pathways related to oxidative phosphorylation and carbon metabolism were upregulated at the transcriptomic level. Moreover, there was a modification of the gut microbial community, with an increase in species richness but a shift towards potentially harmful bacteria. Our findings suggested that exposure to PS MPs affected the overall health of damselfly larvae. Therefore, effective management of MPs to minimize their environmental input is crucial in reducing health risks to aquatic organisms.}, }
@article {pmid39616205, year = {2024}, author = {das Neves, CA and Russi, KL and Alves, CH and Rocha, NC and de Souza, NGL and da Graça Fagundes, AC and de Carvalho, LM and Girardello, R}, title = {Overprescription of antibiotics in Brazilian dental clinics: an evaluation of current practices.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {29796}, pmid = {39616205}, issn = {2045-2322}, mesh = {Humans ; Brazil ; *Anti-Bacterial Agents/therapeutic use ; *Practice Patterns, Dentists'/statistics &amp; numerical data ; Surveys and Questionnaires ; *Dental Clinics ; Dentists ; Antibiotic Prophylaxis ; Male ; Female ; }, abstract = {The use of antibiotics by dentist surgeons faces a lack of consensus among professionals and researchers, whether in relation to prophylaxis, or at least regarding the real need for their use. Recent studies increasingly question the use of prophylactic antibiotic therapy in healthy patients. This study aimed to evaluate the knowledge of dentist surgeons working in offices across Brazil regarding antibiotic use protocols and antibiotic resistance. A questionnaire was made via Google Forms and sent by email. The results showed that most dentists prescribe antibiotics for all surgical procedures performed in their office, regardless of the complexity and the patient. Furthermore, low scientific basis was observed among some of the professionals interviewed regarding the best therapeutic choice and the role of antibiotics in the surgical procedure. The present study highlights the urgent need to improve the knowledge of these professionals in Brazil, to reduce the impact on antibiotic resistance.}, }
@article {pmid39615804, year = {2024}, author = {Ding, J and Xu, J and Wu, H and Li, M and Xiao, Y and Fu, J and Zhu, X and Wu, N and Sun, Q and Liu, Y}, title = {The cross-talk between the metabolome and microbiome in a double-hit neonatal rat model of bronchopulmonary dysplasia.}, journal = {Genomics}, volume = {}, number = {}, pages = {110969}, doi = {10.1016/j.ygeno.2024.110969}, pmid = {39615804}, issn = {1089-8646}, abstract = {Bronchopulmonary dysplasia (BPD), a chronic lung disease in preterm infants, is associated with inflammation and high oxygen exposure. However, the effects of antenatal inflammation and extended hyperoxia on the metabolome and microbiome remain unclear. In this study, pregnant rats received lipopolysaccharide or saline injections on gestational day 20 and were exposed to either 21 % or 80 % oxygen for 4 weeks post-birth. Analysis revealed an increase in Firmicutes, Proteobacteria, and Actinobacteria, with a decrease in Bacteroidetes in BPD rats. Metabolomic analysis identified 78 altered metabolites, primarily lipids, with enrichment in arginine biosynthesis, sphingolipid metabolism, and primary bile acid biosynthesis in BPD rats. Integration analysis revealed strong correlations between intestinal microbiota and metabolites in BPD rats. These findings underscore the impact of antenatal inflammation and prolonged hyperoxia on gut microbiota and serum metabolome, suggesting their role in BPD pathogenesis.}, }
@article {pmid39615665, year = {2024}, author = {Kurukulasooriya, MRP and Tillekeratne, LG and Wijayaratne, WMDGB and Bodinayake, CK and Dilshan, UHBY and De Silva, AD and Nicholson, BP and Østbye, T and Woods, CW and Nagahawatte, AS}, title = {Prevalence and molecular epidemiology of methicillin-resistant Staphylococcus aureus in livestock farmers, livestock, and livestock products in southern Sri Lanka: A one health approach.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {}, number = {}, pages = {105693}, doi = {10.1016/j.meegid.2024.105693}, pmid = {39615665}, issn = {1567-7257}, abstract = {Methicillin-resistant Staphylococcus aureus (MRSA) colonization can lead to subsequent severe infections. Unlike community and hospital-associated types, Livestock-associated MRSA (LA-MRSA) transmits to humans through direct contact with livestock and contaminated livestock products. This study aimed to investigate MRSA prevalence and molecular epidemiology in livestock farmers, livestock, and livestock products, including LA-MRSA presence and MRSA abundance in human and animal nasal microbiome, in southern Sri Lanka using a One Health approach. Nasal swabs from farmers and livestock on 50 farms (Nov 2020 - Dec 2021) and livestock products were collected. MRSA was isolated and confirmed using standard microbiological techniques. Staphylococcal chromosomal cassette mec typing, spa typing, and multilocus sequence typing were performed. Identified clones were compared with hospital isolates. Metagenomics analysis was performed on selected samples. MRSA prevalence was 24.0 % (12/50) in farms, 7.9 % (12/152) in farmers, 2.1 % (5/240) in livestock, and 1.9 % (3/157) in products. Of 372 S. aureus collected from clinical cultures, 59.4 % were MRSA. MRSA clones were identified in farm personnel (CC5/ST5/t002, CC1/ST1/t127, and ST45/CC45/t026), livestock (CC5/ST5/t002), and clinical cultures (CC5/ST5/t002 and CC5/ST6/t304), with ST45/CC45/t026 and CC5/ST6/t304 reported for the first time in Sri Lanka. LA-MRSA clones (ST389/ST9) were not detected. Animals had more diverse nasal microbiomes and lower MRSA abundance (<1.4 %) compared to humans (>82.3 %). MRSA colonization prevalence in southern Sri Lanka was relatively low. Two new clones and no LA-MRSA clones were identified. This study highlights the importance of continuing MRSA surveillance under the One Health framework to identify MRSA transmission between humans, animals, and the environment.}, }
@article {pmid39615647, year = {2024}, author = {Abavisani, M and Faraji, N and Ebadpour, N and Kesharwani, P and Sahebkar, A}, title = {Beyond digestion: Exploring how the gut microbiota modulates human social behaviors.}, journal = {Neuroscience}, volume = {565}, number = {}, pages = {52-62}, doi = {10.1016/j.neuroscience.2024.11.068}, pmid = {39615647}, issn = {1873-7544}, abstract = {For a long time, traditional medicine has acknowledged the gut's impact on general health. Contemporary science substantiates this association through investigations of the gut microbiota, the extensive community of microorganisms inhabiting our gastrointestinal system. These microscopic residents considerably improve digestive processes, nutritional absorption, immunological function, and pathogen defense. Nevertheless, a variety of gastrointestinal and extra-intestinal disorders can result from dysbiosis, an imbalance of the microbial composition of the gut microbiota. A groundbreaking discovery is the gut-brain axis, a complex communication network that links the enteric and central nervous system (CNS). This bidirectional communication allows the brain to influence gut activities and vice versa, impacting mental health and mood disorders like anxiety and depression. The gut microbiota can influence this communication by creating neurotransmitters and short-chain fatty acids, among other biochemical processes. These factors may affect our mental state, our ability to regulate our emotions, and the hypothalamic-pituitary-adrenal (HPA) axis. This study aimed to explore the complex interrelationships between the brain and the gut microbiota. We also conducted a thorough examination of the existing understanding in the area of how microbiota affects social behaviors, including emotions, stress responses, and cognitive functions. We also explored the potential of interventions that focus on the connection between the gut and the brain, such as using probiotics to treat diseases of the CNS. This research opens up new possibilities for addressing mental health and neurological conditions in an innovative manner.}, }
@article {pmid39615570, year = {2024}, author = {Salinas, J and Martinez-Gallardo, MR and Jurado, MM and Suarez-Estrella, F and Lopez-Gonzalez, JA and Estrella-Gonzalez, MJ and Toribio, AJ and Carpena-Istan, V and Lopez, MJ}, title = {Construction of versatile plastic-degrading microbial consortia based on ligninolytic microorganisms associated with agricultural waste composting.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {125333}, doi = {10.1016/j.envpol.2024.125333}, pmid = {39615570}, issn = {1873-6424}, abstract = {The accumulation of plastic in ecosystems is one of the most critical environmental concerns today. Plastic biodegradation using individual microbial cultures has shown limited success, which can be improved by employing microbial consortia with appropriate enzymatic capabilities. This study aims to assemble and characterize microbial consortia using ligninolytic fungi and bacteria isolated from an agricultural waste composting process, with the goal of enhancing the efficiency of plastic biodegradation. The compost microbiome demonstrated plastic-degrading functionality, particularly during the raw material and cooling phases. Ligninolytic microorganisms from compost were characterized for enzymes related to plastic degradation and their ability to colonize plastic films. The genera Bacillus, Pseudomonas, Fusarium, Aspergillus, Scedosporium, and Pseudallescheria exhibited a wide range of activities associated with plastic biodegradation, making them candidates for consortia assembly. The biodegradation of polyethylene using single and consortium cultures revealed that consortia, particularly those combining Bacillus subtilis RBM2 with Fusarium oxysporum RHM1, enhanced degradation efficiency. Additionally, consortia targeting multiple plastics, including virgin and recycled linear low-density polyethylene (LLDPE), polyethylene terephthalate (PET), and polystyrene (PS), showed varying levels of success, with bacterial-bacterial combinations such as Pseudomonas aeruginosa RBM21 and Bacillus subtilis RBM2 demonstrating broad-spectrum plastic degradation. These findings underscore the potential of compost-derived microorganisms for plastic biodegradation and suggest that utilizing microbial consortia offers a promising approach to tackling plastic pollution.}, }
@article {pmid39615475, year = {2024}, author = {Řezáč, M and Řezáčová, V and Heneberg, P}, title = {Differences in the abundance and diversity of endosymbiotic bacteria drive host resistance of Philodromus cespitum, a dominant spider of central European orchards, to selected insecticides.}, journal = {Journal of environmental management}, volume = {373}, number = {}, pages = {123486}, doi = {10.1016/j.jenvman.2024.123486}, pmid = {39615475}, issn = {1095-8630}, abstract = {The ability of tissue endosymbionts to degrade and detoxify agrochemicals is increasingly recognized as a mechanism supporting the survival of arthropods in agroecosystems. Therefore, tissue endosymbionts have the potential to drive insecticide resistance in agrobiont spiders, i.e., in major generalist predators and pest control agents within agroecosystems. We hypothesized that the abundance and diversity of the endosymbiotic bacteria of Philodromus cespitum, a philodromid spider dominating central European apple orchards, vary with regard to differences in predation capacity and drive host insecticide resistance. We provisioned P. cespitum with diets of varying protein and lipid content and topically exposed them to field-relevant doses of commonly used insecticides, namely Mospilan (acetamiprid), Movento (spirotetramat), Gondola (sulfoxaflor), Decis (deltamethrin), Coragen (chlorantraniliprole), and Benevia (cyantraniliprole). The analyses were based on 16S rDNA profiles from lysates of the cephalothorax and legs of the tested spiders. The application of Benevia, Mospilan, and Movento was partially lethal. The spiders that were resistant to the treatments with Benevia, Mospilan, or Movento were associated with the increased relative abundance of Mycoplasmatota by more than one order of magnitude. Additionally, the abundance of other bacteria differed in Mospilan-resistant and Mospilan-sensitive individuals. In contrast, the diet regimens were not associated with any major differences in the microbiome diversity nor the diversity of endosymbionts. Philodromus cespitum hosts assemblages with unexpectedly high beta diversity of endosymbionts. The OTU identified as the alpha proteobacterium endosymbiont of Coelostomidia zealandica was an obligate endosymbiont of the analyzed P. cespitum population. Wolbachia, Rickettsia, and Spiroplasma endosymbionts were also highly prevalent and differed in their responses to the applied treatments. In conclusion, differences in the abundance and diversity of endosymbiotic bacteria drove the resistance of the spider host to selected insecticides.}, }
@article {pmid39615354, year = {2024}, author = {Zhang, Y and He, J and Zeng, H and Xu, D and Li, W and Wang, Y}, title = {Advances in prebiotic carbohydrate-based targeted delivery: Overcoming gastrointestinal challenges for bioactive ingredients.}, journal = {Food chemistry}, volume = {466}, number = {}, pages = {142210}, doi = {10.1016/j.foodchem.2024.142210}, pmid = {39615354}, issn = {1873-7072}, abstract = {Natural bioactive ingredients face challenges in extensive application owing to low oral bioavailability. This can be improved by overcoming gastrointestinal barriers and facilitating targeted release through delivery strategies. This study provides a comprehensive review of targeted delivery systems using prebiotic carbohydrate matrices, focusing on structures, release mechanisms and applications. The bioactive ingredients can be encapsulated into nanohydrogels, nanoparticles, nanoemulsions, micro/nanocapsules and nanofibres to achieve controlled/targeted delivery to predetermined locations via interactions with pH, mucus, microbiome, enzymes and other factors in the colon. In particular, the prebiotic function of carbohydrates is generated by colonic microbiota degradation and fermentation, producing beneficial postbiotics through multiple metabolic pathways. This study provides certain insights into the in-depth development and application of prebiotic carbohydrate-based targeted delivery systems in the fields of food and health.}, }
@article {pmid39615199, year = {2024}, author = {Vaziri, Y}, title = {Dietary influence on cancer progression: Gut health and genomic profiles.}, journal = {Current problems in cancer}, volume = {54}, number = {}, pages = {101159}, doi = {10.1016/j.currproblcancer.2024.101159}, pmid = {39615199}, issn = {1535-6345}, abstract = {This scholarly review comprehensively examines the connection between dietary habits, gut health, cancer prognosis, and genomic profiles. It emphasizes the crucial role of gut microbiota in mediating genomic changes and oncogenic processes through metabolic derivatives.It advocatеs for pеrsonalizеd nutrition stratеgiеs based on individual microbiomе and gеnomic profilеs and proposеs that customized diеtary intеrvеntions could play a crucial rolе in cancеr prеvеntion thеrapy. Thе article highlights thе influеncе of spеcific nutriеnts and such as diеtary fibеr and polyphеnols found in cеrtain foods and dеmonstrating thеir potеntial to altеr gеnе еxprеssions associatеd with inflammation and tumorigеnеsis. Thе rеviеw citеs rеcеnt studiеs that support thе idеa that diеtary modifications can influеncе gеnе rеgulation and thеrеby potеntially altеring cancеr progrеssion. Nevertheless, it calls for morе rigorous rеsеarch including longitudinal and randomizеd studies, to substantiatе thе еvidеncе nеcеssary for developing diеtary guidеlinеs tailorеd for cancеr patiеnts. Thе rеviеw еmphasizеs thе nееd for a multidisciplinary approach and highlight thе importancе of collaboration across thе fiеlds of nutrition gеnomics microbiology and oncology to improve cancеr trеatmеnts and patiеnt quality of lifе. It posits thе rеviеw as a cornеrstonе for a divеrsе audiеncе within thе scientific and mеdical communitimphasizing thе nеcеssity for ongoing rеsеarch in nutritional gеnomics which it dеpicts as a fiеld full of opportunitiеs to transform cancеr carе.}, }
@article {pmid39615192, year = {2024}, author = {Lv, J and Li, X and Zhao, L and Zhang, S and Wang, G and Wang, X and Wang, Y and Chen, X and Yin, C and Mao, Z}, title = {Lactobacillus reuteri metabolites alleviate apple replant disease (ARD) by driving beneficial bacteria to reshape the core root microbiome.}, journal = {Plant physiology and biochemistry : PPB}, volume = {219}, number = {}, pages = {109345}, doi = {10.1016/j.plaphy.2024.109345}, pmid = {39615192}, issn = {1873-2690}, abstract = {Previous studies have shown that the bacterial fertilizer Lactobacillus reuteri (LBR) significantly alleviates apple replant disease (ARD), but the mechanism behind its effectiveness remains unclear. This study investigated the effects of key LBR metabolites on the rhizosphere microbial community. The biocontrol function of extracellular polysaccharides (EPS) was examined and shown to be further enhanced after optimizing the fermentation conditions. The optimized fermentation conditions were found to generate intermediates involved in various plant metabolic pathways, leading to plant growth promotion, increased abundance of beneficial bacteria like Bacillus and Pseudomonas in the rhizosphere soil, and decreased abundance of pathogenic fungi. Through the isolation and identification of rhizosphere microorganisms, a strain of Pseudomonas monteilii with chemotaxis to EPS was isolated, which had growth promotion ability and effectively improved plant resistance and relieves ARD. To further understand the mechanism underlying the inhibitory effect on soil pathogens of microbial aggregations and development in the rhizosphere driven by beneficial bacteria metabolites. These findings offer valuable technical insights for utilizing biocontrol bacteria metabolites in ARD management.}, }
@article {pmid39615045, year = {2024}, author = {Valentino, V and De Filippis, F and Marotta, R and Pasolli, E and Ercolini, D}, title = {Genomic features and prevalence of Ruminococcus species in humans are associated with age, lifestyle, and disease.}, journal = {Cell reports}, volume = {43}, number = {12}, pages = {115018}, doi = {10.1016/j.celrep.2024.115018}, pmid = {39615045}, issn = {2211-1247}, abstract = {The genus Ruminococcus is dominant in the human gut, but higher levels of some species, such as R. gnavus, R. torques, and R. bromii, have been linked to health or disease. In this study, we analyzed >9,000 Ruminococcus metagenome-assembled genomes (MAGs) reconstructed from >5,000 subjects and revealed significant links between the prevalence of some species/subspecies and geographic origin, age, lifestyle, and disease, with subspecies prevalent in specific subpopulations showing divergent metabolic potential. Furthermore, Ruminococcus species from Lachnospiraceae encoded for carbohydrate-active enzymes (CAZy) potentially involved in the metabolism of human N- and O-glycans, whereas those from Oscillospiraceae appear to be more adapted toward fiber metabolism. These new findings contribute to elucidating the potential functional role of Ruminococcus in specific lifestyles and diseases and to decipher the diversity and the adaptation of members of this genus to the human gut.}, }
@article {pmid39614901, year = {2024}, author = {Saadh, MJ and Ahmed, HH and Al-Hussainy, AF and Kaur, I and Kumar, A and Chahar, M and Saini, S and Taher, WM and Alwan, M and Jawad, MJ and Darvishi, M and Alsaikhan, F}, title = {Bile's Hidden Weapon: Modulating the Microbiome and Tumor Microenvironment.}, journal = {Current microbiology}, volume = {82}, number = {1}, pages = {25}, pmid = {39614901}, issn = {1432-0991}, support = {PSAU/2023/R/1444//Prince Sattam bin Abdulaziz University/ ; }, mesh = {Humans ; *Tumor Microenvironment ; *Gastrointestinal Microbiome ; *Bile/metabolism ; *Bile Acids and Salts/metabolism ; *Neoplasms/microbiology ; Animals ; }, abstract = {The human gut microbiome is a dynamic and intricate ecosystem, composed of trillions of microorganisms that play a pivotal role in maintaining overall health and well-being. However, the gut microbiome is constantly exposed to various environmental factors, including the bile produced by the liver, which can significantly impact its composition and function. Bile acids, secreted by the liver and stored in the gallbladder, modulate the gut microbiome, influencing its composition and function. This altered microbiome profile can, in turn, impact the tumor microenvironment (TME), promoting an immunosuppressive environment that favors tumor growth and metastasis. Furthermore, changes in the gut microbiome can also influence the production of bile acids and other metabolites that directly affect cancer cells and their behavior. Moreover, bile acids have been shown to shape the microbiome and increase antibiotic resistance, underscoring the need for targeted interventions. This review provides a comprehensive overview of the intricate relationships between bile, the gut microbiome, and the TME, highlighting the mechanisms by which this interplay drives cancer progression and resistance to therapy. Understanding these complex interactions is crucial for developing novel therapeutic strategies that target the gut-bile-TME axis and improve patient outcomes.}, }
@article {pmid39614602, year = {2024}, author = {Ruiz-Malagón, AJ and Rodríguez-Sojo, MJ and Redondo, E and Rodríguez-Cabezas, ME and Gálvez, J and Rodríguez-Nogales, A}, title = {Systematic review: The gut microbiota as a link between colorectal cancer and obesity.}, journal = {Obesity reviews : an official journal of the International Association for the Study of Obesity}, volume = {}, number = {}, pages = {e13872}, doi = {10.1111/obr.13872}, pmid = {39614602}, issn = {1467-789X}, support = {CTS164//Junta de Andaluc&#xed;a/ ; P18-RT-4930//Instituto de Salud Carlos III/ ; PI18/00826//Instituto de Salud Carlos III/ ; PI19/01058//Instituto de Salud Carlos III/ ; //Fondo Europeo de Desarrollo Regiona/ ; //European Union/ ; }, abstract = {Microbiome modulation is one of the novel strategies in medicine with the greatest future to improve the health of individuals and reduce the risk of different conditions, including metabolic, immune, inflammatory, and degenerative diseases, as well as cancer. Regarding the latter, many studies have reported the role of the gut microbiome in carcinogenesis, formation and progression of colorectal cancer (CRC), as well as its response to different systemic therapies. Likewise, obesity, one of the most important risk factors for CRC, is also well known for its association with gut dysbiosis. Moreover, obesity and CRC display, apart from microbial dysbiosis, chronic inflammation, which participates in their pathogenesis. Although human and murine studies demonstrate the significant impact of the microbiome in regulating energy metabolism and CRC development, little is understood about the contribution of the microbiome to the development of obesity-associated CRC. Therefore, this systematic review explores the evidence for microbiome changes associated with these conditions and hypothesizes that this may contribute to the pathogenesis of obesity-related CRC. Two databases were searched, and different studies on the relationship among obesity, intestinal microbiota and CRC in clinical and preclinical models were selected. Data extraction was carried out by two reviewers independently, and 101 studies were finally considered. Findings indicate the existence of a risk association between obesity and CRC derived from metabolic, immune, and microbial disorders.}, }
@article {pmid39614556, year = {2024}, author = {Gong, M and Yuan, Y and Shi, X and Huang, H and Liu, J and Zhao, J and Xu, Q}, title = {Compound oolong tea ameliorates lipid accumulation through AMPK-PPAR pathway of hepatic lipid metabolism and modulates gut microbiota in HFD induced mice.}, journal = {Food research international (Ottawa, Ont.)}, volume = {196}, number = {}, pages = {115041}, doi = {10.1016/j.foodres.2024.115041}, pmid = {39614556}, issn = {1873-7145}, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Lipid Metabolism/drug effects ; *Diet, High-Fat ; *Liver/metabolism/drug effects ; Mice ; Male ; *Tea/chemistry ; *AMP-Activated Protein Kinases/metabolism ; Obesity/metabolism ; Mice, Inbred C57BL ; Signal Transduction/drug effects ; PPAR gamma/metabolism ; }, abstract = {Based on the modified traditional Chinese formula, Compound Oolong tea (WLT) is composed of six herbal medicines which have beneficial effects. The present study aimed to assess the effects of WLT on lipid metabolism and gut microbiota in the mouse obesity model.Totally 32 mice were randomized into 4 groups including normal control (NC), high-fat diet model (HFD), positive control (PC) receiving atorvastatin 10 mg/kg/d, and WLT group with WLT water extra 300 mg/kg/d. The HFD, PC, WLT groups were fed a High-fat Diet. The results show that body weight, Lee's index, liver index and fat index were reduced in WLT. Moreover, the accumulation of TC, TG, and LDL-C were lower, and the level of serum HDL-C in WLT was higher than HFD. The activities of ALT and AST were reduced, and the glucose tolerance was improved in WLT. Furthermore, the relative gene expression of hepatic such as Pparγ, Lxr, Srebp-1c, Srebp-2, Scd-1, Acc-1, Fas were upregulated, and Hmgcr was downregulated in WLT compared to HFD. The relative protein expression of PPARγ, SREBP-1, FAS, and SCD-1 were decreased, and p-AMPK/AMPK and p-ACC-1/ACC-1 were increased in WLT compared with HFD. In addition, the diversity of gut microbiota was increased in mice, with an increase in Bacteroidota and a decrease in Firmicutes and Desulfovibrionales were decreased in WLT, compared with HFD. Briefly, WLT improves hepatic lipid metabolism through the AMPK-PPAR pathway and regulates the gut microbiome. These findings suggest that WLT could potentially be used as a functional food ingredients for preventing obesity.}, }
@article {pmid39614549, year = {2024}, author = {Wicaksono, WA and Akinyemi, OE and Wassermann, B and Bickel, S and Suwanto, A and Berg, G}, title = {Traditionally produced tempeh harbors more diverse bacteria with more putative health-promoting properties than industrially produced tempeh.}, journal = {Food research international (Ottawa, Ont.)}, volume = {196}, number = {}, pages = {115030}, doi = {10.1016/j.foodres.2024.115030}, pmid = {39614549}, issn = {1873-7145}, mesh = {*Bacteria/genetics/classification/metabolism ; *Food Microbiology ; Humans ; Soy Foods/microbiology ; Fermentation ; Rhizopus/genetics/metabolism ; Hygiene ; Indonesia ; Microbiota ; Fermented Foods/microbiology ; }, abstract = {In recent years, there has been a significant shift towards industrialization in food production, resulting in the implementation of higher hygiene standards globally. Our study focused on examining the impact of hygiene standards on tempeh, a popular Rhizopus-based fermented soybean product native to Indonesia, and now famous around the world. We observed that tempeh produced with standardized hygiene measures exhibited a microbiome with comparable bacterial abundances but a markedly different community structure and function than traditionally produced tempeh. In detail, we found a decreased bacterial abundance of lactobacilli and enterobacteria, bacterial diversity, different indicator taxa, and significantly changed community structure in industrial tempeh. A similar picture was found for functional analysis: the quantity of bacterial genes was similar but qualitative changes were found for genes associated with human health. The resistome of tempeh varied based on its microbiome composition. The higher number of antimicrobial resistance genes in tempeh produced without standardized hygiene measures mainly belong to multidrug efflux pumps known to occur in plant-based food. Our findings were confirmed by functional insights into genomes and metagenome-assembled genomes from the dominant bacteria, e.g. Leuconostoc, Limosilactobacillus, Lactobacillus, Enterococcus, Paenibacillus, Azotobacter and Enterobacter. They harboured an impressive spectrum of genes important for human health, e.g. for production of vitamin B1, B7, B12, and K, iron and zinc transport systems and short chain fatty acid production. In conclusion, industrially produced tempeh harbours a less diverse microbiome than the traditional one. Although this ensures production at large scales as well as biosafety, in the long-term it can lead to potential effects for human gut health.}, }
@article {pmid39614509, year = {2024}, author = {Kim, YM and Choi, E and Cho, TJ and Rhee, MS and Kim, SA}, title = {Microbial profiling of oysters from a processing plant and retail products: Analysis based on culture-dependent methods and 16S rRNA gene sequencing.}, journal = {Food research international (Ottawa, Ont.)}, volume = {196}, number = {}, pages = {115096}, doi = {10.1016/j.foodres.2024.115096}, pmid = {39614509}, issn = {1873-7145}, mesh = {Animals ; *RNA, Ribosomal, 16S/genetics ; *Shellfish/microbiology ; *Bacteria/genetics/classification/isolation &amp; purification ; Food Microbiology ; Microbiota/genetics ; Food Handling/methods ; Ostreidae/microbiology ; Colony Count, Microbial ; Crassostrea/microbiology ; Seasons ; DNA, Bacterial/genetics ; }, abstract = {Oysters (Crassostrea gigas) are one of the most consumed shellfish globally. However, there is a lack of comprehensive microbiome studies that include the processing and distribution stages of oysters. The present study used both culture-based methods and 16S rRNA sequencing to produce comprehensive microbial profiles of oysters in two parts: (1) an oyster processing plant that processes raw and frozen oysters (n = 57) and (2) retail oyster products across two seasons (winter and spring) (n = 112). In the processing plant, shucking increased the aerobic plate count (APC) from 1.86 log CFU/g in freshly harvested oysters to 3.95 log CFU/g in shucked oysters. Controlling the washing process is important, as the APCs decreased after washing and remained level until the final products, raw and frozen oysters (2.54 and 2.34 log CFU/g, respectively). After desalting in the frozen oyster plant, the bacterial community shifted to be dominated by the family Spirochaetaceae, Mycoplasma, and Shigella taxa, indicating a need to control problematic bacteria in the desalting process. SourceTracker analysis revealed that raw materials contributed more to the microbiota of final products than environmental samples. In retail oyster products, APCs were marginally higher in spring (3.58 log CFU/g) than in winter (3.05 log CFU/g) samples. While bacterial count differences were not dramatic, the proportions of taxa in the microbial community differed by season. In winter retail products, Photobacterium (27.91 %) and Aliivibrio (20.42 %) dominated, while spring samples showed a diverse distribution of the family Vibrionaceae (19.90 %), Photobacterium (14.20 %), Psychromonas (11.84 %), and Aliivibrio (7.20 %). These findings contributed to our understanding of oyster microorganisms and identified food safety control points and cross-contamination sources. This in-depth understanding is expected to inform the development of fishery and seafood safety management measures.}, }
@article {pmid39614396, year = {2024}, author = {Matacchione, G and Piacenza, F and Pimpini, L and Rosati, Y and Marcozzi, S}, title = {The role of the gut microbiota in the onset and progression of heart failure: insights into epigenetic mechanisms and aging.}, journal = {Clinical epigenetics}, volume = {16}, number = {1}, pages = {175}, pmid = {39614396}, issn = {1868-7083}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology/genetics ; *Heart Failure/genetics/microbiology/physiopathology ; *Epigenesis, Genetic ; *Aging/genetics ; *DNA Methylation/genetics ; Disease Progression ; Dysbiosis/microbiology/genetics ; Methylamines/metabolism ; Bile Acids and Salts/metabolism ; }, abstract = {BACKGROUND: The gut microbiota (GM) plays a critical role in regulating human physiology, with dysbiosis linked to various diseases, including heart failure (HF). HF is a complex syndrome with a significant global health impact, as its incidence doubles with each decade of life, and its prevalence peaks in individuals over 80 years. A bidirectional interaction exists between GM and HF, where alterations in gut health can worsen the disease's progression.<br><br>MAIN BODY: The "gut hypothesis of HF" suggests that HF-induced changes, such as reduced intestinal perfusion and altered gut motility, negatively impact GM composition, leading to increased intestinal permeability, the release of GM-derived metabolites into the bloodstream, and systemic inflammation. This process creates a vicious cycle that further deteriorates heart function. GM-derived metabolites, including trimethylamine N-oxide (TMAO), short-chain fatty acids (SCFAs), and secondary bile acids (BAs), can influence gene expression through epigenetic mechanisms, such as DNA methylation and histone modifications. These epigenetic changes may play a crucial role in mediating the effects of dysbiotic gut microbial metabolites, linking them to altered cardiac health and contributing to the progression of HF. This process is particularly relevant in older individuals, as the aging process itself has been associated with both dysbiosis and cumulative epigenetic alterations, intensifying the interplay between GM, epigenetic changes, and HF, and further increasing the risk of HF in the elderly.<br><br>CONCLUSION: Despite the growing body of evidence, the complex interplay between GM, epigenetic modifications, and HF remains poorly understood. The dynamic nature of epigenetics and GM, shaped by various factors such as age, diet, and lifestyle, presents significant challenges in elucidating the precise mechanisms underlying this complex relationship. Future research should prioritize innovative approaches to overcome these limitations. By identifying specific metabolite-induced epigenetic modifications and modulating the composition and function of GM, novel and personalized therapeutic strategies for the prevention and/or treatment of HF can be developed. Moreover, targeted research focusing specifically on older individuals is crucial for understanding the intricate connections between GM, epigenetics, and HF during aging.}, }
@article {pmid39614246, year = {2024}, author = {Marín-Sánchez, N and Paredes, R and Borgognone, A}, title = {Exploring potential associations between the human microbiota and reservoir of latent HIV.}, journal = {Retrovirology}, volume = {21}, number = {1}, pages = {21}, pmid = {39614246}, issn = {1742-4690}, support = {847943//European Union's Horizon 2020 Research and Innovation/ ; }, mesh = {Humans ; *HIV Infections/virology/microbiology/immunology ; *Virus Latency ; *HIV-1/physiology ; *Microbiota ; *Gastrointestinal Microbiome ; Virus Replication ; Disease Reservoirs/virology/microbiology ; }, abstract = {BACKGROUND: The rapid establishment and persistence of latent HIV-1 reservoirs is one of the main obstacles towards an HIV cure. While antiretroviral therapy supresses viral replication, it does not eradicate the latent reservoir of HIV-1-infected cells. Recent evidence suggests that the human microbiome, particularly the gut microbiome, may have the potential to modulate the HIV-1 reservoir. However, literature is limited and the exact mechanisms underlying the role of the microbiome in HIV immunity and potential regulation of the viral reservoir remain poorly understood.<br><br>RESULTS: Here, we review updated knowledge on the associations between the human microbiome and HIV reservoir across different anatomical sites, including the gut, the lungs and blood. We provide an overview of the predominant taxa associated with prominent microbiome changes in the context of HIV infection. Based on the current evidence, we summarize the main study findings, with specific focus on consistent bacterial and related byproduct associations. Specifically, we address the contribution of immune activation and inflammatory signatures on HIV-1 persistence. Furthermore, we discuss possible scenarios by which bacterial-associated inflammatory mediators, related metabolites and host immune signatures may modulate the HIV reservoir size. Finally, we speculate on potential implications of microbiome-based therapeutics for future HIV-1 cure strategies, highlighting challenges and limitations inherent in this research field.<br><br>CONCLUSIONS: Despite recent advances, this review underscores the need for further research to deepen the understanding of the complex interplay between the human microbiome and HIV reservoir. Further integrative multi-omics assessments and functional studies are crucial to test the outlined hypothesis and to identify potential therapeutic targets ultimately able to achieve an effective cure for HIV.}, }
@article {pmid39614169, year = {2024}, author = {Tang, H and Du, S and Niu, Z and Zhang, D and Tang, Z and Chen, H and Chen, Z and Zhang, M and Xu, Y and Sun, Y and Fu, X and Norback, D and Shao, J and Zhao, Z}, title = {Nasal, dermal, oral and indoor dust microbe and their interrelationship in children with allergic rhinitis.}, journal = {BMC microbiology}, volume = {24}, number = {1}, pages = {505}, pmid = {39614169}, issn = {1471-2180}, mesh = {Humans ; *Dust/analysis ; Male ; Child ; Female ; *Rhinitis, Allergic/microbiology ; Case-Control Studies ; *RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/isolation &amp; purification/genetics ; *Skin/microbiology ; *Mouth/microbiology ; *Microbiota ; Nasal Cavity/microbiology ; Air Pollution, Indoor/analysis ; Child, Preschool ; Metagenomics/methods ; Nose/microbiology ; }, abstract = {BACKGROUND: Allergic rhinitis (AR) subjects might have their microenvironment changed due to pathogenesis and living environment. Whether the nasal microbe in AR children differs from healthy subjects and how it interplays with dermal, oral and indoor dust microbe needs to be elucidated.<br><br>METHODS: In this case-control study, we analyzed and compared the bacterial characterization and associations in nasal, dermal, oral swab samples and dust samples in 62 children with physician-diagnosed AR(cases) and 51 age- and gender-matched healthy ones with no history of allergic diseases(controls). Full-length 16S rRNA sequencing(swabs) and shotgun metagenomics(dust) were applied. Bacterial diversity, composition, abundance difference characteristics and fast expectation-maximization for microbial source tracking(FEAST) analysis were performed and compared between cases and controls.<br><br>RESULTS: The &#x3b1;-diversity of dust microorganisms in AR was lower than that in control group (P&#x2009;=&#x2009;0.034), and the &#x3b2;-diversity indices of microorganisms in nasal cavity (P&#x2009;=&#x2009;0.020), skin (P&#x2009;=&#x2009;0.001) and dust (P&#x2009;=&#x2009;0.004) were significantly different from those in control group. At species levels, a total of 10, 15, 12, and 15 bacterial species were differentially enriched in either cases or controls in nasal, dermal, oral, and dust samples, respectively(Linear Discriminant Analysis(LDA) score&#x2009;>&#x2009;2, P&#x2009;<&#x2009;0.05). Staphylococcus epidermidis was the single species simultaneously more abundant in nasal, dermal and dust samples in AR children. By FEAST analysis, 8.85% and 10.11% of S. epidermidis in AR dermal and dust samples came from nasal cavity. These proportions were significantly higher than those in controls (2.70% and 3.86%) (P&#x2009;<&#x2009;0.05). The same significantly higher transfer proportions(P&#x2009;<&#x2009;0.05) were observed for Staphylococcus aureus enriched in the nasal cavity in AR children. Classification models by random forest regression at species levels showed, bacterial species enriched in indoor dust, nasal and dermal samples had substantial power in distinguishing AR children from healthy ones, with the highest power in the dust samples (AUC&#x2009;=&#x2009;0.88) followed by nasal(AUC&#x2009;=&#x2009;0.81) and dermal ones(AUC&#x2009;=&#x2009;0.80).<br><br>CONCLUSIONS: Our study presented the microbial enrichment characteristics in AR children both in the living environment(dust) and body sites exposed to environment through inhalation(nasal cavity), contact(skin) and ingestion(oral cavity) pathways, respectively. Nasal S.epidermidis and S.aureus had dominant influences on dust and other body sites in AR children.}, }
@article {pmid39614167, year = {2024}, author = {Mangoma, N and Zhou, N and Ncube, T}, title = {Metagenomic insights into the microbial community of the Buhera soda pans, Zimbabwe.}, journal = {BMC microbiology}, volume = {24}, number = {1}, pages = {510}, pmid = {39614167}, issn = {1471-2180}, mesh = {Zimbabwe ; *Metagenomics ; *Bacteria/genetics/classification/isolation &amp; purification/metabolism ; *Microbiota/genetics ; Salinity ; Phylogeny ; Hydrogen-Ion Concentration ; Archaea/genetics/classification/metabolism/isolation &amp; purification ; Water Microbiology ; }, abstract = {BACKGROUND: Soda pans are unique, natural aquatic environments characterised by elevated salinity and alkalinity, creating a distinctive and often extreme geochemistry. The microbiomes of soda pans are unique, with extremophiles such as halophiles, alkaliphiles and haloalkaliphiles being important. Despite being dominated by mostly unculturable inhabitants, soda pans hold immense biotechnological potential. The application of modern "omics-based" techniques helps us better understand the ecology and true extend of the biotechnological potential of soda pan microbiomes. In this study, we used a shotgun metagenomic approach to determine the microbial diversity and functional profile of previously unexplored soda pans located in Buhera, Eastern Zimbabwe. A combination of titrimetry and inductively coupled plasma optical emission spectroscopy (ICP‒OES) was used to perform physico-chemical analysis of the soda pan water.<br><br>RESULTS: Physicochemical analysis revealed that the Buhera soda pans are highly alkaline, with a pH range of 8.74 to 11.03, moderately saline (2.94 - 7.55 g/L), and have high carbonate (3625 mg/L) and bicarbonate ion (1325 mg/L) alkalinity. High levels of sulphate, phosphate, chloride and fluoride ions were detected. Metagenomic analysis revealed that domain Bacteria dominated the soda pan microbial community, with Pseudomonadota and Bacillota being the dominant phyla. Vibrio was shown to be the predominant genus, followed by Clostridium, Candidatus Brevefilum, Acetoanaerobium, Thioalkalivibrio and Marinilactibacillus. Archaea were also detected, albeit at a low prevalence of 1%. Functional profiling revealed that the Buhera soda pan microbiome is functionally diverse, has hydrolytic-enzyme production potential and is capable of supporting a variety of geochemical cycles.<br><br>CONCLUSIONS: The results of this pioneering study showed that despite their extreme alkalinity and moderate salinity, the Buhera soda pans harbour a taxonomically and functionally diverse microbiome dominated by bacteria. Future work will aim towards establishing the full extent of the soda pan's biotechnological potential, with a particular emphasis on potential enzyme production.}, }
@article {pmid39614121, year = {2024}, author = {}, title = {Do you drink coffee? Ask your gut.}, journal = {Nature}, volume = {}, number = {}, pages = {}, pmid = {39614121}, issn = {1476-4687}, }
@article {pmid39613941, year = {2024}, author = {Hakalehto, E}, title = {Introduction to the Use of Microbial Communities.}, journal = {Advances in biochemical engineering/biotechnology}, volume = {}, number = {}, pages = {}, pmid = {39613941}, issn = {0724-6145}, abstract = {Microbes are the third major group of biospheric organisms after plants and animals. They are responsible for many natural circulations, including the rotation of elements. They return organic carbon for plants' use and dissolve minerals into organic cycles. Microbes contribute to the global gas and water balances. In animal digestion, they partake in the degradation and assimilation of nutrients. Typically, they act as communities where some strains are the most active at a given time point in the prevailing conditions. But they also live in a continuous state of succession, which precludes the maintenance of changeable balances. Whether functioning in soil, in our alimentary tract, or elsewhere, the micro-organisms decisively contribute to the restoration of various balances. As the microbiological scale differs significantly from our comprehension, we must nurture our understanding of the microbiome wherever it occurs. For example, one spoonful of yoghurt contains approximately as many bacterial cells as there are humans residing on Earth. Therefore, such organizational flexibility and interaction are the most advisable modes of operation in microbial biochemistry and biotechnological applications. As microbes tend to form communities, this modus operandi is worth instigating in our process industries and production technologies. The use of microbial mixed cultures most appropriately corresponds to the natural systems. As biocatalysts in human endeavours of biorefining and bioengineering, they have become the most utilizable and producible kind of microbial components. Cooperation with microbes is a prerequisite for the continuous development of sustainable industries and food and health production. The microbial communities can be used to prevent and clean up pollution. In the process design, the microbiological dynamic balances make the highest productivity, repeatability, controllability, and withstanding of entropy. Although their effects have been familiar to our societies, e.g. in the fermentation of foods, their total capacity remains to be put into service. Hopefully, this book could help turn the next page in the development.}, }
@article {pmid39613084, year = {2024}, author = {Kim, EJ and Lee, SH and Kim, TH and Lee, J and Choi, CH and Lee, SJ}, title = {Insect chitosan derived from Hermetia illucens larvae suppresses adipogenic signaling and promotes the restoration of gut microbiome balance.}, journal = {International journal of biological macromolecules}, volume = {284}, number = {Pt 1}, pages = {138168}, doi = {10.1016/j.ijbiomac.2024.138168}, pmid = {39613084}, issn = {1879-0003}, abstract = {Chitosan, the deacetylated form of chitin, is considered a valuable source of compounds in the feed and food industries. However, the impact of Hermetia illucens larvae chitosan (HCS) with specific physicochemical characteristics on obesity mediated by lipid accumulation and microbiome dysbiosis has not been fully elucidated. We purified HCS with a low molecular weight (84 kDa), low crystallinity, and a high deacetylation rate, characterizing it through several analytical techniques, including gel permeation chromatography, FT-IR, [1]H NMR, FE-SEM, and XRD analysis. HCS effectively inhibited the differentiation of 3T3-L1 preadipocytes by suppressing the production of reactive oxygen species. The adipogenic signaling of preadipocytes, mediated by the phosphorylation of mTOR and PPARγ, which are essential for the expression of fatty acid synthase, was attenuated by HCS. In mouse models fed high-fat diets, the oral administration of HCS prevented changes in white adipose tissue and liver weight and reduced plasma levels of total cholesterol. Additionally, the analysis of the microbiota using 16S rRNA revealed that HCS improved dysbiosis by modulating the composition and abundance of specific bacterial genera, including F. rodentium, L. gasseri, L. reuteri, and L. murinus. These findings highlight the potential of HCS as a candidate for the treatment of obesity-related metabolic diseases.}, }
@article {pmid39612986, year = {2024}, author = {Dong, HV and Adamson, P and Pham, DH and Pham, QH and Le, HHL and Pham, LQ and Bui, HTM and Le, GM and Klausner, JD}, title = {Antimicrobial susceptibilities of oral Neisseria from men on HIV pre-exposure prophylaxis in Hanoi, Vietnam.}, journal = {Journal of global antimicrobial resistance}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jgar.2024.11.008}, pmid = {39612986}, issn = {2213-7173}, abstract = {BACKGROUND: Antimicrobial resistance (AMR) in Neisseria gonorrhoeae (NG) is an urgent global health concern. Commensal Neisseria species in the oropharynx are an important reservoir of AMR genes that are transferred to NG, yet few data about AMR among commensal Neisseria in populations at risk for AMR exist.<br><br>METHODS: From May 2022 - December 2023, men in a HIV pre-exposure prophylaxis program in Hanoi, Vietnam, were recruited. Participants self-collected oral specimens using phosphate buffer solution (PBS), for culture on LB agar media containing sucrose, vancomycin and trimethoprim (LBVT.SNR). Oxidase-positive gram-negative diplococci were identified using Remel RapID NH system. Minimum inhibitory concentrations (MICs) to azithromycin, ceftriaxone, cefixime, and doxycycline were determined using Etests.<br><br>RESULTS: There were 42 male participants, the median age was 26 years and 29% (n=12) reported using antibiotics in the past 6 months. In total, 48 Neisseria isolates were recovered; N. sicca/subflava was the most common species (50%; n=24), followed by N. mucosa (38%; n=18). For azithromycin, 85% (n=41) of isolates were resistant with MICs &#x2265;1 ug/ml, including 25% (n=12) with high-level resistance (MICs &#x2265; 256 ug/mL of which 67% (8/12) were N. mucosa. Among non-gonococcal Neisseria isolates, the prevalence of resistance was 6% (n=3) for ceftriaxone, 6% (n=3) for cefixime, and 54% (n=26) for doxycycline; most non-susceptible isolates were N. mucosa.<br><br>CONCLUSION: A High frequency of azithromycin resistance, moderate doxycycline resistance, and low cephalosporin resistance was found in oropharyngeal Neisseria isolates from MSM in a PrEP program in Hanoi, Vietnam. N. mucosa was over-represented among resistant isolates.}, }
@article {pmid39612934, year = {2024}, author = {Almirall, J and Boixeda, R and de la Torre, MC and Torres, A}, title = {Epidemiology and Pathogenesis of Aspiration Pneumonia.}, journal = {Seminars in respiratory and critical care medicine}, volume = {45}, number = {6}, pages = {621-625}, doi = {10.1055/s-0044-1793907}, pmid = {39612934}, issn = {1098-9048}, mesh = {Humans ; *Pneumonia, Aspiration/epidemiology/microbiology ; Risk Factors ; Pneumonia, Ventilator-Associated/epidemiology/microbiology ; Incidence ; Cross Infection/epidemiology/microbiology ; Aged ; Prevalence ; Deglutition Disorders/epidemiology/etiology ; Healthcare-Associated Pneumonia/epidemiology/microbiology ; }, abstract = {Aspiration pneumonia (AP) remains a critical health issue, especially among older and hospitalized patients. This review focuses on understanding the epidemiology and pathogenesis of AP, exploring key risk factors, and proposing diagnostic strategies. Aspiration pneumonia is commonly associated with hospital-acquired pneumonia (HAP) and ventilator-associated pneumonia (VAP), where pathogens introduced into the lungs from gastric aspiration cause infection. Several factors, such as oropharyngeal dysphagia, silent aspiration, and poor oral health, contribute to increased risk, especially in frail elderly populations with chronic comorbidities. Diagnostic criteria for AP are not well-defined, complicating accurate diagnosis. Radiographic evidence of pulmonary infiltrates, history of aspiration, and clinical symptoms, such as cough and fever, guide diagnosis, but the absence of specific biomarkers remains a challenge. Furthermore, the microbiome of the lung, which shares characteristics with the oropharyngeal flora, plays a pivotal role in the development of infection. The incidence of AP is likely to increase given the growing elderly population with factors predisposing them to aspiration. It is one of the most common types of pneumonia in older adults, with its prevalence estimated to range from 5% to 24% in cases of CAP admissions. This revision highlights the growing need for comprehensive diagnostic tools and treatment protocols for AP, especially in high-risk populations such as the elderly and those in long-term care. Understanding the underlying mechanisms and the role of silent aspiration can improve prevention strategies and reduce morbidity and mortality in these vulnerable groups.}, }
@article {pmid39612930, year = {2024}, author = {Galley, JD and Rajasekera, TA and Bennouna, DJ and Batabyal, A and Verosky, B and Woodke, S and Stokes, J and Brown, AK and Murthy, S and Kopec, RE and Gur, TL}, title = {Multifactorial effects of probiotic Parasutterella excrementihominis on gestational inflammation, offspring behaviour and prenatal-stress induced disruptions in tryptophan metabolism.}, journal = {Beneficial microbes}, volume = {}, number = {}, pages = {1-18}, doi = {10.1163/18762891-bja00047}, pmid = {39612930}, issn = {1876-2891}, abstract = {Prenatal stress (PNS) has widespread effects on offspring, including aberrant immune development and behavioural deficits. The microbiome is a mediator of the dissemination of stress effects to the offspring through immunomodulation and metabolite production. Metabolites derived from the mother and their gut microbiota pass to the foetus and can affect immune and nervous development. Stress affects the abundance of such metabolites, including the tryptophan (Trp) pathway, which are involved in immune and nervous system function. We hypothesized that the PNS is associated with dysregulation of Trp metabolism. We further posited that treatment with a Trp-metaboliser Parasutterella excrementihominis would abrogate PNS-associated deleterious effects on offspring development. To test this hypothesis, pregnant mice were exposed to restraint stress and administered P. excrementihominis (Dam n = 3-9; Offspring n = 5-10). PNS increased maternal gut Trp and both maternal and offspring inflammation. P. excrementihominis treatment reduced the PNS-induced excess pool of maternal gut Trp. Some PNS effects on foetal neuroinflammation were reduced in severity due to handling effects from bacterial gavage. However, P. excrementihominis was anti-inflammatory in dam and offspring and anxiolytic in offspring of Pe-treated dams. These data illustrate that elevated Trp levels are associated PNS and its downstream deleterious offspring inflammatory and behavioural outcomes while P. excrementihominis, a Trp-metabolizer, can ameliorate these effects and improve offspring outcomes.}, }
@article {pmid39612711, year = {2024}, author = {Xu, W and Bai, Y and Xu, T and Chen, Y and Wang, J and Li, T and Liu, Z and Liu, H and Ruan, H}, title = {Revealing potential mechanisms of native and non-native snail coexistence through fecal microbiomes and dietary compositions.}, journal = {The Science of the total environment}, volume = {957}, number = {}, pages = {177774}, doi = {10.1016/j.scitotenv.2024.177774}, pmid = {39612711}, issn = {1879-1026}, abstract = {Understanding how animals coexist within an ecosystem is essential for the conservation of biodiversity. In China, large populations of a non-native snail Rumina decollata (a highly invasive species reported by various other countries) coexist with two native snail species (Acusta ravida and Euphaedusa aculus). However, the potential mechanisms that facilitate this non-native and native snail coexistence remain uncertain. Here, we analyzed the fecal microbiomes and dietary compositions of R. decollata, A. ravida, and E. aculus to elucidate the mechanisms that drive the cohabitation of non-native and native species in Nanjing, China. It was found that the composition of the E. aculus fecal microbiome was similar to that of R. decollata, while it was significantly different from that of A. ravida. Furthermore, R. decollata preyed on E. aculus and had similar plant food compositions like A. ravida. These results indicated that the fecal microbiomes of snails may be adaptable to variable environmental conditions, while being minimally influenced by host genetics. R. decollata integrated a portion of the fecal microbes of E. aculus by preying on them. Our findings highlighted that the coexistence of R. decollata with native snails may have been due to abundant environmental resources, which negated the emergence of strong competition. However, the specific dietary changes of R. decollata and their propagation still need to be continuously monitored to better understand the long-term effects of R. decollata on ecosystems. This research provides a new understanding toward the prevention of invasive species and biodiversity conservation.}, }
@article {pmid39612063, year = {2024}, author = {Xu, H and Li, O and Kim, D and Bao, Z and Yang, F}, title = {Gut microbiota and epigenetic age acceleration: a bi-directional Mendelian randomization study.}, journal = {Aging clinical and experimental research}, volume = {36}, number = {1}, pages = {227}, pmid = {39612063}, issn = {1720-8319}, support = {82071581//National Natural Science Foundation of China/ ; XXRC2211//Huadong Hospital Program/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Mendelian Randomization Analysis ; *Aging/genetics ; *Epigenesis, Genetic ; Genome-Wide Association Study ; }, abstract = {BACKGROUND: The gut microbiota is closely related to aging, but the genetic relationship between gut microbiota and aging has not been well investigated. The aim of the study was to explore the association of microbiota with epigenetic age acceleration (EAA) using the Mendelian randomization.<br><br>METHOD: The independent genetic instruments of gut microbiota were obtained from MiBioGen consortium and the Dutch Microbiome Project. EAA data were derived from genome-wide association study. To assess the causal relationship between gut microbiota and EAA, we applied four different methods of Mendelian Randomization (MR) analysis: the inverse variance weighted method (IVW), the MR-Egger regression, the weighted median analysis (WMA), and the weighted mode. Furthermore, sensitivity analyses were conducted to evaluate heterogeneity and horizontal pleiotropy.<br><br>RESULTS: We identified potential causal associations between 12 bacterial taxa and EAA (PIVW and PWMA < 0.05). Among them, species Holdemania_unclassified (OR: 1.31, 95% CI: 1.13-1.52, P&#x2009;=&#x2009;0.0004) retained a strong positive association with GrimAge acceleration. Family Acidaminococcaceae (OR: 0.64, 95% CI: 0.44-0.93, P&#x2009;=&#x2009;0.019) and family Clostridiaceae1 (OR: 0.69, 95% CI: 0.49-0.97 P&#x2009;=&#x2009;0.031) were negative association with GrimAge acceleration. Reverse MR analyses indicated that EAA was associated with 6 bacterial taxa in IVW and WMA. Among them, a strong inverse association was found between Phenoage acceleration and genus Turicibacter (OR: 0.928, 95%CI: 0.888-0.971, PIVW and PWMA < 0.001).<br><br>CONCLUSION: Our study implicates the potential causal effects of specific microbiota on EAA, potentially providing novel insights into the prevention aging through specific gut microbiota.}, }
@article {pmid39612015, year = {2024}, author = {Pathoor, NN and Ganesh, PS and Gopal, RK}, title = {Microbiome interactions: Acinetobacter baumannii biofilms as a co-factor in oral cancer progression.}, journal = {World journal of microbiology &amp; biotechnology}, volume = {40}, number = {12}, pages = {398}, pmid = {39612015}, issn = {1573-0972}, mesh = {*Biofilms/growth &amp; development ; *Acinetobacter baumannii/physiology/pathogenicity ; Humans ; *Mouth Neoplasms/microbiology ; *Microbiota ; Acinetobacter Infections/microbiology ; Disease Progression ; Mouth/microbiology ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial ; }, abstract = {Acinetobacter baumannii (A. baumannii) has long been recognized primarily as a hospital-acquired pathogen. However, recent studies have uncovered a potential link between this bacterium and oral cancer, necessitating a deeper exploration of this relationship. This review examines the relevance of A. baumannii biofilms in the context of oral cancer development. By synthesizing current knowledge, we seek to provide a comprehensive understanding of this emerging area of research and identify critical directions for future investigations. The review emphasizes the remarkable adaptability, environmental resilience, and antibiotic resistance of A. baumannii, delves into the molecular mechanisms of biofilm formation, and their potential connection to oral cancer progression. The review also evaluates how biofilm colonization on oral surfaces and medical devices, along with its role in chronic infections, inflammation, and increased antimicrobial resistance, could contribute to creating a microenvironment favourable for tumor development. This review underscores the broader healthcare implications of A. baumannii biofilms, evaluates current strategies for their prevention and eradication, and calls for interdisciplinary research in this emerging field. By shedding light on the complex interactions between A. baumannii biofilms and oral cancer, it aims to stimulate further research and guide the development of new diagnostic, preventive, and therapeutic strategies in both microbiology and oncology.}, }
@article {pmid39611949, year = {2024}, author = {Makumbi, JP and Leareng, SK and Pierneef, RE and Makhalanyane, TP}, title = {Synergizing Ecotoxicology and Microbiome Data Is Key for Developing Global Indicators of Environmental Antimicrobial Resistance.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {150}, pmid = {39611949}, issn = {1432-184X}, support = {UID 110717//National Research Foundation of South Africa/ ; UID 110717//National Research Foundation of South Africa/ ; }, mesh = {*Microbiota/drug effects ; Humans ; *Ecotoxicology ; Animals ; Risk Assessment ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial ; Public Health ; Drug Resistance, Microbial ; }, abstract = {The One Health concept recognises the interconnectedness of humans, plants, animals and the environment. Recent research strongly supports the idea that the environment serves as a significant reservoir for antimicrobial resistance (AMR). However, the complexity of natural environments makes efforts at AMR public health risk assessment difficult. We lack sufficient data on key ecological parameters that influence AMR, as well as the primary proxies necessary for evaluating risks to human health. Developing environmental AMR 'early warning systems' requires models with well-defined parameters. This is necessary to support the implementation of clear and targeted interventions. In this review, we provide a comprehensive overview of the current tools used globally for environmental AMR human health risk assessment and the underlying knowledge gaps. We highlight the urgent need for standardised, cost-effective risk assessment frameworks that are adaptable across different environments and regions to enhance comparability and reliability. These frameworks must also account for previously understudied AMR sources, such as horticulture, and emerging threats like climate change. In addition, integrating traditional ecotoxicology with modern 'omics' approaches will be essential for developing more comprehensive risk models and informing targeted AMR mitigation strategies.}, }
@article {pmid39611656, year = {2024}, author = {Leclercq, S and Ahmed, H and Amadieu, C and Petit, G and Koistinen, V and Leyrolle, Q and Poncin, M and Stärkel, P and Kok, E and Karhunen, PJ and de Timary, P and Laye, S and Neyrinck, AM and Kärkkäinen, OK and Hanhineva, K and Delzenne, N}, title = {Blood metabolomic profiling reveals new targets in the management of psychological symptoms associated with severe alcohol use disorder.}, journal = {eLife}, volume = {13}, number = {}, pages = {}, pmid = {39611656}, issn = {2050-084X}, support = {ANR-19-NEUR-0003-03//Agence Nationale de la Recherche/ ; R.8013.19//Fonds De La Recherche Scientifique - FNRS/ ; }, mesh = {Humans ; Male ; *Metabolomics ; Adult ; *Alcoholism/metabolism ; Female ; Middle Aged ; *Metabolome ; Gastrointestinal Microbiome ; Chromatography, Liquid ; }, abstract = {BACKGROUND: Alcohol use disorder (AUD) is a global health problem with limited therapeutic options. The biochemical mechanisms that lead to this disorder are not yet fully understood, and in this respect, metabolomics represents a promising approach to decipher metabolic events related to AUD. The plasma metabolome contains a plethora of bioactive molecules that reflects the functional changes in host metabolism but also the impact of the gut microbiome and nutritional habits.<br><br>METHODS: In this study, we investigated the impact of severe AUD (sAUD), and of a 3-week period of alcohol abstinence, on the blood metabolome (non-targeted LC-MS metabolomics analysis) in 96 sAUD patients hospitalized for alcohol withdrawal.<br><br>RESULTS: We found that the plasma levels of different lipids ((lyso)phosphatidylcholines, long-chain fatty acids), short-chain fatty acids (i.e. 3-hydroxyvaleric acid) and bile acids were altered in sAUD patients. In addition, several microbial metabolites, including indole-3-propionic acid, p-cresol sulfate, hippuric acid, pyrocatechol sulfate, and metabolites belonging to xanthine class (paraxanthine, theobromine and theophylline) were sensitive to alcohol exposure and alcohol withdrawal. 3-Hydroxyvaleric acid, caffeine metabolites (theobromine, paraxanthine, and theophylline) and microbial metabolites (hippuric acid and pyrocatechol sulfate) were correlated with anxiety, depression and alcohol craving. Metabolomics analysis in postmortem samples of frontal cortex and cerebrospinal fluid of those consuming a high level of alcohol revealed that those metabolites can be found also in brain tissue.<br><br>CONCLUSIONS: Our data allow the identification of neuroactive metabolites, from interactions between food components and microbiota, which may represent new targets arising in the management of neuropsychiatric diseases such as sAUD.<br><br>FUNDING: Gut2Behave project was initiated from ERA-NET NEURON network (Joint Transnational Call 2019) and was financed by Academy of Finland, French National Research Agency (ANR-19-NEUR-0003-03) and the Fonds de la Recherche Scientifique (FRS-FNRS; PINT-MULTI R.8013.19, Belgium). Metabolomics analysis of the TSDS samples was supported by grant from the Finnish Foundation for Alcohol Studies.}, }
@article {pmid39611592, year = {2024}, author = {Liu, C and Xing, B and Li, Z and Li, J and Xiao, M}, title = {A roadmap of isolating and investigating bacteriophage infecting human gut anaerobes.}, journal = {Essays in biochemistry}, volume = {}, number = {}, pages = {}, doi = {10.1042/EBC20240116}, pmid = {39611592}, issn = {1744-1358}, support = {82250901//National Natural Science Foundation of China (NSFC)/ ; }, abstract = {Bacteriophages, viruses that infect bacteria, play a crucial role in manipulating the gut microbiome, with implications for human health and disease. Despite the vast amount of data available on the human gut virome, the number of cultured phages that infect human gut bacteria-particularly obligate anaerobes-remains strikingly limited. Here, we summarize the resources and basic characteristics of phages that infect the human gut obligate anaerobe. We review various methods for isolating these phages and suggest a strategy for their isolation. Additionally, we outline their impact on the field of viral biology, their interactions with bacteria and humans, and their potential for disease intervention. Finally, we discuss the value and prospects of research on these phages, providing a comprehensive 'Roadmap' that sheds light on the 'dark matter' of phages that infect human gut obligate anaerobes.}, }
@article {pmid39611587, year = {2024}, author = {Sayid, R and van den Hurk, AWM and Rothschild-Rodriguez, D and Herrema, H and de Jonge, PA and Nobrega, FL}, title = {Characteristics of phage-plasmids and their impact on microbial communities.}, journal = {Essays in biochemistry}, volume = {}, number = {}, pages = {}, doi = {10.1042/EBC20240014}, pmid = {39611587}, issn = {1744-1358}, support = {AUF 5188//Amsterdam University Fund/ ; PhD fellowship//Amsterdam Cardiovascular Sciences, Amsterdam University Medical Centers (ACS)/ ; //Bowel Research UK (BRUK)/ ; Aspasia premium (015.017.050)//Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO)/ ; BB/T008768/1//Biotechnology and Biological Sciences Research Council (BBSRC)/ ; Black Futures Research Studentship//University of Southampton (University of Southampton UK)/ ; }, abstract = {Bacteria host various foreign genetic elements, most notably plasmids and bacteriophages (or phages). Historically, these two classes were seen as separate, but recent research has shown considerable interplay between them. Phage-plasmids (P-Ps) exhibit characteristics of both phages and plasmids, allowing them to exist extrachromosomally within bacterial hosts as plasmids, but also to infect and lyse bacteria as phages. This dual functionality enables P-Ps to utilize the modes of transmission of both phage and plasmids, facilitating the rapid dissemination of genetic material, including antibiotic resistance and virulence genes, throughout bacterial populations. Additionally, P-Ps have been found to encode toxin-antitoxin and CRISPR-Cas adaptive immune systems, which enhance bacterial survival under stress and provide immunity against other foreign genetic elements. Despite a growing body of literature on P-Ps, large gaps remain in our understanding of their ecological roles and environmental prevalence. This review aims to synthesise existing knowledge and identify research gaps on the impacts of P-Ps on microbial communities.}, }
@article {pmid39611357, year = {2024}, author = {Kauer, L and Imholt, C and Jacob, J and Berens, C and Kühn, R}, title = {Seasonal shifts and land-use impact: unveiling the gut microbiomes of bank voles (Myodes glareolus) and common voles (Microtus arvalis).}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiae159}, pmid = {39611357}, issn = {1574-6941}, abstract = {Gut microbial diversity influences the health and vitality of the host, yet it is itself affected by internal and external factors, including land-use. The impact of land-use practices on wild rodents' gut microbiomes remains understudied, despite their abundance and potential as reservoirs for zoonotic pathogens. We examined the bacterial and fungal gut microbiomes of bank voles (Myodes glareolus) and common voles (Microtus arvalis) across grassland and forest habitats with varying land-use intensities and types. We collected rodents seasonally and used 16S rRNA and ITS amplicon sequencing for microbe identification. We found significant differences in alpha and beta diversities between the species, with M. arvalis exhibiting higher diversity. Seasonality emerged as a prominent factor influencing microbial diversity, with significant variations between sampling months. While land-use affects the gut microbiome, its impact is subordinate to seasonal variations. Differential abundance analysis underscores the dynamic nature of microbial composition, with seasonal changes playing a predominant role. Overall, our findings highlight the significant influence of seasonality on gut microbiome diversity and composition in wild rodents, reflecting dietary shifts associated with seasonal changes. Understanding the interplay between environmental factors and microbial communities in wild rodents enahnces our knowledge of ecosystem health and resilience, warranting further investigation.}, }
@article {pmid39611305, year = {2024}, author = {Leschonski, KP and Mortensen, MS and Hansen, LBS and Krogh, KBRM and Kabel, MA and Laursen, MF}, title = {Structure-dependent stimulation of gut bacteria by arabinoxylo-oligosaccharides (AXOS): a review.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2430419}, doi = {10.1080/19490976.2024.2430419}, pmid = {39611305}, issn = {1949-0984}, mesh = {*Oligosaccharides/metabolism/pharmacology ; *Gastrointestinal Microbiome ; *Bacteria/genetics/metabolism/classification ; Humans ; Fermentation ; Animals ; Bifidobacterium/genetics/metabolism ; Xylans/metabolism ; Dietary Fiber/metabolism ; Gastrointestinal Tract/microbiology ; }, abstract = {Arabinoxylo-oligosaccharides (AXOS) are non-digestible dietary fibers that potentially confer a health benefit by stimulating beneficial bacteria in the gut. Still, a detailed overview of the diversity of gut bacteria and their specificity to utilize structurally different AXOS has not been provided to date and was aimed for in this study. Moreover, we assessed the genetic information of summarized bacteria, and we extracted genes expected to encode for enzymes that are involved in AXOS hydrolysis (based on the CAZy database). The taxa involved in AXOS fermentation in the gut display a large variety of AXOS-active enzymes in their genome and consequently utilize AXOS to a highly different extent. Clostridia and Bacteroidales are generalists that consume many structurally diverse AXOS, whereas Bifidobacterium are specialists that specifically consume AXOS with a low degree of polymerization. Further complexity is evident from the fact that the exact bacterial species, and in some cases even the bacterial strains (e.g. in Bifidobacterium longum) that are stimulated, highly depend on the specific AXOS molecular structure. Furthermore, certain species in Bifidobacterium and Lactobacillaceae are active as cross-feeders and consume monosaccharides and unbranched short xylo-oligosaccharides released from AXOS. Our review highlights the possibility that (enzymatic) fine-tuning of specific AXOS structures leads to improved precision in targeting growth of specific beneficial bacterial species and strains in the gut.}, }
@article {pmid39611142, year = {2024}, author = {Zhang, L and Zhang, H and Su, S and Jia, Y and Liang, C and Fang, Y and Hong, D and Li, T and Ma, F}, title = {Risk factor assessment and microbiome analysis in peritoneal dialysis-related peritonitis reveal etiological characteristics.}, journal = {Frontiers in immunology}, volume = {15}, number = {}, pages = {1443468}, pmid = {39611142}, issn = {1664-3224}, mesh = {Humans ; *Peritonitis/microbiology/etiology/diagnosis ; *Peritoneal Dialysis/adverse effects ; Male ; Female ; Middle Aged ; Risk Factors ; *Gastrointestinal Microbiome ; Aged ; Risk Assessment ; Adult ; Metagenomics/methods ; High-Throughput Nucleotide Sequencing ; }, abstract = {BACKGROUND: Peritoneal dialysis-related peritonitis (PDRP) is one of the most common complications of peritoneal dialysis (PD). Understanding the risk factors and etiological characteristics is indispensable for infection prevention and improving the outcome and life quality.<br><br>METHODS: A total of 70 PD patients were separated into the PDRP group (n=25) and the control group (n=45). Variables, including gender, age, body mass index, primary diseases, and history of basic diseases, in the two groups were analyzed to assess the risk factors of PDRP. Metagenomic next-generation sequencing (mNGS) and microbial culture were compared in detecting pathogenic microorganisms. Gut microbiota analysis was performed in 35 PDRP patients based on mNGS data.<br><br>RESULTS: Dialysis time and times of dialysate change were the risk factors of PDRP, and times of dialysate change was the independent risk factor of PDRP (p = 0.046). mNGS produced higher sensitivity (65.79%) than microbial culture (36.84%) in identifying pathogenic microorganisms. Staphylococcus aureus and Klebsiella pneumoniae (four cases) were the most frequent pathogens causing PDRP, followed by Staphylococcus capitis (three cases). &#x3b2; diversity of the gut microbiota was significantly different between patients with fewer times of dialysate change (&#x2264;4) and more (>5), as well as between patients with gram-positive (G+) bacterial and gram-negative (G-) bacterial infection.<br><br>CONCLUSION: The dialysis time and times of dialysate changes not only are risk factors for peritonitis in PD patients but also stimulate significant changes in the gut microbiome structure in PDRP patients. These findings may provide a novel viewpoint for the management of patients with PDRP.}, }
@article {pmid39611094, year = {2024}, author = {Hou, G and You, J and Zhuang, Y and Gao, D and Xu, Y and Jiang, W and Li, S and Zhao, X and Chen, T and Zhang, S and Liu, S and Wang, W and Li, S and Cao, Z}, title = {Disorders of acid-base balance promote rumen lipopolysaccharide biosynthesis in dairy cows by modulating the microbiome.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1492476}, pmid = {39611094}, issn = {1664-302X}, abstract = {INTRODUCTION: Disorders of acid-base balance in the rumen of dairy cows have a significant impact on their health and performance. However, the effect of transient differences in pH on susceptibility to subacute ruminal acidosis (SARA) and lipopolysaccharide (LPS) biosynthesis in dairy cows remains unclear.<br><br>METHODS: In this study, milk, serum, and rumen fluid samples from 40 Holstein dairy cows (on d 56 postpartum) with different rumen pH (2-4&#x2009;h after morning feeding) were explored to investigate the difference of susceptibility to SARA and the correlation between microbiome, LPS and inflammation. These cows were categorized into low pH (LPH, pH&#x2009;&#x2264;&#x2009;6.0, n&#x2009;=&#x2009;20) and high pH (HPH, pH&#x2009;&#x2265;&#x2009;6.5, n&#x2009;=&#x2009;20) groups.<br><br>RESULTS: The results showed that LPH group increased the concentrations of total volatile fatty acids, acetate, propionate, butyrate and valerate. However, milk yield and milk compositions were unaffected. Compared to the HPH group, the LPH group increased the concentrations of serum BHBA, NEFA, LPS, HIS, IL-2, IL-6, TNF-&#x3b1;, and MDA, and decreased the concentrations of serum IgA, IgM, IgG, SOD, T-AOC, and mTOR. In addition, the LPH group decreased the copies of Ruminococcus flavefaciens and increased the copies of Fibrobacter succinogenes. Microbial community analysis isupplendicated a significant difference in bacterial composition between the two groups. At the phylum level, Bacteroidota and Firmicutes were enriched in the LPH and HPH groups, respectively. At the genus level, the dominant bacteria in the LPH group were Prevotella. Additionally, the LPH group increased the proportions of Gram-negative phenotypes, potentially pathogenic phenotypes and LPS biosynthesis. The close correlation between two key enzymes for LPS synthesis LpxL and LpxM with rumen pH, inflammatory markers, and microorganisms indicates that low pH may increase the risk of inflammation by facilitating the lysis of Gram-negative bacteria and the release of penta-acylated LPS. Penta-acylated and hexa-acylated LPS may be mainly derived from Prevotella and Succinivibrionaceae_UCG-001, respectively.<br><br>DISCUSSION: Overall, these results support the notion that transient low pH could reflect the risk of cows suffering from SARA and associated inflammation and is strongly associated with penta-acylated LPS. Our findings provide new insights into ruminant health improvement and disease prevention strategies.}, }
@article {pmid39611090, year = {2024}, author = {He, X and Zhang, Y}, title = {Changes in gut flora in patients with epilepsy: a systematic review and meta-analysis.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1480022}, pmid = {39611090}, issn = {1664-302X}, abstract = {BACKGROUND: Epilepsy is a prevalent chronic neurological disorder that is strongly associated with a wide range of psychological, cognitive and social problems. It affects a significant proportion of the global population and has a number of complex etiologies. A growing body of research indicates that there is a strong association between epilepsy and the gut microbiota. Indeed, a substantial body of research has investigated the potential role of epilepsy in relation to the gut microbiota, examining alterations in the abundance, diversity, and relative abundance of the gut microbiota in patients with epilepsy.<br><br>METHODS: This study was conducted in accordance with the PRISMA guidelines and included multiple studies that met specific criteria. A keyword search was conducted in the following databases: PubMed, Embase, and Web of Science. The data extraction and quality assessment were conducted by two independent researchers. A systematic review and meta-analysis of the relationship between patients with epilepsy and gut flora was conducted using the R 4.3.4 software.<br><br>RESULTS: The results of the analyses indicated that the intestinal flora of patients with epilepsy did not differ significantly in alpha diversity compared to healthy controls. However, the relative abundance of specific flora, such as Verrucomicrobia and Ackermannia was significantly increased in patients, whereas Lactobacillus was significantly decreased.<br><br>CONCLUSION: The relationship between epilepsy and gut flora is reciprocal. The present meta-analysis demonstrated that there were no statistically significant alterations in the overall characteristics of the intestinal flora of the patients. However, significant changes were observed in the relative abundance of certain phyla and genera. Consequently, it is hypothesized that epilepsy can cause changes in the relative abundance of specific flora in patients. Furthermore, in conjunction with previous studies, it is believed that changes in intestinal flora can also have an effect on seizures. For example, Lactobacillus may be a beneficial genus that potentially reduces seizures. Conversely, the effect of Akkermansia is two-sided.}, }
@article {pmid39610873, year = {2024}, author = {Wu, H and Liu, Y and Han, Y and Liu, B and Chen, S and Ye, Z and Li, J and Xie, L and Wu, X}, title = {Integrated Analysis of Gut Microbiome, Inflammation, and Neuroimaging Features Supports the Role of Microbiome-Gut-Brain Crosstalk in Schizophrenia.}, journal = {Schizophrenia bulletin open}, volume = {5}, number = {1}, pages = {sgae026}, pmid = {39610873}, issn = {2632-7899}, abstract = {BACKGROUND AND HYPOTHESIS: Gut microbiota has been implicated in the pathogenesis of schizophrenia (SZ) and relevant changes in the brain, but the underlying mechanism remains elusive. This study aims to investigate the microbiota-gut-brain crosstalk centered on peripheral inflammation in SZ patients.<br><br>STUDY DESIGN: We recruited a cohort of 182 SZ patients and 120 healthy controls (HC). Multi-omics data, including fecal 16S rRNA, cytokine data, and neuroimaging data, were collected and synthesized for analysis. Multi-omics correlations and mediation analyses were utilized to determine the associations of gut microbiome with inflammatory cytokines and neuroimaging characteristics. Additionally, machine learning models for effective SZ diagnosis were separately generated based on gut microbial and neuroimaging data.<br><br>STUDY RESULTS: Gut microbial dysbiosis, characterized by a decrease in butyrate-producing bacteria and an increase in proinflammatory bacteria, has been identified in SZ patients. These key microbial taxa were associated with increased inflammatory cytokines, potentially through mediating lipid metabolic pathways such as steroid biosynthesis and linoleic acid metabolism. Further analysis revealed altered microbial genera to be correlated with disrupted gray matter volume and regional homogeneity in SZ patients. Importantly, certain inflammatory cytokines mediated the relationship between the SZ-enriched genus Succinivibrio and aberrant activity of anterior cingulate cortex and left inferior temporal gyrus in the SZ group. Moreover, the classification model based on gut microbial data showed comparable efficacy to the model based on brain functional signatures in SZ diagnosis.<br><br>CONCLUSIONS: This study presents evidence for the dysregulated microbiota-gut-brain axis in SZ and emphasizes the central role of peripheral inflammation.}, }
@article {pmid39610787, year = {2024}, author = {Zecha, JAEM and Raber-Durlacher, JE and Brandt, BW and Buijs, MJ and Zaura, E and de Lange, J and Smeele, LE and Laheij, AMGA}, title = {Oral microbial changes, oral mucositis and febrile neutropenia during myelosuppressive chemotherapy in patients diagnosed with a solid tumor or lymphoma.}, journal = {Frontiers in oral health}, volume = {5}, number = {}, pages = {1461463}, pmid = {39610787}, issn = {2673-4842}, abstract = {OBJECTIVES: To evaluate the possible changes of the oral microbiome during myelosuppressive chemotherapy (CT) and to investigate the potential relationship between the oral microbiome, the presence of oral mucositis (OM) and febrile neutropenia (FN).<br><br>METHODS: A prospective, longitudinal, observational study was conducted in patients receiving myelosuppressive CT for a solid tumor or lymphoma. Oral rinsing samples were retrieved before, during and after the start of CT, but also when OM or FN was present. The samples were analyzed using 16S rRNA gene amplicon sequencing and statistical analysis was performed using alpha (Shannon) and beta (PERMANOVA) diversity analyses. Furthermore, differential abundances were analyzed using ALDEx2v1.32.0. Differences between groups were calculated using the Mann Whitney U-test, Kruskal-Wallis test and Wilcoxon Signed Rank using R.<br><br>RESULTS: Forty-six patients, with a mean follow up of 114 days, were included for analysis and a total of 138 oral rinsing samples were available in the CLR-transformed data for PERMANOVA and 137 samples-for alpha diversity calculation. Significant changes in alpha diversity were seen when OM or FN was present. Moreover, significant changes were seen in beta diversity during the course of the CT treatment and when OM was present. Genera showing substantial changes in relative abundance were Streptococcus during the course of CT treatment and Prevotella, Fusobacterium, Selenomonas, Actinomyces and Leptotrichia when OM was present.<br><br>CONCLUSION: Changes in the oral microbiome were observed during the CT-regimen and when OM was present. Furthermore, changes of the oral microbiota during FN episodes were observed; however, larger studies should be performed to substantiate our results.}, }
@article {pmid39610673, year = {2024}, author = {Li, A and Yue, M and Ye, X and Gaietto, K and Wang-Erickson, AF and Chen, W}, title = {Diversity and Meta-Analysis of Microbial Differential Abundance in Nasal Metatranscriptomic Profiles of Asthma.}, journal = {Journal of respiratory biology and translational medicine}, volume = {1}, number = {4}, pages = {}, pmid = {39610673}, issn = {3006-6514}, abstract = {Asthma affects millions worldwide and involves complex genetic, immunological, and environmental factors. The nasal microbiome is increasingly recognized for its role in asthma development, but inconsistent results and small sample sizes have limited a clear understanding. We aimed to clarify the nasal microbiome's role in asthma using large datasets and meta-transcriptomic analysis. RNA-seq data was analyzed from two large public studies: GALA II (694 children of Puerto Rican heritage; 441 asthmatics, 253 controls) and CAAPA (562 individuals of African ancestry; 265 asthmatics, 297 controls). After quality control and host read removal, microbial reads were annotated using Kraken2. α and β diversity analyses compared microbial diversity between asthmatic and control groups. Differential abundance analysis was conducted separately, controlling for age and sex, with results combined via meta-analysis. We found that asthmatic patients exhibited significantly higher α diversity indices (Shannon, Berger-Parker, Inverse Simpson, Fisher's) in nasal microbiota compared to controls in GALA II, with similar trends in CAAPA. β diversity analysis showed significant differences in microbial composition in GALA II data. Differential abundance analysis identified 20 species in GALA II and 9 species in CAAPA significantly associated with asthma. Meta-analysis revealed 11 species significantly associated with asthma, including Mycobacterium_tuberculosis. Our study demonstrates increased nasal microbiome α diversity in asthmatic patients and identifies specific microbial species associated with asthma risk. These findings enhance understanding of asthma pathogenesis from the nasal microbiome perspective and may inform future research and therapeutic strategies.}, }
@article {pmid39610501, year = {2024}, author = {Babu, DD and Mehdi, S and Krishna, KL and Lalitha, MS and Someshwara, CK and Pathak, S and Pesaladinne, UR and Rajashekarappa, RK and Mylaralinga, PS}, title = {Diabetic neuropathy: understanding the nexus of diabetic neuropathy, gut dysbiosis and cognitive impairment.}, journal = {Journal of diabetes and metabolic disorders}, volume = {23}, number = {2}, pages = {1589-1600}, pmid = {39610501}, issn = {2251-6581}, abstract = {OBJECTIVES: Diabetic neuropathy is a traditional and one of the most prevalent complications of diabetes mellitus. The exact pathophysiology of diabetic neuropathy is not fully understood. However, oxidative stress and inflammation are proven to be one of the major underlying mechanisms of neuropathy which is described in detail. Gut dysbiosis is being studied for various neurological disorders and its impact on diabetic neuropathy is also explained. Diabetic neuropathy also causes loss in an individual's quality of life and one such adverse event is cognitive dysfunction. The interrelation between the neuropathy, cognitive dysfunction and gut is reviewed.<br><br>METHODS: The exact mechanism is not understood but several hypotheses, cross-sectional studies and systematic reviews suggest a relationship between cognition and neuropathy. The review has collected data from various review and research publications that justifies this inter-relationship.<br><br>RESULTS: The multifactorial etiology and pathophysiology of diabetic neuropathy is described with special emphasis on the role of gut dysbiosis. There might exist a correlation between the neuropathy and cognitive impairment caused simultaneously in diabetic patients.<br><br>CONCLUSIONS: This review summarizes the relationship that might exist between diabetic neuropathy, cognitive dysfunction and the impact of disturbed gut microbiome on its development and progression.}, }
@article {pmid39610253, year = {2024}, author = {Li, D and Wan, M and Xue, L and Zhang, Z and Qiu, Y and Mei, F and Tang, N and Yu, C and Yu, Y and Chen, T and Ding, X and Yang, Q and Liu, Q and Gu, P and Jia, W and Chen, Y and Chen, P}, title = {Zinc promotes microbial p-coumaric acid production that protects against cholestatic liver injury.}, journal = {Cell host &amp; microbe}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.chom.2024.11.002}, pmid = {39610253}, issn = {1934-6069}, abstract = {Cholestatic liver disease (CLD) is a common liver disorder with limited treatment options. Here, we demonstrate that zinc (Zn) supplementation can alter the gut microbiome to mitigate cholestatic liver injury. Oral Zn altered the microbiota of mice and humans (this study was registered at clinicaltrials.gov [NCT05597137]), increasing the abundance of Blautia producta (B. producta) and promoting the generation of p-coumaric acid. Additionally, p-coumaric acid concentrations were negatively correlated with liver injury parameters in CLD patients. In mice, the protective effects of Zn were partially mediated by p-coumaric acid, which directly bound to nicotinamide adenine dinucleotide phosphate (NADPH) oxidase 2 (NOX2) and suppressed the production of reactive oxygen species (ROS) in hepatocytes, thus preventing hepatocyte cell death and liver damage. Additionally, knocking out the histidine ammonia-lyase, which catalyzes the conversion of tyrosine to p-coumaric acid in B. producta, blunted the protective effects of Zn. These findings highlight a host-microbiota interaction that is stimulated by Zn supplementation, providing potential benefits for CLD.}, }
@article {pmid39610133, year = {2024}, author = {Wang, X and Sun, Q}, title = {Ultra-Processed Foods and the Impact on Cardiometabolic Health: The Role of Diet Quality.}, journal = {Diabetes &amp; metabolism journal}, volume = {48}, number = {6}, pages = {1047-1055}, doi = {10.4093/dmj.2024.0659}, pmid = {39610133}, issn = {2233-6087}, support = {UM1 CA186107/NH/NIH HHS/United States ; U01 CA176726/NH/NIH HHS/United States ; U01 CA167552/NH/NIH HHS/United States ; P01 CA87969/NH/NIH HHS/United States ; R01 HL034594/NH/NIH HHS/United States ; R01 HL035464/NH/NIH HHS/United States ; R01 HL60712/NH/NIH HHS/United States ; R01 DK120870/NH/NIH HHS/United States ; R01 DK126698/NH/NIH HHS/United States ; R01 DK119268/NH/NIH HHS/United States ; U2C DK129670/NH/NIH HHS/United States ; DK119268/NH/NIH HHS/United States ; R01 ES022981/NH/NIH HHS/United States ; R21 AG070375/NH/NIH HHS/United States ; }, mesh = {Humans ; *Fast Foods/adverse effects ; *Nutritive Value ; *Food Handling ; *Diet ; Gastrointestinal Microbiome ; Cardiovascular Diseases/etiology/prevention &amp; control ; Diet, Healthy ; Food, Processed ; }, abstract = {The consumption of ultra-processed foods (UPFs) has surged globally, raising significant public health concerns due to their associations with a range of adverse health outcomes. This review aims to elucidate potential health impacts of UPF intake and underscore the importance of considering diet quality when interpreting study findings. UPF group, as classified by the Nova system based on the extent of industrial processing, contains numerous individual food items with a wide spectrum of nutrient profiles, as well as differential quality as reflected by their potential health effects. The quality of a given food may well misalign with the processing levels so that a UPF food can be nutritious and healthful whereas a non-UPF food can be of low quality and excess intake of which may lead to adverse health consequences. The current review argues that it is critical to focus on the nutritional content and quality of foods and their role within the overall dietary pattern rather than only the level of processing. Further research should dissect health effects of diet quality and food processing, investigate the health impacts of ingredients that render the UPF categorization, understand roles of metabolomics and the gut microbiome in mediating and modulating the health effects of food processing, and consider environmental sustainability in UPF studies. Emphasizing nutrient-dense healthful foods and dietary patterns shall remain the pivotal strategy for promoting overall health and preventing chronic diseases.}, }
@article {pmid39610111, year = {2024}, author = {Zancarini, A and Le Signor, C and Terrat, S and Aubert, J and Salon, C and Munier-Jolain, N and Mougel, C}, title = {Medicago truncatula genotype drives the plant nutritional strategy and its associated rhizosphere bacterial communities.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.20272}, pmid = {39610111}, issn = {1469-8137}, support = {P10061//Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement/ ; 089201PPO24S00901//Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement/ ; //R&#xe9;gion Bourgogne/ ; }, abstract = {Harnessing the plant microbiome through plant genetics is of increasing interest to those seeking to improve plant nutrition and health. While genome-wide association studies (GWAS) have been conducted to identify plant genes driving the plant microbiome, more multidisciplinary studies are required to assess the relationships among plant genetics, plant microbiome and plant fitness. Using a metabarcoding approach, we characterized the rhizosphere bacterial communities of a core collection of 155 Medicago truncatula genotypes along with the plant phenotype and investigated the plant genetic effects through GWAS. The different genotypes within the M. truncatula core collection showed contrasting growth and nutritional strategies but few loci were associated with these ecophysiological traits. To go further, we described its associated rhizosphere bacterial communities, dominated by Proteobacteria, Actinobacteria and Bacteroidetes, and defined a core rhizosphere bacterial community. Next, the occurrences of bacterial candidates predicting plant ecophysiological traits of interest were identified using random forest analyses. Some of them were heritable and plant loci were identified, pinpointing genes related to response to hormone stimulus, systemic acquired resistance, response to stress, nutrient starvation or transport, and root development. Together, these results suggest that plant genetics can affect plant growth and nutritional strategies by harnessing keystone bacteria in a well-connected interaction network.}, }
@article {pmid39609882, year = {2024}, author = {Cloarec, LA and Bacchetta, T and Bruto, M and Leboulanger, C and Grossi, V and Brochier-Armanet, C and Flandrois, JP and Zurmely, A and Bernard, C and Troussellier, M and Agogué, H and Ader, M and Oger-Desfeux, C and Oger, PM and Vigneron, A and Hugoni, M}, title = {Lineage-dependent partitioning of activities in chemoclines defines Woesearchaeota ecotypes in an extreme aquatic ecosystem.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {249}, pmid = {39609882}, issn = {2049-2618}, mesh = {*Archaea/classification/genetics/metabolism ; *Lakes/microbiology ; *Phylogeny ; *Ecotype ; Ecosystem ; Metagenomics ; Microbiota ; Genome, Archaeal ; Water Microbiology ; Biodiversity ; }, abstract = {BACKGROUND: DPANN archaea, including Woesearchaeota, encompass a large fraction of the archaeal diversity, yet their genomic diversity, lifestyle, and role in natural microbiomes remain elusive. With an archaeal assemblage naturally enriched in Woesearchaeota and steep vertical geochemical gradients, Lake Dziani Dzaha (Mayotte) provides an ideal model to decipher their in-situ activity and ecology.<br><br>RESULTS: Using genome-resolved metagenomics and phylogenomics, we identified highly diversified Woesearchaeota populations and defined novel halophilic clades. Depth distribution of these populations in the water column showed an unusual double peak of abundance, located at two distinct chemoclines that are hotspots of microbial diversity in the water column. Genome-centric metatranscriptomics confirmed this vertical distribution and revealed a fermentative activity, with acetate and lactate as end products, and active cell-to-cell processes, supporting strong interactions with other community members at chemoclines. Our results also revealed distinct Woesearchaeota ecotypes, with different transcriptional patterns, contrasted lifestyles, and ecological strategies, depending on environmental/host conditions.<br><br>CONCLUSIONS: This work provides novel insights into Woesearchaeota in situ activity and metabolism, revealing invariant, bimodal, and adaptative lifestyles among halophilic Woesearchaeota. This challenges our precepts of an invariable host-dependent metabolism for all the members of this taxa and revises our understanding of their contributions to ecosystem functioning and microbiome assemblage. Video Abstract.}, }
@article {pmid39609876, year = {2024}, author = {Ren, Y and Huang, P and Zhang, L and Tang, Y and He, S and Li, H and Huang, X and Ding, Y and Liu, L and Liu, L and He, X}, title = {Multi-omics landscape of childhood simple obesity: novel insights into pathogenesis and biomarkers discovery.}, journal = {Cell &amp; bioscience}, volume = {14}, number = {1}, pages = {145}, pmid = {39609876}, issn = {2045-3701}, support = {820MS168//Hainan Provincial Natural Science Foundation of China/ ; 822RC871//Hainan Provincial Natural Science Foundation of China/ ; 820QN413//Hainan Provincial Natural Science Foundation of China/ ; 20A200345//Key Research and Development Project of Hainan Province/ ; 2023SK4018//the Science and Technology Program of Hunan Province/ ; 2024ZZTS0161//Fundamental Research Funds for the Center Universities of Central South University/ ; 2024JJ8249//Department Joint Fund of Hunan Province/ ; WSJK2024MS237//Hainan Province Health Science and Technology Innovation Joint Project/ ; QRCBT202121//Hainan Province Clinical Medical Center, the Excellent Talent Team of Hainan Province/ ; }, abstract = {BACKGROUND: The increasing incidence of childhood obesity annually has led to a surge in physical and mental health risks, making it a significant global public health concern. This study aimed to discover novel biomarkers of childhood simple obesity through integrative multi-omics analysis, uncovering their potential connections and providing fresh research directions for the complex pathogenesis and treatment strategies.<br><br>METHODS: Transcriptome, untargeted metabolome, and 16&#xa0;S rDNA sequencing were conducted on subjects to examine transcripts, metabolites in blood, and gut microflora in stool.<br><br>RESULTS: Transcriptomic analysis identified 599 differentially expressed genes (DEGs), of which 25 were immune-related genes, and participated in immune pathways such as antimicrobial peptides, neutrophil degranulation, and interferons. The optimal random forest model based on these genes exhibited an AUC of 0.844. The metabolomic analysis examined 71 differentially expressed metabolites (DEMs), including 12 immune-related metabolites. Notably, lauric acid showed an extremely strong positive correlation with BMI and showed a good discriminative power for obesity (AUC&#x2009;=&#x2009;0.82). DEMs were found to be significantly enriched in four metabolic pathways, namely "Aminoacyl-tRNA biosynthesis", "Valine leucine and isoleucine biosynthesis, and Glycine", "Serine and threonine metabolism", and "Biosynthesis of unsaturated fatty acids". Microbiome analysis revealed 12 differential gut microbiotas (DGMs) at the phylum and genus levels, with p_Firmicutes dominating in the obese group and g_Escherichia-Shigella in the normal group. Subsequently, a Random Forest model was developed based on the DEMs, immune-related DEGs, and metabolites with an AUC value of 0.912. The 14 indicators identified by this model could potentially serve as a set of biomarkers for obesity. The analysis of the inter-omics correlation network found 233 pairs of significant correlations. DEGs BPIFA1, BPI, and SAA1, DEMs Dimethy(tetradecyl)amine, Deoxycholic acid, Pathalic anhydride, and DL-Alanine, and DGMs g_Intestinimonas and g_Turicibacter showed strong connectivity within the network, constituting a large proportion of interactions.<br><br>CONCLUSION: This study presents the first comprehensive description of the multi-omics characteristics of childhood simple obesity, recognizing promising biomarkers. Immune-related markers offer a new perspective for researching the immunological mechanisms underlying obesity and its associated complications. The revealed interactions among these biomarkers contribute to a deeper understanding the intricate biological regulatory networks associated with obesity.}, }
@article {pmid39609794, year = {2024}, author = {Zheng, R and Xiang, X and Shi, Y and Xie, J and Xing, L and Zhang, T and Zhou, Z and Zhang, D}, title = {Gut microbiota and mycobiota change with feeding duration in mice on a high-fat and high-fructose diet.}, journal = {BMC microbiology}, volume = {24}, number = {1}, pages = {504}, pmid = {39609794}, issn = {1471-2180}, support = {kh2301027//Changsha Major Science and Technology Project/ ; 82070884//National Natural Science Foundation of China/ ; 2024JJ5550//Natural Science Foundation of Hunan Province/ ; DKME202213//Key laboratory of diabetes immunology, ministry of education/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; Male ; *Diet, High-Fat/adverse effects ; *Mice, Inbred C57BL ; Mice ; *Fructose/administration &amp; dosage/adverse effects ; *Bacteria/classification/isolation &amp; purification/genetics ; *Non-alcoholic Fatty Liver Disease/microbiology/etiology ; Fungi/classification/isolation &amp; purification/genetics ; Colon/microbiology ; }, abstract = {BACKGROUND: Metabolic dysfunction-associated fatty liver disease (MAFLD), formerly known as nonalcoholic fatty liver disease (NAFLD), is becoming the most common chronic liver disease. The gut microbiome is regarded to play a crucial role in MAFLD, but the specific changes of gut microbiome, especially fungi, in different stages of MAFLD are not well understood. This study aimed to observe the longitudinal changes of colon bacteria and fungi of mice at different feeding duration of a high-fat and high-fructose diet (HFHFD), and explore the association between the changes and the progression of MAFLD.<br><br>METHODS: Twenty-eight male C57BL6J mice were randomly assigned to the normal diet (ND) group and HFHFD group. At the 8th and 16th weeks, mice were sacrificed to compare the diversity, composition, and co-abundance network of bacteria and fungi in colon contents among groups.<br><br>RESULTS: HFHFD-8W mice exhibited increases in Candida and Dorea, and decreases in Oscillospira and Prevotella in comparison to ND-8W mice, HFHFD-16W mice had increases in Bacteroides, Candida, Desulfovibrio, Dorea, Lactobacillus, and Rhodotorula, and decreases in Akkermansia, Aspergillus, Sterigmatomyces, and Vishniacozyma in comparison to ND-16W mice. And compared to HFHFD-8W mice, HFHFD-16W mice had increases in Desulfovibrio, Lactobacillus, Penicillium, and Rhodotorula, and decreases in Talaromyces and Wallemia. Spearman and GEE correlation analysis revealed that Bacteroides, Candida, Desulfovibrio, and Lactobacillus positively correlated with NAFLD activity score (NAS).<br><br>CONCLUSION: Gut microbiota and mycobiota undergo diverse changes at different stages of MAFLD.<br><br>CLINICAL TRIAL NUMBER: Not applicable.}, }
@article {pmid39609616, year = {2024}, author = {Kim, M and Parrish, RC and Tisza, MJ and Shah, VS and Tran, T and Ross, M and Cormier, J and Baig, A and Huang, CY and Brenner, L and Neuringer, I and Whiteson, K and Harris, JK and Willis, AD and Lai, PS}, title = {Host DNA depletion on frozen human respiratory samples enables successful metagenomic sequencing for microbiome studies.}, journal = {Communications biology}, volume = {7}, number = {1}, pages = {1590}, pmid = {39609616}, issn = {2399-3642}, support = {R21 AI175965/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; *Metagenomics/methods ; *Microbiota/genetics ; *Sputum/microbiology ; *Cystic Fibrosis/microbiology ; Bronchoalveolar Lavage Fluid/microbiology ; Freezing ; Adult ; Cryopreservation ; Female ; High-Throughput Nucleotide Sequencing/methods ; Bacteria/genetics/isolation &amp; purification/classification ; Sequence Analysis, DNA/methods ; Male ; Respiratory System/microbiology ; }, abstract = {Most respiratory microbiome studies use amplicon sequencing due to high host DNA. Metagenomics sequencing offers finer taxonomic resolution, phage assessment, and functional characterization. We evaluated five host DNA depletion methods on frozen nasal swabs from healthy adults, sputum from people with cystic fibrosis (pwCF), and bronchoalveolar lavage (BAL) from critically ill patients. Median sequencing depth was 76.4 million reads per sample. Untreated nasal, sputum, and BAL had 94.1%, 99.2%, and 99.7% host reads, respectively. Host depletion effects varied by sample type, generally increasing microbial reads, species and functional richness; this was mediated by higher effective sequencing depth. Rarefaction curves showed species richness saturation at 0.5-2 million microbial reads. Most methods did not change Morisita-Horn dissimilarity for BAL and nasal samples although the proportion of gram-negative bacteria decreased for sputum from pwCF. Freezing did not affect the viability of Staphylococcus aureus but reduced the viability of Pseudomonas aeruginosa and Enterobacter spp.; this was mitigated by adding a cryoprotectant. QIAamp-based host depletion minimally impacted gram-negative viability even in non-cryoprotected frozen isolates. While some host depletion methods may shift microbial composition, metagenomics sequencing without host depletion severely underestimates microbial diversity of respiratory samples due to shallow effective sequencing depth and is not recommended.}, }
@article {pmid39609496, year = {2024}, author = {Ahmad, W and Coffman, L and Ray, RL and Balan, V and Weerasooriya, A and Khan, AL}, title = {Microbiome diversity and variations in industrial hemp genotypes.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {29560}, pmid = {39609496}, issn = {2045-2322}, mesh = {*Cannabis/microbiology/genetics ; *Microbiota/genetics ; *Genotype ; *Bacteria/genetics/classification ; *Rhizosphere ; *Fungi/genetics/classification ; Soil Microbiology ; Plant Roots/microbiology ; Biodiversity ; Endophytes/genetics ; Cannabidiol ; Plant Leaves/microbiology ; }, abstract = {Microbes like bacteria and fungi are crucial for host plant growth and development. However, environmental factors and host genotypes can influence microbiome composition and diversity in plants such as industrial hemp (Cannabis sativa L.). Herein, we evaluated the endophytic and rhizosphere microbial communities of two cannabidiol (CBD; Sweet Sensi and Cherry Wine) and two fibers (American Victory and Unknown). The four hemp varieties showed significant variations in microbiome diversity. The roots had significantly abundant fungal and bacterial endophyte diversity indices, whereas the stem had higher fungal than bacterial diversity. Interestingly, the soil system showed no significant diversity variation across CBD vs. fiber genotypes. In fungal phyla, Ascomycota and Basidiomycota were significantly more abundant in roots and stems than leaves in CBD-rich genotypes compared to fiber-rich genotypes. The highly abundant bacterial phyla were Proteobacteria, Acidobacteria, and Actinobacteria. We found 16 and 11 core-microbiome bacterial and fungal species across genotypes. Sphingomonas, Pseudomonas, and Bacillus were the core bacteria of fiber genotypes with high abundance compared to CBD genotypes. Contrarily, Microbacterium, and Rhizobium were significantly higher in CBD than fiber. The Alternaria and Gibberella formed a core-fungal microbiome of fiber-genotype than CBD. Contrarily, Penicillium, and Nigrospora were significantly more abundant in CBD than fiber genotypes. In conclusion, specific hemp genotypes recruit specialized microbial communities in the rhizosphere and phyllosphere. Utilizing the core-microbiome species can help to maintain and improve the growth of hemp plants and to target specialized traits of the genotype.}, }
@article {pmid39609243, year = {2024}, author = {Komeya, M and Lundy, SD}, title = {Microbiome-based Therapeutics: Cutting-edge Innovation.}, journal = {European urology focus}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.euf.2024.10.011}, pmid = {39609243}, issn = {2405-4569}, abstract = {From bacillus Calmette-Guérin to cutting-edge research, the microbiome has played an integral role in urology treatments and will continue to do so for many generations to come.}, }
@article {pmid39609102, year = {2024}, author = {Li, W and Liu, Y and Zheng, X and Han, J and Shi, A and Wong, CC and Wang, R and Jing, X and Li, Y and Fan, S and Zhang, C and Chen, Y and Guo, G and Yu, J and She, J}, title = {Rewiring Tryptophan Metabolism via Programmable Probiotic Integrated by Dual-Layered Microcapsule Protects against Inflammatory Bowel Disease in Mice.}, journal = {ACS nano}, volume = {}, number = {}, pages = {}, doi = {10.1021/acsnano.4c12801}, pmid = {39609102}, issn = {1936-086X}, abstract = {Intestinal dysbiosis and the associated l-tryptophan metabolic disorder are pivotal in inflammatory bowel disease progression, leading to a compromised intestinal barrier integrity. Remedying the dysfunction in tryptophan metabolism has emerged as a promising therapeutic strategy. Herein, we reprogram the tryptophan metabolism in situ by EcN-TRP@A/G, encapsulating the engineered probiotic, EcN-TRP, with enhanced tryptophan synthesis capacity, for sustained modulation, thereby restoring intestinal barrier function and microbial homeostasis. The pH-responsive dual-layered EcN-TRP@A/G microcapsule developed via high-voltage electrospraying and liquid interface self-assembly, preserved probiotic viability in the harsh gastrointestinal milieu, and facilitated targeted colon release. Bioluminescent tracking in mice reveals a 22.84-fold increase in EcN-TRP@A/G viability and distribution compared to naked EcN-TRP. Targeted metabolomics highlights EcN-TRP@A/G's modulation of the tryptophan-indole pathway. Oral administration of EcN-TRP@A/G sustained elevates indole metabolites, particularly indole-3-acetic acid and indole-3-propionic acid, in colon tissue for up to 7 days. In IBD mice, EcN-TRP@A/G improves intestinal permeability, reduces inflammation, and recovers the gut microbiome by enhancing beneficial bacteria abundance like Prevotellaceae_UCG-001 and Anaerostipes while suppressing pathogenic strains like Escherichia-Shigella. Our findings offer a cost-effective approach, harnessing the probiotic metabolic potential in situ through engineered modifications for effective IBD treatment.}, }
@article {pmid39608999, year = {2024}, author = {Climacosa, FMM and Anlacan, VMM and Gordovez, FJA and Reyes, JCB and Tabios, IKB and Manalo, RVM and Cruz, JMC and Asis, JLB and Razal, RB and Abaca, MJM and Dacasin, AB and Espiritu, APN and Gapaz, NCLL and Lee Yu, MHL}, title = {Monitoring drug Efficacy through Multi-Omics Research initiative in Alzheimer's Disease (MEMORI-AD): A protocol for a multisite exploratory prospective cohort study on the drug response-related clinical, genetic, microbial and metabolomic signatures in Filipino patients with Alzheimer's disease.}, journal = {BMJ open}, volume = {14}, number = {11}, pages = {e078660}, doi = {10.1136/bmjopen-2023-078660}, pmid = {39608999}, issn = {2044-6055}, mesh = {Humans ; *Alzheimer Disease/drug therapy/genetics ; Philippines ; Prospective Studies ; Aged ; Cholinesterase Inhibitors/therapeutic use ; Rivastigmine/therapeutic use ; Donepezil/therapeutic use ; Cross-Sectional Studies ; Memantine/therapeutic use ; Male ; Female ; Metabolomics ; Gastrointestinal Microbiome/drug effects ; Multiomics ; }, abstract = {INTRODUCTION: Dementia is one of the leading causes of disability among older people aged 60 years and above, with majority eventually being diagnosed with Alzheimer's disease (AD). Pharmacological agents approved for dementia include acetylcholinesterase enzyme (AChE) inhibitors like rivastigmine, donepezil and galantamine and the N-methyl-D-aspartate (NMDA) receptor antagonist memantine, prescribed as monotherapy or in combination with each other, depending on the severity of disease. There is currently no available study demonstrating the clinical response to these drugs for AD in the Filipino population. Hence, this protocol aims to characterise the clinical, genetic, microbial and metabolic factors associated with drug responses to donepezil, rivastigmine and/or memantine for AD in a cohort of Filipinos with late-onset AD.<br><br>METHODS AND ANALYSIS: This protocol involves a multisite descriptive study that will use two study designs: (1) a descriptive, cross-sectional study to characterise the clinical profile of Filipino dementia patients with AD and (2) an exploratory prospective cohort study to investigate drug response-related genetic, gut microbiome and metabolome signatures of a subset of the recruited AD patients. At least 153 patients with mild or moderate AD aged 65 years old and above will be recruited regardless of their treatment status. A subset of these patients (n=60) who meet inclusion and exclusion criteria will be included further in the exploratory cohort study. These patients will be grouped according to their baseline medications and will be observed for treatment response in 6 months. The cognitive, functional and behavioural domains of patients and levels of functioning will be measured using different assessment tools. Drug responses of Filipino patients will then be investigated employing multi-omics technology to characterise genetic variations via whole exome sequencing, gut microbiome profile via shotgun metagenomic sequencing and metabolome profile via liquid chromatography with mass spectrometry.<br><br>ETHICS AND DISSEMINATION: The study has received ethical clearance from the Department of Health Single Joint Research Ethics Board (SJREB-2022-15). Results of psychometric scales will be made available to enrolled patients. The study results will be presented at national/international conferences and published in international peer-reviewed scientific journals, and summaries of the results will be provided to the study funders and institutional review boards of the three tertiary referral hospitals.<br><br>TRIAL REGISTRATION NUMBER: Philippine Health Research Registry ID PHRR230220-0054116; ClinicalTrials.gov ID NCT05801380.}, }
@article {pmid39608384, year = {2024}, author = {Gopal, RK and Sankar Ganesh, P and Pathoor, NN and Viswanathan, A}, title = {Enhancing microbiome-based biomarkers: challenges and opportunities.}, journal = {The Lancet. Microbe}, volume = {}, number = {}, pages = {101032}, doi = {10.1016/j.lanmic.2024.101032}, pmid = {39608384}, issn = {2666-5247}, }
@article {pmid39608378, year = {2024}, author = {Hussain, A and Koser, N and Aun, SM and Siddiqui, MF and Malik, S and Ali, SA}, title = {Deciphering the role of probiotics in mental health: a systematic literature review of psychobiotics.}, journal = {Beneficial microbes}, volume = {}, number = {}, pages = {1-22}, doi = {10.1163/18762891-bja00053}, pmid = {39608378}, issn = {1876-2891}, abstract = {Probiotics are live microorganisms that, when administered in adequate amounts, confer a health benefit to the host. The selection criteria for probiotics include strain safety, viability, tolerance, metabolite production and/or the ability to modulate the immune system. Probiotics are commonly used in industries, such as food, agriculture, medicine, biotechnology, pharmaceuticals, and aquaculture. Recently, the medicinal applications of probiotics have gained attention and are being explored for the prevention and treatment of various diseases. One emerging area of interest is their potential role in psychological disorders. Mental illnesses, characterised by disturbances in behaviour, mood, thinking, and emotions, affect over one billion people globally. While various preventive and treatment options for mental disorders exists, each is associated with certain limitations. A new avenue being explored is the gut-brain axis, a complex bi-directional communication between the gut and the brain, that is facilitated by hormonal, neuronal, humoral, and immunological pathways. This system plays an important role in mental health. Probiotics, as a key modulator of the gut microbiome, could play a vital role in this communication. However, the underlying mechanisms remain to be explored. Probiotics may act through the production of metabolites and neuroactive substances, as well as through immunomodulation and cytokine production. Current data shows promising effects on stress, mood, and depression, presenting probiotics as a potential natural treatment option for psychological disorders. Nevertheless, major limitations in the existing research include insufficient clinical outcomes, limited sample sizes, and variable dosing. Future advancements may be achieved through stratifications based on gut microbiota, the use of next-generation probiotic strains, and the conduct of comprehensive validation studies.}, }
@article {pmid39608339, year = {2024}, author = {Gu, Y and Jiao, J and Xu, H and Chen, Y and He, X and Wu, X and Wang, J and Chen, X and He, H and Yan, W}, title = {Intercropping improves the yield by increasing nutrient metabolism capacity and crucial microbial abundance in root of Camellia oleifera in purple soil.}, journal = {Plant physiology and biochemistry : PPB}, volume = {219}, number = {}, pages = {109318}, doi = {10.1016/j.plaphy.2024.109318}, pmid = {39608339}, issn = {1873-2690}, abstract = {Intercropping system influences the endophytic microbial abundance, hormone balance, nutrient metabolism and yield, but the molecular mechanism of yield advantage in Camellia oleifera intercropping with peanut is not clear. In this study, the C. oleifera monoculture (CK) and C. oleifera-peanut intercropping (CP) treatments in purple soil were conducted, and the physicochemical properties, gene expressions, signal pathways and crucial microbial abundances were investigated to reveal the molecular mechanism of the yield advantage of intercropped C. oleifera. The results showed that the intercropping system increased in contents of pigment, carbohydrate, available nitrogen and phosphorus in leaf and root, as well as the abundances of Burkholderia, Ralstonia, Delftia, Pseudoalteromonas and Caulobacter, enhanced the relative expression levels of CoSPS, CoGBE, CoGlgP, CoGBSS/GlgA genes to promote sugar metabolism, decreased the relative expression levels of CoASA, CoTSB, CoPAI, CoTDC and CoCYP71A13 genes for inhibiting IAA biosynthesis and signal transduction, as well as microbial diversity, Fusarium, Albifimbria and Coniosporium abundances in root, ultimately improved the fruit yield of C. oleifera. These findings indicate that intercropping system improves the fruit yield by enhancing the nutrient metabolism capability and crucial microbial abundances in root of C. oleifera in purple soil.}, }
@article {pmid39608222, year = {2024}, author = {Padilha, MDM and Melo, FTV and Laurentino, RV and da Silva, ANMR and Feitosa, RNM}, title = {Dysregulation in the microbiota by HBV and HCV infection induces an altered cytokine profile in the pathobiome of infection.}, journal = {The Brazilian journal of infectious diseases : an official publication of the Brazilian Society of Infectious Diseases}, volume = {29}, number = {1}, pages = {104468}, doi = {10.1016/j.bjid.2024.104468}, pmid = {39608222}, issn = {1678-4391}, abstract = {Viral hepatitis is a public health problem, about 1 million people die due to complications of this viral disease, the etiological agents responsible for inducing cirrhosis and cellular hepatocarcinoma are HBV and HCV, both hepatotropic viruses that cause asymptomatic infection in most cases. The regulation of the microbiota performs many physiological functions, which can induce normal intestinal function and produce essential nutrients for the human body. Metabolites derived from gut microbiota or direct regulation of host immunity and metabolism have been reported to profoundly affect tumorigenesis in liver disease. If the microbiota is unbalanced, both exogenous and symbiotic microorganisms can affect a pathological process. It is well understood that the microbiota plays a role in viral diseases and infections, specifically the hepatic portal pathway has been linked to the gut-liver axis. In HBV and HCV infections, the altered bacterial representatives undergo a state of dysbiosis, with subsequent establishment of the pathobiome with overexpression of taxons such as Bacteroides, Clostridium, Lactobacillus, Enterobacter, and Enterococcus. This dysregulated microbiome induces a microenvironment conducive to the development of hepatic complications in patients with acute and chronic HBV and HCV infection, with subsequent dysregulation of cytokines IFN-α/β, TNF-α, IL-1β, TGF-β, IL-6 and IL-10, which alter the dysfunction and damage of the hepatic portal system. In view of the above, this review aimed to correlate the pathophysiological mechanisms in HBV and HCV infection, the dysregulation of the microbiome in patients infected with HBV and HCV, the most altered cytokines in the microbiome, and the most altered bacterial representatives in the pathobiome of infection.}, }
@article {pmid39608199, year = {2024}, author = {Bhat, AH and Malik, IM and Tak, H and Ganai, BA and Bharti, P}, title = {Host, parasite, and microbiome interaction: Trichuris ovis and its effect on sheep gut microbiota.}, journal = {Veterinary parasitology}, volume = {333}, number = {}, pages = {110356}, doi = {10.1016/j.vetpar.2024.110356}, pmid = {39608199}, issn = {1873-2550}, abstract = {Sheep that are infected with gastrointestinal helminths experience a significant impact on their health and productivity. Among the helminths, nematodes like Haemonchus contortus, Oesophagostomum spp., Bunostomum trigonocephalum, Nematodirus battus, Trichostrongylus spp. and Teladorsagia circumcincta are particularly pathogenic. Understanding the interactions among parasites, hosts, and their microbiomes is crucial in developing new approaches in the management of parasites. This study examines the bacterial profile of Trichuris ovis, a highly prevalent nematode among Kashmir Merino sheep, and the influence of nematode infection on the caecal microbiome of its host. Sheep were selected based on T. ovis infection status, and samples were collected from infected and non-infected caecum. The 16S rRNA metagenomic analysis revealed distinct microbial communities in T. ovis, infected caecum, and non-infected caecum. Proteobacteria dominated the T. ovis microbiome, while infected caecum was rich in Bacteroidota and Spirochaetota, and non-infected caecum had a higher proportion of Firmicutes and Verrucomicrobiota. At the genus level, T. ovis was predominantly associated with Escherichia/Shigella, while infected caecum had higher proportions of Bacteroides, Prevotella, and Treponema. Non-infected caecum was characterized by WCHB1-41, Prevotella, and Succiniclasticum like genera. Alpha and beta diversity indicated significant differences in microbiome among the groups, with higher diversity observed in infected caecum. The study found T. ovis infection significantly alters the caecal microbiome of sheep, introducing potentially pathogenic bacteria and reducing beneficial ones. These findings underscore the complex relationship between host, parasite, and microbiome, highlighting the need for comprehensive strategies to manage helminth infections and their broader ecological impacts.}, }
@article {pmid39607975, year = {2024}, author = {Abbasi, AM and Nasir, S and Bajwa, AA and Akbar, H and Ali, MM and Rashid, MI}, title = {A comparative study of the microbiomes of the ticks Rhipicephalus microplus and Hyalomma anatolicum.}, journal = {Parasite (Paris, France)}, volume = {31}, number = {}, pages = {74}, pmid = {39607975}, issn = {1776-1042}, support = {HEC-GCF-273//Higher Education Commission, Pakistan/ ; }, mesh = {Animals ; *Rhipicephalus/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Ixodidae/microbiology ; *Microbiota ; Pakistan ; Phylogeny ; Symbiosis ; Female ; Gastrointestinal Microbiome ; Coxiella/genetics/isolation &amp; purification/classification ; Bacteria/classification/genetics/isolation &amp; purification ; }, abstract = {Hyalomma anatolicum and Rhipicephalus microplus are tick species that are important vectors of numerous pathogens affecting both humans and livestock. Endosymbionts, such as Coxiella-like endosymbionts (CLE), Francisella-like endosymbionts (FLE), and Candidatus Midichloria, play a crucial role in the physiology and vector competence of these ticks. In this study, we investigated the microbial composition of H. anatolicum and R. microplus from four geographically distinct regions of Pakistan to assess whether environmental differences influence their microbiomes. We analyzed the ticks' gut microbiome targeting the V3-V4 hypervariable region of 16S rRNA for Illumina 16S metagenome NGS sequencing and processed overall 144 ticks. Analysis of gut bacterial composition resulted in observation of 1200 R. microplus and 968 H. anatolicum unique amplicon sequencing variants (ASVs). Relative abundance, Alpha diversity (Shannon, Faith's phylogenetic distance) and beta diversity metrics (Bray-Curtis, Jaccard and UniFrac) were analyzed and revealed that H. anatolicum ticks have significantly unique and diverse microbial communities with Acinetobacter indicus and Francisella-like endosymbionts dominating as opposed to Candidatus Midichloria. Rhipicephalus microplus exhibited results consistent with the previous studies with no major changes in microbiome including Coxiella-like endosymbionts as the major contributor. These findings suggest that geographical and environmental factors play a significant role in shaping the tick microbiome, with potential consequences for disease transmission and tick survivability. Further research is needed to elucidate the functional roles of these microbial shifts and their impact on public health and livestock in affected regions.}, }
@article {pmid39607793, year = {2024}, author = {Özdemir, A and Buyuktuncer, Z}, title = {Dietary legumes and gut microbiome: a comprehensive review.}, journal = {Critical reviews in food science and nutrition}, volume = {}, number = {}, pages = {1-15}, doi = {10.1080/10408398.2024.2434725}, pmid = {39607793}, issn = {1549-7852}, abstract = {The gut microbiome plays a crucial role in human health, affecting metabolic, immune, and cognitive functions. While the impact of various dietary components on the microbiome is well-studied, the effect of legumes remains less explored. This review examines the influence of legume consumption on gut microbiome composition, diversity, and metabolite production, based on 10 human and 21 animal studies. Human studies showed mixed results, with some showing increased microbial diversity and others finding no significant changes. However, legume consumption was linked to increases in beneficial bacteria like Bifidobacterium and Faecalibacterium. Animal studies generally indicated enhanced microbial diversity and composition changes, though these varied by legume type and the host's health. Some studies highlighted legume-induced shifts in bacteria associated with better metabolic health. Overall, the review emphasizes the complexity of legume-microbiome interactions and the need for standardized methodologies and longitudinal studies. While legumes have the potential to positively affect the gut microbiome, the effects are nuanced and depend on context. Future research should investigate the long-term impacts of legume consumption on microbiome stability and its broader health implications, particularly for disease prevention and dietary strategies.}, }
@article {pmid39607629, year = {2024}, author = {Chua, HC and Pham, S and Lombardi, DA and Hot, E and Mody, L}, title = {Patient Satisfaction Scale Following a Laxative for Antibiotic Washout Prior to Oral Microbiome Therapy.}, journal = {Advances in therapy}, volume = {}, number = {}, pages = {}, pmid = {39607629}, issn = {1865-8652}, abstract = {INTRODUCTION: Administration of fecal microbiota spores, live-brpk [Vowst Oral Spores (VOS)], an oral microbiome therapeutic approved for prevention of recurrent Clostridioides difficile infection in adults, requires antibiotic washout using a laxative prior to administration. Patient acceptability of the prerequisite laxative is important. This study assessed psychometric properties of the Antibiotic Washout Patient Satisfaction Scale (AWPSS) which was minimally modified from a previously validated patient satisfaction scale for bowel preparation prior to colonoscopy.<br><br>METHODS: Patients from the ECOSPOR IV trial who received a laxative preparation prior to oral administration of VOS and were administered the AWPSS were included. Reliability and construct validity of the AWPSS were evaluated.<br><br>RESULTS: AWPSS data were available for 110 patients; all completed all 6 items of the AWPSS, supporting its acceptability. Domain 1 mean/median transformed total scores of 105.9/100 [range (best-worst), 0-300] suggested that patients were satisfied with the laxative preparation; a Cronbach's alpha of 0.81 showed acceptable reliability. Almost all patients (97.3%) reported they were able to consume the entire laxative solution as instructed and would take it again if needed (95.5%). Higher satisfaction with the laxative preparation predicted higher acceptability of future use if needed (lower score) with mean/median of 101.7/100 and 195.0/200.00 for those who were willing or not willing to accept, respectively (P&#xa0;=&#xa0;0.008).<br><br>CONCLUSIONS: AWPSS is a valid and reliable 6-item patient-reported outcome measure for use in patients requiring a laxative prior to oral microbiome therapy. AWPSS showed antibiotic washout was well tolerated and predicted that patients would be willing to consume the laxative in the future if needed.}, }
@article {pmid39607612, year = {2024}, author = {Qasem, HH and El-Sayed, WM}, title = {The bacterial microbiome and cancer: development, diagnosis, treatment, and future directions.}, journal = {Clinical and experimental medicine}, volume = {25}, number = {1}, pages = {12}, pmid = {39607612}, issn = {1591-9528}, mesh = {Humans ; *Neoplasms/therapy/microbiology/diagnosis ; *Dysbiosis ; *Microbiota ; Bacteria/classification/genetics ; Probiotics/therapeutic use ; }, abstract = {The term "microbiome" refers to the collection of bacterial species that reside in the human body's tissues. Sometimes, it is used to refer to all microbial entities (bacteria, viruses, fungi, and others) which colonize the human body. It is now generally acknowledged that the microbiome plays a critical role in the host's physiological processes and general well-being. Changes in the structure and/or function of the microbiome (dysbiosis) are linked to the development of many diseases including cancer. The claim that because of their negatively charged membrane, cancer cells are more vulnerable to some bacteria than normal cells and that is how the link between these bacteria and cancer evolved has been refuted. Furthermore, the relationship between the microbiome and cancer is more evident in the emerging field of cancer immunotherapy. In this narrative review, we detailed the correlation between the presence/absence of specific bacterial species and the development, diagnosis, prognosis, and treatment of some types of cancer including colorectal, lung, breast, and prostate cancer. In addition, we discussed the mechanisms of microbiome-cancer interactions including genotoxin production, the role of free radicals, modification of signaling pathways in host cells, immune modulation, and modulation of drug metabolism by microbiome. Future directions and clinical application of microbiome in the early detection, prognosis, and treatment of cancer emphasizing on the role of fecal transplantation, probiotics, prebiotics, and microbiome biomarkers were also considered.}, }
@article {pmid39607539, year = {2024}, author = {Lv, JL and Bai, Y and Lv, YE and Chen, CC and Qin, XM and Du, GH and Zhou, YZ}, title = {Integrated colon microbiome and metabolomics to elucidate the antidepressant mechanisms of the Radix Bupleuri-Radix Paeoniae Alba herb pair.}, journal = {Metabolic brain disease}, volume = {40}, number = {1}, pages = {45}, pmid = {39607539}, issn = {1573-7365}, support = {202102130501010//Key Research and Development Program of Shanxi Province/ ; 202204051002011//The special fund for Science and Technology Innovation Teams of Shanxi Province/ ; 81673572//National Natural Science Foundation of China/ ; 2024-021//Research Project Supported by Shanxi Scholarship Council of China/ ; 202403021211150//Supported by Fundamental Research Program of Shanxi Province/ ; }, mesh = {Animals ; *Antidepressive Agents/pharmacology/therapeutic use ; *Gastrointestinal Microbiome/drug effects ; Male ; Rats ; *Metabolomics ; *Paeonia ; *Depression/metabolism/drug therapy/microbiology ; *Rats, Sprague-Dawley ; Stress, Psychological/metabolism/drug therapy ; Bupleurum ; Drugs, Chinese Herbal/pharmacology/therapeutic use ; Colon/metabolism/drug effects/microbiology ; }, abstract = {Radix Bupleuri-Radix Paeoniae Alba herb pair (RB-RPA) is the fundamental medication combination of many classic antidepressant prescriptions, and RB-RPA's antidepressant effect is well established. For an extended period, the involvement of intestinal flora in the progression of depression has been widely acknowledged. However, it remains unclear whether RB-RPA could modulate intestinal microbiota disturbances and metabolic abnormalities induced by depression. The research explores the antidepressant mechanism of RB-RPA in chronic unpredictable mild stress (CUMS) rats in terms of intestinal flora and metabolites. We identified critical gut microbial species and metabolites associated with the antidepressant effects of RB-RPA using 16 S rRNA sequencing and Liquid Chromatography-Mass Spectrometry (LC-MS) metabolomics. And then, correlation analysis between critical microbiota and differential metabolites was conducted. The results demonstrate that RB-RPA significantly ameliorated depressive-like behavior in CUMS rats. RB-RPA improved intestinal flora disorders in depressed rats mainly by increasing the abundance of Lactobacillus (especially L. johnsonii), and ameliorated tryptophan synthesis and metabolism disorders in depressed rats and restored the levels of tryptophan and tryptophan microbial metabolites, such as indoleacrylic acid and 4-indoleacetaldehyde. Notably, correlation analysis showed that Lactobacillus had a significant positive correlation with tryptophan, indoleacrylic acid, and 4-indoleacetaldehyde. In conclusion, RB-RPA can improve the disorder of intestinal flora by increasing the abundance of Lactobacillus and improve the metabolic disorder of depressed rats by regulating tryptophan metabolism, thus exerting antidepressant effects.}, }
@article {pmid39607509, year = {2024}, author = {Bahat, H and Paret, M and Uzan, A and Klainer, H and Sharon, E and Turjeman, S and Koren, O and Goldman, M and Youngster, I}, title = {Fecal microbiome composition in neonates with or without urinary tract infection.}, journal = {Pediatric nephrology (Berlin, Germany)}, volume = {}, number = {}, pages = {}, pmid = {39607509}, issn = {1432-198X}, abstract = {BACKGROUND: Most infants with febrile urinary tract infection (UTI) do not have an underlying anatomical risk factor. Thus, other non-anatomical risk factors should be considered. Since the most common pathogens arise from the fecal microbiota, our aim was to investigate whether the gut microbiota composition differs between febrile infants younger than 2 months with or without UTI.<br><br>METHODS: In this prospective, case-control, pilot study, we performed 16S ribosomal ribonucleic acid amplicon sequencing to characterize gut microbiota of febrile neonates with and without UTI admitted to the pediatric ward at Shamir Medical Center between February 2019 and May 2021.<br><br>RESULTS: The study cohort included 42 febrile neonates: 17 with and 25 without febrile UTI. We found a significant difference in beta diversity (i.e. between-sample/study group similarity indices) between the UTI and non-UTI group (p&#x2009;=&#x2009;0.016). There were also distinct differences in the relative abundance of the 20 most prevalent genera. Furthermore, several genera were significantly enriched in the UTI group, with others dominating the non-UTI group. Streptococci were underrepresented in the UTI group. There was no difference in alpha diversity (i.e. within-sample diversity/richness) between groups.<br><br>CONCLUSION: Febrile neonates with UTI have a different fecal microbiota composition (beta-diversity), but not alpha diversity, in comparison to febrile neonates without UTI. A larger study is warranted to confirm these findings and their potential applications.}, }
@article {pmid39607341, year = {2024}, author = {Merk, LN and Shur, AS and Jena, S and Munoz, J and Brubaker, DK and Murray, RM and Green, LN}, title = {Diagnostic and Therapeutic Microbial Circuit with Application to Intestinal Inflammation.}, journal = {ACS synthetic biology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acssynbio.3c00668}, pmid = {39607341}, issn = {2161-5063}, abstract = {Bacteria genetically engineered to execute defined therapeutic and diagnostic functions in physiological settings can be applied to colonize the human microbiome, providing in situ surveillance and conditional disease modulation. However, many engineered microbes can only respond to single-input environmental factors, limiting their tunability, precision, and effectiveness as living diagnostic and therapeutic systems. For engineering microbes to improve complex chronic disorders such as inflammatory bowel disease, the bacteria must respond to combinations of stimuli in the proper context and time. This work implements a previously characterized split activator AND logic gate in the probiotic Escherichia coli strain Nissle 1917 (EcN). Our system can respond to two input signals: the inflammatory biomarker tetrathionate and a second input signal, anhydrotetracycline (aTc), for manual control. We report 4-6 fold induction with a minimal leak when the two chemical signals are present. We model the AND gate dynamics using chemical reaction networks and tune parameters in silico to identify critical perturbations that affect our circuit's selectivity. Finally, we engineer the optimized AND gate to secrete a therapeutic anti-inflammatory cytokine IL-22 using the hemolysin secretion pathway in the probiotic E. coli strain. We used a germ-free transwell model of the human gut epithelium to show that our engineering bacteria produce similar host cytokine responses compared to recombinant cytokine. Our study presents a scalable workflow to engineer cytokine-secreting microbes driven by logical signal processing. It demonstrates the feasibility of IL-22 derived from probiotic EcN with minimal off-target effects in a gut epithelial context.}, }
@article {pmid39606796, year = {2024}, author = {Wang, Z and Yang, S and Liu, L and Mao, A and Kan, H and Yu, F and Ma, X and Feng, L and Zhou, T}, title = {The gut microbiota-derived metabolite indole-3-propionic acid enhances leptin sensitivity by targeting STAT3 against diet-induced obesity.}, journal = {Clinical and translational medicine}, volume = {14}, number = {12}, pages = {e70053}, pmid = {39606796}, issn = {2001-1326}, support = {82470455//National Natural Science Foundation of China/ ; 82025005//National Natural Science Foundation of China/ ; 91939301//National Natural Science Foundation of China/ ; 81622007//National Natural Science Foundation of China/ ; }, mesh = {*Obesity/metabolism/drug therapy ; Animals ; *Gastrointestinal Microbiome/drug effects ; *Leptin/metabolism ; Mice ; *STAT3 Transcription Factor/metabolism ; *Indoles/pharmacology/metabolism ; *Diet, High-Fat/adverse effects ; Male ; Mice, Inbred C57BL ; Disease Models, Animal ; }, abstract = {Obesity is associated with the gut microbiome. Here, we report that gut commensal Clostridia bacteria regulate host energy balance through the tryptophan-derived metabolite indole-3-propionic acid (IPA). IPA acts as an endogenous leptin sensitiser to counteract obesity. Mechanistically, IPA is secreted from the gut into the circulation, and then targets to the STAT3 in the hypothalamic appetite regulation centre, promoting its phosphorylation and nuclear translocation, which enhances the body's response to leptin, and regulates the balance between appetite and energy metabolism. The in vitro pull-down assays involving site-directed mutagenesis demonstrate that Trp623 in the SH2 domain is the key binding site for STAT3-IPA interaction. High-fat diet (HFD), rather than genetic factors, induces excessive secretion of antimicrobial peptides by Paneth cells, inhibiting the growth of Clostridia in the gut and resulting in decreased production of the beneficial metabolite IPA. IPA or Clostridium sporogenes supplement effectively controls weight gain, improves glucose metabolism, and reduces inflammation in DIO mice. IPA fails to achieve such effects in ob/ob mice, while exogenous leptin administration restores the therapeutic effect of IPA. Our study suggests that the IPA-based gut-brain axis regulates host metabolism, and supplementation with microbiome-derived IPA could be a promising intervention strategy for treating obesity.}, }
@article {pmid39606663, year = {2024}, author = {Özkan, S and Bay, V and Cömert Acar, M and Yalcın, S}, title = {Partial replacement of soybean with local alternative sources: effects on behavior, cecal microbiota, and intestinal histomorphometry of local chickens.}, journal = {Frontiers in veterinary science}, volume = {11}, number = {}, pages = {1463301}, pmid = {39606663}, issn = {2297-1769}, abstract = {Interest in partially replacing soybean meal in poultry diets with alternative protein sources such as agri-industrial by-products and black soldier fly (BSF, Hermetia illucens) has gained significant attention due to sustainability concerns. This study aimed to evaluate the effects of broiler diets in which soybean meal was partially substituted with agri-industrial by-products with or without BSF larvae meal, on the behavior, intestinal histomorphometry, and microbiome profile of a local broiler chicken strain. There were three dietary treatments. (1) A corn-soybean-based diet (Control), (2) a diet in which soybean was partly replaced (SPR) with local agri-industrial by-products, namely sunflower meal, brewers' dried grain, and wheat middlings, and (3) a diet in which BSF (5%) meal was added to SPR (SPR+BSF). Behavior was recorded on days 14, 35, and 49 at the pen level. On day 55, intestinal segments and cecal contents were collected from eight chickens per pen for histomorphometry and microbiome analysis. Dietary manipulations did not affect the behavior of broiler chickens (P > 0.05) suggesting that the experimental diets had no influence on behavior. A significant interaction between the intestinal segment and diets revealed that the SPR and SPR+BSF diets decreased duodenal villus height (VH) compared to the control diet (P < 0.05). However, this effect was not consistent across all of intestinal segments. Diet did not affect villus height to crypt depth ratio (VH/CD; P > 0.05), indicating no significant impact on the absorptive capacity of the digestive system. Firmicutes and Bacteroidetes were the dominant phyla in the cecal samples. Colidextribacter and Oscillibacter spp. were more abundant in chickens fed the SPR diet compared to those fed the control diet. The SPR+BSF diet resulted in higher abundance of Rikenella and Colidextribacter spp. compared to the control diet, while Desulfovibrio, Ruminococcus torques group, and Lachnoclostridium were more abundant in the ceca of birds fed the SPR diet than those fed SPR+BSF. In conclusion, replacement of soybean with agri-industrial by-products and BSF larvae meal could regulate the cecal microbiota composition without negatively affecting the behavior and intestinal histomorphometry of the local chickens.}, }
@article {pmid39606458, year = {2024}, author = {Lozupone, C and O'Connor, J and Fouquier, J and Neff, C and Sterrett, J and Marden, T and Fiorillo, S and Siebert, J and Schneider, J and Nusbacher, N and Noe, A and Higgins, B and Higgins, J and Campbell, T and Palmer, B}, title = {Agrarian Diet Improves Metabolic Health in HIV-positive Men with Prevotella-Rich Microbiomes: Results from a Randomized Trial.}, journal = {Research square}, volume = {}, number = {}, pages = {}, doi = {10.21203/rs.3.rs-5349309/v1}, pmid = {39606458}, issn = {2693-5015}, abstract = {This study aimed to assess the impact a high-fiber/low-fat agrarian diet (AD) on inflammation and metabolic outcomes in HIV positive men who have sex with men (MSM). Since the gut microbiome of MSM has been shown to have a striking resemblance to individuals in agrarian cultures, including being Prevotella-rich and Bacteroides-poor, we hypothesized that they would have particularly strong health benefits from consumption of a diet matched to their microbiome type. Sixty-six participants, including 36 HIV-positive MSM (HIV(+)MSM), 21 HIV-negative MSM, and 9 HIV negative men who have sex with women were randomized to either an AD or a high-fat western diet (WD) for four weeks. The AD reduced low-density lipoprotein cholesterol in HIV(+)MSM, with more significant reductions predicted by Prevotella-rich/Bacteroides-poor microbiomes at baseline. The AD also reduced T cell exhaustion and pro-inflammatory intermediate monocytes and altered host transcription in the colonic mucosa. Our findings suggest that tailoring diet interventions to baseline microbiome type can help promote metabolic health in HIV(+)MSM.}, }
@article {pmid39606371, year = {2024}, author = {Jeong, S and Tollison, T and Brochu, H and Chou, H and Yu, T and Baghaie, P and Yount, KS and Darville, T and Peng, X and O'Connell, CM}, title = {Aptima Combo2-avoiding variants detected in cervical and endometrial specimens from a cohort of sexually active cisgender women during 16S microbiome profiling.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.11.13.24316066}, pmid = {39606371}, abstract = {BACKGROUND: Performance of a 16S rRNA analysis of the cervicovaginal microbiome of 220 participants recruited into the T Cell Response against Chlamydia (TRAC) cohort between February 2011 and August 2014 in Allegheny County, Pennsylvania USA surprisingly detected DNA encoding chlamydial 16S rRNA in samples from seven participants who had tested negatively for Chlamydia trachomatis (CT) and DNA encoding gonococcal 16S rRNA from five participants who had tested negatively for Neisseria gonorrhoeae (NG) infection with the Aptima Combo2 assay (Hologic).<br><br>METHODS: We used targeted PCR amplification followed by sequencing to characterize the chlamydial 23S rRNA locus and qPCR to detect gonococcal DNA in residual diagnostic swab eluates or DNA used to generate 16S rRNA libraries.<br><br>RESULTS: Discrepant specimens that contained chlamydial DNA carried a diagnostic-avoidant, G1526A variant in the 23S rRNA locus identical to variants previously detected in Finland, Denmark, and the UK. PCR validation of gonococcal DNA was confirmed for all participants who had tested negatively, with stochastic effects consistent with infection levels close to the limit of detection by the diagnostic assay.<br><br>CONCLUSIONS: These data indicate that this probe-avoidant CT mutant, and possibly others, were circulating in the northeastern US prior to their detection and characterization in 2019 and subsequently. Although infrequent, documentation of false negative results for CT indicates a need for clinicians to consider performance of a second test that uses alternate PCR probes if patients have persistent symptoms or have known contact to an infected sex partner and their initial NAAT is negative.}, }
@article {pmid39606341, year = {2024}, author = {Scalzo, PL and Marshall, A and Soriano, S and Curry, K and Dulay, M and Hodics, T and Quigley, EM and Treangen, TJ and Piskorz, MM and Villapol, S}, title = {Gut microbiome dysbiosis and immune activation correlate with somatic and neuropsychiatric symptoms in COVID-19 patients.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.11.18.24317428}, pmid = {39606341}, abstract = {COVID-19 patients often exhibit altered immune responses and neuropsychiatric symptoms during hospitalization. However, the potential interactions with gut microbiome profiles have not been fully characterized. Here, COVID-19 disease severity was classified as low (27.4%), moderate (29.8%), and critical (42.8%). Fever (66.1%) and cough (55.6%) were common symptoms. Additionally, 27.3% reported somatic symptoms, 27.3% experienced anxiety, 39% had depressive symptoms, and 80.5% reported stress. Gut microbiome profiling was performed using full-length 16S rRNA gene sequencing. Elevated interleukin-6 levels were observed in the most severe cases, indicating systemic inflammation. Reduced gut bacterial diversity was more pronounced in women and obese patients and correlated with higher disease severity. The presence of the genus Mitsuokella was significantly associated with increased physical, stress, anxiety, and depressive symptoms, and Granulicatella with critically ill patients. These findings suggest a link between mental health status, systemic inflammation, and gut dysbiosis in COVID-19 patients, emphasizing the potential of microbiome-targeted therapies to improve recovery and reduce severe complications.}, }
@article {pmid39606148, year = {2024}, author = {Xiao, L and Zhao, F}, title = {Exploring the frontier of microbiome biomarker discovery with artificial intelligence.}, journal = {National science review}, volume = {11}, number = {11}, pages = {nwae325}, pmid = {39606148}, issn = {2053-714X}, }
@article {pmid39604606, year = {2024}, author = {}, title = {Decoding ageing: Handan Melike Dönertaş on microbiomes, AI and improving lifespan and healthspan.}, journal = {Communications biology}, volume = {7}, number = {1}, pages = {1579}, doi = {10.1038/s42003-024-07246-7}, pmid = {39604606}, issn = {2399-3642}, abstract = {Investigating the complexities of ageing through computational biology, Handan Melike Dönertaş shares her journey from evolutionary genomics research at Middle East Technical University to leading her own lab at the Leibniz Institute on Ageing. Her team is developing and applying computational approaches aiming to advance our understanding of the microbiome and ageing.}, }
@article {pmid39610545, year = {2024}, author = {Ejtahed, HS and Hasani-Ranjbar, S and Soroush, AR and Larijani, B}, title = {Multidimensional perspective of obesity; prevention to treatment.}, journal = {Journal of diabetes and metabolic disorders}, volume = {23}, number = {2}, pages = {1485-1489}, pmid = {39610545}, issn = {2251-6581}, abstract = {OBJECTIVE: An increasing prevalence of overweight and obesity across the world can lead to serious health complications. The present narrative review highlighted the results of research on obesity management affiliated to the Endocrinology and Metabolism Research Institute (EMRI), Tehran University of Medical Sciences.<br><br>METHODS: All documents from the EMRI focused on obesity topics were searched using PubMed and Scopus databases up to December 2019.<br><br>RESULTS: EMRI research projects conducted in obesity field cover several topics including childhood obesity, epidemiology of obesity, roles of genetic factors and gut microbiota in excess weight, as well as weight management by medicinal herbs and nutritional interventions. The increasing prevalence of excess-weight in children and adults indicates that conventional weight management strategies alone are not successful in obesity control and complementary therapies including herbal medicine could be helpful. Moreover, clarifying the role of the human genome and microbiome in different responses of individuals to dietary recommendations could be effective in achieving personalized nutrition.<br><br>CONCLUSION: Further population-based studies focusing on national and international collaborations are needed to progress more practical strategies to face with obesity challenge in different age ranges.}, }
@article {pmid39610549, year = {2024}, author = {Ejtahed, HS and Hasani-Ranjbar, S and Soroush, AR and Siadat, SD and Larijani, B}, title = {Microbiota research in Iran; current knowledge and future perspective.}, journal = {Journal of diabetes and metabolic disorders}, volume = {23}, number = {2}, pages = {1479-1484}, pmid = {39610549}, issn = {2251-6581}, abstract = {OBJECTIVE: As the gut microbiota has attracted considerable attention in recent years, the aim of the present study is introducing a new microbiota research group at Endocrinology and Metabolism Research Institute (EMRI) that collaborates with national and international research centers for microbiome research projects management.<br><br>METHODS: All the documents from EMRI focused on the microbiota field were collected using PubMed, Scopus, and Web of Science electronic databases from the inception up to June 2020.<br><br>RESULTS: Findings of the EMRI research projects on the microbiota field were reviewed in this study and we highlighted some specific primary results of gut microbiota composition in the Iranian population. Moreover, applications of the developed Microbiota Database are introduced.<br><br>CONCLUSION: Enhancement of investment in this field and interdisciplinary collaborations are needed to progress our knowledge about the Iranian gut microbiota composition and develop microbiota modulating interventions over the next decade.}, }
@article {pmid39606113, year = {2024}, author = {Hanif, MS and Tayyab, M and Baillo, EH and Islam, MM and Islam, W and Li, X}, title = {Plant microbiome technology for sustainable agriculture.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1500260}, pmid = {39606113}, issn = {1664-302X}, abstract = {Plants establish specific interactions with microorganisms, which are vital for promoting growth and resilience. Although advancements in microbiome modulation technologies show great potential for sustainable agriculture, several challenges have hindered the wider application of plant microbiomes in the field. These challenges may include inconsistent microbial colonization, competition with native microbiota, and environmental variability. Current strategies, while promising, often yield inconsistent results in real-world agricultural settings, highlighting the need for more refined approaches. Agricultural practices and plant genotypes significantly influence the composition and function of plant-associated microbiota. A data-driven strategy that incorporates genomic profiling, environmental assessments, and optimized delivery systems is essential for selecting effective microbial strains. Additionally, refining farming practices, such as crop rotation, intercropping, and reduced tillage, along with robust plant breeding programs, can greatly enhance crop health and productivity.}, }
@article {pmid39606112, year = {2024}, author = {Skarlupka, JH and Cox, MS and Steinberger, AJ and Sbardellati, DL and McClure, JC and Bickhart, DM and Scheftgen, AJ and Zuniga-Chaves, I and Wolfe, LA and Paget, E and Skadron, C and Attipetty, N and Suen, G}, title = {Corrigendum: Oral swabs as a proxy for direct ruminal microbiome sampling in Holstein dairy cows is correlated with sample color.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1501270}, doi = {10.3389/fmicb.2024.1501270}, pmid = {39606112}, issn = {1664-302X}, abstract = {[This corrects the article DOI: 10.3389/fmicb.2024.1466375.].}, }
@article {pmid39606108, year = {2024}, author = {Liu, H and Zhang, Y and Li, H and Chen, S and Zhang, J and Ding, W}, title = {Characteristics of soil microbial community assembly patterns in fields with serious occurrence of tobacco Fusarium wilt disease.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1482952}, pmid = {39606108}, issn = {1664-302X}, abstract = {INTRODUCTION: Fusarium wilt disease (FWD) of tobacco is a destructive disease caused by Fusarium spp. in tobacco-growing regions worldwide. The Fusarium spp. infection may alter the composition and structure of the tobacco root microbial community; however, the relationship between these factors under large-scale geographical conditions in China remains underexplored.<br><br>METHODS: In the context of this investigation, soil samples from the rhizosphere of tobacco plants were procured from fields afflicted with FWD and those devoid of the disease in the Hanzhong region of Shaanxi province, as well as in the Sanmenxia and Nanyang regions of Henan province. These regions are recognized for the commercial cultivation of tobacco. The examination focused on discerning the influence of tobacco FWD on the composition and configuration of the rhizosphere microbial community, along with their co-occurrence patterns. This scrutiny was underpinned by targeted PCR amplification and high-throughput sequencing (amplicon sequencing) of the 16S rRNA gene and the ITS1 region.<br><br>RESULTS: The amplicon data analyses showed that FWD influenced the microbial structure and composition of the tobacco rhizosphere soil. FWD had a greater impact on the microbiome of the tobacco fungal community than on the microbiome of the bacterial community. Healthy plants had the ability to recruit potential beneficial bacteria. Diseased plants were more susceptible to colonization by other pathogenic fungi, but they still had the capacity to recruit potential beneficial bacteria. The analysis of microbial intra- and inter-kingdom networks further indicated that FWD destabilized microbial networks. In the overall microbial interaction, microorganisms primarily interacted within their boundaries, but FWD increased the proportion of interactions occurring across boundaries. In addition, FWD could disrupt the interactions within microbial network modules.<br><br>DISCUSSION: This study provides evidence that FWD can cause changes in the composition and network of microbial communities, affecting the interactions among various microorganisms, including bacteria and fungi. These findings contribute to our understanding of how plant microbiomes change due to disease. Furthermore, they add to our knowledge of the mechanisms that govern the assembly and interactions of microbial communities under the influence of FWD.}, }
@article {pmid39606106, year = {2024}, author = {Lu, Z and Zhang, T and Zhao, Y and Pang, Y and Guo, M and Zhu, X and Li, Y and Li, Z}, title = {The influence of host genotype and gut microbial interactions on feed efficiency traits in pigs.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1459773}, pmid = {39606106}, issn = {1664-302X}, abstract = {Feed efficiency and growth performance are economically important traits in pigs. Precious studies have been revealed that both genetics and gut microbes could influence host phenotypes, however, the mechanisms by which they affect pig growth and feed efficiency remain poorly understood. In this study, 361 crossbred Duroc × (Landrace × Yorkshire) commercial pigs were genotyped using GeneSeek Porcine SNP50K BeadChip, and the microbiotas from fecal samples were acquired using microbial 16S rRNA gene sequencing technology to investigate the impact of host genetics and gut microorganisms on growth and feed efficiency. The results showed that the heritability and enterobacterial force ranged from 0.27 to 0.46 and 0 to 0.03, respectively. Genome-wide association studies (GWAS) identified seven significant SNPs to be associated with growth and feed efficiency, and several genes, including AIF1L, ASS1, and QRFP were highlighted as candidates for the analyzed traits. Additionally, microbiome-genome-wide association studies GWAS revealed potential links between CCAR2, EGR3, GSTM3, and GPR61 genes and the abundance of microorganisms, such as Trueperella, Victivallis, and Erysipelatoclostridium. In addition, six microbial genera linked to growth and feed efficiency were identified as follows Lachnospiraceae_UCG-005, Prevotellaceae_UCG-003, Prevotellaceae_NK3B31_group, Prevotella_1, Prevotella_9, and Veillonella. Our findings provide novel insights into the factors influencing host phenotypic complexity and identify potential microbial targets for enhancing pig feed efficiency through selective breeding. This could aid in the development of strategies to manipulate the gut microbiota to optimize growth rates and feed efficiency in pig breeding.}, }
@article {pmid39605655, year = {2024}, author = {O'Connor, LC and Kang, WK and Vo, P and Spinelli, JB and Alkema, MJ and Byrne, AB}, title = {Comamonas aquatica inhibits TIR-1/SARM1 induced axon degeneration.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.11.20.622298}, pmid = {39605655}, issn = {2692-8205}, abstract = {Emerging evidence suggests the microbiome critically influences the onset and progression of neurodegenerative diseases; however, the identity of neuroprotective bacteria and the molecular mechanisms that respond within the host remain largely unknown. We took advantage of Caenorhabditis elegans' well characterized nervous system and ability to eat uni-bacterial diets to determine how metabolites and neuroprotective molecules from single species of bacteria suppress degeneration of motor neurons. We found Comamonas aquatica significantly protects against degeneration induced by overexpressing a key regulator of axon degeneration, TIR-1/SARM1. Genetic analyses and metabolomics reveal Comamonas protects against neurodegeneration by providing sufficient Vitamin B12 to activate METR-1/MTR methionine synthase in the intestine, which then lowers toxic levels of homocysteine in TIR-1-expressing animals. Defining a molecular pathway between Comamonas and neurodegeneration adds significantly to our understanding of gut-brain interactions and, given the prominent role of homocysteine in neurodegenerative disorders, reveals how such a bacterium could protect against disease.}, }
@article {pmid39605612, year = {2024}, author = {Cumbo, F and Truglia, S and Weitschek, E and Blankenberg, D}, title = {Feature selection with vector-symbolic architectures: a case study on microbial profiles of shotgun metagenomic samples of colorectal cancer.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.11.18.624180}, pmid = {39605612}, issn = {2692-8205}, abstract = {UNLABELLED: The continuingly decreasing cost of next-generation sequencing has recently led to a significant increase in the number of microbiome-related studies, providing invaluable information for understanding host-microbiome interactions and their relation to diseases. A common approach in metagenomics consists of determining the composition of samples in terms of the amount and types of microbial species that populate them, with the goal to identify microbes whose profiles are able to differentiate samples under different conditions with advanced feature selection techniques. Here we propose a novel backward variable selection method based on the hyperdimensional computing paradigm, which takes inspiration from how the human brain works in the classification of concepts by encoding features into vectors in a high-dimensional space. We validated our method on public metagenomic samples collected from patients affected by colorectal cancer in a case/control scenario, by performing a comparative analysis with other state-of-the-art feature selection methods, obtaining promising results.<br><br>AUTHOR SUMMARY: Characterizing the microbial composition of metagenomic samples is crucial for identifying potential biomarkers that can distinguish between healthy and diseased states. However, the high dimensionality and complexity of metagenomic data present significant challenges in the context of accurately selecting features. Our backward variable selection method, based on the hyperdimensional computing paradigm, offers a promising approach to overcoming these challenges. By effectively reducing the feature space while preserving essential information, this method enhances the ability to detect critical microbial signatures associated with diseases like colorectal cancer, leading to more precise diagnostic tools.}, }
@article {pmid39605610, year = {2024}, author = {Sterrett, JD and Quinn, KD and Doenges, KA and Nusbacher, NM and Levens, CL and Armstrong, ML and Reisdorph, RM and Smith, H and Saba, LM and Kuhn, KA and Lozupone, CA and Reisdorph, NA}, title = {Appearance of green tea compounds in plasma following acute green tea consumption is modulated by the gut microbiome in mice.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.07.11.603097}, pmid = {39605610}, issn = {2692-8205}, abstract = {UNLABELLED: Studies have suggested that phytochemicals in green tea have systemic anti-inflammatory and neuroprotective effects. However, the mechanisms behind these effects are poorly understood, possibly due to differential metabolism of phytochemicals resulting from variation in gut microbiome composition. To unravel this complex relationship, our team utilized a novel combined microbiome analysis and metabolomics approach applied to low complexity microbiome (LCM) and human colonized (HU) gnotobiotic mice treated with an acute dose of powdered matcha green tea. A total of 20 LCM mice received 10 distinct human fecal slurries for an n=2 mice per human gut microbiome; 9 LCM mice remained un-colonized with human slurries throughout the experiment. We performed untargeted metabolomics on green tea and plasma to identify green tea compounds that were found in plasma of LCM and HU mice that had consumed green tea. 16S ribosomal RNA gene sequencing was performed on feces of all mice at study end to assess microbiome composition. We found multiple green tea compounds in plasma associated with microbiome presence and diversity (including acetylagmatine, lactiflorin, and aspartic acid negatively associated with diversity). Additionally, we detected strong associations between bioactive green tea compounds in plasma and specific gut bacteria, including associations between spiramycin and Gemmiger , and between wildforlide and Anaerorhabdus . Additionally, some of the physiologically relevant green tea compounds are likely derived from plant-associated microbes, highlighting the importance of considering foods and food products as meta-organisms. Overall, we describe a novel workflow for discovering relationships between individual food compounds and composition of the gut microbiome.<br><br>IMPORTANCE: Foods contain thousands of unique and biologically important compounds beyond the macro- and micro-nutrients listed on nutrition facts labels. In mammals, many of these compounds are metabolized by the community of microbes in the colon. These microbes may impact the thousands of biologically important compounds we consume; therefore, understanding microbial metabolism of food compounds will be important for understanding how foods impact health. We used metabolomics to track green tea compounds in plasma of mice with and without complex microbiomes. From this, we can start to recognize certain groups of green tea-derived compounds that are impacted by mammalian microbiomes. This research presents a novel technique for understanding microbial metabolism of food-derived compounds in the gut, which can be applied to other foods.}, }
@article {pmid39605587, year = {2024}, author = {Andermann, TM and Zeng, K and Guirales-Medrano, S and Groth, A and Ramachandran, BC and Sun, S and Sorgen, AA and Hill, L and Bush, AT and Liu, H and Jones, C and Roach, J and Conlon, BP and Rao, G and Chao, NJ and Fodor, AA and Sung, AD}, title = {The impact of transplant location on the gut microbiome and resistome in patients undergoing hematopoietic stem cell transplantation at home versus in the hospital.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.11.19.624359}, pmid = {39605587}, issn = {2692-8205}, abstract = {OBJECTIVES: Home-based hematopoietic stem cell transplantation (HCT) is a novel approach that has the potential to improve outcomes, however, the impact of transplant location on the gut microbiome remains uncharacterized. We hypothesized that patients randomized to undergo home HCT would have higher gut taxonomic diversity and lower antimicrobial resistance (AMR) gene abundance compared to those undergoing standard hospital HCT.<br><br>METHODS: We identified 28 patients enrolled in Phase II randomized trials of home (n=16) v. hospital (n=12) HCT at Duke and performed shotgun metagenomic sequencing of stools to compare taxonomic and AMR gene composition between groups. We performed a secondary analysis of patients from each group transplanted at an outpatient infusion clinic with those who underwent standard inpatient HCT ("outpatient" v. "inpatient").<br><br>RESULTS: No significant differences in duration of hospitalization were found in those randomized to home v. hospital HCT. Taxonomic and AMR gene &#x3b1;- and &#x3b2;-diversity were comparable. In contrast, secondary analyses demonstrated that patients from both home and hospital groups transplanted at an outpatient infusion clinic spent significantly less time in the hospital and demonstrated higher taxonomic &#x3b1;-diversity and differential &#x3b2;-diversity compared to standard inpatient HCT, although AMR gene &#x3b1;-diversity did not differ, and comparisons were confounded by both differences in transplant type and use of antibiotics.<br><br>CONCLUSIONS: Randomization by transplant location did not impact the gut microbiota to the same extent as the duration of hospitalization, although secondary analyses were heavily confounded. Even when taxonomic differences were observed, AMR genes were similar between groups.}, }
@article {pmid39605476, year = {2024}, author = {Macadangdang, BR and Wang, Y and Woodward, C and Revilla, JI and Shaw, BM and Sasaninia, K and Makanani, SK and Berruto, C and Ahuja, U and Miller, JF}, title = {Targeted protein evolution in the gut microbiome by diversity-generating retroelements.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.11.15.621889}, pmid = {39605476}, issn = {2692-8205}, abstract = {Diversity-generating retroelements (DGRs) accelerate evolution by rapidly diversifying variable proteins. The human gastrointestinal microbiota harbors the greatest density of DGRs known in nature, suggesting they play adaptive roles in this environment. We identified >1,100 unique DGRs among human-associated Bacteroides species and discovered a subset that diversify adhesive components of Type V pili and related proteins. We show that Bacteroides DGRs are horizontally transferred across species, that some are highly active while others are tightly controlled, and that they preferentially alter the functional characteristics of ligand-binding residues on adhesive organelles. Specific variable protein sequences are enriched when Bacteroides strains compete with other commensal bacteria in gnotobiotic mice. Analysis of >2,700 DGRs from diverse phyla in mother-infant pairs shows that Bacteroides DGRs are preferentially transferred to vaginally delivered infants where they actively diversify. Our observations provide a foundation for understanding the roles of stochastic, targeted genome plasticity in shaping host-associated microbial communities.}, }
@article {pmid39605433, year = {2024}, author = {Cortés-Martín, A and Buttimer, C and Maier, JL and Tobin, CA and Draper, LA and Ross, RP and Kleiner, M and Hill, C and Shkoporov, AN}, title = {Adaptations in gut Bacteroidales facilitate stable co-existence with their lytic bacteriophages.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.11.17.624012}, pmid = {39605433}, issn = {2692-8205}, abstract = {BACKGROUND: Bacteriophages (phages) and bacteria within the gut microbiome persist in long-term stable coexistence. These interactions are driven by eco-evolutionary dynamics, where bacteria employ a variety of mechanisms to evade phage infection, while phages rely on counterstrategies to overcome these defences. Among the most abundant phages in the gut are the crAss-like phages that infect members of the Bacteroidales, in particular Bacteroides . In this study, we explored some of the mechanisms enabling the co-existence of four phage-Bacteroidales host pairs in vitro using a multi-omics approach (transcriptomics, proteomics and metabolomics). These included three Bacteroides species paired with three crAss-like phages (Bacteroides intestinalis and ϕcrAss001, Bacteroides xylanisolvens and ϕcrAss002, and an acapsular mutant of Bacteroides thetaiotaomicron with DAC15), and Parabacteroides distasonis paired with the siphovirus ϕPDS1.<br><br>RESULTS: We show that phase variation of individual capsular polysaccharides (CPSs) is the primary mechanism promoting phage co-existence in Bacteroidales, but this is not the only strategy. Alternative resistance mechanisms, while potentially less efficient than CPS phase variation, can be activated to support bacterial survival by regulating gene expression and resulting in metabolic adaptations, particularly in amino acid degradation pathways. These mechanisms, also likely regulated by phase variation, enable bacterial populations to persist in the presence of phages, and vice versa . An acapsular variant of B. thetaiotaomicron demonstrated broader transcriptomic, proteomic, and metabolomic changes, supporting the involvement of additional resistance mechanisms beyond CPS variation.<br><br>CONCLUSIONS: This study advances our understanding of long-term phage-host interaction, offering insights into the long-term persistence of crAss-like phages and extending these observations to other phages, such as &#x3d5;PDS1. Knowledge of the complexities of phage-bacteria interactions is essential for designing effective phage therapies and improving human health through targeted microbiome interventions.}, }
@article {pmid39605394, year = {2024}, author = {Kabonick, S and Verma, K and Modesto, JL and Pearce, VH and Winokur, KM and Groisman, EA and Townsend, GE}, title = {Hierarchical glycolytic pathways control the carbohydrate utilization regulator in human gut Bacteroides.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.11.13.623061}, pmid = {39605394}, issn = {2692-8205}, abstract = {Human dietary choices control the gut microbiome. Industrialized populations consume abundant glucose and fructose, resulting in microbe-dependent intestinal disorders. Simple sugars inhibit the carbohydrate utilization regulator (Cur), a transcription factor in the prominent gut bacterial phylum, Bacteroidetes . Cur encodes products necessary for carbohydrate utilization, host immunomodulation, and intestinal colonization. Here, we demonstrate how simple sugars decrease Cur activity in the mammalian gut. Our findings in two Bacteroides species show that ATP-dependent fructose-1,6-bisphosphate (FBP) synthesis is necessary for glucose or fructose to inhibit Cur, but dispensable for growth because of an essential pyrophosphate (PPi)-dependent enzyme. Furthermore, we show that ATP-dependent FBP synthesis is required to regulate Cur in the gut but does not contribute to fitness when cur is absent, indicating PPi is sufficient to drive glycolysis in these bacteria. Our findings reveal how sugar-rich diets inhibit Cur, thereby disrupting Bacteroides fitness and diminishing products that are beneficial to the host.}, }
@article {pmid39605370, year = {2024}, author = {Sakamachi, Y and Wiley, E and Solis, A and Johnson, CG and Meng, X and Hussain, S and Lipinski, JH and O'Dwyer, DN and Randall, T and Malphurs, J and Papas, B and Wu, BG and Li, Y and Kugler, M and Mehta, S and Trempus, CS and Thomas, SY and Li, JL and Zhou, L and Karmaus, PW and Fessler, MB and McGrath, JA and Gibson, K and Kass, DJ and Gleiberman, A and Walts, A and Invernizzi, R and Molyneaux, PL and Yang, IV and Zhang, Y and Kaminski, N and Segal, LN and Schwartz, DA and Gudkov, AV and Garantziotis, S}, title = {Toll-Like-Receptor 5 protects against pulmonary fibrosis by reducing lung dysbiosis.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.04.30.591719}, pmid = {39605370}, issn = {2692-8205}, abstract = {UNLABELLED: Idiopathic pulmonary fibrosis (IPF) is a devastating pulmonary disease with no curative treatment other than lung transplantation. IPF results from maladaptive responses to lung epithelial injury, but the underlying mechanisms remain unclear. Here, we show that deficiency in the innate immune receptor, toll-like receptor 5 (TLR5), is associated with IPF in humans and with increased susceptibility to epithelial injury and experimental fibrosis in mice, while activation of lung epithelial TLR5 through a synthetic flagellin analogue protects from experimental fibrosis. Mechanistically, epithelial TLR5 activation induces antimicrobial gene expression and ameliorates dysbiosis after lung injury. In contrast, TLR5 deficiency in mice and IPF patients is associated with lung dysbiosis. Elimination of the microbiome in mice through antibiotics abolishes the protective effect of TLR5 and reconstitution of the microbiome rescues the observed phenotype. In aggregate, TLR5 deficiency is associated with IPF and dysbiosis in humans and in the murine model of pulmonary fibrosis. Furthermore, TLR5 protects against pulmonary fibrosis in mice and this protection is mediated by effects on the microbiome.<br><br>ONE-SENTENCE SUMMARY: Deficiency in the innate immune receptor TLR5 is a risk factor for pulmonary fibrosis, because TLR5 prevents microbial dysbiosis after lung injury.}, }
@article {pmid39605360, year = {2024}, author = {Dai, Y and Qian, Y and Qu, Y and Guan, W and Xie, J and Wang, D and Butler, C and Dashper, S and Carroll, I and Divaris, K and Liu, Y and Wu, D}, title = {Longitudinal Microbiome-based Interpretable Machine Learning for Identification of Time-Varying Biomarkers in Early Prediction of Disease Outcomes.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.10.18.619118}, pmid = {39605360}, issn = {2692-8205}, abstract = {Information generated from longitudinally-sampled microbial data has the potential to illuminate important aspects of development and progression for many human conditions and diseases. Identifying microbial biomarkers and their time-varying effects can not only advance our understanding of pathogenetic mechanisms, but also facilitate early diagnosis and guide optimal timing of interventions. However, longitudinal predictive modeling of highly noisy and dynamic microbial data (e.g., metagenomics) poses analytical challenges. To overcome these challenges, we introduce a robust and interpretable machine-learning-based longitudinal microbiome analysis framework, LP-Micro, that encompasses: (i) longitudinal microbial feature screening via a polynomial group lasso, (ii) disease outcome prediction implemented via machine learning methods (e.g., XGBoost, deep neural networks), and (iii) interpretable association testing between time points, microbial features, and disease outcomes via permutation feature importance. We demonstrate in simulations that LP-Micro can not only identify incident disease-related microbiome taxa but also offers improved prediction accuracy compared to existing approaches. Applications of LP-Micro in two longitudinal microbiome studies with clinical outcomes of childhood dental disease and weight loss following bariatric surgery yield consistently high prediction accuracy. The identified critical early predictive time points are informative and aligned with clinical expectations.}, }
@article {pmid39605271, year = {2024}, author = {Zhu, S and Teng, Z}, title = {[The characteristics of pharyngea microbiological in children with obstructive sleep apnea].}, journal = {Lin chuang er bi yan hou tou jing wai ke za zhi = Journal of clinical otorhinolaryngology head and neck surgery}, volume = {38}, number = {12}, pages = {1178-1182}, doi = {10.13201/j.issn.2096-7993.2024.12.017}, pmid = {39605271}, issn = {2096-7993}, mesh = {Humans ; *Sleep Apnea, Obstructive/microbiology ; *Microbiota ; Child ; *Pharynx/microbiology ; Male ; Female ; Prevotella/isolation &amp; purification ; Haemophilus/isolation &amp; purification ; Veillonella/isolation &amp; purification ; RNA, Ribosomal, 16S/genetics ; Child, Preschool ; Proteobacteria/isolation &amp; purification ; }, abstract = {Objective:This study aimed to explore the possible pathogenesis of OSA from the perspective of microbiology by evaluate the change in pharyngeal microbiome of OSA children, and provide new ideas for clinical prevention, diagnosis and treatment. Methods:Randomly enrolled 20 children with OSA as OSA group and 20 children without OSA as control group. The swallow swab of each children been collected. Using 16srDNA sequencing to investigate the characteristics of pharyngeal microbiome. Results:The α-diversity showed that the Chao1and Observe-Otus index has significantly increased in the OSA group, and the β-diversity was significantly different between the two groups. The relative abundance of Haemophilus（Proteobacteria） increased but that of Veillonella（member of Firmicutes） and Prevotella-7 and Prevotella（member of Bacteroidota） decreased in the OSA group compared to control group. Conclusion:The pharyngeal microbial richness are decreased significantly and composition are disrupted in children with OSA. This microbiome analysis provides a new understanding about the pathogenesis of OSA in children.}, }
@article {pmid39605107, year = {2024}, author = {Abdelwahab, SI and Taha, MME and Jerah, AA and Farasani, A and Abdullah, SM and Aljahdali, IA and Ibrahim, R and Oraibi, O and Oraibi, B and Alfaifi, HA and Alzahrani, AH and Babiker, YOH}, title = {Artificial intelligence and microbiome research: Evolution of hotspots, research trends, and thematic-based narrative review.}, journal = {Cellular and molecular biology (Noisy-le-Grand, France)}, volume = {70}, number = {10}, pages = {182-192}, doi = {10.14715/cmb/2024.70.10.24}, pmid = {39605107}, issn = {1165-158X}, mesh = {*Artificial Intelligence ; Humans ; *Microbiota/physiology ; Bibliometrics ; Machine Learning ; Biomedical Research/trends ; Gastrointestinal Microbiome/physiology ; }, abstract = {Artificial intelligence (AI) and microbiome have emerged in recent years as transformative fields with far-reaching implications for various biomedical domains. This paper presents a comprehensive bibliometric analysis examining the intersection of AI and the microbiome (AIM). The study aims to provide information on this interdisciplinary field's research landscape, trends, and emerging topics. Using a systematic approach, data-driven studies were extracted from the Scopus database on 23 November 2023 and analyzed using the VOSviewer and Bibliometrix applications. The regression coefficient of 0.94 and the yearly growth rate of 7.46% in AIM production indicate a consistent increase over time. Identification of essential contributors, organizations, and nations illuminated cooperative networks and research hotspots. The trend themes are the gut microbiome, disease prediction, machine learning, transfer learning, categorization, big data, artificial neural networks, chronic rhinosinusitis, epidemiology, COPD, and bronchoalveolar lavage. These hot issues in AIM reflect the present emphasis on research and developments in our knowledge of the microbiome's function in health, sickness, and individualized treatment. The findings give researchers, policymakers, and industry experts a thorough picture of the research environment and guide future paths in AIM's fascinating and promising subject.}, }
@article {pmid39605068, year = {2024}, author = {Yue, C and Ma, X and Yang, W and Liu, Y and Yang, Z and Hou, R and Yan, X and Yang, M and Su, X and Liu, S}, title = {Characterization of Bacteroides fragilis from the vagina of a giant panda (Ailuropoda melanoleuca) with vaginitis.}, journal = {BMC veterinary research}, volume = {20}, number = {1}, pages = {528}, pmid = {39605068}, issn = {1746-6148}, mesh = {Female ; Animals ; *Ursidae/microbiology ; *Bacteroides fragilis/isolation &amp; purification/genetics ; *RNA, Ribosomal, 16S/genetics ; *Phylogeny ; *Vagina/microbiology ; Anti-Bacterial Agents/therapeutic use/pharmacology ; Vaginitis/veterinary/microbiology/drug therapy ; Bacteroides Infections/veterinary/microbiology/drug therapy ; Drug Resistance, Bacterial ; }, abstract = {BACKGROUND: Bacteroides fragilis is a prevalent anaerobic bacterium typically resides in the human vagina. It is known to potentially induce infections under specific conditions. Interestingly, there have been no previous reports of B. fragilis being isolated from the vagina of giant pandas.<br><br>CASE PRESENTATION: A novel strain of anaerobic bacteria was isolated from the vaginal tract of a giant panda exhibiting symptoms of vaginitis. This strain, designated as GPBF01, was identified as Bacteroides fragilis, a species commonly found in the vaginal microbiome of humans and other animals. After purifying of the single colony, a series of evaluations were conducted including morphological examination, physiological and biochemical identification, antibiotic resistance analysis, resistance genes detection, 16S rRNA sequence, and phylogenetic tree sequence analysis to investigate its biological characteristics. The findings indicated the presence of a predominant anaerobic bacterium, which was identified as B. fragilis and temporarily named GPBF01 with unique biological traits not previously.<br><br>CONCLUSIONS: This study is the first to report B. fragilis in the vaginal tract of giant pandas. The analysis of antibiotic resistance patterns among anaerobic bacteria, as conducted in this research, is critical for informing the selection of appropriate antimicrobial agents in the clinical treatment of vaginitis in this species. The findings of this report substantially enhance the scientific basis needed to understand the etiology and refine therapeutic approaches for vaginitis in giant pandas.}, }
@article {pmid39605008, year = {2024}, author = {Bush, JR and Alfa, MJ}, title = {Consumption of resistant potato starch produces changes in gut microbiota that correlate with improvements in abnormal bowel symptoms: a secondary analysis of a clinical trial.}, journal = {BMC nutrition}, volume = {10}, number = {1}, pages = {152}, pmid = {39605008}, issn = {2055-0928}, abstract = {BACKGROUND: Studies have linked a lack of dietary fibre, including resistant starch (RS), to disease-associated changes in intestinal bacteria. Healthy people often report abnormal bowel symptoms (ABS), including bloating, constipation, abdominal pain, and diarrhea, however, connections between these symptoms and the gut microbiota are poorly understood. Determining correlations between ABS and taxonomic groups may provide predictive value for using prebiotics to mitigate ABS in combination with stool microbiome testing.<br><br>METHODS: Post hoc analysis of a three-arm randomized, double-blind, placebo-controlled clinical trial evaluating the effects of 3.5&#xa0;g and 7&#xa0;g resistant potato starch (RPS) doses or placebo was conducted. The study population (n&#x2009;=&#x2009;70) were healthy adults aged 18-69 years old living in and around Guelph, ON. Participants evaluated their stools using the Bristol Stool Chart and also recorded any ABS daily. The presence of ABS was compared between treatment arms at baseline and changes in ABS were compared within treatment arms over 1- and 4-week periods. Pearson correlation analysis was used to identify significant relationships between changes in ABS and changes in bacterial taxa.<br><br>RESULTS: Abdominal pain, belching, bloating, constipation, diarrhea, gas, and feeling unwell were reported by participants at low levels at baseline. Neither RPS nor placebo had significant effects on mean ABS scores. However, we identified positive correlations between treatment-dependent changes in symptoms and changes in Granulicatella, Haemophilus, Lachnospira, Olsenella, Papillibacter, Turicibacter, unclassified Enterobacteriaceae, unclassified Fusobacteriaceae, unclassified Pasteurellaceae, and unclassified Gammaproteobacteria. We also identified negative correlations between treatment-dependent changes in symptoms and changes in Anaerotruncus, Dorea, RFN20, Victivallis, unclassified Coriobacteriaceae, and unclassified Oxalobacteraceae. These Pearson correlations were significant after correction for repeated testing. The mean relative abundance of these taxa did not change in response to treatment. Finally, macronutrient intake was unaffected by RPS or placebo treatments.<br><br>CONCLUSION: Changes in ABS can be positively or negatively correlated with changes in specific gut microbiota, creating opportunities for personalized microbiome-targeted interventions to resolve ABS.<br><br>TRIAL REGISTRATION: The trial was registered at ClinicalTrials.gov (NCT05242913) on February 16, 2022.}, }
@article {pmid39604724, year = {2024}, author = {Knight, CG and Nicolitch, O and Griffiths, RI and Goodall, T and Jones, B and Weser, C and Langridge, H and Davison, J and Dellavalle, A and Eisenhauer, N and Gongalsky, KB and Hector, A and Jardine, E and Kardol, P and Maestre, FT and Schädler, M and Semchenko, M and Stevens, C and Tsiafouli, M&#x391; and Vilhelmsson, O and Wanek, W and de Vries, FT}, title = {Soil microbiomes show consistent and predictable responses to extreme events.}, journal = {Nature}, volume = {}, number = {}, pages = {}, pmid = {39604724}, issn = {1476-4687}, abstract = {Increasing extreme climatic events threaten the functioning of terrestrial ecosystems[1,2]. Because soil microbes govern key biogeochemical processes, understanding their response to climate extremes is crucial in predicting the consequences for ecosystem functioning[3,4]. Here we subjected soils from 30 grasslands across Europe to four contrasting extreme climatic events under common controlled conditions (drought, flood, freezing and heat), and compared the response of soil microbial communities and their functioning with those of undisturbed soils. Soil microbiomes exhibited a small, but highly consistent and phylogenetically conserved, response under the imposed extreme events. Heat treatment most strongly impacted soil microbiomes, enhancing dormancy and sporulation genes and decreasing metabolic versatility. Microbiome response to heat in particular could be predicted by local climatic conditions and soil properties, with soils that do not normally experience the extreme conditions being imposed being most vulnerable. Our results suggest that soil microbiomes from different climates share unified responses to extreme climatic events, but that predicting the extent of community change may require knowledge of the local microbiome. These findings advance our understanding of soil microbial responses to extreme events, and provide a first step for making general predictions about the impact of extreme climatic events on soil functioning.}, }
@article {pmid39604625, year = {2024}, author = {Huelsmann, M and Schubert, OT and Ackermann, M}, title = {A framework for understanding collective microbiome metabolism.}, journal = {Nature microbiology}, volume = {9}, number = {12}, pages = {3097-3109}, pmid = {39604625}, issn = {2058-5276}, support = {180575//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; 180575//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; 180575//Schweizerischer Nationalfonds zur F&#xf6;rderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; 542389//Simons Foundation/ ; 542395//Simons Foundation/ ; 101023360//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 Marie Sk&#x142;odowska-Curie Actions (H2020 Excellent Science - Marie Sk&#x142;odowska-Curie Actions)/ ; }, mesh = {*Microbiota/physiology ; *Bacteria/metabolism/genetics ; Proteome/metabolism ; Carbon Cycle ; Selection, Genetic ; Humans ; Metabolic Networks and Pathways ; Bacterial Proteins/metabolism/genetics ; }, abstract = {Microbiome metabolism underlies numerous vital ecosystem functions. Individual microbiome members often perform partial catabolism of substrates or do not express all of the metabolic functions required for growth. Microbiome members can complement each other by exchanging metabolic intermediates and cellular building blocks to achieve a collective metabolism. We currently lack a mechanistic framework to explain why microbiome members adopt partial metabolism and how metabolic functions are distributed among them. Here we argue that natural selection for proteome efficiency-that is, performing essential metabolic fluxes at a minimal protein investment-explains partial metabolism of microbiome members, which underpins the collective metabolism of microbiomes. Using the carbon cycle as an example, we discuss motifs of collective metabolism, the conditions under which these motifs increase the proteome efficiency of individuals and the metabolic interactions they result in. In summary, we propose a mechanistic framework for how collective metabolic functions emerge from selection on individuals.}, }
@article {pmid39604623, year = {2024}, author = {Procházková, N and Laursen, MF and La Barbera, G and Tsekitsidi, E and Jørgensen, MS and Rasmussen, MA and Raes, J and Licht, TR and Dragsted, LO and Roager, HM}, title = {Gut physiology and environment explain variations in human gut microbiome composition and metabolism.}, journal = {Nature microbiology}, volume = {9}, number = {12}, pages = {3210-3225}, pmid = {39604623}, issn = {2058-5276}, support = {NNF19OC0056246//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF19OC0056246//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF19OC0056246//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF19OC0056246//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF19OC0056246//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF19OC0056246//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF19OC0056246//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF19OC0056246//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Feces/microbiology ; Adult ; Hydrogen-Ion Concentration ; Male ; Female ; Bacteria/classification/metabolism/genetics/isolation &amp; purification ; Gastrointestinal Transit/physiology ; Young Adult ; Middle Aged ; Diet ; Fermentation ; Gastrointestinal Tract/microbiology/metabolism ; Methane/metabolism ; Healthy Volunteers ; }, abstract = {The human gut microbiome is highly personal. However, the contribution of gut physiology and environment to variations in the gut microbiome remains understudied. Here we performed an observational trial using multi-omics to profile microbiome composition and metabolism in 61 healthy adults for 9 consecutive days. We assessed day-to-day changes in gut environmental factors and measured whole-gut and segmental intestinal transit time and pH using a wireless motility capsule in a subset of 50 individuals. We observed substantial daily fluctuations, with intra-individual variations in gut microbiome and metabolism associated with changes in stool moisture and faecal pH, and inter-individual variations accounted for by whole-gut and segmental transit times and pH. Metabolites derived from microbial carbohydrate fermentation correlated negatively with the gut passage time and pH, while proteolytic metabolites and breath methane showed a positive correlation. Finally, we identified associations between segmental transit time/pH and coffee-, diet-, host- and microbial-derived metabolites. Our work suggests that gut physiology and environment are key to understanding the individuality of the human gut microbial composition and metabolism.}, }
@article {pmid39604530, year = {2024}, author = {Shokoohi, E and Masoko, P}, title = {Microbiome of Xiphinema elongatum (Nematoda, Longidoridae), isolated from water berry.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {29494}, pmid = {39604530}, issn = {2045-2322}, mesh = {Animals ; *Microbiota ; *Soil Microbiology ; South Africa ; Nematoda/microbiology ; Bacteria/classification/isolation &amp; purification/genetics ; Soil/parasitology ; Fruit/microbiology/parasitology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The soil microbiome is crucial for the environment and significantly impacts the ecosystem. Understanding the microbiome and its interaction with soil microorganisms is essential for improving ecological and environmental strategies. In this study, Xiphinema elongatum nematodes were collected from water berry in Sovenga Hills, Limpopo Province, South Africa, and were analyzed their associated bacterial communities using metabarcoding analysis. The findings revealed that X. elongatum forms associations with a wide range of bacterial species. Among the most abundant species identified, we found Sphingomonas sp., a bacterial species commonly found in various habitats and primarily beneficial to plants, and Candidatus Xiphinematobacter, a bacterial species commonly found in nematode species of Xiphinema as an endosymbiont. The analysis using principal component analysis (PCA) revealed that the abundance of X. elongatum in the soil is inversely correlated with clay content (r = -0.52) and soil pH levels (r = -0.98), and directly correlated with soil sand content (r = 0.88). This study provides valuable insights into the bacterial species associated with plant-parasitic nematodes in trees in South Africa. It underscores the presence of various potentially detrimental and beneficial nematode-associated bacteria. The results could potentially influence the overall quality of the soil, leading to implications for the productivity and yield of fruit crops. Additionally, the results help us understand the interaction between bacteria and X. elongatum.}, }
@article {pmid39604394, year = {2024}, author = {Akiyama, S and Nishijima, S and Kojima, Y and Kimura, M and Ohsugi, M and Ueki, K and Mizokami, M and Hattori, M and Tsuchiya, K and Uemura, N and Kawai, T and Bork, P and Nagata, N}, title = {Multi-biome analysis identifies distinct gut microbial signatures and their crosstalk in ulcerative colitis and Crohn's disease.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {10291}, pmid = {39604394}, issn = {2041-1723}, mesh = {Humans ; *Colitis, Ulcerative/microbiology/genetics/virology ; *Crohn Disease/microbiology ; *Gastrointestinal Microbiome/genetics ; *Feces/microbiology ; Male ; *Metagenomics/methods ; Female ; *Bacteriophages/genetics ; Adult ; Escherichia coli/genetics/metabolism ; Middle Aged ; Japan ; Fungi/genetics ; Bacteria/genetics/metabolism/classification ; Metagenome/genetics ; Saccharomyces cerevisiae/genetics ; Bifidobacterium/genetics ; Virome/genetics ; Enterococcus faecium/genetics/pathogenicity ; Fatty Acids, Volatile/metabolism ; Young Adult ; China ; Case-Control Studies ; }, abstract = {The integrative multi-kingdom interaction of the gut microbiome in ulcerative colitis (UC) and Crohn's disease (CD) remains underinvestigated. Here, we perform shotgun metagenomic sequencing of feces from patients with UC and CD, and healthy controls in the Japanese 4D cohort, profiling bacterial taxa, gene functions, and antibacterial genes, bacteriophages, and fungi. External metagenomic datasets from the US, Spain, the Netherlands, and China were analyzed to validate our multi-biome findings. We found that Enterococcus faecium and Bifidobacterium spp. were enriched in both diseases. Enriched Escherichia coli was characteristic of CD and was linked to numerous antibiotic resistance genes involved in efflux pumps and adherent-invasive Escherichia coli virulence factors. Virome changes correlated with shifts in the bacteriome, including increased abundances of phages encoding pathogenic genes. Saccharomyces paradoxus and Saccharomyces cerevisiae were enriched in UC and CD, respectively. Saccharomyces cerevisiae and Escherichia coli had negative associations with short-chain fatty acid (SCFA)-producing bacteria in CD. Multi-biome signatures and their interactions in UC and CD showed high similarities between Japan and other countries. Since bacteria, phages, and fungi formed multiple hubs of intra- or trans-kingdom networks with SCFA producers and pathobionts in UC and CD, an approach targeting the interaction network may hold therapeutic promise.}, }
@article {pmid39604384, year = {2024}, author = {Lima, HS and Mancine, N and Peruchi, GB and Francisco, CS and Wang, N and de Souza, RSC and Armanhi, JSL and Coletta-Filho, HD}, title = {Microbial community of cultivated and uncultivated citrus rhizosphere microbiota in Brazil.}, journal = {Scientific data}, volume = {11}, number = {1}, pages = {1294}, pmid = {39604384}, issn = {2052-4463}, mesh = {*Citrus/microbiology ; *Microbiota ; Brazil ; *Rhizosphere ; *RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; Bacteria/classification/genetics ; Plant Roots/microbiology ; }, abstract = {The rhizosphere microbiome is known to contain beneficial microorganisms that promote plant growth and increase tolerance to abiotic and biotic stresses. Understanding citrus microbiome diversity and the percentage of diversity that can be recovered in the laboratory is essential for developing innovative approaches to improve plant health and promote sustainable agricultural practices. However, information about the citrus root microbiome, especially in the context of exploring commercial citrus growing areas to identify beneficial plant growth-promoting rhizobacteria (PGPR), is scarce. Here, we present the microbiome data of healthy citrus trees sampled from geographical regions of São Paulo and Amazonas States, in Brazil. The resulting rhizosphere microbiome data comprise an average of 126,180 and 138,707 high-quality reads for the 16S rRNA V3-V4 and ITS1-5F regions, respectively. The taxonomic analysis of cultivated diversity revealed a total of 91 bacterial genera recovered in the laboratory. These data provide valuable information for understanding how the microbiome supports citrus plants in different environments and for developing new strategies to improve crop productivity by using PGPR.}, }
@article {pmid39604327, year = {2024}, author = {Saeed, H and Díaz, LA and Gil-Gómez, A and Burton, J and Bajaj, J and Romero-Gomez, M and Arrese, M and Arab, JP and Khan, MQ}, title = {Microbiome-Centered Therapies for the Management of Metabolic Dysfunction-Associated Steatotic Liver Disease.}, journal = {Clinical and molecular hepatology}, volume = {}, number = {}, pages = {}, doi = {10.3350/cmh.2024.0811}, pmid = {39604327}, issn = {2287-285X}, abstract = {Metabolic dysfunction-associated steatotic liver disease (MASLD) is a significant global health issue, affecting over 30% of the population worldwide due to the rising prevalence of metabolic risk factors such as obesity and type 2 diabetes mellitus (T2DM). This spectrum of liver disease ranges from isolated steatosis to more severe forms such as steatohepatitis, fibrosis, and cirrhosis. Recent studies highlight the role of gut microbiota in MASLD pathogenesis, showing that dysbiosis significantly impacts metabolic health and the progression of liver disease. This review critically evaluates current microbiome-centered therapies in MASLD management, including prebiotics, probiotics, synbiotics, fecal microbiota transplantation (FMT), and emerging therapies such as engineered bacteria and bacteriophage therapy. We explore the scientific rationale, clinical evidence, and potential mechanisms by which these interventions influence MASLD. The gut-liver axis is crucial in MASLD, with notable changes in microbiome composition linked to disease progression. For instance, specific microbial profiles and reduced alpha diversity are associated with MASLD severity. Therapeutic strategies targeting the microbiome could modulate disease progression by improving gut permeability, reducing endotoxin-producing bacteria, and altering bile acid metabolism. Although promising, these therapies require further research to fully understand their mechanisms and optimize their efficacy. This review integrates findings from clinical trials and experimental studies, providing a comprehensive overview of microbiome-centered therapies' potential in managing MASLD. Future research should focus on personalized strategies, utilizing microbiome features, blood metabolites, and customized dietary interventions to enhance the effectiveness of these therapies.}, }
@article {pmid39603890, year = {2024}, author = {Sutherland, DB and Kato, LM and Fagarasan, S}, title = {Breaking down IgA: Tomasiella immunophila enlightens microbiome-immune interactions.}, journal = {Trends in immunology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.it.2024.11.003}, pmid = {39603890}, issn = {1471-4981}, abstract = {The recent discovery by Lu and colleagues of Tomasiella immunophila, a bacterium that degrades IgA, offers insights into microbial influences on mucosal immunity and evolutionary immune trade-offs. By modulating IgA titers, T. immunophila influences the dynamic interactions and balance between the host and pathogen. This has implications for immune health, microbiome research, and therapeutics.}, }
@article {pmid39603824, year = {2024}, author = {Li, N and Wang, M and Liu, F and Wu, P and Wu, F and Xiao, H and Kang, Q and Li, Z and Yang, S and Wu, G and Tan, X and Yang, Q}, title = {Bioorthogonal Engineering of Bacterial Outer Membrane Vesicles for NIR-II Fluorescence Imaging-Guided Synergistic Enhanced Immunotherapy.}, journal = {Analytical chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.analchem.4c04449}, pmid = {39603824}, issn = {1520-6882}, abstract = {The efficacy of immunotherapy in treating triple-negative breast cancer (TNBC) has been restricted due to its low immunogenicity and suppressive immune microenvironment. Bacterial outer membrane vesicles (OMVs) have emerged as innovative immunotherapeutic agents in antitumor therapy by stimulating the innate immune system, but intricate modifications and undesirable multiple dose administration severely hinder their utility. Herein, a two-step bacterial metabolic labeling technique was utilized for the bioorthogonal engineering of OMVs. At first, d-propargylglycine (DPG, an alkyne-containing d-amino acid) was introduced into the incubation process of probiotic Escherichia coli 1917 (Ecn) to produce DPG-functionalized OMVs, which were subsequently conjugated with azide-functionalized new indocyanine green (IR820) to yield OMV-DPG-IR820. The combination of phototherapy and immunostimulation of OMV-DPG-IR820 effectively arouses adaptive immune responses, causing maturation of dendritic cells, infiltration of T cells, repolarization of the M2 macrophage to the M1 macrophage, and upregulation of inflammatory factors. Remarkably, OMV-DPG-IR820 demonstrated tumor-targeting capabilities with guidance provided by near-infrared II (NIR-II) fluorescence imaging, leading to remarkable inhibition on both primary and distant tumors and preventing metastasis without causing noticeable adverse reactions. This study elucidates a sophisticated bioorthogonal engineering strategy for the design and production of functionalized OMVs and provides novel perspectives on the microbiome-mediated reversal of TNBC through a precise and efficient immunotherapy.}, }
@article {pmid39603712, year = {2024}, author = {Arrington, HB and Lee, SG and Lee, JH and Covi, JA}, title = {Assessment of the cyst wall and surface microbiota in dormant embryos of the Antarctic calanoid copepod, Boeckella poppei.}, journal = {Environmental microbiology reports}, volume = {16}, number = {6}, pages = {e70035}, doi = {10.1111/1758-2229.70035}, pmid = {39603712}, issn = {1758-2229}, support = {PE24160//Korea Polar Research Institute (KOPRI)/ ; PM24030//Korea Polar Research Institute (KOPRI)/ ; 20200610//Korea Institute of Marine Science &amp; Technology Promotion (KIMST)/ ; //Ministry of Oceans and Fisheries/ ; //National Science Foundation/ ; //National Science Foundation/ ; //College of Arts and Sciences, University of North Carolina at Wilmington/ ; }, mesh = {Animals ; *Copepoda/microbiology ; *Microbiota ; Antarctic Regions ; RNA, Ribosomal, 16S/genetics ; Embryo, Nonmammalian/microbiology ; Microscopy, Electron, Scanning ; Biofilms/growth &amp; development ; Bacteria/genetics/classification/isolation &amp; purification/metabolism ; Zooplankton/microbiology ; }, abstract = {Embryos of zooplankton from inland waters and estuaries can remain viable for years in an extreme state of metabolic suppression. How these embryos resist microbial attack with limited metabolic capacity for immune defence or repair is unknown. As a first step in evaluating resistance to microbial attack in dormant zooplankton, surface colonization of the Antarctic freshwater copepod, Boeckella poppei, was evaluated. Scanning electron micrographs demonstrate the outer two layers of a five-layered cyst wall in B. poppei fragment and create a complex environment for microbial colonization. By contrast, the third layer remains undamaged during years of embryo storage in native sediment. The absence of damage to the third layer indicates that it is resistant to degradation by microbial enzymes. Scanning electron microscopy and microbiome analysis using the 16S ribosomal subunit gene and internal transcribed spacer (ITS) region demonstrate the presence of a diverse microbial community on the embryo surface. Coverage of the embryos with microbial life varies from a sparse population with individual microbes to complete coverage by a thick biofilm. Extracellular polymeric substance binds debris and provides a structural element for the microbial community. Frequent observation of bacterial fission indicates that the biofilm is viable in stored sediments.}, }
@article {pmid39603509, year = {2024}, author = {Shiraz, MG and Nielsen, J and Widmann, J and Chung, KHK and Davis, TP and Rasmussen, C and Scavenius, C and Enghild, JJ and Martin-Gallausiaux, C and Singh, Y and Javed, I and Otzen, DE}, title = {Young rat microbiota extracts strongly inhibit fibrillation of α-synuclein and protect neuroblastoma cells and zebrafish against α-synuclein toxicity.}, journal = {Molecules and cells}, volume = {}, number = {}, pages = {100161}, doi = {10.1016/j.mocell.2024.100161}, pmid = {39603509}, issn = {0219-1032}, abstract = {The clinical manifestations of Parkinson's Disease (PD) are driven by aggregation of α-Synuclein (α-Syn) in the brain. However, there is increasing evidence that PD may be initiated in the gut and thence spread to the brain, e.g. via the vagus nerve. Many studies link PD to changes in the gut microbiome, and bacterial amyloid has been shown to stimulate α-syn aggregation. Yet we are not aware of any studies reporting on a direct connection between microbiome components and α-Syn aggregation. Here we report that soluble extract from the gut microbiome of the rats, particularly young rats transgenic for PD, show a remarkably strong ability to inhibit in vitro α-Syn aggregation and keep it natively unfolded and monomeric. The active component(s) are heat-labile molecule(s) of around 30-100 kDa size which are neither nucleic acid nor lipid. Proteomic analysis identified several proteins whose concentrations in different rat samples correlated with the samples' anti-inhibitory activity, while a subsequent pulldown assay linked the protein chaperone DnaK with the inhibitory activity of young rat's microbiome, confirmed in subsequent in vitro assays. Remarkably, the microbiome extracts also protected neuroblastoma SH-SY5Y cells and zebrafish embryos against α-Syn toxicity. Our study sheds new light on the gut microbiome as a potential source of protection against PD and opens up for new microbiome-based therapeutic strategies.}, }
@article {pmid39603488, year = {2024}, author = {Wang, Y and Wu, W and Zeng, F and Meng, X and Peng, M and Wang, J and Chen, Z and Liu, W}, title = {The role of kynurenine pathway metabolism mediated by exercise in the microbial-gut-brain axis in Alzheimer's disease.}, journal = {Experimental neurology}, volume = {}, number = {}, pages = {115070}, doi = {10.1016/j.expneurol.2024.115070}, pmid = {39603488}, issn = {1090-2430}, abstract = {In recent years, the role of the microbiome-gut-brain axis in the pathogenesis of Alzheimer's disease (AD) has garnered increasing attention. Specifically, tryptophan metabolism via the kynurenine pathway (KP) plays a crucial regulatory role in this axis. This study reviews how exercise regulates the microbiome-gut-brain axis by influencing kynurenine pathway metabolism, thereby exerting resistance against AD. This paper also discusses how exercise positively impacts AD via the microbiome-gut-brain axis by modulating the endocrine, autonomic nervous, and immune systems. Although the specific mechanisms are not fully understood, research indicates that exercise may optimize tryptophan metabolism by promoting the growth of beneficial microbiota and inhibiting harmful microbiota, producing substances that are beneficial to the nervous system and combating AD. The aim of this review is to provide new perspectives and potential intervention strategies for the prevention and treatment of AD by exploring the links between exercise, KP and the gut-brain axis.}, }
@article {pmid39603393, year = {2024}, author = {Chen, Z and Liu, S and Song, F and Hou, Z and Zhou, H and Fan, Y and Wang, R and Liu, Z}, title = {Integrated metabolome and microbiome strategy reveals the therapeutic effect of nervonic acid on Alzheimer's disease rats.}, journal = {The Journal of nutritional biochemistry}, volume = {}, number = {}, pages = {109813}, doi = {10.1016/j.jnutbio.2024.109813}, pmid = {39603393}, issn = {1873-4847}, abstract = {Alzheimer's disease (AD) is a complex neurodegenerative disease. Nervonic acid is a component of breast milk and is also found in fish oil and specific vegetable oils. Studies have shown that nervonic acid is essential for the development of the human nervous system. In this study, Morris water maze (MWM) test and pathological analysis showed that nervonic acid could improve cognitive deficits and brain nerve damage in AD rats. Then, through sequencing, we found that nervonic acid increased the abundance of beneficial bacteria such as Lactobacillus and Bacteroides, and decreased the abundance of Pseudomonadaceae_Pseudomonas. Not only that, nervonic acid also regulates the production of short-chain fatty acids (SCFA) and the levels of 29 fecal metabolites, and affects the metabolism of linoleic acid, α-linolenic acid, arachidonic acid, and sphingolipid. Finally, we verified the regulatory effect of nervonic acid on metabolic enzyme activity.}, }
@article {pmid39603332, year = {2024}, author = {Wai-Yan Tang, J and Cheuk-Fung Hau, C and Tong, WM and Watt, RM and Yiu, CKY and Kar-Man Shum, K}, title = {Alterations of Oral Microbiota in Young Children with Autism: Unraveling Potential Biomarkers for Early Detection.}, journal = {Journal of dentistry}, volume = {}, number = {}, pages = {105486}, doi = {10.1016/j.jdent.2024.105486}, pmid = {39603332}, issn = {1879-176X}, abstract = {OBJECTIVES: This study investigated the oral microbiota in young children with autism spectrum disorder (ASD) to determine possible alterations in microbial composition and identify potential biomarkers for early detection.<br><br>METHODS: Dental plaque samples from 25 children with ASD (aged 3-6 years; M&#x202f;=&#x202f;4.79, SD&#x202f;=&#x202f;0.83) and 30 age- and sex-matched typically developing (TD) children were analyzed using 16S rRNA sequencing.<br><br>RESULTS: The results showed lower bacterial diversity in children with ASD compared to controls, with distinct microbial compositions in the ASD and TD groups. Six discriminatory species (Microbacterium flavescens, Leptotrichia sp. HMT-212, Prevotella jejuni, Capnocytophaga leadbetteri, Leptotrichia sp. HMT-392, and Porphyromonas sp. HMT-278) were identified in the oral microbiota of ASD children, while five discriminatory species (Fusobacterium nucleatum subsp. polymorphum, Schaalia sp. HMT-180, Leptotrichia sp. HMT-498, Actinomyces gerencseriae, and Campylobacter concisus) were identified in TD controls. A model generated by random forest and leave-one-out cross-validation achieved an accuracy of 0.813. Receiver operating characteristic analysis yielded a sensitivity of 0.778, a specificity of 0.857, and an AUC (area under curve) of 0.937 (95% CI: 0.82 - 1.00) for differentiating children with and without ASD.<br><br>CONCLUSION: The present study has unveiled significant disparities in the oral microbial composition between ASD and TD children.<br><br>SIGNIFICANCE: These findings contribute to understanding the microbiome-brain connection in ASD and its implications for early detection and management. Further research is needed to validate these oral bacterial biomarkers and explore their mechanistic association with ASD pathophysiology.}, }
@article {pmid39603245, year = {2024}, author = {Pietrasanta, C and Carlosama, C and Lizier, M and Fornasa, G and Jost, TR and Carloni, S and Giugliano, S and Silvestri, A and Brescia, P and De Ponte Conti, B and Braga, D and Mihula, M and Morosi, L and Bernardinello, A and Ronchi, A and Martano, G and Mosca, F and Penna, G and Grassi, F and Pugni, L and Rescigno, M}, title = {Prenatal antibiotics reduce breast milk IgA and induce dysbiosis in mouse offspring, increasing neonatal susceptibility to bacterial sepsis.}, journal = {Cell host &amp; microbe}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.chom.2024.11.001}, pmid = {39603245}, issn = {1934-6069}, abstract = {Antibiotics (Abx) are administered to 20%-30% of pregnant women, but their effects on neonatal immune development are poorly understood. We show that newborn mice born to Abx-treated dams are more susceptible to late-onset sepsis. This susceptibility is linked to lower maternal breast milk immunoglobulin A (IgA), neonatal fecal IgA, and IgA coating of intestinal bacteria, thus causing the translocation of intestinal pathobionts. Weaned young adults born to Abx-treated mothers had reduced IgA+ plasma cells in the ileum and colon, fecal secretory IgA (SIgA), colonic CD4[+] T regulatory lymphocytes and T helper 17-like lymphocytes, and a less diverse fecal microbiome. However, treatment with apyrase, which restores SIgA secretion, prompted IgA production in breast milk and protected pups from sepsis. Additionally, breast milk from untreated mothers rescued the phenotypes of pups born to Abx-treated mothers. Our data highlight the impact of prenatal Abx on breast milk IgA and their long-term influence on intestinal mucosal immune function mediated by breastfeeding.}, }
@article {pmid39603188, year = {2024}, author = {Xie, C and Liang, Q and Cheng, J and Yuan, Y and Xie, L and Ji, J}, title = {Transplantation of fecal microbiota from low to high residual feed intake chickens: Impacts on RFI, microbial community and metabolites profiles.}, journal = {Poultry science}, volume = {104}, number = {1}, pages = {104567}, doi = {10.1016/j.psj.2024.104567}, pmid = {39603188}, issn = {1525-3171}, abstract = {Improving feed efficiency is vital to bolster profitability and sustainability in poultry production. Although several studies have established links between gut microbiota and feed efficiency, the direct effects remain unclear. In this study, two distinct lines of Huiyang bearded chickens, exhibiting significant differences in residual feed intake (RFI), were developed after 15 generations of selective breeding. Fecal microbiota transplantation (FMT) from low RFI (LRFI) chickens to high RFI (HRFI) chickens resulted in a reduction trend in RFI, decreasing from 5.65 to 4.49 in the HRFI recipient chickens (HFMT). Microbiota composition and functional profiles in LRFI and HFMT chickens formed a distinct cluster compared to HRFI chickens. Using 16S rDNA sequencing and RandomForest analysis, Slackia, Peptococcus, Blautia, and Dorea were identified as key microbial markers associated with feed efficiency. Additionally, untargeted metabolomics identified common differential metabolites between HFMT and LRFI vs. HRFI groups. Correlation analysis showed significant correlations between these microbial markers and differential metabolites. These findings provide a foundation for microbiome-based strategies to improve feed efficiency in poultry.}, }
@article {pmid39602985, year = {2024}, author = {Gao, X and Chen, J and Yu, K and Bu, Y and Wang, L and Yu, X}, title = {Exposure to polypropylene microplastics induces the upregulation of protein digestion-associated genes and microbiome reorganization in the octocoral Junceella squamata.}, journal = {Marine pollution bulletin}, volume = {210}, number = {}, pages = {117331}, doi = {10.1016/j.marpolbul.2024.117331}, pmid = {39602985}, issn = {1879-3363}, abstract = {Microplastics, a new type of pollutants found in coral reefs, have attracted increasing attention. However, most of the current research focuses on the scleractinian corals and few reports on Octocorallia. To reveal the impact of microplastic exposure on Octocorallia, we analyzed the transcriptional response of the coral hosts Junceella squamata along with changes to the diversity and community structure of its symbiotic bacteria following exposure to polystyrene microplastics. These results suggest that the microplastics have adverse impacts on nutrient metabolism and absorption in J. squamata. The symbiotic bacteria of J. squamata exhibited a clear response after exposure to microplastics, which may also reflect an adaptation mechanism of corals, and help to maintain the physiological function of coral symbiotic function under the exposure of microplastics. This study has revealed the impact of microplastic exposure on J. squamata, providing new insights for coral protection against the background of increased microplastics pollution.}, }
@article {pmid39602306, year = {2024}, author = {Pasolli, E and Mauriello, IE and Avagliano, M and Cavaliere, S and De Filippis, F and Ercolini, D}, title = {Bifidobacteriaceae diversity in the human microbiome from a large-scale genome-wide analysis.}, journal = {Cell reports}, volume = {43}, number = {12}, pages = {115027}, doi = {10.1016/j.celrep.2024.115027}, pmid = {39602306}, issn = {2211-1247}, abstract = {We performed a large-scale genome-wide analysis aiming to investigate the prevalence and strain-level diversity of Bifidobacteriaceae species in the human microbiome. We considered 9,528 publicly available human metagenomes and integrated them with 1,192 isolate genomes from different sources. The prevalence and abundance of Bifidobacteriaceae species in humans was linked to multiple host characteristics: they were reduced in older people and enriched in populations characterized by Westernized lifestyles with geography-specific patterns. Phylogenetic analysis highlighted 110 Bifidobacteriaceae species-level genome bins (SGBs), with 32 found in humans and 8 in food and probiotic sources. Functional annotation revealed a great diversity in carbohydrate-active enzyme families across these SGBs. We found potential subspecies for most of the SGBs prevalent in humans and identified patterns driven by age and geography. We provided evidence that strains used in probiotics were rarely identified in humans, with the only exception represented by Bifidobacterium animalis. We finally evaluated that the abundance of Bifidobacteriaceae species exhibited moderate and variable capabilities to predict health status in case-control studies.}, }
@article {pmid39602230, year = {2024}, author = {Millot, M and Imbert, C and Pouget, C and Girardot, M and Mambu, L}, title = {Lichen and its Microbiome as an Untapped Source of Anti-biofilm Compounds.}, journal = {Chemistry &amp; biodiversity}, volume = {}, number = {}, pages = {e202401557}, doi = {10.1002/cbdv.202401557}, pmid = {39602230}, issn = {1612-1880}, abstract = {Lichen substances have been firstly described in the 1870s and most of them have been evaluated for their activity on planktonic microorganisms (bacteria and fungi). More recently, microorganisms colonizing the lichen thallus have been isolated and identified giving access to a wild diversity of culturable microorganisms. The increasing research in lichens associated microbiome in recent years, has emphased a wide range of metabolites as a potential source of bioactive compounds. In parallel, humans are facing microbial resistance to conventional antimicrobial drugs. One of the reasons is the biofilm lifestyle of microorganisms. Indeed, the aggregation of microbial communities inside biofilms is now well-known and characterized and some possible ways to fight and destroy biofilms are identified (quorum sensing inhibitors,…). The present review aims to summarize the anti-biofilm potential of lichen metabolites and those from their associated microorganisms (bacteria and/or fungi). Are the metabolites isolated from lichens and their associated fungi displaying any anti-biofilm activity? This literature synthesis highlights the metabolites of interest as new anti-biofilm drugs and shows the lack of current biological research dealing with biofilm and lichen metabolites. Only two lichen metabolites, usnic acid and evernic acid, have been evaluated both as antifungal and antibacterial biofilm compounds.}, }
@article {pmid39602070, year = {2024}, author = {Ehis-Eriakha, CB and Chikere, CB and Akaranta, O and Akemu, SE}, title = {A comparative assesment of biostimulants in microbiome-based ecorestoration of polycyclic aromatic hydrocarbon polluted soil.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {}, number = {}, pages = {}, pmid = {39602070}, issn = {1678-4405}, abstract = {Polycyclic aromatic hydrocarbons (PAHs) pose severe environmental and public health risks due to their harmful and persistent nature. Therefore, developing sustainable and effective methods for PAH remediation is crucial. This study explores the biostimulation potential of various nutrient supplements in enhancing the metabolic activities of indigenous oleophilic bacteria to PAH degradation and removal. The physicochemical and microbiological characterization of the soil sample obtained from the aged crude oil spill site prior to bioremediation revealed the presence of PAH and other hydrocarbons, reduced nutrient availability as well as an appreciable population of PAH degrading bacteria such as strains of Pseudomonas, Enterobacter, Kosakonia and Staphylococcus. The polluted soil treatment was conducted in six microcosms representing each nutrient supplement: casmes-CM, cocodust-CCD and osmocote-OSM slow-release fertilizers, NPK 20:10:10, casmes + cow dung - CM + CD and a control (unamended soil). Each pot contained 4 kg of soil spiked with 4% Escravos crude oil to a final concentration of 989 mg/kg of PAH, respectively. All treatments enhanced the activity of the indigenous bacteria to promote PAH removal (> 50%) after 35 days although CM + CD had the highest biostimulation effect (B. E.) of 56% with 71.77% PAH attenuation followed by NPK treatment with B. E. of 54.9% and 70.4% PAH removal, respectively. The order of degradation of PAHs from lowest to highest is: control > casmes > osmocote > cocodust > NPK > CM + CD. First-order kinetic model revealed soil microcosm amended with CM + CD had a higher k value (0.0342 day-1) and lower t½ (18.48 day) and this was relatively followed by NPK treated soil. Biostimulation is an effective bioremediation approach to PAH degradation, however, a combined nutrient regimen in the presence of PAH-degrading microbes is more potent and eco-friendly in driving this process.}, }
@article {pmid39574575, year = {2024}, author = {Nickols, WA and McIver, LJ and Walsh, A and Zhang, Y and Nearing, JT and Asnicar, F and Punčochář, M and Segata, N and Nguyen, LH and Hartmann, EM and Franzosa, EA and Huttenhower, C and Thompson, KN}, title = {Evaluating metagenomic analyses for undercharacterized environments: what's needed to light up the microbial dark matter?.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {39574575}, issn = {2692-8205}, support = {R24 DK110499/DK/NIDDK NIH HHS/United States ; U19 AI110820/AI/NIAID NIH HHS/United States ; }, abstract = {Non-human-associated microbial communities play important biological roles, but they remain less understood than human-associated communities. Here, we assess the impact of key environmental sample properties on a variety of state-of-the-art metagenomic analysis methods. In simulated datasets, all methods performed similarly at high taxonomic ranks, but newer marker-based methods incorporating metagenomic assembled genomes outperformed others at lower taxonomic levels. In real environmental data, taxonomic profiles assigned to the same sample by different methods showed little agreement at lower taxonomic levels, but the methods agreed better on community diversity estimates and estimates of the relationships between environmental parameters and microbial profiles.}, }
@article {pmid39601988, year = {2024}, author = {Rekadwad, BN and Shouche, YS and Jangid, K}, title = {Oil spill pollution and diversity analyses of resistant bacteria isolated from soil across the Arabian Sea and Bay of Bengal coastlines.}, journal = {Environmental monitoring and assessment}, volume = {196}, number = {12}, pages = {1265}, pmid = {39601988}, issn = {1573-2959}, mesh = {*Bacteria/classification/isolation &amp; purification/genetics ; *Petroleum Pollution ; *Environmental Monitoring ; India ; *Soil Microbiology ; Biodiversity ; Bays/microbiology ; Drug Resistance, Bacterial ; }, abstract = {Pelagic transport causes oil pollution via international tanker routes in the open ocean across southern Asia and the Indian Territory. Nutrient-rich runoff from residential, commercial, and industrial wastes, oil tanker mishaps, and sailing flags have all resulted in pollution. The natural flow of ocean water from east to west dragged pollutants into Indian Territory. We have investigated that the severe deposition of oil spills and biohazardous wastes is causing faunal mortality. Microbiome analyses helped us understand the sample's microbial load. 16S amplicon metagenome analysis, followed by enumeration and confirmation using molecular methods, indicates the presence of diverse microbial profiles. The presence of non-native hydrocarbon- and AMR-resistant bacterial taxa, such as Brevundimonas, Staphylococcus spp., Mycolicibacterium, Spingomonas spp., Bacillus spp., Chitinophaga spp., Priestia spp., Domibacillus spp., Rossellomorea spp., and Acinetobacter spp., confirms the impacts of oil and urban pollution. This indicates that the coastal soil of Goa and Andhra Pradesh has hydrocarbon- and antibiotic-resistant bacteria, which confirms that the present pollution status and that high-traffic recreational activities put biodiversity and humans at risk of getting illnesses linked to antibiotic resistance.}, }
@article {pmid39601776, year = {2024}, author = {Mavros, CF and Bongers, M and Neergaard, FBF and Cusimano, F and Sun, Y and Kaufman, A and Richardson, M and Kammler, S and Kristensen, M and Sommer, MOA and Wang, HH}, title = {Bacteria Engineered to Produce Serotonin Modulate Host Intestinal Physiology.}, journal = {ACS synthetic biology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acssynbio.4c00453}, pmid = {39601776}, issn = {2161-5063}, abstract = {Bacteria in the gastrointestinal tract play a crucial role in intestinal motility, homeostasis, and dysfunction. Unraveling the mechanisms by which microbes impact the host poses many challenges due to the extensive array of metabolites produced or metabolized by bacteria in the gut. Here, we describe the engineering of a gut commensal bacterium, Escherichia coli Nissle 1917, to biosynthesize the human metabolite serotonin for examining the effects of microbially produced biogenic amines on host physiology. Upon oral administration to mice, our engineered bacteria reach the large intestine, where they produce serotonin. Mice treated with serotonin-producing bacteria exhibited biological changes in the gut at transcriptional and physiological levels. This work establishes a novel framework employing engineered bacteria to modulate luminal serotonin levels and suggests potential clinical applications of modified microbial therapeutics to address gut disorders in humans.}, }
@article {pmid39601521, year = {2024}, author = {Atkinson, CGF and Kerns, KA and Hendrickson, EL and He, X and Bor, B and McLean, JS}, title = {Complete genome of Nanosynbacter sp. strain BB002, isolated and cultivated from a site of periodontal disease.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0063724}, doi = {10.1128/mra.00637-24}, pmid = {39601521}, issn = {2576-098X}, abstract = {Nanosynbacter sp. strain BB002, was isolated from the human oral cavity on its basibiont bacterial host Actinomyces sp. oral taxon 171 strain F0337, related to Actinomyces oris. As a member of the Saccharibacteria within the candidate phylum radiation group (CPR), its reduced genome facilitates the survival as an ultrasmall (<0.2 μm) epibiont.}, }
@article {pmid39601429, year = {2024}, author = {Wang, Y and Wang, Y and Zhou, Y and Feng, Y and Sun, T and Xu, J}, title = {Tumor-related fungi and crosstalk with gut fungi in the tumor microenvironment.}, journal = {Cancer biology &amp; medicine}, volume = {}, number = {}, pages = {}, doi = {10.20892/j.issn.2095-3941.2024.0240}, pmid = {39601429}, issn = {2095-3941}, support = {82373113 to XJ//National Natural Science Foundation of China/ ; 22-321-31-04 to ST//Shenyang Public Health R&amp;D Special Project/ ; XLYC1907160 to XJ//Liaoning Revitalization Talents Program/ ; YXJL-2020-0941-0752 to ST//Beijing Medical Award Foundation/ ; CORP-239-N27 to CH//Beijing Medical Award Foundation/ ; 320.6750.2020-12-21//Wu Jieping Medical Foundation/ ; 320.6750.2020-6-30 to ST//Wu Jieping Medical Foundation/ ; 202229 to ST//Fundamental Research Funds for the Central Universities/ ; 202230 to XJ//Fundamental Research Funds for the Central Universities/ ; }, abstract = {Most studies on the human gut microbiome have focused on the bacterial fraction rather than fungal biomics, which as resulted in an incomplete understanding of the fungal microbiome. Recent advances in microbiota detection and next-generation sequencing technology have boosted an increase in research on fungi. Symbiotic fungi have become increasingly influential in health and disease and modulate various physiologic functions within the host. Fungal infections can result in high morbidity and mortality rates and are life-threatening in some immunocompromised patients. In addition to bacterial dysbiosis, alterations in fungal communities are important and have been linked to many diseases, including asthma, mental illness, and various cancers. When investigating cancer it is imperative to consider the role of fungi alongside viruses and bacteria. This review examined the impact of intestinal fungi and peri-tumor fungi on tumorigenesis, cancer progression, and response to anticancer therapies. The review highlights the specific involvement of some fungal species in cancers include digestive tract tumors such as colorectal, pancreatic, liver, and gastric cancers, as well as non-digestive tract tumors such as lung, melanoma, breast, and ovarian cancers. Furthermore, fungal mechanisms of action, including fungus-host recognition and immune regulation, biofilm formation, toxin and metabolite production in the tumor microenvironment, and the complex effects of fungus-bacteria interactions on tumorigenesis and development, highlight the significance of potential biomarkers in cancer diagnosis and treatment.}, }
@article {pmid39601281, year = {2024}, author = {Rios-Carlos, M and Cervantes-García, D and Córdova-Dávalos, LE and Bermúdez-Humarán, LG and Salinas, E}, title = {Unraveling the gut-skin axis in atopic dermatitis: exploiting insights for therapeutic strategies.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2430420}, doi = {10.1080/19490976.2024.2430420}, pmid = {39601281}, issn = {1949-0984}, mesh = {*Dermatitis, Atopic/microbiology/therapy/drug therapy ; Humans ; *Gastrointestinal Microbiome ; *Skin/microbiology ; *Probiotics/therapeutic use ; *Prebiotics/administration &amp; dosage ; Animals ; Bacteria/metabolism/classification ; Fatty Acids, Volatile/metabolism ; }, abstract = {Gut microbiota exert functions of high importance in the intestine. Furthermore, there is increasing evidence for its role in immune regulation and maintenance of homeostasis in many physiological processes taking place in distant tissues. In particular, in this review, we explore the impact of metabolites produced by the gut microbiota on the development of atopic dermatitis (AD). Probiotics and prebiotics balance the microbiota and promote the generation of bacterial metabolites, such as short-chain fatty acids and tryptophan derivates, which promote the regulation of the exacerbated AD immune response through regulatory T cells and IL-10 and TGF-β cytokines. Metabolites also have a direct action on keratinocytes once they reach the bloodstream. Besides, probiotics decrease the levels of metabolites associated with AD onset, such as phenols. Understanding all these crosstalk processes between the gut and the skin reveals a number of possibilities, mainly through the manipulation of the gut microbiome, which may represent therapeutic strategies that can contribute to the standard treatments of AD patients to improve their quality of life.}, }
@article {pmid39601125, year = {2024}, author = {Cao, H and Tian, Q and Chu, L and Wu, L and Gao, H and Gao, Q}, title = {Lycium ruthenicum Murray anthocyanin-driven neuroprotection modulates the gut microbiome and metabolome of MPTP-treated mice.}, journal = {Food &amp; function}, volume = {}, number = {}, pages = {}, doi = {10.1039/d4fo01878h}, pmid = {39601125}, issn = {2042-650X}, abstract = {Emerging evidence suggests that Parkinson's disease (PD) is strongly associated with altered gut microbiota. The present study investigated the prophylactic effects of anthocyanins (ACNs) from Lycium ruthenicum Murray on Parkinson's disease based on microbiomics and metabolomics. In this study, sixty-six adult male C57BL/6J mice were randomized into the control group, model group, positive drug (Madopar) group, and low-, medium- and high-dose ACN groups. Behavioral experiments were conducted and pathological indicators were determined. Fresh feces were collected for microbiomic analysis using 16S rRNA sequencing. Urine and serum were analyzed by the UPLC-MS method for untargeted metabolomics. The results demonstrated that ACNs ameliorated 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP)-induced motor deficits, dopamine neuron death, and glial cell activation, while 100 mg kg[-1] and 200 mg kg[-1] ACNs were more neuroprotective than 50 mg kg[-1]. Mice with PD-like phenotypes have an altered gut microbiota composition, and ACNs may regulate this disorder by causing an increase in Firmicutes/Bacteroidota ratio and abundance of norank_f__Eubacterium_coprostanoligenes_group and a decrease in the abundance of norank_f__Muribaculaceae, Coriobacteriaceae_UCG-002 and Parvibacter. Furthermore, ACNs increased 14 urinary key metabolites such as DIMBOA-Glc and tauroursodeoxycholic acid, decreased N,N-dimethyllysine, and increased 12 serum key metabolites such as 1-methylguanine and 1-nitro-5-glutathionyl-6-hydroxy-5,6-dihydronaphthalene, and decreased lamivudine-monophosphate and 5-butyl-2- methylpyridine. The present study reveals that ACNs are protective against MPTP-induced PD in mice by modulating anti-inflammatory flora in the gut and endogenous metabolites in serum/urine, and the key mechanisms may be related to Coriobacteriaceae_UCG-002 and glycerophospholipid metabolic pathways. Our findings provide new insights into the pathogenesis and potential treatment of Parkinson's disease.}, }
@article {pmid39600755, year = {2024}, author = {Castro-Vidal, ZA and Mathew, F and Ibrahim, AA and Shubhangi, F and Cherian, RR and Choi, HK and Begum, A and Ravula, HK and Giri, H}, title = {The Role of Gastrointestinal Dysbiosis and Fecal Transplantation in Various Neurocognitive Disorders.}, journal = {Cureus}, volume = {16}, number = {10}, pages = {e72451}, pmid = {39600755}, issn = {2168-8184}, abstract = {This review explores the critical role of the human microbiome in neurological and neurodegenerative disorders, focusing on gut-brain axis dysfunction caused by dysbiosis, an imbalance in gut bacteria. Dysbiosis has been linked to diseases such as Alzheimer's disease, Parkinson's disease (PD), multiple sclerosis (MS), and stroke. The gut microbiome influences the central nervous system (CNS) through signaling molecules, including short-chain fatty acids, neurotransmitters, and metabolites, impacting brain health and disease progression. Emerging therapies, such as fecal microbiota transplantation (FMT), have shown promise in restoring microbial balance and alleviating neurological symptoms, especially in Alzheimer's and PD. Additionally, nutritional interventions such as probiotics, prebiotics, and specialized diets are being investigated for their ability to modify gut microbiota and improve patient outcomes. This review highlights the therapeutic potential of gut microbiota modulation but emphasizes the need for further clinical trials to establish the safety and efficacy of these interventions in neurological and mental health disorders.}, }
@article {pmid39600698, year = {2024}, author = {Liu, X and Li, B and Liang, L and Han, J and Mai, S and Liu, L}, title = {From microbes to medicine: harnessing the power of the microbiome in esophageal cancer.}, journal = {Frontiers in immunology}, volume = {15}, number = {}, pages = {1450927}, pmid = {39600698}, issn = {1664-3224}, mesh = {Humans ; *Esophageal Neoplasms/therapy/microbiology/immunology ; *Dysbiosis/therapy/microbiology ; *Gastrointestinal Microbiome/immunology ; Animals ; Probiotics/therapeutic use ; Microbiota/immunology ; }, abstract = {Esophageal cancer (EC) is a malignancy with a high incidence and poor prognosis, significantly influenced by dysbiosis in the esophageal, oral, and gut microbiota. This review provides an overview of the roles of microbiota dysbiosis in EC pathogenesis, emphasizing their impact on tumor progression, drug efficacy, biomarker discovery, and therapeutic interventions. Lifestyle factors like smoking, alcohol consumption, and betel nut use are major contributors to dysbiosis and EC development. Recent studies utilizing advanced sequencing have revealed complex interactions between microbiota dysbiosis and EC, with oral pathogens such as Porphyromonas gingivalis and Fusobacterium nucleatum promoting inflammation and suppressing immune responses, thereby driving carcinogenesis. Altered esophageal microbiota, characterized by reduced beneficial bacteria and increased pathogenic species, further exacerbate local inflammation and tumor growth. Gut microbiota dysbiosis also affects systemic immunity, influencing chemotherapy and immunotherapy efficacy, with certain bacteria enhancing or inhibiting treatment responses. Microbiota composition shows potential as a non-invasive biomarker for early detection, prognosis, and personalized therapy. Novel therapeutic strategies targeting the microbiota-such as probiotics, dietary modifications, and fecal microbiota transplantation-offer promising avenues to restore balance and improve treatment efficacy, potentially enhancing patient outcomes. Integrating microbiome-focused strategies into current therapeutic frameworks could improve EC management, reduce adverse effects, and enhance patient survival. These findings highlight the need for further research into microbiota-tumor interactions and microbial interventions to transform EC treatment and prevention, particularly in cases of late-stage diagnosis and poor treatment response.}, }
@article {pmid39600316, year = {2024}, author = {Chen, S and Wang, C and Zou, X and Li, H and Yang, G and Su, X and Mo, Z}, title = {Multi-omics insights implicate the remodeling of the intestinal structure and microbiome in aging.}, journal = {Frontiers in genetics}, volume = {15}, number = {}, pages = {1450064}, pmid = {39600316}, issn = {1664-8021}, abstract = {BACKGROUND: Aging can impair the ability of elderly individuals to fight infections and trigger persistent systemic inflammation, a condition known as inflammaging. However, the mechanisms underlying the development of inflammaging remain unknown.<br><br>METHODS: We conducted 16S rRNA sequencing of intestinal contents from young and old C57BL/6J mice to elucidate changes in gut microbiota diversity and microbial community composition after aging. Aging-related differential bacterial taxa were then identified, and their abundance trends were validated in human samples. The variances in intestinal barrier function and circulating endotoxin between groups were also assessed. Furthermore, widely targeted metabolomics was conducted to characterize metabolic profiles after aging and to investigate the key metabolic pathways enriched by the differential metabolites.<br><br>RESULTS: Our findings demonstrated an increase in relative proportion of pathogenic bacteria with age, a trend also revealed in healthy populations of different age groups. Additionally, aging individuals exhibited reduced intestinal barrier function and increased circulating endotoxin levels. Widely targeted metabolomics revealed a significant increase in various secondary bile acid metabolites after aging, positively correlated with the relative abundance of several aging-related bacterial taxa. Furthermore, old group had lower levels of various anti-inflammatory or beneficial metabolites. Enrichment analysis identified the starch and sucrose metabolism pathway as potentially the most significantly impacted signaling pathway during aging.<br><br>CONCLUSION: This study aimed to provide insights into the complex interactions involved in organismal inflammaging through microbial multi-omics. These findings lay a solid foundation for future research aimed at identifying novel biomarkers for the clinical diagnosis of aging-related diseases or potential therapeutic targets.}, }
@article {pmid39600252, year = {2024}, author = {Grupstra, CGB and Meyer-Kaiser, KS and Bennett, MJ and Andres, MO and Juszkiewicz, DJ and Fifer, JE and Da-Anoy, JP and Gomez-Campo, K and Martinez-Rugerio, I and Aichelman, HE and Huzar, AK and Hughes, AM and Rivera, HE and Davies, SW}, title = {Holobiont Traits Shape Climate Change Responses in Cryptic Coral Lineages.}, journal = {Global change biology}, volume = {30}, number = {11}, pages = {e17578}, doi = {10.1111/gcb.17578}, pmid = {39600252}, issn = {1365-2486}, support = {2048589//The National Science Foundation's Division of Ocean Sciences/ ; 2048678//The National Science Foundation's Division of Ocean Sciences/ ; }, mesh = {*Anthozoa/microbiology/physiology ; Animals ; *Climate Change ; *Coral Reefs ; *Symbiosis ; Microbiota ; Dinoflagellida/physiology ; }, abstract = {As ocean warming threatens reefs worldwide, identifying corals with adaptations to higher temperatures is critical for conservation. Genetically distinct but morphologically similar (i.e. cryptic) coral populations can be specialized to extreme habitats and thrive under stressful conditions. These corals often associate with locally beneficial microbiota (Symbiodiniaceae photobionts and bacteria), obscuring the main drivers of thermal tolerance. Here, we leverage a holobiont (massive Porites) with high fidelity for C15 photobionts to investigate adaptive variation across classic ("typical" conditions) and extreme reefs characterized by higher temperatures and light attenuation. We uncovered three cryptic lineages that exhibit limited micro-morphological variation; one lineage dominated classic reefs (L1), one had more even distributions (L2), and a third was restricted to extreme reefs (L3). L1 and L2 were more closely related to populations ~4300 km away, suggesting that some lineages are widespread. All corals harbored Cladocopium C15 photobionts; L1 and L2 shared a photobiont pool that differed in composition between reef types, yet L3 mostly harbored unique photobiont strains not found in the other lineages. Assemblages of bacterial partners differed among reef types in lineage-specific ways, suggesting that lineages employ distinct microbiome regulation strategies. Analysis of light-harvesting capacity and thermal tolerance revealed adaptive variation underpinning survival in distinct habitats: L1 had the highest light absorption efficiency and lowest thermal tolerance, suggesting that it is a classic reef specialist. L3 had the lowest light absorption efficiency and the highest thermal tolerance, showing that it is an extreme reef specialist. L2 had intermediate light absorption efficiency and thermal tolerance, suggesting that is a generalist lineage. These findings reveal diverging holobiont strategies to cope with extreme conditions. Resolving coral lineages is key to understanding variation in thermal tolerance among coral populations, can strengthen our understanding of coral evolution and symbiosis, and support global conservation and restoration efforts.}, }
@article {pmid39600222, year = {2024}, author = {Lu, SSM and Rutegård, M and Häggström, C and Gylfe, &#xc5; and Harlid, S and Van Guelpen, B}, title = {Prior antibiotics exposure is associated with an elevated risk of surgical site infections, including anastomotic leakage, after colon cancer but not rectal cancer surgery: A register-based study of 38,839 patients.}, journal = {International journal of cancer}, volume = {}, number = {}, pages = {}, doi = {10.1002/ijc.35269}, pmid = {39600222}, issn = {1097-0215}, support = {RV-932777//Region V&#xe4;sterbotten/ ; LP 17-2154//the Lions Cancer Research Foundation in Northern Sweden/ ; //the Knut and Alice Wallenberg Foundation/ ; }, abstract = {Gut microbiota composition has been implicated in surgical site complications after colorectal cancer surgery. Antibiotics affect gut microbiota, but evidence for a role in surgical site complications is inconclusive. We aimed to investigate use of prescription antibiotics during the years before surgery in relation to the risk of surgical site infections, including anastomotic leakage, within 30 days after surgery. Cardiovascular/neurological complications and the urinary antiseptic methenamine hippurate, for which there is no clear link with the microbiota, were used as negative controls. We conducted a patient cohort study using complete population data from Swedish national registers between 2005 and 2020. The final study population comprised 26,527 colon cancer and 12,312 rectal cancer cases with a 4.5 year exposure window. In colon cancer patients, antibiotics use was associated with a higher risk of surgical site infections (adjusted odds ratio (aOR) for any versus no use = 1.20, 95% confidence interval (CI) 1.10-1.33) and anastomotic leakage in particular (aOR =1.19, 95% CI 1.03-1.36), both with dose-response relationships for increasing cumulative antibiotics use (Ptrend = <0.001 and Ptrend = 0.047, respectively). Conversely, associations in rectal cancer patients, as well as for the negative controls cardiovascular/neurological complications and methenamine hippurate, were null. In conclusion, prescription antibiotics use up to 4.5 years before colorectal cancer surgery is associated with a higher risk of surgical site infections, including anastomotic leakage, after colon cancer but not rectal cancer surgery. These findings support a role for antibiotics-induced intestinal dysbiosis in surgical site infections.}, }
@article {pmid39600051, year = {2024}, author = {Rashad, S}, title = {Queuosine tRNA Modification: Connecting the Microbiome to the Translatome.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {}, number = {}, pages = {e2400213}, doi = {10.1002/bies.202400213}, pmid = {39600051}, issn = {1521-1878}, support = {23H02741//Japan Society for the Promotion of Science/ ; }, abstract = {Transfer RNA (tRNA) modifications play an important role in regulating mRNA translation at the codon level. tRNA modifications can influence codon selection and optimality, thus shifting translation toward specific sets of mRNAs in a dynamic manner. Queuosine (Q) is a tRNA modification occurring at the wobble position. In eukaryotes, queuosine is synthesized by the tRNA-guanine trans-glycosylase (TGT) complex, which incorporates the nucleobase queuine (or Qbase) into guanine of the GUN anticodons. Queuine is sourced from gut bacteria and dietary intake. Q was recently shown to be critical for cellular responses to oxidative and mitochondrial stresses, as well as its potential role in neurodegenerative diseases and brain health. These unique features of Q provide an interesting insight into the regulation of mRNA translation by gut bacteria, and the potential health implications. In this review, Q biology is examined in the light of recent literature and nearly 4 decades of research. Q's role in neuropsychiatric diseases and cancer is highlighted and discussed. Given the recent interest in Q, and the new findings, more research is needed to fully comprehend its biological function and disease relevance, especially in neurobiology.}, }
@article {pmid39599889, year = {2024}, author = {Meléndez-Vázquez, NM and Gomez-Manzano, C and Godoy-Vitorino, F}, title = {Oncolytic Virotherapies and Adjuvant Gut Microbiome Therapeutics to Enhance Efficacy Against Malignant Gliomas.}, journal = {Viruses}, volume = {16}, number = {11}, pages = {}, doi = {10.3390/v16111775}, pmid = {39599889}, issn = {1999-4915}, support = {2U54CA096297-16/BC/NCI NIH HHS/United States ; R25 GM061838/GM/NIGMS NIH HHS/United States ; 2U54MD007600/MD/NIMHD NIH HHS/United States ; R01CA256006/BC/NCI NIH HHS/United States ; }, mesh = {*Oncolytic Virotherapy/methods ; Humans ; *Gastrointestinal Microbiome ; *Oncolytic Viruses/genetics ; *Brain Neoplasms/therapy ; *Glioma/therapy ; Animals ; Immunotherapy/methods ; Glioblastoma/therapy ; Combined Modality Therapy ; }, abstract = {Glioblastoma (GBM) is the most prevalent malignant brain tumor. Current standard-of-care treatments offer limited benefits for patient survival. Virotherapy is emerging as a novel strategy to use oncolytic viruses (OVs) for the treatment of GBM. These engineered and non-engineered viruses infect and lyse cancer cells, causing tumor destruction without harming healthy cells. Recent advances in genetic modifications to OVs have helped improve their targeting capabilities and introduce therapeutic genes, broadening the therapeutic window and minimizing potential side effects. The efficacy of oncolytic virotherapy can be enhanced by combining it with other treatments such as immunotherapy, chemotherapy, or radiation. Recent studies suggest that manipulating the gut microbiome to enhance immune responses helps improve the therapeutic efficacy of the OVs. This narrative review intends to explore OVs and their role against solid tumors, especially GBM while emphasizing the latest technologies used to enhance and improve its therapeutic and clinical responses.}, }
@article {pmid39599772, year = {2024}, author = {Das, A and Gutkoska, J and Tadassa, Y and Jia, W}, title = {Enhanced Recovery and Detection of Highly Infectious Animal Disease Viruses by Virus Capture Using Nanotrap[®] Microbiome A Particles.}, journal = {Viruses}, volume = {16}, number = {11}, pages = {}, doi = {10.3390/v16111657}, pmid = {39599772}, issn = {1999-4915}, mesh = {Animals ; *Real-Time Polymerase Chain Reaction/methods ; Viruses/isolation &amp; purification/genetics/classification ; Virus Diseases/diagnosis/veterinary/virology ; Sensitivity and Specificity ; Microbiota ; Cell Line ; }, abstract = {This study reports the use of Nanotrap[®] Microbiome A Particles (NMAPs) to capture and concentrate viruses from diluted suspensions to improve their recovery and sensitivity to detection by real-time PCR/RT-PCR (qPCR/RT-qPCR). Five highly infectious animal disease viruses including goatpox virus (GTPV), sheeppox virus (SPPV), lumpy skin disease virus (LSDV), peste des petits ruminants virus (PPRV), and African swine fever virus (ASFV) were used in this study. After capture, the viruses remained viable and recoverable by virus isolation (VI) using susceptible cell lines. To assess efficacy of recovery, the viruses were serially diluted in phosphate-buffered saline (PBS) or Eagle's Minimum Essential Medium (EMEM) and then subjected to virus capture using NMAPs. The NMAPs and the captured viruses were clarified on a magnetic stand, reconstituted in PBS or EMEM, and analyzed separately by VI and virus-specific qPCR/RT-qPCR. The PCR results showed up to a 100-fold increase in the sensitivity of detection of the viruses following virus capture compared to the untreated viruses from the same dilutions. Experimental and clinical samples were subjected to virus capture using NMAPs and analyzed by PCR to determine diagnostic sensitivity (DSe) that was comparable (100%) to that determined using untreated (-NMAPs) samples. NMAPs were also used to capture spiked viruses from EDTA whole blood (EWB). Virus capture from EWB was partially blocked, most likely by hemoglobin (HMB), which also binds NMAPs and outcompetes the viruses. The effect of HMB could be removed by either dilution (in PBS) or using HemogloBind™ (Biotech Support Group; Monmouth Junction, NJ, USA), which specifically binds and precipitates HMB. Enhanced recovery and detection of viruses using NMAPs can be applicable to other highly pathogenic animal viruses of agricultural importance.}, }
@article {pmid39599756, year = {2024}, author = {Horvath, A and Haller, R and Feldbacher, N and Habisch, H and Žukauskaitė, K and Madl, T and Stadlbauer, V}, title = {Probiotic Therapy of Gastrointestinal Symptoms During COVID-19 Infection: A Randomized, Double-Blind, Placebo-Controlled, Remote Study.}, journal = {Nutrients}, volume = {16}, number = {22}, pages = {}, doi = {10.3390/nu16223970}, pmid = {39599756}, issn = {2072-6643}, support = {Project 3.23//Austrian Research Promotion Agency/ ; KLI 741//FWF Austrian Science Fund/ ; P28854//FWF Austrian Science Fund/ ; I3792//FWF Austrian Science Fund/ ; DOC-130//FWF Austrian Science Fund/ ; DK-MCD//FWF Austrian Science Fund/ ; W1226//FWF Austrian Science Fund/ ; 864690//Austrian Research Promotion Agency/ ; 870454//Austrian Research Promotion Agency/ ; //Integrative Metabolism Research Center Graz/ ; //Austrian Infrastructure Program 2016/2017/ ; //Styrian Government (Zukunftsfonds, doc.fund program)/ ; //City of Graz/ ; Flagship project//BioTechMed-Graz/ ; }, mesh = {Humans ; *Probiotics/therapeutic use/administration &amp; dosage ; Male ; *COVID-19/therapy ; Female ; *Gastrointestinal Microbiome ; Middle Aged ; Double-Blind Method ; *Feces/microbiology ; Adult ; *SARS-CoV-2 ; *Quality of Life ; Gastrointestinal Diseases/therapy/microbiology ; Aged ; Quarantine ; Telemedicine ; }, abstract = {BACKGROUND: The novel coronavirus (SARS-CoV-2) led to gastrointestinal manifestations in up to 50% of cases, with diarrhea being common, and probiotics have been suggested as a potential treatment.<br><br>AIM: This study aimed to assess changes in the microbiome and the effects of a multispecies probiotic in patients with COVID-19 in home quarantine through a fully remote telemedical approach.<br><br>METHODS: Thirty patients were randomized to receive either the Ecologic AAD probiotic (Winclove Probiotics, Amsterdam, The Netherlands), on the market as OMNi-BiOTiC 10 (Allergosan, Austria), or a placebo for 30 days in a 2:1 ratio. Respiratory and gastrointestinal symptoms were monitored in 2-10-day intervals via online surveys, and five stool samples were collected during the 30-day study period for microbiome and metabolomics analyses. Twenty-four healthy volunteers served as controls.<br><br>RESULTS: Of the 30 patients, 26 completed this study (10 placebo, 16 probiotic). Patients reported respiratory symptoms and a diminished gastrointestinal quality of life, both of which improved significantly during the study period, irrespective of the intervention. Compared to controls, infected patients showed significant alterations in the fecal microbiome (p = 0.002), including an increase in Bacteroidetes and decreases in Christensenellaceae, Ruminococcaceae, and Gammaproteobacteria, along with metabolomic changes. Probiotic treatment significantly modulated the patients' microbiome beta diversity (p = 0.001) and introduced the Enterococcus faecium W54 strain. Symptoms, COVID-19-related taxa, and the fecal metabolome were not affected by the intervention.<br><br>CONCLUSIONS: Patients with mild COVID-19 disease in home quarantine exhibited respiratory symptoms, a reduced gastrointestinal quality of life, and changes in the fecal microbiome and metabolome.}, }
@article {pmid39599747, year = {2024}, author = {Kajdas, AA and Żebrowska, A and Zalewska-Janowska, A and Czerwonogrodzka-Senczyna, A}, title = {The Role of Nutrition in the Pathogenesis and Treatment of Autoimmune Bullous Diseases-A Narrative Review.}, journal = {Nutrients}, volume = {16}, number = {22}, pages = {}, doi = {10.3390/nu16223961}, pmid = {39599747}, issn = {2072-6643}, mesh = {Humans ; *Autoimmune Diseases/diet therapy ; *Skin Diseases, Vesiculobullous/diet therapy/therapy/drug therapy ; Diet ; Nutritional Status ; Dietary Supplements ; Pemphigus/therapy/diet therapy/drug therapy ; Female ; }, abstract = {Autoimmune bullous diseases (AIBDs) are a group of conditions marked by the formation of blisters and erosions on the skin and mucous membranes. It occurs in all age groups, slightly more often affecting women. Several factors may be linked to the development of AIBDs, with nutrition being one of them. The literature mentions various food products and food ingredients acting as disease modifiers. Given the complex relationship between bullous diseases and nutrition, the current literature on AIBDs has been reviewed, with an emphasis on the influence of dietary modifications, various diets, and the nutritional consequences of these conditions. This review summarizes the role of nutrition in the pathogenesis and treatment of the following AIBDs: (i) pemphigus, (ii) bullous pemphigoid and mucous membrane pemphigoid, (iii) dermatitis herpetiformis, and (iv) epidermolysis bullosa acquisita. Several nutrients and dietary factors have been studied for their potential roles in triggering or exacerbating AIBDs. The key nutrients and their potential impacts include thiols and bulb vegetables (Allium), phenols, tannic acid, tannins, phycocyanin, isothiocyanates, all trans-retinoic acids, cinnamic acid, and walnut antigens. Many patients with ABIDs may require supplementation, particularly of vitamin D and B3, calcium, potassium, zinc, selenium, and cobalt. In addition, various diets play an important role. A soft diet is recommended for individuals with issues in the oral cavity and/or esophagus, particularly for those who experience difficulties with biting or swallowing. This approach is commonly used in managing pemphigus. A high-protein, high-calcium diet, DASH (Dietary Approaches to Stop Hypertension), and the Mediterranean diet are utilized during long-term glucocorticoid therapy. However, in dermatitis herpetiformis it is advisable to follow a gluten-free diet and eliminate iodine from the diet. When it comes to herbal supplements, Algae (Spirulina platensis), Echinacea, and St. John's wort (Hyperitum perforatum) enhance the ABIDs, while Cassia fistula may be recommended in the treatment of erosions in pemphigus vulgaris. Fast foods enhance the development of ABIDs. However, the pathomechanism is not yet fully understood. Future researchers should more precisely define the relationships between nutrients and nutrition and blistering diseases by also looking at, i.e., genetic predispositions, microbiome differences, or exposure to stress.}, }
@article {pmid39599742, year = {2024}, author = {Al-Habsi, N and Al-Khalili, M and Haque, SA and Elias, M and Olqi, NA and Al Uraimi, T}, title = {Health Benefits of Prebiotics, Probiotics, Synbiotics, and Postbiotics.}, journal = {Nutrients}, volume = {16}, number = {22}, pages = {}, doi = {10.3390/nu16223955}, pmid = {39599742}, issn = {2072-6643}, support = {(SR/AGR/Food/23/01)//His Majesty Trust Funds/ ; }, mesh = {Humans ; *Prebiotics/administration &amp; dosage ; *Probiotics/administration &amp; dosage ; *Synbiotics/administration &amp; dosage ; *Gastrointestinal Microbiome ; Fecal Microbiota Transplantation ; Functional Food ; }, abstract = {The trillions of microbes that constitute the human gut microbiome play a crucial role in digestive health, immune response regulation, and psychological wellness. Maintaining gut microbiota is essential as metabolic diseases are associated with it. Functional food ingredients potentially improving gut health include prebiotics, probiotics, synbiotics, and postbiotics (PPSPs). While probiotics are living bacteria that provide health advantages when ingested sufficiently, prebiotics are non-digestible carbohydrates that support good gut bacteria. Synbiotics work together to improve immunity and intestinal health by combining probiotics and prebiotics. Postbiotics have also demonstrated numerous health advantages, such as bioactive molecules created during probiotic fermentation. According to a recent study, PPSPs can regulate the synthesis of metabolites, improve the integrity of the intestinal barrier, and change the gut microbiota composition to control metabolic illnesses. Additionally, the use of fecal microbiota transplantation (FMT) highlights the potential for restoring gut health through microbiota modulation, reinforcing the benefits of PPSPs in enhancing overall well-being. Research has shown that PPSPs provide several health benefits, such as improved immunological function, alleviation of symptoms associated with irritable bowel disease (IBD), decreased severity of allergies, and antibacterial and anti-inflammatory effects. Despite encouraging results, many unanswered questions remain about the scope of PPSPs' health advantages. Extensive research is required to fully realize the potential of these functional food components in enhancing human health and well-being. Effective therapeutic and prophylactic measures require further investigation into the roles of PPSPs, specifically their immune-system-modulating, cholesterol-lowering, antioxidant, and anti-inflammatory characteristics.}, }
@article {pmid39599737, year = {2024}, author = {Naghibi, M and Pont-Beltran, A and Lamelas, A and Llobregat, L and Martinez-Blanch, JF and Rojas, A and Álvarez, B and López Plaza, B and Arcos Castellanos, L and Chenoll, E and Vijayakumar, V and Day, R}, title = {Effect of Postbiotic Bifidobacterium longum CECT 7347 on Gastrointestinal Symptoms, Serum Biochemistry, and Intestinal Microbiota in Healthy Adults: A Randomised, Parallel, Double-Blind, Placebo-Controlled Pilot Study.}, journal = {Nutrients}, volume = {16}, number = {22}, pages = {}, doi = {10.3390/nu16223952}, pmid = {39599737}, issn = {2072-6643}, support = {TOLERA IDI-20170876//Spanish Ministry of Economy and Competitiveness, under the CDTI Project TOLERA IDI-20170876/ ; NA//Archer Daniels Midland (United States)/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; Double-Blind Method ; Pilot Projects ; Male ; Adult ; Female ; *Bifidobacterium longum ; *Probiotics/administration &amp; dosage ; *Feces/microbiology ; Middle Aged ; Quality of Life ; Irritable Bowel Syndrome/microbiology/blood/therapy ; Young Adult ; Leukocyte L1 Antigen Complex/analysis/blood ; }, abstract = {OBJECTIVES: A randomised, double-blind, placebo-controlled pilot trial was conducted to assess the effect of heat-treated Bifidobacterium longum CECT 7347 (HT-ES1) in healthy adults with mild to moderate digestive symptoms. A total of 60 participants were recruited and received either HT-ES1 or an identical placebo for 8 weeks with a further follow-up at week 10.<br><br>METHODS: This study monitored changes in the total Gastrointestinal Symptom Rating Scale for IBS score (GSRS-IBS), Irritable Bowel Syndrome Symptom Severity Scale (IBS-SSS), IBS Quality of Life index (IBS-QoL), gut microbiome using 16S rRNA sequencing, and the Visceral Sensitivity Index, as well as a range of biochemical markers, anthropometric parameters, and adverse events.<br><br>RESULTS: While minimal changes were observed in gastrointestinal (GI) symptoms, the HT-ES1 group showed a significant decrease in total and non-HDL cholesterol compared to the placebo. The intervention group also exhibited a significant increase in the abundance of the genera Faecalibacterium and Anaerobutyricum, both of which were positively correlated with butyrate concentrations. Faecal calprotectin significantly increased over time in the placebo group but remained stable in the HT-ES1 group.<br><br>CONCLUSIONS: Overall, these findings suggest that HT-ES1 may promote gut health by increasing butyrate-producing bacteria in the gut, maintaining normal levels of faecal calprotectin and reducing serum cholesterol.}, }
@article {pmid39599727, year = {2024}, author = {Roth, MS and d'Aujourd'hui, M and Künstner, A and Hirose, M and Olbrich, M and Ibrahim, S and Hartmann, K and Roduit, C and Busch, H and Bellutti Enders, F}, title = {Characterization of the Gut and Skin Microbiome over Time in Young Children with IgE-Mediated Food Allergy.}, journal = {Nutrients}, volume = {16}, number = {22}, pages = {}, doi = {10.3390/nu16223942}, pmid = {39599727}, issn = {2072-6643}, mesh = {Humans ; *Immunoglobulin E/blood ; *Food Hypersensitivity/microbiology/immunology ; Female ; Male ; *Skin/microbiology/immunology ; *Gastrointestinal Microbiome ; Infant ; Prospective Studies ; RNA, Ribosomal, 16S/genetics ; Pilot Projects ; Microbiota ; Feces/microbiology ; Child, Preschool ; Dysbiosis/microbiology ; Bacteria/classification/immunology/genetics/isolation &amp; purification ; }, abstract = {BACKGROUND/OBJECTIVES: The prevalence of food allergy (FA) in children is increasing. Dysbiosis of the microbiome has been linked to FA but needs to be better understood. We aimed to characterize the gut and skin microbiome of young food-allergic children over time and within different types of immunoglobulin E (IgE)-mediated FA.<br><br>METHODS: We studied 23 patients, as a pilot study of an ongoing prospective multicenter cohort study including children < 2y with newly diagnosed IgE-mediated FA. Samples (feces/skin swabs) were collected at enrollment and at 1-year follow-up and sequenced for the bacterial 16S rRNA gene (hypervariable v1-v2 region).<br><br>RESULTS: Gut and skin bacterial diversity was significantly higher in patients compared with controls and increased over time (beta test, Shannon diversity, p < 0.01). Within different types of IgE-mediated FA, bacterial diversity was similar. Community composition differed significantly over time and within IgE-mediated FA types (PERMANOVA: p < 0.01). Several significantly different genus abundances were revealed. We observed a positive correlation between high total IgE and a high abundance of the genus Collinsella in patients with a higher number of allergies/sensitizations (&#x2265;3), and patients with tree nut and/or peanut allergy.<br><br>CONCLUSIONS: This study revealed an increased bacterial diversity in children with FA compared with non-atopic children. Importantly, the gut and skin microbiome differed in their composition over time and within different types of IgE-mediated FA. These findings contribute to the understanding of microbiome changes in children with FA and indicate the potential of the genus Collinsella as a biomarker for tree nut and/or peanut allergy and possibly for allergy persistence.}, }
@article {pmid39599721, year = {2024}, author = {Ng, CYJ and Zhong, L and Ng, HS and Goh, KS and Zhao, Y}, title = {Managing Type 2 Diabetes Mellitus via the Regulation of Gut Microbiota: A Chinese Medicine Perspective.}, journal = {Nutrients}, volume = {16}, number = {22}, pages = {}, doi = {10.3390/nu16223935}, pmid = {39599721}, issn = {2072-6643}, mesh = {*Diabetes Mellitus, Type 2/microbiology/therapy ; *Gastrointestinal Microbiome/physiology ; Humans ; *Medicine, Chinese Traditional/methods ; *Drugs, Chinese Herbal/therapeutic use ; Akkermansia ; Acupuncture Therapy/methods ; Bifidobacterium ; Animals ; }, abstract = {Type 2 Diabetes Mellitus (T2DM) is a metabolic disorder characterized by insulin resistance and inadequate insulin production. Given the increased frequency of T2DM and the health issues it can cause, there is an increasing need to develop alternative T2DM management strategies. One such approach is Chinese Medicine (CM), a complementary therapy widely used in T2DM treatment. Given the emphasis on gut microbiota in current research, studying CM in the treatment of T2DM via gut microbiota modulation could be beneficial. Scope and approach: The use of various CM methods for managing T2DM via gut microbiota modulation is highlighted in this review. Following an introduction of the gut microbiota and its role in T2DM pathogenesis, we will review the potential interactions between gut microbiota and T2DM. Thereafter, we will review various CM treatment modalities that modulate gut microbiota and provide perspectives for future research. Key findings and discussion: In T2DM, Akkermansia, Bifidobacterium, and Firmicutes are examples of gut microbiota commonly imbalanced. Studies have shown that CM therapies can modulate gut microbiota, leading to beneficial effects such as reduced inflammation, improved metabolism, and improved immunity. Among these treatment modalities, Chinese Herbal Medicine and acupuncture are the most well-studied, and several in vivo studies have demonstrated their potential in managing T2DM by modulating gut microbiota. However, the underlying biomolecular mechanisms of actions are not well elucidated, which is a key area for future research. Future studies could also investigate alternate CM therapies such as moxibustion and CM exercises and conduct large-scale clinical trials to validate their effectiveness in treatment.}, }
@article {pmid39599719, year = {2024}, author = {Senaprom, S and Namjud, N and Ondee, T and Bumrungpert, A and Pongpirul, K}, title = {Sugar Composition of Thai Desserts and Their Impact on the Gut Microbiome in Healthy Volunteers: A Randomized Controlled Trial.}, journal = {Nutrients}, volume = {16}, number = {22}, pages = {}, doi = {10.3390/nu16223933}, pmid = {39599719}, issn = {2072-6643}, support = {FOODF67300006//Thailand Science Research and Innovation Fund Chulalongkorn University/ ; //The 90th Anniversary of Chulalongkorn University, Ratchadaphisek Somphot Fund/ ; //The Second Century Fund (C2F) for PhD Scholarship, Chulalongkorn University/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; Adult ; Male ; Thailand ; Female ; Young Adult ; *Healthy Volunteers ; *Feces/microbiology ; Middle Aged ; Adolescent ; RNA, Ribosomal, 16S/genetics ; Bacteria/classification/genetics ; Dietary Sugars ; Southeast Asian People ; }, abstract = {BACKGROUND: The relationship between consuming Thai desserts-predominantly composed of carbohydrates-and gut microbiome profiles remains unclear. This study aimed to evaluate the effects of consuming various Thai desserts with different GI values on the gut microbiomes of healthy volunteers.<br><br>METHODS: This open-label, parallel randomized clinical trial involved 30 healthy individuals aged 18 to 45 years. Participants were randomly assigned to one of three groups: Phetchaburi's Custard Cake (192 g, low-GI group, n = 10), Saraburi's Curry Puff (98 g, medium-GI group, n = 10), and Lampang's Crispy Rice Cracker (68 g, high-GI group, n = 10), each consumed alongside their standard breakfast. Fecal samples were collected at baseline and 24 h post-intervention for metagenomic analysis of gut microbiome profiles using 16S rRNA gene sequencing.<br><br>RESULTS: After 24 h, distinct trends in the relative abundance of various gut microbiota were observed among the dessert groups. In the high-GI dessert group, the abundance of Collinsella and Bifidobacterium decreased compared to the low- and medium-GI groups, while Roseburia and Ruminococcus showed slight increases. Correlation analysis revealed a significant negative relationship between sugar intake and Lactobacillus abundance in the medium- and high-GI groups, but not in the low-GI group. Additionally, a moderately negative association was observed between Akkermansia abundance and sugar intake in the high-GI group. These bacteria are implicated in energy metabolism and insulin regulation. LEfSe analysis identified Porphyromonadaceae and Porphyromonas as core microbiota in the low-GI group, whereas Klebsiella was enriched in the high-GI group, with no predominant bacteria identified in the medium-GI group.<br><br>CONCLUSIONS: The findings suggest that Thai desserts with varying GI levels can influence specific gut bacteria, though these effects may be temporary.}, }
@article {pmid39599707, year = {2024}, author = {Farella, I and D'Amato, G and Orellana-Manzano, A and Segura, Y and Vitale, R and Clodoveo, ML and Corbo, F and Faienza, MF}, title = {"OMICS" in Human Milk: Focus on Biological Effects on Bone Homeostasis.}, journal = {Nutrients}, volume = {16}, number = {22}, pages = {}, doi = {10.3390/nu16223921}, pmid = {39599707}, issn = {2072-6643}, mesh = {Humans ; *Milk, Human/chemistry ; *Homeostasis ; *Bone and Bones/metabolism ; Gastrointestinal Microbiome/physiology ; Proteomics/methods ; Bone Development/drug effects ; Infant ; Insulin-Like Growth Factor I/metabolism ; Metabolomics/methods ; Oligosaccharides/pharmacology ; MicroRNAs/metabolism ; Bone Density/drug effects ; }, abstract = {Human milk (HM) is a complex biofluid rich in nutrients and bioactive compounds essential for infant health. Recent advances in omics technologies-such as proteomics, metabolomics, and transcriptomics-have shed light on the influence of HM on bone development and health. This review discusses the impact of various HM components, including proteins, lipids, carbohydrates, and hormones, on bone metabolism and skeletal growth. Proteins like casein and whey promote calcium absorption and osteoblast differentiation, supporting bone mineralization. Long-chain polyunsaturated fatty acids like docosahexaenoic acid (DHA) contribute to bone health by modulating inflammatory pathways and regulating osteoclast activity. Additionally, human milk oligosaccharides (HMOs) act as prebiotics, improving gut health and calcium bioavailability while influencing bone mineralization. Hormones present in HM, such as insulin-like growth factor 1 (IGF-1), leptin, and adiponectin, have been linked to infant growth, body composition, and bone density. Research has shown that higher IGF-1 levels in breast milk are associated with increased weight gain, while leptin and adiponectin influence fat mass and bone metabolism. Emerging studies have also highlighted the role of microRNAs (miRNAs) in regulating key processes like adipogenesis and bone homeostasis. Furthermore, microbiome-focused techniques reveal HM's role in establishing a balanced infant gut microbiota, indirectly influencing bone development by enhancing nutrient absorption. Although current findings are promising, comprehensive longitudinal studies integrating omics approaches are needed to fully understand the intricate relationships among maternal diet, HM composition, and infant bone health. Bridging these gaps could offer novel dietary strategies to optimize skeletal health during infancy, advancing early-life nutrition science.}, }
@article {pmid39599702, year = {2024}, author = {Ostrowska, M and Nowosad, K and Mikoluc, B and Szczerba, H and Komon-Janczara, E}, title = {Changes in the Gut and Oral Microbiome in Children with Phenylketonuria in the Context of Dietary Restrictions-A Preliminary Study.}, journal = {Nutrients}, volume = {16}, number = {22}, pages = {}, doi = {10.3390/nu16223915}, pmid = {39599702}, issn = {2072-6643}, support = {VKT/MN-7/T&#x17b;/21//University of Life Sciences in Lublin/ ; 2022/06/X/NZ9/00519//National Science Center/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; *Phenylketonurias/diet therapy/microbiology ; Child ; Male ; Female ; *Mouth/microbiology ; *RNA, Ribosomal, 16S/genetics ; Child, Preschool ; Bacteria/classification/isolation &amp; purification/genetics ; Microbiota ; Diet ; Case-Control Studies ; Phylogeny ; }, abstract = {BACKGROUND: Phenylketonuria (PKU) is a metabolic disorder that necessitates dietary restrictions, potentially impacting the composition of gut and oral microbiota. This study aimed to compare the microbiota composition between children with PKU and healthy controls.<br><br>METHODS: Using 16S rRNA gene sequencing, we analysed microbial communities at six phylogenetic levels.<br><br>RESULTS: Our findings revealed significant differences in the gut microbiota: Euryarchaeota was more abundant in controls (p = 0.01), while Bacilli and Lactobacillales were higher in PKU children (p = 0.019). Methanobacteriales were significantly elevated in controls (p = 0.01). At the genus and species levels, PKU children had higher Streptococcus and Eubacterium dolichum (p = 0.019, p = 0.015), whereas controls had more Barnesiella, Coprococcus, and Faecalibacterium prausnitzii (p = 0.014, p = 0.019, p = 0.014). In the oral microbiota, control children exhibited significantly higher Bacteroidetes (p = 0.032), while PKU children had increased Bacilli and Betaproteobacteria (p = 0.0079, p = 0.016). Streptococcus and Neisseria were more prevalent in PKU (p = 0.0079, p = 0.016).<br><br>CONCLUSIONS: These results suggest that PKU and its dietary management significantly alter the gut and oral microbiota composition. Understanding these microbial shifts could have implications for managing PKU and improving patient outcomes.}, }
@article {pmid39599673, year = {2024}, author = {Lorefice, L and Zoledziewska, M}, title = {Propionic Acid Impact on Multiple Sclerosis: Evidence and Challenges.}, journal = {Nutrients}, volume = {16}, number = {22}, pages = {}, doi = {10.3390/nu16223887}, pmid = {39599673}, issn = {2072-6643}, mesh = {*Multiple Sclerosis/drug therapy ; Humans ; *Propionates/therapeutic use ; *Gastrointestinal Microbiome/drug effects ; Animals ; Dietary Supplements ; }, abstract = {Accumulating evidence suggests that multiple sclerosis (MS) is an environmentally influenced disorder with contributions from life-time exposure to factors including Epstein-Barr virus infection or shifts in microbiome, diet and lifestyle. One suggested factor is a deficiency in propionic acid, a short-chain fatty acid produced by gut bacteria that may contribute to the disease pathology both in animal models and in human cases of MS. Propionate appears to exert beneficial effects on the immune, peripheral and central nervous systems of people with MS (pwMS), showing immunoregulatory, neuroprotective and neurogenerative effects. These functions are crucial, given that MS is characterized by immune-mediated damage of myelin in the central nervous system. Accordingly, propionate supplementation or a modulated increase in its levels through the microbiome and diet may help counteract the pro-inflammatory state in MS by directly regulating immune system and/or by decreasing permeability of gut barrier and blood-brain barrier. This could potentially improve outcomes when used with immune-modulating therapy. However, while its broad effects are promising, further large clinical trials are necessary to evaluate its efficacy and safety in pwMS and clarify its role as a complementary therapeutic strategy. This review provides a comprehensive analysis of the evidence, challenges and limitations concerning propionic acid supplementation in MS.}, }
@article {pmid39599626, year = {2024}, author = {Horvath, A and Habisch, H and Prietl, B and Pfeifer, V and Balazs, I and Kovacs, G and Foris, V and John, N and Kleinschek, D and Feldbacher, N and Grønbæk, H and Møller, HJ and Žukauskaitė, K and Madl, T and Stadlbauer, V}, title = {Alteration of the Gut-Lung Axis After Severe COVID-19 Infection and Modulation Through Probiotics: A Randomized, Controlled Pilot Study.}, journal = {Nutrients}, volume = {16}, number = {22}, pages = {}, doi = {10.3390/nu16223840}, pmid = {39599626}, issn = {2072-6643}, support = {Project 3.23//Austrian Research Promotion Agency/ ; KLI 741//FWF Austrian Science Fund/ ; P28854//FWF Austrian Science Fund/ ; I3792//FWF Austrian Science Fund/ ; DOC-130//FWF Austrian Science Fund/ ; DK-MCD//FWF Austrian Science Fund/ ; W1226//FWF Austrian Science Fund/ ; 864690//Austrian Research Promotion Agency/ ; 870454//Austrian Research Promotion Agency/ ; //Integrative Metabolism Research Center Graz/ ; //Austrian Infrastructure Program 2016/2017/ ; //Styrian Government (Zukunftsfonds, doc. fund program)/ ; //City of Graz/ ; Flagship project//BioTechMed-Graz/ ; }, mesh = {Humans ; *Probiotics/therapeutic use/administration &amp; dosage ; Pilot Projects ; *COVID-19/therapy ; *Gastrointestinal Microbiome ; Male ; Female ; Middle Aged ; *Lung ; *SARS-CoV-2 ; Aged ; Metabolome ; Adult ; Feces/microbiology ; Biomarkers/blood ; Severity of Illness Index ; }, abstract = {BACKGROUND: The gut-lung axis could be a potential therapeutic target for improving post-acute COVID-19 symptoms, and probiotics have been proposed as possible modulators.<br><br>AIM: We conducted a pilot study to understand alterations in the gut-lung axis and to explore the effects of a probiotic in post-acute COVID-19 disease.<br><br>METHODS: We included patients after severe COVID-19 disease (sCOV, n = 21) in a randomized, placebo-controlled trial to test the effect of a probiotic (Pro-Vi 5, Institute Allergosan, Graz, Austria) in a six-month intervention and used patients after mild disease (mCOV, n = 10) as controls, to compare the intestinal microbiome, metabolome, and patient-reported outcomes and biomarkers along the gut-lung axis at baseline and throughout probiotic intervention.<br><br>RESULTS: Compared to mCOV patients, sCOV patients showed lower microbial richness, which was significantly improved by probiotic intervention. A reorganization of Ruminococcaceae and Lachnospiraceae taxa was observed in sCOV patients but remained unaffected by the intervention. Serum metabolome showed a dysregulation of lipoproteins in accordance with higher BMI and comorbidities in sCOV patients. HDL and LDL fractions/components were temporarily decreased in the probiotic group. Stool metabolome was altered at baseline in sCOV patients and an increase in L-DOPA after 3 months and butyrate after 6 months of intervention could be observed. Probiotics partially improved reduced quality of life and modulated altered immune responses in sCOV patients. Increased intestinal permeability at baseline remained unaffected.<br><br>CONCLUSION: The study provides evidence of long-term alterations of the gut-lung axis after severe COVID-19 infection and suggests that probiotics can modulate the biomarkers of the gut-lung axis.}, }
@article {pmid39599625, year = {2024}, author = {Inoue, R and Hosomi, K and Park, J and Sakaue, H and Yumioka, H and Kamitani, H and Kinugasa, Y and Harano, K and Syauki, AY and Doi, M and Kageyama, S and Yamamoto, K and Mizuguchi, K and Kunisawa, J and Irie, Y}, title = {Clinical Phenotypes Associated with the Gut Microbiome in Older Japanese People with Care Needs in a Nursing Home.}, journal = {Nutrients}, volume = {16}, number = {22}, pages = {}, doi = {10.3390/nu16223839}, pmid = {39599625}, issn = {2072-6643}, support = {22ae0121035s0102, 22gm1010006h0004, 22ae0121042h0002, 22ae0121035s0102//Japan Agency for Medical Research and Development/ ; 20AC5004//Ministry of Health and Welfare of Japan and Public/Private R&amp;D Investment Strategic Expan-sion Progra/ ; 21K11730//Japan Society for the Promotion of Science/ ; }, mesh = {Humans ; *Nursing Homes ; *Gastrointestinal Microbiome ; Male ; Female ; Aged, 80 and over ; Aged ; *Phenotype ; Japan ; *Frailty ; *Nutritional Status ; Frail Elderly ; Dementia/microbiology ; Homes for the Aged ; Geriatric Assessment/methods ; Asian People ; East Asian People ; }, abstract = {BACKGROUND: Frailty increases the risk of needing nursing care and significantly affects the life and functional prognosis of older individuals. Early detection and tailored interventions are crucial for maintaining and enhancing their life functions. Recognizing distinct clinical phenotypes is essential for devising appropriate interventions. This study aimed to explore diverse frailty phenotypes, focusing on poor nutrition in older Japanese individuals through observational research.<br><br>METHODS: Twenty-one nursing home residents underwent a comprehensive survey covering physical, blood, dietary, cardiac, cognitive, nutritional, nursing care, frailty, agitated behavior, and gut microbiome assessments (high-throughput 16S rRNA gene sequencing). Using clustering analysis with 239 survey items (excluding gut microbiome), participants were classified into subgroups based on clinical phenotypes, and group characteristics were compared through analysis.<br><br>RESULTS: Individuals with moderate or severe frailty and suspected dementia formed subgroups with distinct clinical phenotypes based on nutritional, defecation, and nursing care statuses. The gut microbiome significantly varied among these groups (p = 0.007), indicating its correlation with changes in clinical phenotype. Nutritional status differences suggested poor nutrition as a differentiating factor in the core clinical phenotype.<br><br>CONCLUSIONS: This study proposes that the gut microbiome differs based on the clinical phenotype of Japanese older individuals with frailty, and targeted interventions addressing the gut microbiome may contribute to preventing frailty in this population.}, }
@article {pmid39599623, year = {2024}, author = {Yang, J and Ou, W and Lin, G and Wang, Y and Chen, D and Zeng, Z and Chen, Z and Lu, X and Wu, A and Lin, C and Liang, Y}, title = {PAMK Ameliorates Non-Alcoholic Steatohepatitis and Associated Anxiety/Depression-like Behaviors Through Restoring Gut Microbiota and Metabolites in Mice.}, journal = {Nutrients}, volume = {16}, number = {22}, pages = {}, doi = {10.3390/nu16223837}, pmid = {39599623}, issn = {2072-6643}, mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Non-alcoholic Fatty Liver Disease/metabolism ; Mice ; *Depression ; *Anxiety ; Male ; *Atractylodes/chemistry ; *Disease Models, Animal ; *Polysaccharides/pharmacology ; *Behavior, Animal/drug effects ; Mice, Inbred C57BL ; Liver/metabolism/drug effects ; Drugs, Chinese Herbal/pharmacology ; Diet, Western/adverse effects ; }, abstract = {OBJECTIVES: Long-term Western diet-induced non-alcoholic steatohepatitis (NASH) can lead to liver cirrhosis and NASH-associated hepatocellular carcinoma, which are end-stage liver diseases. Meanwhile, NASH is associated with mental burden and worsens as the disease progresses. Atractylodes Macrocephala Koidz (AMK) is one of the main ingredients of Shenling Baizhu San, and the effect of Polysaccharide from AMK ameliorates (PAMK), as an important medicinal ingredient of AMK, on NASH and associated anxiety/depression-like behaviors is still unclear.<br><br>METHODS: This study investigated the protective effect of PAMK on NASH and associated anxiety/depression-like behaviors through a Western diet-induced NASH mice model.<br><br>RESULTS: showed that PAMK decreased the concentrations of liver TC, TG, and serum AST and ALT, improving glucose tolerance, and reducing liver steatosis and fibrosis. Moreover, the expression of liver IL-6, IL-1&#x3b2;, TNF-&#x3b1;, IL-18 and MCP-1 could be reduced by PAMK significantly. Additionally, PAMK decreased anxiety/depression-like behaviors and expression of IL-6, IL-1&#x3b2;, TNF-&#x3b1;, and MCP-1 in the hippocampus. 16S rRNA gene sequencing revealed that PAMK diminished the Firmicutes/Bacteroidetes ratio and abundance of Faecalibaculum_rodentium, and increased the abundance of Muribaculaceae. This might be related to gene abundance of Pentose, the glucuronate interconversions pathway and carbohydrate enzymes (GH1, GH4). Serum metabolomics suggested that PC (18:5e/2:0), PC (16:2e/2:0), Lysopc 20:4, PC (16:0/2:0), and LPC 19:0 upregulated significantly after PAMK intervention, together with the enrichment of carbon metabolism and Citrate cycle pathways specially.<br><br>CONCLUSIONS: PAMK as a potential prebiotic ameliorated NASH and associated anxiety/depression-like behaviors in mice, probably by regulating Faecalibaculum_rodentium, carbohydrate enzymes and lipid metabolites.}, }
@article {pmid39599583, year = {2024}, author = {De La Barrera, S and De La Barrera, B and Legault, MA and Gamache, I and Manousaki, D}, title = {Association Between Circulating Vitamin K Levels, Gut Microbiome, and Type 1 Diabetes: A Mendelian Randomization Study.}, journal = {Nutrients}, volume = {16}, number = {22}, pages = {}, doi = {10.3390/nu16223795}, pmid = {39599583}, issn = {2072-6643}, mesh = {Humans ; *Mendelian Randomization Analysis ; *Diabetes Mellitus, Type 1/microbiology/blood/genetics ; *Gastrointestinal Microbiome ; *Vitamin K/blood ; *Genome-Wide Association Study ; Male ; Female ; Polymorphism, Single Nucleotide ; Risk Factors ; }, abstract = {BACKGROUND/OBJECTIVES: Nutritional deficiencies have been proposed as possible etiological causes for autoimmune diseases, among which type 1 diabetes (T1D). Vitamin K (VK) has potentially positive effects on type 2 diabetes, but its role on T1D in humans remains largely unknown. We aimed to examine the presence of a causal association between VK and T1D using a Mendelian randomization (MR) approach.<br><br>METHODS: Genetic variants from a genome-wide association study (GWAS) for VK (N = 2138 Europeans) were used as instruments in our two-sample MR study to investigate whether circulating VK levels are causally associated with the risk of T1D in a large European T1D GWAS cohort (18,942 cases/520,580 controls). Through a multivariable MR (MVMR), the effects of both VK and specific gut microbiota on T1D were investigated given that the gut microbiome synthesizes VK.<br><br>RESULTS: We found that changes in levels of circulating VK did not affect T1D risk in our univariate two-sample MR, but this study had limited power to detect small effects of VK (OR for T1D of less than 0.8). However, our MVMR indicated a suggestive association of VK with the risk of T1D adjusting for two different gut microbiome populations.<br><br>CONCLUSIONS: In conclusion, VK levels are unlikely to significantly affect the risk of T1D, but small effects cannot be excluded, and the role of gut microbiome in this association should be further investigated.}, }
@article {pmid39599558, year = {2024}, author = {Druszczynska, M and Sadowska, B and Kulesza, J and Gąsienica-Gliwa, N and Kulesza, E and Fol, M}, title = {The Intriguing Connection Between the Gut and Lung Microbiomes.}, journal = {Pathogens (Basel, Switzerland)}, volume = {13}, number = {11}, pages = {}, doi = {10.3390/pathogens13111005}, pmid = {39599558}, issn = {2076-0817}, abstract = {Recent advances in microbiome research have uncovered a dynamic and complex connection between the gut and lungs, known as the gut-lung axis. This bidirectional communication network plays a critical role in modulating immune responses and maintaining respiratory health. Mediated by immune interactions, metabolic byproducts, and microbial communities in both organs, this axis demonstrates how gut-derived signals, such as metabolites and immune modulators, can reach the lung tissue via systemic circulation, influencing respiratory function and disease susceptibility. To explore the implications of this connection, we conducted a systematic review of studies published between 2001 and 2024 (with as much as nearly 60% covering the period 2020-2024), using keywords such as "gut-lung axis", "microbiome", "respiratory disease", and "immune signaling". Studies were selected based on their relevance to gut-lung communication mechanisms, the impact of dysbiosis, and the role of the gut microbiota in respiratory diseases. This review provides a comprehensive overview of the gut-lung microbiome axis, emphasizing its importance in regulating inflammatory and immune responses linked to respiratory health. Understanding this intricate pathway opens new avenues for microbiota-targeted therapeutic strategies, which could offer promising interventions for respiratory diseases like asthma, chronic obstructive pulmonary disease, and even infections. The insights gained through this research underscore the potential of the gut-lung axis as a novel target for preventative and therapeutic approaches in respiratory medicine, with implications for enhancing both gut and lung health.}, }
@article {pmid39599549, year = {2024}, author = {Du, C and Zhang, Y and Zhang, H and Zhang, H and Liu, J and Shen, N}, title = {Bibliometric Analysis of Research Trends and Prospective Directions of Lung Microbiome.}, journal = {Pathogens (Basel, Switzerland)}, volume = {13}, number = {11}, pages = {}, doi = {10.3390/pathogens13110996}, pmid = {39599549}, issn = {2076-0817}, support = {2022YFC2303200//National Key Research and Development Program of China/ ; No. 010071//Beijing Key Clinical Specialty Funding/ ; No.82202415//National Natural Science Foundation of China/ ; }, abstract = {The lung microbiome has emerged as a pivotal area of research in human health. Despite the increasing number of publications, there is a lack of research that comprehensively and objectively presents the current status of lung microbiome-related studies. Thus, this study aims to address this gap by examining over two decades of publications through bibliometric analysis. The original bibliographic data of this study were obtained from the Web of Science Core Collection, focusing on publications from 2003 to 2023. The analysis included the data extraction and examination of authors, affiliations, countries, institutions, abstracts, keywords, references, publication dates, journals, citations, H-indexes, and journal impact factors. A total of 845 publications were identified, showing an increasing trend in both publications and citations over the years, particularly in the last decade. The analysis highlighted the most productive authors, institutions, and countries/regions, and identified potential partners for interested researchers. Co-citation analysis revealed that lung microbiome- and infectious/pulmonary disease-related studies are at the forefront of the field. The hotspots and frontiers of the lung microbiome field have progressed from basic composition to exploring specific mechanisms and the clinical value of diseases. In conclusion, this study provides a comprehensive overview of the current research status and trends in the field of the lung microbiome over the past two decades and highlights the areas that need more attention and research efforts. It offers valuable insights for researchers and institutions and identifies key hotspots and frontiers, which can serve as references for related researchers and future research.}, }
@article {pmid39599495, year = {2024}, author = {Mousavi, A and Thaker, KN and Ackerman, JE and Diaz, N and Martin, R and Tipton, CD and Tallman, N and Henao, LM and Nassiri, N and Veale, J and Ackerman, AL and Scotland, KB}, title = {Exploring Condition-Specific Variability in the Ureteral Stent Microbiome.}, journal = {Pathogens (Basel, Switzerland)}, volume = {13}, number = {11}, pages = {}, doi = {10.3390/pathogens13110942}, pmid = {39599495}, issn = {2076-0817}, support = {N/A//Urology Care Foundation Medical Student Fellowship Grant/ ; N/A//Viola Hyde Surgical Research Scholarship/ ; N/A//UCLA Innovation Award/ ; }, abstract = {(1) Background: Indwelling ureteral stents are commonly used urological devices to maintain ureteral patency, yet they have been associated with complications such as infections. Some studies have shown that bacteria adhere to and create an antimicrobial-resistant biofilm on stents. One factor that may impact biofilm formation is the original condition informing stent placement, such as kidney stones and renal allografts. Both kidney stones and renal allografts are independently associated with infection, yet the differential stent microbiomes of these populations remain poorly characterized. Our objective was to characterize these microbiomes in order to inform urological health practice and help prevent ureteral stent-associated infections. (2) Methods: Stents were collected from kidney stone and renal transplant recipients undergoing routine cystoscopic stent removal. Microbial DNA was extracted from stents and analyzed using 16S Next Generation Sequencing. Descriptive statistics, alpha diversity, and beta diversity methods were used for statistical analysis. (3) Results: The microbiome of ureteral stents in kidney stone and transplant patients is composed of unique species, each with different biofilm-forming abilities. (4) Conclusions: Our findings demonstrate that the microbiome of stents differs based on preceding condition. It is important to conduct future studies that explore this microbiome further to understand what type of stent-associated infection someone may develop based on their initial condition.}, }
@article {pmid39598705, year = {2024}, author = {Gościniak, A and Lainé, E and Cielecka-Piontek, J}, title = {How Do Cyclodextrins and Dextrans Affect the Gut Microbiome? Review of Prebiotic Activity.}, journal = {Molecules (Basel, Switzerland)}, volume = {29}, number = {22}, pages = {}, doi = {10.3390/molecules29225316}, pmid = {39598705}, issn = {1420-3049}, support = {Preludium BIS (2020/39/O/NZ7/03441)//National Science Center/ ; }, mesh = {*Prebiotics ; *Gastrointestinal Microbiome/drug effects ; *Cyclodextrins/pharmacology/chemistry ; Humans ; Animals ; Fatty Acids, Volatile/metabolism ; Bacteria/drug effects/metabolism ; }, abstract = {The modulation of the gut microbiome through dietary components has garnered significant attention for its potential health benefits. Prebiotics, non-digestible food ingredients that promote the growth of beneficial gut bacteria, play a crucial role in maintaining gut health, enhancing immune function, and potentially preventing various metabolic and inflammatory disorders. This review explores the prebiotic activity of cyclodextrins and dextrans, focusing on their ability to influence gut microbiota composition and function. Both cyclodextrins and dextrans have demonstrated the capacity to promote the growth of beneficial bacterial populations, while also impacting short-chain fatty acid production, crucial for gut health.}, }
@article {pmid39598283, year = {2024}, author = {Mederle, AL and Dima, M and Stoicescu, ER and Căpăstraru, BF and Levai, CM and Hațegan, OA and Maghiari, AL}, title = {Impact of Gut Microbiome Interventions on Glucose and Lipid Metabolism in Metabolic Diseases: A Systematic Review and Meta-Analysis.}, journal = {Life (Basel, Switzerland)}, volume = {14}, number = {11}, pages = {}, doi = {10.3390/life14111485}, pmid = {39598283}, issn = {2075-1729}, abstract = {BACKGROUND: The gut microbiome is increasingly recognized as a key player in metabolic health, influencing glucose and lipid metabolism through various mechanisms. However, the efficacy of gut microbiota-targeted interventions, such as probiotics, prebiotics, fecal microbiota transplantation (FMT), and diet-based treatments, remains unclear for specific metabolic outcomes. In this study, the aim was to evaluate the impact of these interventions on the glucose and lipid parameters in individuals with metabolic diseases such as diabetes mellitus (DM), obesity, and metabolic syndrome.<br><br>METHODS: This systematic review and meta-analysis included 41 randomized controlled trials that investigated the effects of gut microbiota-targeted treatments on metabolic parameters such as fasting glucose, glycated hemoglobin (HbA1c), homeostatic model assessment for insulin resistance (HOMA-IR), total cholesterol, low-density lipoprotein cholesterol (LDL-C), high-density lipoprotein cholesterol (HDL-C), and triglycerides. A comprehensive search was conducted using databases like PubMed, Google Scholar, and Scopus, focusing on interventions targeting the gut microbiota. A meta-analysis was performed using random-effects models, with effect sizes calculated for each outcome. Risk of bias was assessed using the Cochrane Risk of Bias tool.<br><br>RESULTS: Gut microbiota-targeted interventions significantly reduced fasting glucose, HbA1c, HOMA-IR, total cholesterol, LDL-C, and triglycerides, with moderate heterogeneity observed across studies. The interventions also led to modest increases in HDL-C levels. Probiotic and synbiotic interventions showed the most consistent benefits in improving both glucose and lipid profiles, while FMT yielded mixed results. Short-term interventions showed rapid microbial shifts but less pronounced metabolic improvements, whereas longer-term interventions had more substantial metabolic benefits.<br><br>CONCLUSIONS: In this study, it is demonstrated that gut microbiota-targeted interventions can improve key metabolic outcomes, offering a potential therapeutic strategy for managing metabolic diseases. However, the effectiveness of these interventions varies depending on the type, duration, and population characteristics, highlighting the need for further long-term studies to assess the sustained effects of microbiota modulation on metabolic health.}, }
@article {pmid39598237, year = {2024}, author = {Min, M and Tarmaster, A and Bodemer, A and Sivamani, RK}, title = {The Influence of a Plant-Based Diet on Skin Health: Inflammatory Skin Diseases, Skin Healing, and Plant-Based Sources of Micro- and Macro-Nutrients.}, journal = {Life (Basel, Switzerland)}, volume = {14}, number = {11}, pages = {}, doi = {10.3390/life14111439}, pmid = {39598237}, issn = {2075-1729}, abstract = {Dietary patterns have been shown to worsen or alleviate several dermatological diseases. A well-balanced, plant-based diet is known to have anti-inflammatory, probiotic, and antioxidant properties, along with weight loss-promoting effects. Moreover, a plant-based diet has a low glycemic load, improving metabolic disease. Due to these qualities, plant-based diets may have beneficial effects on inflammatory skin conditions. In this review, we aim to discuss the possible mechanisms by which a plant-based diet reduces disease severity in psoriasis, acne, hidradenitis suppurativa, and atopic dermatitis. We also aim to clarify how a plant-based diet may influence skin healing and identify sources of vitamins, nutrients, fatty acids, and protein in a well-balanced, plant-based diet. We performed a literature search on PubMed/MEDLINE databases with the following keywords: "plant-based" OR "vegan" OR "vegetarian" OR "meat" OR "diet" AND "psoriasis" OR "hidradenitis suppurativa" OR "acne" OR "atopic dermatitis" OR "skin healing" OR "dermatology". Our findings demonstrate that plant-based foods may improve inflammatory skin diseases by supporting the gut microbiome, exerting anti-inflammatory effects, providing barrier support, and improving glycemic control. With the proper education, there is an abundance of plant-based food sources or supplements that contain riboflavin, vitamin B12, vitamin A, omega-3 fatty acids, and protein, thereby ameliorating the risk of nutritional deficiencies. Thus, a plant-based diet may have therapeutic potential in dermatology. In spite of the evidence available, there is a paucity of clinical studies focusing specifically on plant-based diets and dermatologic conditions and further investigation is warranted.}, }
@article {pmid39598196, year = {2024}, author = {Shalmon, G and Ibrahim, R and Israel-Elgali, I and Grad, M and Shlayem, R and Shapira, G and Shomron, N and Youngster, I and Scheinowitz, M}, title = {Gut Microbiota Composition Positively Correlates with Sports Performance in Competitive Non-Professional Female and Male Runners.}, journal = {Life (Basel, Switzerland)}, volume = {14}, number = {11}, pages = {}, doi = {10.3390/life14111397}, pmid = {39598196}, issn = {2075-1729}, abstract = {There is still a pressing need for further investigation to bridge the gap in understanding the differences in gut microbiota composition between female runners and their male counterparts. We aimed to determine the gut microbiota composition in competitive non-professional female and male runners and to correlate the gut bacteria to performance. Our study included 40 subjects, of which 22 were runners (13 males and 9 females) and 18 control subjects (9 males and 9 females, representing the general population who perform light physical activity with a weekly running volume of ≤5 km per week). Fecal specimens were collected and analyzed for taxonomic profiling to compare species' relative abundances between males and females based on the results of 16SrRNA analysis. Bacterial alpha and beta diversity were assessed to determine the differences in microbial composition between runners and controls, and between sexes. Each participant underwent a maximal oxygen consumption test and a time-to-exhaustion test at 85% of the measured VO2max. Blood lactate was collected every 5 min during the tests. Bacterial alpha diversity showed a significant difference (p = 0.04) between runners and controls. Taxonomic analysis of gut microbiota composition showed a lower Enterobacteriaceae abundance and a higher Methanosphaera abundance in runners compared with the control group. Ten different bacteria (Methanosphaera, Mitsuokella, Prevotellaceae, Megamonas, Rothia, Oscillospira, Bacteroides, Odoribacter, Blautia massiliensis, Butyricicoccus_pullicaecorum) were positively correlated with exercise (VO2max, lactate blood levels, time to exhaustion, and weekly training volume). We found no significant differences in the gut microbiota composition between male and female runners. Gut microbiota composition positively correlates with sports performance in competitive non-professional female and male runners, and female runners show similar gut microbiome diversity to male runners.}, }
@article {pmid39598083, year = {2024}, author = {Neiroukh, D and Hajdarpasic, A and Ayhan, C and Sultan, S and Soliman, O}, title = {Gut Microbial Taxonomy and Its Role as a Biomarker in Aortic Diseases: A Systematic Review and Future Perspectives.}, journal = {Journal of clinical medicine}, volume = {13}, number = {22}, pages = {}, doi = {10.3390/jcm13226938}, pmid = {39598083}, issn = {2077-0383}, abstract = {Background/Objectives: Evidence of the association between the gut microbiome and cardiovascular diseases has accumulated. An imbalance or dysbiosis of this system has been shown to play a role in the pathogenesis of cardiovascular events, including aortic diseases. We aimed to elucidate the findings of the gut microbial taxonomy associated with aortic diseases and their subtypes. Furthermore, we sought to investigate whether gut microbiome dysbiosis can be used as a biomarker for aortic disease detection and to identify which species can be disease-specific. Methods: A systematic search was conducted using the Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) guidelines for original research papers on gut microbiome composition in patients with aortic disease, using patients without aortic disease as the control (i.e., healthy controls). The databases PubMed, Scopus, Cochrane, and Web of Science were used by employing the medical subject headings (MeSH) terms "aortic diseases", "microbiome"," microbiota", and "taxa" before August 2024. We extracted the study characteristics, study population, and gut microbiome in aortic disease, including microbiota taxa diversity and abundance, regardless of taxa level. The National Institutes of Health (NIH) Quality Assessment Tool was used to assess study quality. Data were synthesized narratively to address the heterogeneity of the studies. Results: In this review, twelve studies that have identified gut microbial species and their potential impact on aortic disease pathogenesis were included. The studies showed the phyla dominance of Bacillota, Pseudomonadota, Actinomycetota, Bacteroidota, and Euryarchaeota in aortic disease patients. We also included the taxa sequencing methods and those used to extract the microorganisms. Aortic diseases were categorized into Takayasu's arteritis, giant cell arteritis, aortic aneurysm, and aortic dissection. Aortic disease patients had a higher rate of dysbiosis when compared to the healthy control groups, with significantly different microbiome composition. Conclusions: Patients with aortic disease exhibit a distinct difference between their gut microbiota composition and that of the healthy controls, which suggests a potential biomarker role of gut dysbiosis. Further exploration of the microbiome and its metagenome interface can help identify its role in aortic disease pathogenesis in depth, generating future therapeutic options. However, a unified methodology is required to identify potential microbial biomarkers in cardiovascular and cardiometabolic diseases.}, }
@article {pmid39598069, year = {2024}, author = {Marfil-Cantón, M and Prados-Carmona, A and Cebolla-Verdugo, M and Husein-ElAhmed, H and Campos, F and Ruiz-Villaverde, R}, title = {Anti-OX40 Biological Therapies in the Treatment of Atopic Dermatitis: A Comprehensive Review.}, journal = {Journal of clinical medicine}, volume = {13}, number = {22}, pages = {}, doi = {10.3390/jcm13226925}, pmid = {39598069}, issn = {2077-0383}, abstract = {Introduction. Atopic dermatitis (AD) is the most prevalent inflammatory dermatological disorder, affecting a significant percentage of the global population. This chronic disease has a multifactorial and intricate pathogenesis, influenced by genetic predisposition, skin barrier dysfunction, immune dysregulation, neuroimmune mechanisms, and alterations in the skin microbiome, among other factors. Methods. The treatment of AD has faced significant clinical challenges due to the ineffectiveness of conventional therapies. However, recent advances in understanding its pathophysiology have led to the introduction of new therapeutic options. Recently, the OX40 receptor has been identified as a key factor in the development of AD. Recent studies have demonstrated that blocking the OX40 ligand with monoclonal antibodies significantly and sustainably improves the signs and symptoms of moderate to severe AD. Results. A comprehensive review of the available literature on anti-OX40 treatments in atopic dermatitis that evaluates their mechanism of action, their clinical efficacy, and the prospects of this promising therapeutic option for improving AD management is provided. Conclusions. Anti-OX40 and anti-OX40L blockers are a promising therapeutic alternative for the management of moderate-severe atopic dermatitis. Prospective analytical studies are needed to determine whether this new therapeutic target represents a qualitative advance in modifying the progression of the disease.}, }
@article {pmid39598018, year = {2024}, author = {Marchlewicz, M and Sagan, P and Grabowska, M and Kiedrowicz, M and Kruk, J and Gill, K and Piasecka, M and Duchnik, E}, title = {The Role of Vitamin D3 Deficiency and Colonization of the Oral Mucosa by Candida Yeast-like Fungi in the Pathomechanism of Psoriasis.}, journal = {Journal of clinical medicine}, volume = {13}, number = {22}, pages = {}, doi = {10.3390/jcm13226874}, pmid = {39598018}, issn = {2077-0383}, support = {WNoZ-324/S/2024//Pomeranian Medical University/ ; }, abstract = {Psoriasis is a chronic inflammatory skin disease with complex pathogenesis and variable severity. Performed studies have indicated the impact of vitamin D3 deficiency on the pathogenesis of psoriasis and its severity. However, there is no clear evidence of the influence of the mucosal microbiome on the onset and progression of psoriasis. This review aims to present the current evidence on the role of vitamin D3 and colonization of the oral mucosa by Candida yeast-like fungi in the pathogenesis of psoriasis. Candida albicans is a common yeast that can colonize the skin and mucosal surfaces, particularly in individuals with weakened immune systems or compromised skin barriers. In psoriasis, the skin's barrier function is disrupted, potentially making patients more susceptible to fungal infections such as Candida. Since patients with psoriasis are at increased risk of metabolic syndrome, they may experience the vicious circle effect in which chronic inflammation leads to obesity. Vitamin D3 deficiency is also associated with microbiological imbalance, which may promote excessive growth of Candida fungi. Under normal conditions, the intestinal and oral microflora support the immune system. Vitamin D3 deficiency, however, leads to disruption of this balance, which allows Candida to overgrow and develop infections.}, }
@article {pmid39597764, year = {2024}, author = {Zobrist, Y and Doulberis, M and Biedermann, L and Leventhal, GE and Rogler, G}, title = {Anthocyanin-Rich Extract Mitigates the Contribution of the Pathobiont Genus Haemophilus in Mild-to-Moderate Ulcerative Colitis Patients.}, journal = {Microorganisms}, volume = {12}, number = {11}, pages = {}, doi = {10.3390/microorganisms12112376}, pmid = {39597764}, issn = {2076-2607}, support = {33IC30_166844/SNSF_/Swiss National Science Foundation/Switzerland ; }, abstract = {Anthocyanins (ACs) have been shown to elicit anti-inflammatory and antioxidant effects in animal models of ulcerative colitis (UC). Furthermore, we previously observed in a double-blind randomized trial in UC patients that biochemical disease activity tended to be lower in patients that were exposed to AC. Here, we report on the changes in the fecal microbiome composition in these patients upon AC exposure. UC patients received a 3 g daily dose of an AC-rich bilberry extract (ACRE) for eight weeks. We determined the microbiome composition in longitudinal stool samples from 24 patients and quantified the degree of change over time. We also correlated the relative abundances of individual microbial taxa at different timepoints to fecal concentrations of calprotectin, a proxy for inflammation. Microbiome composition did not change over time as a result of the intervention, in terms of both alpha and beta diversity. However, before the intervention, the abundance of Haemophilus parainfluenzae was positively correlated with fecal calprotectin concentrations, and this correlation persisted in placebo-treated subjects throughout the study. In contrast, the correlation between H. parainfluenzae and calprotectin vanished in ACRE-treated subjects, while the relative abundance of H. parainfluenzae did not change. Our results suggest that ACRE treatment mitigates the contribution of H. parainfluenzae to inflammation. Further research is warranted to better comprehend the role of microbial composition in response to medical therapy including AC-rich extract in UC patients.}, }
@article {pmid39597757, year = {2024}, author = {Duffy, HR and Ashton, NN and Blair, A and Hooper, N and Stulce, P and Williams, DL}, title = {Regulatory Standard for Determining Preoperative Skin Preparation Efficacy Underreports True Dermal Bioburden in a Porcine Model.}, journal = {Microorganisms}, volume = {12}, number = {11}, pages = {}, doi = {10.3390/microorganisms12112369}, pmid = {39597757}, issn = {2076-2607}, support = {2139322//National Science Foundation/ ; NA//L.S. Peery Foundation (Department of Orthopeadics, University of Utah)/ ; }, abstract = {Medical device companies and regulatory bodies rely on a nondestructive bacterial sampling technique specified by the American Society for Testing and Materials (ASTM E1173-15) to test preoperative skin preparations (PSPs). Despite the widespread use of PSPs, opportunistic skin-flora pathogens remain the most significant contributor to surgical site infections, suggesting that the ASTM testing standard may be underreporting true dermal bioburden. We hypothesized that ASTM E1173-15 may fail to capture deep skin-dwelling flora. To test this hypothesis, we applied ASTM E1173-15 and a full-thickness skin sampling technique, which we established previously through application to the backs of seven pigs (Yorkshire/Landrace hybrid) following a clinically used PSP (4% chlorhexidine gluconate). The results showed that samples quantified using the full-thickness skin method consistently cultured more bacteria than the ASTM standard, which principally targeted surface-dwelling bacteria. Following PSP, the ASTM standard yielded 1.05 ± 0.24 log10 CFU/cm[2], while the full-thickness tissue method resulted in 3.24 ± 0.24 log10 CFU/cm[2], more than a 2 log10 difference (p < 0.001). Immunofluorescence images corroborated the data, showing that Staphylococcus epidermidis was present in deep skin regions with or without PSP treatment. Outcomes suggested that a full-thickness sampling technique may better evaluate PSP technologies as it resolves bioburdens dwelling in deeper skin regions.}, }
@article {pmid39597740, year = {2024}, author = {Taufer, CR and da Silva, J and Rampelotto, PH}, title = {In Silico Analysis of Probiotic Bacteria Changes Across COVID-19 Severity Stages.}, journal = {Microorganisms}, volume = {12}, number = {11}, pages = {}, doi = {10.3390/microorganisms12112353}, pmid = {39597740}, issn = {2076-2607}, support = {88887.513461/2020-00//CAPES/ ; }, abstract = {The gut microbiota plays a crucial role in modulating the immune response during COVID-19, with several studies reporting significant alterations in specific bacterial genera, including Akkermansia, Bacteroides, Bifidobacterium, Faecalibacterium, Lactobacillus, Oscillospira, and Ruminococcus. These genera are symbionts of the gut microbiota and contribute to host health. However, comparing results across studies is challenging due to differences in analysis methods and reference databases. We screened 16S rRNA raw datasets available in public databases on COVID-19, focusing on the V3-V4 region of the bacterial genome. In total, seven studies were included. All samples underwent the same bioinformatics pipeline, evaluating the differential abundance of these seven bacterial genera at each level of severity. The reanalysis identified significant changes in differential abundance. Bifidobacterium emerged as a potential biomarker of disease severity and a therapeutic target. Bacteroides presented a complex pattern, possibly related to disease-associated inflammation or opportunistic pathogen growth. Lactobacillus showed significant changes in abundance across the COVID-19 stages. On the other hand, Akkermansia and Faecalibacterium did not show significant differences, while Oscillospira and Ruminococcus produced statistically significant results but with limited relevance to COVID-19 severity. Our findings reveal new insights into the differential abundance of key bacterial genera in COVID-19, particularly Bifidobacterium and Bacteroides.}, }
@article {pmid39597739, year = {2024}, author = {Sun, X and Liu, Y and He, L and Kuang, Z and Dai, S and Hua, L and Jiang, Q and Wei, T and Ye, P and Zeng, H}, title = {Response of Yields, Soil Physiochemical Characteristics, and the Rhizosphere Microbiome to the Occurrence of Root Rot Caused by Fusarium solani in Ligusticum chuanxiong Hort.}, journal = {Microorganisms}, volume = {12}, number = {11}, pages = {}, doi = {10.3390/microorganisms12112350}, pmid = {39597739}, issn = {2076-2607}, support = {2023NSFSC1262//the Natural Science Foundation of Sichuan Province of China/ ; SCCXTD-2024-19//Sichuan Innovation Team of the Chinese National Modern Agriculture Industry Technology System/ ; CARS-21-21//National Chinese Medicinal Materials Technology System/ ; 2022ZZCX078//Sichuan Provincial Finance Independent Innovation Project/ ; }, abstract = {Ligusticum chuanxiong Hort. is considered an important medicinal herb with extremely high economic value and medicinal value due to its various effects, including anti-oxidation, sedative action, hepatoprotection, and invigorating blood circulation. However, L. chuanxiong cultivation is hampered by various plant diseases, especially the root rot caused by Fusarium solani, hindering the sustainable development of the L. chuanxiong industry. The occurrence of soil-borne diseases is closely linked to imbalances in the microbial community structure. Here, we studied the yields, rhizosphere microbiota, and soil physiochemical characteristics of healthy and diseased L. chuanxiong plants affected by root rot with high-throughput sequencing and microbial network analysis, aiming to explore the relationships between soil environmental factors, microbiomes, and plant health of L. chuanxiong. According to the results, L. chuanxiong root rot significantly decreased the yields, altered microbial community diversity and composition, enriched more pathogenic fungi, recruited some beneficial bacteria, and reduced microbial interaction network stability. The Mantel test showed that soil organic matter and pH were the major environmental factors modulating plant microbiome assembly. The root rot severity was significantly affected by soil physiochemical properties, including organic matter, cation exchange capacity, available nitrogen, phosphorus, potassium, and pH. Furthermore, two differential microbes that have great potential in the biocontrol of L. chuanxiong root rot were dug out in the obtained results, which were the genera Trichoderma and Bacillus. This study provided a theoretical basis for further studies revealing the microecological mechanism of L. chuanxiong root rot and the ecological prevention and control of L. chuanxiong root rot from a microbial ecology perspective.}, }
@article {pmid39597729, year = {2024}, author = {Alexandrescu, L and Suceveanu, AP and Stanigut, AM and Tofolean, DE and Axelerad, AD and Iordache, IE and Herlo, A and Nelson Twakor, A and Nicoara, AD and Tocia, C and Dumitru, A and Dumitru, E and Condur, LM and Aftenie, CF and Tofolean, IT}, title = {Intestinal Insights: The Gut Microbiome's Role in Atherosclerotic Disease: A Narrative Review.}, journal = {Microorganisms}, volume = {12}, number = {11}, pages = {}, doi = {10.3390/microorganisms12112341}, pmid = {39597729}, issn = {2076-2607}, abstract = {Recent advances have highlighted the gut microbiota as a significant contributor to the development and progression of atherosclerosis, which is an inflammatory cardiovascular disease (CVD) characterized by plaque buildup within arterial walls. The gut microbiota, consisting of a diverse collection of microorganisms, impacts the host's metabolism, immune responses, and lipid processing, all of which contribute to atherosclerosis. This review explores the complex mechanisms through which gut dysbiosis promotes atherogenesis. We emphasize the potential of integrating microbiota modulation with traditional cardiovascular care, offering a holistic approach to managing atherosclerosis. Important pathways involve the translocation of inflammatory microbial components, modulation of lipid metabolism through metabolites such as trimethylamine-N-oxide (TMAO), and the production of short-chain fatty acids (SCFAs) that influence vascular health. Studies reveal distinct microbial profiles in atherosclerosis patients, with increased pathogenic bacteria (Megamonas, Veillonella, Streptococcus) and reduced anti-inflammatory genera (Bifidobacterium, Roseburia), highlighting the potential of these profiles as biomarkers and therapeutic targets. Probiotics are live microorganisms that have health benefits on the host. Prebiotics are non-digestible dietary fibers that stimulate the growth and activity of beneficial gut bacteria. Interventions targeting microbiota, such as probiotics, prebiotics, dietary modifications, and faecal microbiota transplantation (FMT), present effective approaches for restoring microbial equilibrium and justifying cardiovascular risk. Future research should focus on longitudinal, multi-omics studies to clarify causal links and refine therapeutic applications.}, }
@article {pmid39597728, year = {2024}, author = {Martín-Cereceda, M and de Cos-Gandoy, A and Williams, RAJ and Elliott, D and Serrano-Bellón, A and Pérez-Uz, B and Sanchez-Jimenez, A}, title = {Cast from the Past? Microbial Diversity of a Neolithic Stone Circle.}, journal = {Microorganisms}, volume = {12}, number = {11}, pages = {}, doi = {10.3390/microorganisms12112338}, pmid = {39597728}, issn = {2076-2607}, support = {PR44/21-29928//Universidad Complutense de Madrid/ ; }, abstract = {We studied the microbial diversity colonizing limestone rock pools at a Neolithic Monument (Arbor Low, Derbyshire, England). Five pools were analyzed: four located at the megaliths of the stone circle and one pool placed at the megalith at the Gib Hill burial mound 300 m distant. Samples were taken from rock pool walls and sediments, and investigated through molecular metabarcoding. The microbiome consisted of 23 phyla of bacteria (831 OTUs), 4 phyla of archaea (19 OTUs), and 27 phyla of microbial eukarya (596 OTUs). For bacteria, there were statistically significant differences in wall versus sediment populations, but not between pools. For archaea and eukarya, significant differences were found only between pools. The most abundant bacterial phylum in walls was Cyanobacteriota, and Pseudomonadota in sediments. For archaea and microbial eukarya, the dominant phyla were Euryarcheota and Chlorophyta, respectively, in both wall and sediments. The distant pool (P5) showed a markedly different community structure in phyla and species, habitat discrimination, and CHN content. Species sorting and dispersal limitation are discussed as mechanisms structuring the microbiome assemblages and their spatial connectivity. The Arbor Low microbiome is composed of terrestrial representatives common in extreme environments. The high presence of Cyanobacteriota and Chlorophyta in the Arbor Low stones is troubling, as these microorganisms can induce mechanical disruption by penetrating the limestone matrix through endolithic/chasmoendolithic growth. Future research should focus on the metabolic traits of strains to ascertain their implication in bioweathering and/or biomineralization.}, }
@article {pmid39597723, year = {2024}, author = {Huang, CW and Liu, SY and Bhattarai, BP and Lee, TY and Chang, HT and Lin, HC and Weng, HM and Huang, HH and Lin, JS and Lee, JW}, title = {Live Multi-Strain Probiotics Enhance Growth Performance by Regulating Intestinal Morphology and Microbiome Population in Weaning Piglets.}, journal = {Microorganisms}, volume = {12}, number = {11}, pages = {}, doi = {10.3390/microorganisms12112334}, pmid = {39597723}, issn = {2076-2607}, support = {N/A//SYNBIO TECH INC./ ; }, abstract = {The effects of different forms of multi-strain probiotics on weaning piglets are limitedly addressed. Thus, this study investigated the effects of live or inanimate multi-strain probiotics comprising Lactobacillus plantarum, Streptococcus thermophilus, and Bacillus subtilis on growth performance, intestinal morphology, fecal microbiota, short-chain fatty acids, and intestinal gene expression of weaning piglets. A total of 160 weaning piglets (4 weeks old) were randomly allocated into four treatments (CON: basal diet; AB: basal diet with 110 ppm and 66 ppm colistin in the weaning and nursery phases, respectively; LP: basal diet with 2.0 × 10[9] CFU/kg live probiotics; and IP: basal diet with 2.0 × 10[9] CFU/kg inanimate probiotics). Piglets fed with LP had significantly lower FCR compared to those of the CON and IP groups in week 4 to week 8 (p < 0.05). Moreover, the LP group had significantly higher villus height (VH) compared with AB at week 6, lower crypt depth (CD) compared with IP, and higher VH/CD ratio compared to other treatments at week 10 (p < 0.05), which indicate healthier intestinal morphology. Probiotic treatments (LP and IP) increased Bifidobacterium population compared to CON at week 6 and lowered Enterobacteriaceae at week 6 and week 10 (p < 0.05). Regarding gene expressions of intestinal integrity, LP showed significantly higher TFF3 expression compared with CON and AB at week 6 and compared with other treatments in jejunum at week 10 (p < 0.05). IP treatment had significantly higher MUC2 expression compared to other treatments at week 6 and week 10 (p < 0.05). Overall, live multi-strain probiotics improved growth efficiency by enhancing gut integrity and microbiome balance, making them a potential antibiotic alternative to ameliorate weaning stress and promote productive performance in weaning piglets.}, }
@article {pmid39597722, year = {2024}, author = {Khalil, M and Di Ciaula, A and Mahdi, L and Jaber, N and Di Palo, DM and Graziani, A and Baffy, G and Portincasa, P}, title = {Unraveling the Role of the Human Gut Microbiome in Health and Diseases.}, journal = {Microorganisms}, volume = {12}, number = {11}, pages = {}, doi = {10.3390/microorganisms12112333}, pmid = {39597722}, issn = {2076-2607}, abstract = {The human gut is a complex ecosystem that supports billions of living species, including bacteria, viruses, archaea, phages, fungi, and unicellular eukaryotes. Bacteria give genes and enzymes for microbial and host-produced compounds, establishing a symbiotic link between the external environment and the host at both the gut and systemic levels. The gut microbiome, which is primarily made up of commensal bacteria, is critical for maintaining the healthy host's immune system, aiding digestion, synthesizing essential nutrients, and protecting against pathogenic bacteria, as well as influencing endocrine, neural, humoral, and immunological functions and metabolic pathways. Qualitative, quantitative, and/or topographic shifts can alter the gut microbiome, resulting in dysbiosis and microbial dysfunction, which can contribute to a variety of noncommunicable illnesses, including hypertension, cardiovascular disease, obesity, diabetes, inflammatory bowel disease, cancer, and irritable bowel syndrome. While most evidence to date is observational and does not establish direct causation, ongoing clinical trials and advanced genomic techniques are steadily enhancing our understanding of these intricate interactions. This review will explore key aspects of the relationship between gut microbiota, eubiosis, and dysbiosis in human health and disease, highlighting emerging strategies for microbiome engineering as potential therapeutic approaches for various conditions.}, }
@article {pmid39597687, year = {2024}, author = {Zamorano-Martín, F and Chumaceiro, G and Navarro-Torres, P and Borroni, D and Urbinati, F and Molina, &#xc1; and Paytuví-Gallart, A and Rocha-de-Lossada, C}, title = {A Comparative Analysis of the Ocular Microbiome: Insights into Healthy Eyes and Anophthalmic Sockets.}, journal = {Microorganisms}, volume = {12}, number = {11}, pages = {}, doi = {10.3390/microorganisms12112298}, pmid = {39597687}, issn = {2076-2607}, abstract = {The purpose of this study is to characterize the ocular surface microbiota of patients with an anophthalmic cavity. An eNAT with 1 mL of Liquid Amies Medium was used to collect samples. Microbial DNA from anophthalmic socket and healthy fellow control eye samples was isolated and sequenced. Raw reads were analyzed with GAIA (v 2.02). The richness and Shannon alpha diversity metrics, as well as Bray-Curtis beta diversity and Wilcoxon signed-rank test values, were computed with R packages such as phyloseq, mia, or DESeq2 to allow for microbiome analysis. Principal coordinate analysis (PCoA) was performed using the function plotReducedDim from the R package scater. The different taxonomic profiles were described under the concept of eye community state type (ECST). The microbiomes of both eyes from 25 patients with an anophthalmic cavity were analyzed in this study. While the microbial communities of paired eyes from the same patients showed notable dissimilarity, no consistent patterns emerged when comparing healthy eyes to anophthalmic sockets. Alpha diversity values did not significantly differ between healthy eyes and anophthalmic socket samples, though there was considerable variability within each group. Notably, anophthalmic socket samples generally exhibited lower abundances of genera such as Staphylococcus, Enterococcus, Paenibacillus, and Sediminibacterium compared to their healthy counterparts. Microbial variability between healthy eyes and anophthalmic sockets may be due to anatomical differences. Further research is needed to determine whether patients without anophthalmic sockets exhibit similar microbiome patterns in both eyes.}, }
@article {pmid39597681, year = {2024}, author = {Scharf, SA and Friedrichs, L and Bock, R and Borrelli, M and MacKenzie, C and Pfeffer, K and Henrich, B}, title = {Oxford Nanopore Technology-Based Identification of an Acanthamoeba castellanii Endosymbiosis in Microbial Keratitis.}, journal = {Microorganisms}, volume = {12}, number = {11}, pages = {}, doi = {10.3390/microorganisms12112292}, pmid = {39597681}, issn = {2076-2607}, abstract = {(1) Background: Microbial keratitis is a serious eye infection that carries a significant risk of vision loss. Acanthamoeba spp. are known to cause keratitis and their bacterial endosymbionts can increase virulence and/or treatment resistance and thus significantly worsen the course of the disease. (2) Methods and Results: In a suspected case of Acanthamoeba keratitis, in addition to Acanthamoeba spp., an endosymbiont of acanthamoebae belonging to the taxonomic order of Holosporales was detected by chance in a bacterial 16S rDNA-based pan-PCR and subsequently classified as Candidatus Paracaedibacter symbiosus through an analysis of an enlarged 16S rDNA region. We used Oxford Nanopore Technology to evaluate the usefulness of whole-genome sequencing (WGS) as a one-step diagnostics method. Here, Acanthamoeba castellanii and the endosymbiont Candidatus Paracaedibacter symbiosus could be directly detected at the species level. No other microbes were identified in the specimen. (3) Conclusions: We recommend the introduction of WGS as a diagnostic approach for keratitis to replace the need for multiple species-specific qPCRs in future routine diagnostics and to enable an all-encompassing characterisation of the polymicrobial community in one step.}, }
@article {pmid39597659, year = {2024}, author = {Mongruel, ACB and Medici, EP and Machado, RZ and Clay, K and André, MR}, title = {Characterization of the Blood Bacterial Microbiota in Lowland Tapirs (Tapirus terrestris), a Vulnerable Species in Brazil.}, journal = {Microorganisms}, volume = {12}, number = {11}, pages = {}, doi = {10.3390/microorganisms12112270}, pmid = {39597659}, issn = {2076-2607}, support = {2019/26403-0//Funda&#xe7;&#xe3;o de Apoio &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2022/13016-1//Funda&#xe7;&#xe3;o de Apoio &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2020/12037-0//Funda&#xe7;&#xe3;o de Apoio &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 2022/08543-2//Funda&#xe7;&#xe3;o de Apoio &#xe0; Pesquisa do Estado de S&#xe3;o Paulo/ ; 303701/2021-8//National Council for Scientific and Technological Development/ ; }, abstract = {Microbiome studies targeting hypervariable regions of the 16S rRNA gene are suitable for understanding interactions between animals and their associated bacteria. While many studies focus on the gut microbiome, assessments of blood microbiota remain scarce despite the prevalence of blood-borne pathogens in vertebrates. This study aimed to investigate the bacterial community in blood samples from 79 living and 7 road-killed lowland tapirs (Tapirus terrestris), a vulnerable species, sampled in two biomes in midwestern Brazil: Pantanal and Cerrado. Animals were categorized by condition (living or road-killed), sex, age, and biome. V3-V4 16S rRNA fragments were obtained from 86 blood samples and 4 negative controls. After filtering contaminants, 13,742,198 sequences representing 2146 ASVs were analyzed. Alpha diversity significantly differed by condition, while beta diversity differed by condition, site, and age (adults vs. sub-adults). For living animals (79/86 samples), alpha diversity showed no significant differences, but beta diversity differed by age. Different vector-borne bacterial pathogens, including Anaplasmataceae, Bartonella, and Borrelia spp., were detected. Additionally, evidence of transient translocation of microbial communities from other body regions to the bloodstream was observed. Amplification of bacterial 16S rRNA from blood samples of wild T. terrestris provided novel information about the diversity of blood-borne microbiota of lowland tapirs, members of a poorly studied mammalian family. Next-generation sequencing proved to be a valuable tool for screening potential vector-borne pathogens in this host.}, }
@article {pmid39597645, year = {2024}, author = {Biennier, S and Fontaine, M and Duquenoy, A and Schwintner, C and Doré, J and Corvaia, N}, title = {Narrative Review: Advancing Dysbiosis Treatment in Onco-Hematology with Microbiome-Based Therapeutic Approach.}, journal = {Microorganisms}, volume = {12}, number = {11}, pages = {}, doi = {10.3390/microorganisms12112256}, pmid = {39597645}, issn = {2076-2607}, abstract = {This review explores the complex relationship between gut dysbiosis and hematological malignancies, focusing on graft-versus-host disease (GvHD) in allogeneic hematopoietic stem cell transplantation (allo-HSCT) recipients. We discuss how alterations in microbial diversity and composition can influence disease development, progression, and treatment outcomes in blood cancers. The mechanisms by which the gut microbiota impacts these conditions are examined, including modulation of immune responses, production of metabolites, and effects on intestinal barrier function. Recent advances in microbiome-based therapies for treating and preventing GvHD are highlighted, with emphasis on full ecosystem standardized donor-derived products. Overall, this review underscores the growing importance of microbiome research in hematology-oncology and its potential to complement existing treatments and improve outcomes for thousands of patients worldwide.}, }
@article {pmid39597635, year = {2024}, author = {Dharmarathne, G and Kazi, S and King, S and Jayasinghe, TN}, title = {The Bidirectional Relationship Between Cardiovascular Medications and Oral and Gut Microbiome Health: A Comprehensive Review.}, journal = {Microorganisms}, volume = {12}, number = {11}, pages = {}, doi = {10.3390/microorganisms12112246}, pmid = {39597635}, issn = {2076-2607}, abstract = {Cardiovascular diseases (CVDs) are a leading cause of widespread morbidity and mortality. It has been found that the gut and oral microbiomes differ in individuals with CVDs compared to healthy individuals. Patients with CVDs often require long-term pharmacological interventions. While these medications have been extensively studied for their cardiovascular benefits, emerging research indicates that they may also impact the diversity and composition of the oral and gut microbiomes. However, our understanding of how these factors influence the compositions of the oral and gut microbiomes in individuals remains limited. Studies have shown that statins and beta-blockers, in particular, cause gut and oral microbial dysbiosis, impacting the metabolism and absorption of these medications. These alterations can lead to variations in drug responses, highlighting the need for personalized treatment approaches. The microbiome's role in drug metabolism and the impact of CVD medications on the microbiome are crucial in understanding these variations. However, there are very few studies in this area, and not all medications have been studied, emphasizing the necessity for further research to conclusively establish cause-and-effect relationships and determine the clinical significance of these interactions. This review will provide evidence of how the oral and gut microbiomes in patients with cardiovascular diseases (CVDs) interact with specific drugs used in CVD treatment.}, }
@article {pmid39597633, year = {2024}, author = {Panee, J and Qin, Y and Deng, Y}, title = {Associations of Chronic Marijuana Use with Changes in Salivary Microbiome.}, journal = {Microorganisms}, volume = {12}, number = {11}, pages = {}, doi = {10.3390/microorganisms12112244}, pmid = {39597633}, issn = {2076-2607}, support = {P20GM103466, U54MD007601, P30GM114737, P20GM139753, U54GM138062, and P30CA071789/NH/NIH HHS/United States ; }, abstract = {The legalization of marijuana (MJ) for medicinal and recreational use has raised concerns about its potential impact on health, including oral health. While MJ use has been linked to poor oral health, its effects on the composition of the oral microbiome remain unclear. This cross-sectional study analyzed saliva samples from chronic MJ users (n = 18) and nonusers (n = 20) to investigate MJ-related changes in salivary microbiome composition. We identified significant differences in the relative abundance of 16 taxa, including seven species, such as Megasphaera micronucliformis, Prevotella melaninogenica, and Streptococcus anginosus. Additionally, five species showed positive correlations with cumulative lifetime MJ use, including Streptococcus vestibularis and Streptococcus parasanguinis. By grouping salivary microbial communities into clusters based on their association with periodontal health, we found that the cluster with species associated with poor periodontal health had the highest percentage of MJ users. Moreover, MJ use significantly contributed to variance in microbial communities in individuals with relatively good periodontal health. These findings suggest that chronic MJ use is associated with alterations in the salivary microbiome, highlighting its potential broader impact on oral and systemic health.}, }
@article {pmid39597631, year = {2024}, author = {Li, Q and Wu, Y and Qi, X and Liu, Z and Wang, C and Ma, X and Ma, Y}, title = {Prickly Ash Seeds Improve the Ruminal Epithelial Development and Growth Performance of Hu Sheep by Modulating the Rumen Microbiota and Metabolome.}, journal = {Microorganisms}, volume = {12}, number = {11}, pages = {}, doi = {10.3390/microorganisms12112242}, pmid = {39597631}, issn = {2076-2607}, support = {KJJC-LX-2023-05//Technology Integration Technology Project of Linxia Beef and Sheep Industry Development Re-search Institute/ ; 23JRRA1448//Science and Technology Plan Project of Gansu Province/ ; GAU-XKTD-2022-20//Discipline Team Project of Gansu Agricultural University/ ; }, abstract = {It is known that the addition of feed rich in bioactive components to animal diets will affect rumen fermentation parameters and flora structure. However, research on the regulatory effects of prickly ash seeds (PASs) during rumen development or on the rumen microbiome and its metabolites in sheep is limited. The current study was designed to explore the effects of PASs on sheep rumen development and growth performance using metagenomics and metabolomics. Eighteen 3-month-old Hu lambs were randomly allotted to three different dietary treatment groups: 0% (basal diet, CK), 3% (CK with 3% PAS, low-dose PAS, LPS), and 6% (CK with 6% PAS, high-dose PAS, HPS) PASs. The lambs were slaughtered to evaluate production performance. Our results showed that dietary PAS addition improved the average daily gain and reduced the F/G ratio of the experimental animals. Additionally, the height and width of the rumen papilla in the treatment groups were significantly higher than those in the CK group. The fermentation parameters showed that the levels of acetate and butyrate were significantly higher in the LPS group than in the CK and HPS groups. The propionate levels in the HPS group were significantly higher than those in the CK and LPS groups. Metagenomics analysis revealed that PAS dietary supplementation improved the abundance of Clostridiales and Bacteroidales and reduced the abundance of Prevotella, Butyrivibrio, and Methanococcus. Metabolomic analyses revealed that increased metabolite levels, such as those of serotonin, L-isoleucine, and L-valine, were closely related to growth-related metabolic pathways. The correlations analyzed showed that papilla height and muscular thickness were positively and negatively correlated with serotonin and L-valine, respectively. Average daily gain (ADG) was positively and negatively correlated with L-valine and several Prevotella, respectively. In addition, muscular thickness was positively correlated with Sodaliphilus pleomorphus, four Prevotella strains, Sarcina_sp_DSM_11001, and Methanobrevibacter_thaueri. Overall, PAS addition improved sheep growth performance by regulating beneficial microorganism and metabolite abundances, facilitating bacterial and viral invasion resistance.}, }
@article {pmid39597630, year = {2024}, author = {Arone, GJ and Ocaña, R and Sánchez, A and Villadas, PJ and Fernández-López, M}, title = {Benefits of Crotalaria juncea L. as Green Manure in Fertility and Soil Microorganisms on the Peruvian Coast.}, journal = {Microorganisms}, volume = {12}, number = {11}, pages = {}, doi = {10.3390/microorganisms12112241}, pmid = {39597630}, issn = {2076-2607}, support = {PE501079087-2022//Prociencia-Concytec, Per&#xfa;/ ; }, abstract = {The soils of the Barranca valley are among the best soils in Peru, but with so many years of application of agrochemicals and other agricultural practices, they are losing their productive capacity. Consequently, it was suggested to assess the impact of Crotalaria juncea L. as a green manure on soil fertility and the populations of bacteria and fungi present in the soil. Crotalaria was cultivated for 75 days and incorporated as green manure. After 90 days, the presence of bacteria and fungi was evaluated. Metabarcoding was employed, and the 16S rRNA and ITS2 amplicons were sequenced using the Illumina MiSeq platform. The sequences were processed using various bioinformatics tools. The results indicate that soils have a high diversity of bacteria and fungi. Likewise, in plots where the presence and action of natural biocontrol is suppressed (C0 and P0), pathogenic fungi increase their population in the fallow period (C1), while in P1, the addition of Crotalaria as a green manure promotes an increase in the population of bacteria and fungi, and at the same time it suppresses pathogenic fungi. The genera (bacterial and/or fungal) that increase due to the effect of Crotalaria are beneficial because they are involved as degraders of organic matter, promotion of plant growth and biological control of pathogens. Crotalaria is an alternative to improve soil fertility, increase the beneficial bacterial population, and reduce pathogenic fungi.}, }
@article {pmid39597621, year = {2024}, author = {Trojacka, E and Izdebska, J and Szaflik, J and Przybek-Skrzypecka, J}, title = {The Ocular Microbiome: Micro-Steps Towards Macro-Shift in Targeted Treatment? A Comprehensive Review.}, journal = {Microorganisms}, volume = {12}, number = {11}, pages = {}, doi = {10.3390/microorganisms12112232}, pmid = {39597621}, issn = {2076-2607}, abstract = {A healthy ocular surface is inhabited by microorganisms that constitute the ocular microbiome. The core of the ocular microbiome is still a subject of debate. Numerous culture-dependent and gene sequencing studies have revealed the composition of the ocular microbiome. There was a confirmed correlation between the ocular microbiome and ocular surface homeostasis as well as between ocular dysbiosis and pathologies such as blepharitis, microbial keratitis, and conjunctivitis. However, the role of the ocular microbiome in the pathogenesis and treatment of ocular surface diseases remains unclear. This article reviews available data on the ocular microbiome and microbiota, their role in maintaining ocular homeostasis, and the impact of dysbiosis on several ophthalmic disorders. Moreover, we aimed to discuss potential treatment targets within the ocular microbiota.}, }
@article {pmid39597610, year = {2024}, author = {Gáspár, Z and Nagavci, B and Szabó, BG and Lakatos, B}, title = {Gut Microbiome Alteration in HIV/AIDS and the Role of Antiretroviral Therapy-A Scoping Review.}, journal = {Microorganisms}, volume = {12}, number = {11}, pages = {}, doi = {10.3390/microorganisms12112221}, pmid = {39597610}, issn = {2076-2607}, abstract = {(1) Background: The gut microbiota plays a crucial role in chronic immune activation associated with human immunodeficiency virus (HIV) infection, acquired immune deficiency syndrome (AIDS) pathogenesis, non-AIDS-related comorbidities, and mortality among people living with HIV (PLWH). The effects of antiretroviral therapy on the microbiome remain underexplored. This study aims to map the evidence of the impact of integrase strand transfer inhibitors (INSTI) and non-nucleoside reverse transcriptase inhibitors (NNRTI) on the gut microbiota of PLWH. (2) Methods: A scoping review was conducted using PubMed, Web of Science, and Embase, with reports collected following PRISMA for Scoping Reviews (PRISMA-ScR). (3) Results: Evidence suggests that INSTI-based regimes generally promote the restoration of alpha diversity, bringing it closer to that of seronegative controls, while beta diversity remains largely unchanged. INSTI-based therapies are suggested to be associated with improvements in microbiota composition and a tendency toward reduced inflammatory markers. In contrast, NNRTI-based treatments demonstrate limited recovery of alpha diversity and are linked to an increase in proinflammatory bacteria. (4) Conclusions: Based on the review of the current literature, it is indicated that INSTI-based antiretroviral therapy (ART) therapy facilitates better recovery of the gut microbiome.}, }
@article {pmid39597606, year = {2024}, author = {Qiao, Y and Feng, Q and Wang, Q and Zhao, Q and Zhu, S and Zhao, F and Wang, Z and Zhang, R and Wang, J and Yu, Y and Han, H and Dong, H}, title = {Alteration in the Gut Microbiota of Chickens Resistant to Eimeria tenella Infection.}, journal = {Microorganisms}, volume = {12}, number = {11}, pages = {}, doi = {10.3390/microorganisms12112218}, pmid = {39597606}, issn = {2076-2607}, support = {Grant No. 2023YFD18024//National Key Research and Development Program of China/ ; XZ202401ZY0052//Key Research and Development of Science and Technology Plan in Tibet Autonomous Region/ ; Grant No. 32373038//National Natural Science Foundation of China/ ; NPRC-2019-194-30//National Parasitic Resources Center/ ; }, abstract = {Avian coccidiosis, caused by several species of Eimeria, is a widespread and economically important poultry disease that inflicts severe losses in the poultry industry. Understanding the interplay between Eimeria and gut microbiota is critical for controlling coccidiosis and developing innovative treatments to ensure good poultry health. In the present study, chickens were immunized six times with a low dose of Eimeria tenella, resulting in complete immunity against Eimeria infection. The results of fecal microbiota transplantation showed that the gut microbiota of immunized chickens induced a certain degree of resistance to coccidial infection. To investigate the types of intestinal microbiota involved in the development of resistance to Eimeria, the intestinal contents and fecal samples from both immunized and unimmunized groups were collected for 16S rRNA gene sequencing. The results showed that, at the genus level, the abundance of the Eubacterium coprostanoligenes group, Erysipelatoclostridium, Shuttleworthia, and Colidextribacter was significantly increased in the intestinal content of immunized chickens, whereas the abundance of Eisenbergiella was significantly decreased. In fecal samples, the abundance of Clostridiaceae and Muribaculaceae significantly increased, whereas that of Bacillales significantly decreased. These findings will help to elucidate the interactions between E. tenella and the gut microbiota of chickens, providing a basis for isolating E. tenella-resistant strains from the gut microbiome and developing new vaccines against coccidiosis.}, }
@article {pmid39597602, year = {2024}, author = {Fernandes, GVO and Mosley, GA and Ross, W and Dagher, A and Martins, BGDS and Fernandes, JCH}, title = {Revisiting Socransky's Complexes: A Review Suggesting Updated New Bacterial Clusters (GF-MoR Complexes) for Periodontal and Peri-Implant Diseases and Conditions.}, journal = {Microorganisms}, volume = {12}, number = {11}, pages = {}, doi = {10.3390/microorganisms12112214}, pmid = {39597602}, issn = {2076-2607}, abstract = {This review aimed to identify newly discovered bacteria from individuals with periodontal/peri-implant diseases and organize them into new clusters (GF-MoR complexes) to update Socransky's complexes (1998). For methodological development, the PCC (Population, Concept, Context) strategy was used for the focus question construction: "In patients with periodontal and/or peri-implant disease, what bacteria (microorganisms) were detected through laboratory assays?" The search strategy was applied to PubMed/MEDLINE, PubMed Central, and Embase. The search key terms, combined with Boolean markers, were (1) bacteria, (2) microbiome, (3) microorganisms, (4) biofilm, (5) niche, (6) native bacteria, (7) gingivitis), (8) periodontitis, (9) peri-implant mucositis, and (10) peri-implantitis. The search was restricted to the period 1998-2024 and the English language. The bacteria groups in the oral cavity obtained/found were retrieved and included in the GF-MoR complexes, which were based on the disease/condition, presenting six groups: (1) health, (2) gingivitis, (3) peri-implant mucositis, (4) periodontitis, (5) peri-implantitis, and (6) necrotizing and molar-incisor (M-O) pattern periodontitis. The percentual found per group refers to the number of times a specific bacterium was found to be associated with a particular disease. A total of 381 articles were found: 162 articles were eligible for full-text reading (k = 0.92). Of these articles, nine were excluded with justification, and 153 were included in this review (k = 0.98). Most of the studies reported results for the health condition, periodontitis, and peri-implantitis (3 out of 6 GF-MoR clusters), limiting the number of bacteria found in the other groups. Therefore, it became essential to understand that bacterial colonization is a dynamic process, and the bacteria present in one group could also be present in others, such as those observed with the bacteria found in all groups (Porphyromonas gingivalis, Tannarela forsythia, Treponema denticola, and Aggregatibacter actinomycetemcomitans) (GF-MoR's red triangle). The second most observed bacteria were grouped in GF-MoR's blue triangle: Porphyromonas spp., Prevotela spp., and Treponema spp., which were present in five of the six groups. The third most detected bacteria were clustered in the grey polygon (GF-MoR's grey polygon): Fusobacterium nucleatum, Prevotella intermedia, Campylobacter rectus, and Eikenella corrodens. These three geometric shapes had the most relevant bacteria to periodontal and peri-implant diseases. Specifically, per group, GF-MoR's health group had 58 species; GF-MoR's gingivitis group presented 16 bacteria; GF-MoR's peri-implant mucositis included 17 bacteria; GF-MoR's periodontitis group had 101 different bacteria; GF-MoR's peri-implantitis presented 61 bacteria; and the last group was a combination of necrotizing diseases and molar-incisor (M-I) pattern periodontitis, with seven bacteria. After observing the top seven bacteria of all groups, all of them were found to be gram-negative. Groups 4 and 5 (periodontitis and peri-implantitis) presented the same top seven bacteria. For the first time in the literature, GF-MoR's complexes were presented, gathering bacteria data according to the condition found and including more bacteria than in Socransky's complexes. Based on this understanding, this study could drive future research into treatment options for periodontal and peri-implant diseases, guiding future studies and collaborations to prevent and worsen systemic conditions. Moreover, it permits the debate about the evolution of bacterial clusters.}, }
@article {pmid39597593, year = {2024}, author = {Le Doujet, T and Haugen, P}, title = {The Microbiota of the Outer Gut Mucus Layer of the Migrating Northeast Arctic Cod (Gadus morhua) as Determined by Shotgun DNA Sequencing.}, journal = {Microorganisms}, volume = {12}, number = {11}, pages = {}, doi = {10.3390/microorganisms12112204}, pmid = {39597593}, issn = {2076-2607}, support = {257146//ERA-MarineBiotech/ ; 000000//UiT The Arctic University of Norway/ ; }, abstract = {Animals form functional units with their microbial communities, termed metaorganisms. Despite extensive research on some model animals, microbial diversity in many species remains unexplored. Here, we describe the taxonomic profile of the microbes from the outer gut mucus layer from the Northeast Arctic cod using a shotgun DNA sequencing approach. We focused on the mucus to determine if its microbial composition differs from that of the fecal microbiota, which could reveal unique microbial interactions and functions. Metagenomes from six individuals were analyzed, revealing three different taxonomic profiles: Type I is dominated in numbers by Pseudomonadaceae (44%) and Xanthomonadaceae (13%), Type II by Vibrionaceae (65%), and Type III by Enterobacteriaceae (76%). This stands in sharp contrast to the bacterial diversity of the transient gut content (i.e., feces). Additionally, binning of assembled reads followed by phylogenomic analyses place a high-completeness bin of Type I within the Pseudomonas fluorescens group, Type II within the Photobacterium phosphoreum clade, and Type III within the Escherichia/Shigella group. In conclusion, we describe the adherent bacterial diversity in the Northeast Arctic cod's intestine using shotgun sequencing, revealing different taxonomic profiles compared to the more homogenous transient microbiota. This suggests that the intestine contains two separate and distinct microbial populations.}, }
@article {pmid39597592, year = {2024}, author = {Maynez-Perez, A and Jahuey-Martínez, FJ and Martínez-Quintana, JA and Hume, ME and Anderson, RC and Corral-Luna, A and Rodríguez-Almeida, FA and Castillo-Castillo, Y and Felix-Portillo, M}, title = {The Rumen Microbiome Composition of Raramuri Criollo and European Cattle in an Extensive System.}, journal = {Microorganisms}, volume = {12}, number = {11}, pages = {}, doi = {10.3390/microorganisms12112203}, pmid = {39597592}, issn = {2076-2607}, support = {OF-511-6/18-8538//PRODEP/ ; }, abstract = {Understanding the relationship between Raramuri Criollo cattle (RC) and their microbial ruminal ecosystem will help identify advantageous characteristics of adapted cattle as alternatives to achieve sustainable beef production systems. Our objective was to characterize the rumen microbiome of RC in comparison to Angus and Hereford breeds (European, E) and the cross between them (E × RC). Ruminal fluid was collected from 63 cows in their second productive cycle after grazing in the same paddock for 45 d, in the dry (n = 28) and rain (n = 35) seasons. DNA from ruminal fluid was isolated for 16s rRNA gene next-generation sequencing. The data were analyzed with QIIME2 and compared against the SILVA 16s rRNA database. Beta diversity was different (p < 0.05) between RC and E in both seasons. A microbial core was represented by the most abundant phyla. Planctomycetes and Spirochaetes represented above 1% in the rain season and below 1% in the dry one, whereas Euryarchaeota was below 1% and around 3%, respectively. LEfSe analysis identified differentiated (p < 0.05) key microbial groups that explain the differences between lineages at different taxonomic levels, reflecting the ability of the rumen ecosystem of RC cattle to adapt to hostile environmental conditions by having microbial groups specialized in the degradation of highly fibrous content.}, }
@article {pmid39597582, year = {2024}, author = {Hu, S and Zhang, X and Yang, F and Nie, H and Lu, X and Guo, Y and Zhao, X}, title = {Multimodal Approaches Based on Microbial Data for Accurate Postmortem Interval Estimation.}, journal = {Microorganisms}, volume = {12}, number = {11}, pages = {}, doi = {10.3390/microorganisms12112193}, pmid = {39597582}, issn = {2076-2607}, support = {2023JC17//Ministry of Public Security science and technology strong police basic work plan/ ; 2023JSYJC11//Ministry of Public Security Technology Research Program/ ; 2023JB001//Central Public-Interest Scientific Institution Basal Research/ ; }, abstract = {Accurate postmortem interval (PMI) estimation is critical for forensic investigations, aiding case classification and providing vital trial evidence. Early postmortem signs, such as body temperature and rigor mortis, are reliable for estimating PMI shortly after death. However, these indicators become less useful as decomposition progresses, making late-stage PMI estimation a significant challenge. Decomposition involves predictable microbial activity, which may serve as an objective criterion for PMI estimation. During decomposition, anaerobic microbes metabolize body tissues, producing gases and organic acids, leading to significant changes in skin and soil microbial communities. These shifts, especially the transition from anaerobic to aerobic microbiomes, can objectively segment decomposition into pre- and post-rupture stages according to rupture point. Microbial communities change markedly after death, with anaerobic bacteria dominating early stages and aerobic bacteria prevalent post-rupture. Different organs exhibit distinct microbial successions, providing valuable PMI insights. Alongside microbial changes, metabolic and volatile organic compound (VOC) profiles also shift, reflecting the body's biochemical environment. Due to insufficient information, unimodal models could not comprehensively reflect the PMI, so a muti-modal model should be used to estimate the PMI. Machine learning (ML) offers promising methods for integrating these multimodal data sources, enabling more accurate PMI predictions. Despite challenges such as data quality and ethical considerations, developing human-specific multimodal databases and exploring microbial-insect interactions can significantly enhance PMI estimation accuracy, advancing forensic science.}, }
@article {pmid39597569, year = {2024}, author = {Miura, H and Tsukahara, T and Inoue, R}, title = {Whole-Genome Metagenomic Analysis of Functional Profiles in the Fecal Microbiome of Farmed Sows with Different Reproductive Performances.}, journal = {Microorganisms}, volume = {12}, number = {11}, pages = {}, doi = {10.3390/microorganisms12112180}, pmid = {39597569}, issn = {2076-2607}, support = {23K14070//JSPS KAKENHI/ ; }, abstract = {Recent studies suggested an association between the reproductive performance of sows and their gut microbiota. To understand how the gut microbiota affect the reproductive performances of sows, we conducted a whole-genome metagenomic analysis on the fecal microbial functional profiles of sows with high and low reproductive performances. We used 60 sows from six farms (10 sows/farm), including 30 sows from three farms with higher reproductive performances (the mean number of weaned piglets/sow/year) (group H) and 30 sows from three farms with lower performances (group L). Fecal microbial DNA was subjected to a whole-genome metagenomic analysis. Biomarker exploration analysis identified "carbohydrate transport and metabolism" as the most discriminative function enriched in group H. Further analysis of carbohydrate-active enzymes revealed that the fecal microbiome of group H had a greater capacity to degrade dietary fiber, specifically cellulose and pectin. Group H also exhibited higher fecal short-chain fatty acid (SCFA) concentrations than group L, with the abundances of cellulose- and pectin-degrading genes showing significant positive correlations with fecal SCFA concentrations. Taxonomic analysis indicated greater contributions of Prevotella, Treponema, Ruminococcus, and Fibrobacter to cellulose and pectin degradation in the fecal microbiome in group H. In conclusion, higher reproductive performances of sows were, at least in part, associated with a greater microbial capacity for degrading cellulose and pectin, resulting in a higher SCFA production in the hindgut.}, }
@article {pmid39597568, year = {2024}, author = {Jung, Y and Kim, I and Jung, DR and Ha, JH and Lee, EK and Kim, JM and Kim, JY and Jang, JH and Bae, JT and Shin, JH and Cho, YS}, title = {Aging-Induced Changes in Cutibacterium acnes and Their Effects on Skin Elasticity and Wrinkle Formation.}, journal = {Microorganisms}, volume = {12}, number = {11}, pages = {}, doi = {10.3390/microorganisms12112179}, pmid = {39597568}, issn = {2076-2607}, support = {HP23C0061//Korea Health Industry Development Institute/Republic of Korea ; }, abstract = {Skin aging involves biomechanical changes like decreased elasticity, increased wrinkle formation, and altered barrier function. The skin microbiome significantly impacts this process. Here, we investigated the effects of decreased Cutibacterium acnes abundance and increase in other skin microorganisms on skin biomechanical properties in 60 healthy Koreans from Seoul, divided into younger (20-29 years) and older (60-75 years) groups. Metagenomic sequencing and skin assessments showed that the older group exhibited decreased C. acnes dominance and increased microbial diversity, correlating with reduced skin elasticity and increased wrinkles. In the younger age group, the enriched pathways included zeatin biosynthesis, distinct biotin metabolism pathways, and cofactor and vitamin metabolism in the younger age group, whereas pathways related to lipid metabolism, energy metabolism, and responses to environmental stressors, including UV damage and pollution, were enriched in the older group, according to functional analysis results. Network analysis indicated higher microbial connectivity in the younger group, suggesting a more stable community, whereas the older group's community displayed higher modularity, indicating more independent and specialized clusters. This study enhances our understanding of the impact of skin microbiome changes on skin aging, particularly the anti-aging effects of C. acnes. Future research should focus on the physiological mechanisms of skin microbiota on skin aging and explore therapeutic potentials to enhance skin health.}, }
@article {pmid39597565, year = {2024}, author = {Liu, J and Zhou, L and Lan, Y and Fan, J}, title = {Breed Selection of Poplars Imposes Greater Selection Pressure on the Rhizosphere Bacterial Community.}, journal = {Microorganisms}, volume = {12}, number = {11}, pages = {}, doi = {10.3390/microorganisms12112176}, pmid = {39597565}, issn = {2076-2607}, support = {2021YFD2201205 and 2021YFD2201203//National Key Research and Development Program of China/ ; }, abstract = {Breed selection alters the coevolution of plant-microbiome associations that have developed over long periods of natural evolution. We investigated the effects of breed selection on the rhizosphere microbiomes and metabolites of hybrid parents (I101 and 84K) and their offspring (Q1-Q5) using metagenomics and untargeted metabolomics. Rhizosphere archaeal, bacterial and fungal community β-diversity significantly differed among hybrid parents and offspring, but only the dominant bacterial phyla and bacterial community α-diversity revealed significant differences. Approximately 5.49%, 14.90% and 7.86% of the archaeal, bacterial and fungal species significantly differed among the poplar hybrid parents and offspring. Rhizosphere microbial functional genes and metabolites were both clustered into the following three groups: I101 and 84K; Q2 and Q4; and Q1, Q3 and Q5. Compared with the hybrid parents, 15 phytochemical compounds were enriched in the hybrid offspring and explained 7.15%, 18.24% and 6.68% of the total variation in the archaeal, bacterial and fungal community compositions, respectively. Rhizosphere metabolites significantly affected the bacterial community, rather than the archaeal and fungal communities. Our observations suggested that poplar breed selection imposed greater selection pressure on the rhizosphere bacterial community, which was mainly driven by metabolites.}, }
@article {pmid39597554, year = {2024}, author = {Lee, YJ and Lee, S and Kim, B and Kwak, D and Kim, T and Seo, MG}, title = {Gut Microbiome Diversity and Composition in Captive Siberian Tigers (Panthera tigris altaica): The Influence of Diet, Health Status, and Captivity on Microbial Communities.}, journal = {Microorganisms}, volume = {12}, number = {11}, pages = {}, doi = {10.3390/microorganisms12112165}, pmid = {39597554}, issn = {2076-2607}, abstract = {The gut microbiome is essential for the health of carnivorous mammals, including the endangered Siberian tiger (Panthera tigris altaica). However, limited research exists on the gut microbiome of captive Siberian tigers, especially regarding how diet and health status influence microbial diversity. This study addresses this gap by investigating the gut microbiome diversity and composition of six captive-born Siberian tigers housed at the Baekdudaegan National Arboretum in South Korea, using 16S rRNA gene sequencing. The study aimed to examine how diet and health status influence microbial communities, providing baseline data for managing captive tigers. Alpha diversity analysis revealed significant variation in microbial richness and evenness, with Tigers 2 and 6 exhibiting the highest microbial diversity and Tiger 3 the lowest, likely due to its surgical history and limited diet. Beta diversity analysis showed distinct microbial community structures influenced by diet and health. Taxonomic profiling identified Firmicutes and Bacteroidota as the dominant phyla, with Clostridium sensu stricto more prevalent in healthier tigers, while Escherichia-Shigella and Proteobacteria were abundant in tigers with lower diversity, suggesting dysbiosis. Comparisons with other tiger species confirm that diet, health, and captivity significantly shape the gut microbiome. These findings highlight the need for personalized health management in captive environments.}, }
@article {pmid39597538, year = {2024}, author = {Yilmaz, G and Chan, M and Lau, CH and Capitani, S and Kang, M and Charron, P and Hoover, E and Topp, E and Guan, J}, title = {How Gut Microbiome Perturbation Caused by Antibiotic Pre-Treatments Affected the Conjugative Transfer of Antimicrobial Resistance Genes.}, journal = {Microorganisms}, volume = {12}, number = {11}, pages = {}, doi = {10.3390/microorganisms12112148}, pmid = {39597538}, issn = {2076-2607}, support = {Phase VI Shared Priority Project Management Plan on Antimicrobial Resistance//Government of Canada Genomics R&amp;D Initiative/ ; }, abstract = {The global spread of antimicrobial resistance genes (ARGs) poses a significant threat to public health. While antibiotics effectively treat bacterial infections, they can also induce gut dysbiosis, the severity of which varies depending on the specific antibiotic treatment used. However, it remains unclear how gut dysbiosis affects the mobility and dynamics of ARGs. To address this, mice were pre-treated with streptomycin, ampicillin, or sulfamethazine, and then orally inoculated with Salmonella enterica serovar Typhimurium and S. Heidelberg carrying a multi-drug resistance IncA/C plasmid. The streptomycin pre-treatment caused severe microbiome perturbation, promoting the high-density colonization of S. Heidelberg and S. Typhimurium, and enabling an IncA/C transfer from S. Heidelberg to S. Typhimurium and a commensal Escherichia coli. The ampicillin pre-treatment induced moderate microbiome perturbation, supporting only S. Heidelberg colonization and the IncA/C transfer to commensal E. coli. The sulfamethazine pre-treatment led to mild microbiome perturbation, favoring neither Salmonella spp. colonization nor a conjugative plasmid transfer. The degree of gut dysbiosis also influenced the enrichment or depletion of the ARGs associated with mobile plasmids or core commensal bacteria, respectively. These findings underscore the significance of pre-existing gut dysbiosis induced by various antibiotic treatments on ARG dissemination and may inform prudent antibiotic use practices.}, }
@article {pmid39597536, year = {2024}, author = {Kim, WJ and Jung, G and Kim, T and Kim, J and Hurh, BS and Kim, H and Soung, DY}, title = {Heat-Killed Lactobacillus paracasei SMB092 Reduces Halitosis by Stimulating the Expression of β-Defensins in Oral Keratinocytes.}, journal = {Microorganisms}, volume = {12}, number = {11}, pages = {}, doi = {10.3390/microorganisms12112147}, pmid = {39597536}, issn = {2076-2607}, support = {the Technology Innovation Program (20008991)//the Ministry of Trade, Industry &amp; Energy (MOTIE, Korea)/ ; }, abstract = {The purpose of this study is to evaluate Lactobacillus paracasei SMB092 as a prophylactic agent for oral pathogens. We examined the physical interaction of SMB092 with a host by identifying the presence of mucus-binding (MuB) protein domains and the capacity of the mucin binding. We determined the role of heat-killed SMB092 in host oral immunity by quantifying the mRNA levels of β-defensins (BDs), Toll-like receptors (TLRs), and their cofactors (CD14/CD36) in normal human oral keratinocytes (HOK-16B cells). To assess the clinically relevant oral health effects of heat-killed SMB092, the growth of Porphyromonas (P.) gingivalis and the production of a volatile sulfur compound (H2S) were also measured in the filtered condition media (FCM) obtained from its cultures with HOK-16B cells. SMB092 possessed 14 putative MuB protein domains and was attached to mucin. Significant amounts of hBD1/2 and TLR2/6 were expressed in heat-killed SMB092-treated HOK-16B cells. The specific neutralization of TLR2 attenuated the expression of hBD1/2 and CD14/CD36. The FCM inhibited the growth of P. gingivalis and the production of H2S. Our data indicate that heat-killed SMB092 may contribute to a healthy oral microbiome as an immune stimulant in the production of BDs via the activation of the TLR2/6 signaling pathway.}, }
@article {pmid39597509, year = {2024}, author = {Pérez-Bustamante, IS and Cruz-Flores, R and López-Carvallo, JA and Sánchez-Serrano, S}, title = {Effect of the 16S rRNA Gene Hypervariable Region on the Microbiome Taxonomic Profile and Diversity in the Endangered Fish Totoaba macdonaldi.}, journal = {Microorganisms}, volume = {12}, number = {11}, pages = {}, doi = {10.3390/microorganisms12112119}, pmid = {39597509}, issn = {2076-2607}, support = {O0F154//Center for Scientific Research and Higher Education at Ensenada/ ; }, abstract = {Understanding the intricate dynamics of fish microbiota through 16S rRNA amplicon sequencing is pivotal for ecological insights and effective disease management. However, this approach faces challenges including the co-amplification of host mitochondrial sequences and the variability in bacterial composition influenced by the selected 16S rRNA gene regions. To overcome these limitations, we conducted a comprehensive investigation to identify the most suitable 16S rRNA region for bacterial microbial analysis in endangered fish Totoaba macdonaldi, an endemic species of significant ecological and economic importance in Mexico. Targeting four distinct hypervariable regions (V1-V2, V2-V3, V3-V4, and V5-V7) of the 16S rRNA gene, we determined the microbial composition within the distal intestine. A total of 40 microbiomes were sequenced. Our findings underscore the critical impact of region selection on the accuracy of microbiota analysis. The V3-V4 region detected the highest number of bacterial taxa and exhibited significantly higher alpha diversity indices, demonstrating the highest taxonomic resolution. This study emphasizes the necessity of meticulous 16S rRNA region selection for fish microbiota analysis, particularly in native species of ecological and economic significance such as the endangered T. macdonaldi, where information is limited. Such optimization enhances the reliability and applicability of microbiota studies in fisheries management and conservation efforts.}, }
@article {pmid39597084, year = {2024}, author = {Ko, Y and Alaedin, S and Fernando, D and Zhou, J and Ho, V}, title = {A Review of Fecal Microbiota Transplantation in Children-Exploring Its Role in the Treatment of Inflammatory Bowel Diseases.}, journal = {Medicina (Kaunas, Lithuania)}, volume = {60}, number = {11}, pages = {}, doi = {10.3390/medicina60111899}, pmid = {39597084}, issn = {1648-9144}, mesh = {Humans ; *Fecal Microbiota Transplantation/methods ; Child ; *Inflammatory Bowel Diseases/therapy/microbiology ; Gastrointestinal Microbiome ; Treatment Outcome ; }, abstract = {Background and Objectives: There is an increasing use of fecal matter transplantation (FMT) worldwide as research into the impact of the gut microbiome in various disease states is growing. FMT is the transfer of stool from a healthy human donor to a patient for the purpose of restoring intestinal dysbiosis. This review will assess the efficacy and safety of FMT in the treatment of pediatric inflammatory bowel diseases (IBDs) and explore the future directions of the use of FMT in children. Materials and Methods: A systematic review was performed where a literature search of publications published prior to 15 September 2023 was performed. Efficacy outcomes and safety data as well as microbiome analysis were reviewed from the studies where applicable. Results: Nine studies on UC and two studies on CD satisfied eligibility criteria and individually analysed. Most of the studies provided microbiome analyses. Conclusions: FMT is a safe treatment for paediatric IBD, and is shown to be effective in inducing clinical response by some studies. However the lack of randomized controlled trials limited the results of our study.}, }
@article {pmid39596994, year = {2024}, author = {Loperfido, A and Rizzo, D and Fionda, B and Mureddu, L and Tondo, A and Tagliaferri, L and Bellocchi, G and Delogu, G and Bussu, F}, title = {The Potential Role of the Microbiome in the Pathogenesis of Nasal Tumors: A Comprehensive Review.}, journal = {Medicina (Kaunas, Lithuania)}, volume = {60}, number = {11}, pages = {}, doi = {10.3390/medicina60111808}, pmid = {39596994}, issn = {1648-9144}, mesh = {Humans ; *Microbiota/physiology ; *Nose Neoplasms/microbiology/etiology ; Dysbiosis/complications ; Carcinoma, Squamous Cell/microbiology/etiology ; Carcinogenesis ; }, abstract = {Cancers of the nose, and especially the nose vestibule, represent a significant challenge for clinicians due to their rarity, the intricate nature of surrounding vital structures, the nonspecific early symptoms, and the etiological factors that are not completely understood. Emerging research suggests that alterations in the nasal microbiome, also known as microbial dysbiosis, may contribute to the pathogenesis of those malignancies through mechanisms involving chronic inflammation, immune modulation, and cellular changes. The aims of this paper are to review the current literature covering the nasal microbiome's role in carcinogenesis, particularly in the context of squamous cell carcinoma, and to explore how microbial dysbiosis might foster a pro-tumorigenic environment. It further discusses potential future directions for research and therapeutic approaches.}, }
@article {pmid39596938, year = {2024}, author = {Lee, YH and Jung, J and Hong, JY}, title = {Oral Microbial Changes in Oral Squamous Cell Carcinoma: Focus on Treponema denticola, Lactobacillus casei, and Candida albicans.}, journal = {Medicina (Kaunas, Lithuania)}, volume = {60}, number = {11}, pages = {}, doi = {10.3390/medicina60111753}, pmid = {39596938}, issn = {1648-9144}, support = {KMDF_PR_20200901_0023, 9991006696//Korea Medical Device Development Fund grant/ ; }, mesh = {Humans ; *Lacticaseibacillus casei ; Male ; Female ; *Candida albicans/isolation &amp; purification/pathogenicity ; Middle Aged ; *Carcinoma, Squamous Cell/microbiology ; Aged ; *Mouth Neoplasms/microbiology ; Adult ; *Treponema denticola/isolation &amp; purification ; Prospective Studies ; Saliva/microbiology ; Real-Time Polymerase Chain Reaction ; Mouth/microbiology ; }, abstract = {Background and Objectives: In this study, we aimed to explore the oral bacteria and fungi that can help discern oral squamous cell carcinoma (OSCC) and investigate the correlations between multiple key pathogens. Materials and Methods: Twelve participants (8 females and 4 males; mean age, 54.33 ± 20.65 years) were prospectively recruited into three groups: Group 1: healthy control, Group 2: patients with stomatitis, and Group 3: patients with OSCC, with 4 individuals in each group. Unstimulated whole saliva samples from these participants were analyzed using real-time PCR to assess the presence and abundance of 14 major oral bacterial species and Candida albicans. Results: The analysis revealed significant differences for certain microorganisms, namely, Treponema denticola (T. denticola), Lactobacillus casei (L. casei), and Candida albicans. T. denticola was most abundant in the OSCC group (5,358,692.95 ± 3,540,767.33), compared to the stomatitis (123,355.54 ± 197,490.86) and healthy control (9999.21 ± 11,998.40) groups. L. casei was undetectable in the healthy control group but was significantly more abundant in the stomatitis group (1653.94 ± 2981.98) and even higher in the OSCC group (21,336.95 ± 9258.79) (p = 0.001). A similar trend was observed for C. albicans, with DNA copy numbers rising from the healthy control (464.29 ± 716.76) to the stomatitis (1861.30 ± 1206.15) to the OSCC group (9347.98 ± 5128.54) (p = 0.006). The amount of T. denticola was positively correlated with L. casei (r = 0.890, p < 0.001) and C. albicans (r = 0.724, p = 0.008). L. casei's DNA copy number was strongly correlated with C. albicans (r = 0.931, p < 0.001). These three oral microbes exhibited strong positive correlations with each other and had various direct or indirect relationships with other species. Conclusions: In the OSCC group, T. denticola, L. casei, and C. albicans exhibited strong positive correlations with one another, further emphasizing the need for a deeper understanding of the complex microbial interactions in the OSCC environment.}, }
@article {pmid39596844, year = {2024}, author = {Jeong, JY and Kim, J and Kim, M and Park, S}, title = {Efficacy of High-Dose Synbiotic Additives for Deoxynivalenol Detoxification: Effects on Blood Biochemistry, Histology, and Intestinal Microbiome in Weaned Piglets.}, journal = {Biology}, volume = {13}, number = {11}, pages = {}, doi = {10.3390/biology13110889}, pmid = {39596844}, issn = {2079-7737}, support = {PJ015002//This research was funded by the Cooperative Research Program for Agriculture, Science, and Technology Development (Project No. PJ015002), Rural Development Administration, Republic of Korea, and the 2024 RDA Fellowship Program of the National Institute of/ ; }, abstract = {Deoxynivalenol (DON) is a common mycotoxin observed in cereal grains, and feed contamination poses health risks to pigs. Biological antidotes, such as synbiotics (SYNs), have garnered attention for mitigating DON toxicity. This study aimed to assess the efficacy of SYNs by comparing the blood biochemistry, histology, and gut microbiome of weaned piglets. A 4-week trial was conducted on 32 weaned piglets. After a week of diet and environmental adaptation, the pigs were divided into four groups: (1) control (CON, n = 8); (2) SYN (n = 8); (3) DON (n = 8); and (4) DON+SYN (n = 8). The SYN supplementation of weaned piglets increased the final body weight (21.71 ± 0.93 vs. 20.73 ± 0.84), average daily gain (0.38 ± 0.02 vs. 0.34 ± 0.02), and gain-to-feed ratio (0.49 ± 0.04 vs. 0.43 ± 0.02), and decreased the feed conversion ratio (2.14 ± 0.14 vs. 2.39 ± 0.13) compared to the DON group. A high dose of DON induced liver and colon fibrosis and liver and cecum apoptosis, which were alleviated by SYNs. Glucose in the DON group (84.9 ± 3.7) was significantly lower than in the control (101.3 ± 4.2). Additionally, both the DON and DON+SYN groups exhibited higher creatine (0.9 ± 0.0 and 0.9 ± 0.1) and lower cholesterol (88.3 ± 3.2 and 90.0 ± 4.8) levels (p < 0.05). In conclusion, SYNs alleviated DON toxicity, indicating its potential as an antidote for specific biomarkers.}, }
@article {pmid39596843, year = {2024}, author = {Uddipto, K and Quinlivan, JA and Mendz, GL}, title = {The Existence of an Intra-Amniotic Microbiome: Assessing a Controversy.}, journal = {Biology}, volume = {13}, number = {11}, pages = {}, doi = {10.3390/biology13110888}, pmid = {39596843}, issn = {2079-7737}, abstract = {The existence of intra-amniotic and placental microbiomes during pregnancy has been the source of considerable debate, with research yielding conflicting evidence. This study evaluated investigations into the putative presence of these microbiomes in healthy pregnancies by identifying design and data interpretation issues, particularly concerning contamination in samples with low-density bacterial DNA. Positive findings from diverse populations suggest a consistent presence of microbiota in the intra-amniotic space. Negative conclusions regarding the existence of these prenatal microbiomes emphasise the impact of contamination in the analysis of samples with low-density bacterial DNA. This study concluded that there is no definitive evidence to refute the existence of intra-amniotic microbiomes in healthy pregnancies. Also, it provides suggestions for controlling potential contamination factors in future research on intra-amniotic and placental microbial populations.}, }
@article {pmid39596789, year = {2024}, author = {Hurley, J}, title = {Structural Equation Modelling as a Proof-of-Concept Tool for Mediation Mechanisms Between Topical Antibiotic Prophylaxis and Six Types of Blood Stream Infection Among ICU Patients.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {13}, number = {11}, pages = {}, doi = {10.3390/antibiotics13111096}, pmid = {39596789}, issn = {2079-6382}, support = {Rural Clinical Training and Support (RCTS) program.//Australian Government Department of Health and Ageing/ ; }, abstract = {Whether exposing the microbiome to antibiotics decreases or increases the risk of blood stream infection with Pseudomonas aeruginosa, Staphylococcus aureus, Acinetobacter, and Candida among ICU patients, and how this altered risk might be mediated, are critical research questions. Addressing these questions through the direct study of specific constituents within the microbiome would be difficult. An alternative tool for addressing these research questions is structural equation modelling (SEM). SEM enables competing theoretical causation networks to be tested 'en bloc' by confrontation with data derived from the literature. These causation models have three conceptual steps: exposure to specific antimicrobials are the key drivers, clinically relevant infection end points are the measurable observables, and the activity of key microbiome constituents on microbial invasion serve as mediators. These mediators, whether serving to promote, to impede, or neither, are typically unobservable and appear as latent variables in each model. SEM methods enable comparisons through confronting the three competing models, each versus clinically derived data with the various exposures, such as topical or parenteral antibiotic prophylaxis, factorized in each model. Candida colonization, represented as a latent variable, and concurrency are consistent promoters of all types of blood stream infection, and emerge as harmful mediators.}, }
@article {pmid39596708, year = {2024}, author = {Gyraitė, G and Kataržytė, M and Espinosa, RP and Kalvaitienė, G and Lastauskienė, E}, title = {Microbiome and Resistome Studies of the Lithuanian Baltic Sea Coast and the Curonian Lagoon Waters and Sediments.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {13}, number = {11}, pages = {}, doi = {10.3390/antibiotics13111013}, pmid = {39596708}, issn = {2079-6382}, support = {S-PD-22-80//Lietuvos Mokslo Taryba/ ; }, abstract = {BACKGROUND: the widespread use of antibiotics in human and veterinary medicine has contributed to the global challenge of antimicrobial resistance, posing significant environmental and public health risks.<br><br>OBJECTIVES: this study aimed to examine the microbiome and resistome dynamics across a salinity gradient, analyzing water and sediment samples from the Baltic Sea coast and the Curonian Lagoon between 2017 and 2023.<br><br>METHODS: the composition of the water and sediment bacterial community was determined by Full-Length Amplicon Metagenomics Sequencing, while ARG detection and quantification were performed using the SmartChipTM Real-Time PCR system.<br><br>RESULTS: the observed differences in bacterial community composition between the Baltic Sea coast and the Curonian Lagoon were driven by variations in salinity and chlorophyll a (chl a) concentration. The genera associated with infectious potential were observed in higher abundances in sediment than in water samples. Over 300 genes encoding antibiotic resistance (ARGs), such as aminoglycosides, beta-lactams, and multidrug resistance genes, were identified. Of particular interest were those ARGs that have previously been detected in pathogens and those currently classified as a potential future threat. Furthermore, our findings reveal a higher abundance and a distinct profile of ARGs in sediment samples from the lagoon compared to water.<br><br>CONCLUSIONS: these results suggest that transitional waters such as lagoons may serve as reservoirs for ARGs, and might be influenced by anthropogenic pressures and natural processes such as salinity fluctuation and nutrient cycling.}, }
@article {pmid39596705, year = {2024}, author = {Moraes, BDGC and Martins, RCR and Fonseca, JVDS and Franco, LAM and Pereira, GCO and Bartelli, TF and Cortes, MF and Scaccia, N and Santos, CF and Musqueira, PT and Otuyama, LJ and Pylro, VS and Mariano, L and Rocha, V and Witkin, SS and Sabino, E and Guimaraes, T and Costa, SF}, title = {Impact of Exogenous Lactiplantibacillus plantarum on the Gut Microbiome of Hematopoietic Stem Cell Transplantation Patients Colonized by Multidrug-Resistant Bacteria: An Observational Study.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {13}, number = {11}, pages = {}, doi = {10.3390/antibiotics13111010}, pmid = {39596705}, issn = {2079-6382}, support = {FAPESP//001/ ; }, abstract = {Background:Lactiplantibacillus plantarum can inhibit the growth of multidrug-resistant organisms (MDROs) and modulate the gut microbiome. However, data on hematopoietic stem cell transplantation (HSCT) are scarce. Aim: In an observational study, we assessed the impact of L. plantarum on the modulation of the gut microbiome in HSCT patients colonized by MDROs. Methods: Participants were allocated to an intervention group (IG = 22) who received capsules of L. plantarum (5 × 10[9] CFU) twice per day until the onset of neutropenia or a control group (CG = 20). The V4 region of the 16S bacterial rRNA gene was sequenced in 87 stool samples from a subset of 33 patients (IG = 20 and CG = 13). The Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt2) program was used to predict metagenome functions. Results:L. plantarum demonstrated an average 86% (±11%) drug-target engagement at 43 (±29) days of consumption and was deemed safe, well-tolerated, and associated with an increase in the abundance of the Lactobacillales (p < 0.05). A significant increase in Lactococcus and a reduction in Turicibacter (p < 0.05) were identified on the second week of L. plantarum use. Although Enterococcus abundance had a greater rise in the CG (p = 0.07), there were no significant differences concerning the Gram-negative MDROs. No serious adverse effects were reported in the IG. We observed a greater, non-significant pyruvate fermentation to propanoate I (p = 0.193) relative abundance in the IG compared with the CG. L. plantarum use was safe and tolerable by HSCT patients. Conclusions: While L. plantarum is safe and may impact Enterococcus and Turicibacter abundance, it showed no impact on Gram-negative MDRO abundance in HSCT patients.}, }
@article {pmid39596695, year = {2024}, author = {Sánchez, MC and Hernández, P and Velapatiño, &#xc1; and Cuba, E and Ciudad, MJ and Collado, L}, title = {Illumina Sequencing in Conjunction with Propidium Monoazide to Identify Live Bacteria After Antiseptic Treatment in a Complex Oral Biofilm: A Study Using an Ex Vivo Supragingival Biofilm Model.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {13}, number = {11}, pages = {}, doi = {10.3390/antibiotics13111000}, pmid = {39596695}, issn = {2079-6382}, abstract = {Background/Objectives: The evaluation of the efficacy of antibacterial treatments in complex oral ecosystems is limited by the inability to differentiate live from dead bacteria using omic techniques. The objective of this study was therefore to assess the ability of the combination of the 16S rRNA Illumina sequencing methodology and the action of propidium monoazide (PMA) to study viable bacterial profiles in oral biofilms after exposure to an antiseptic compound. Methods: Cariogenic supragingival biofilms were developed in an ex vivo model for 96 h, using saliva from healthy volunteers. The biofilms were treated with 0.12% chlorhexidine (CHX) combined with 0.05% cetylpyridinium chloride (CPC), for 60 s, using phosphate buffered saline as a control. After exposure, each biofilm was treated or not with PMA to then extract the bacterial DNA, quantify it by Qubit, quantify the bacterial population using qPCR, and perform the metataxonomic study of the samples using Illumina 16S rRNA sequencing. Results: A significantly lower DNA concentration in the PMA-treated biofilms (p < 0.05 compared with those not exposed to PMA) was observed. The viable bacterial count obtained by qPCR differed significantly from the total bacterial count in the biofilm samples exposed to the antiseptic (p < 0.05). The viable microbiome differed significantly from the total bacterial profile of the samples treated with CHX/CPC after exposure to PMA (p < 0.05 at the α- and β-diversity levels). Conclusions: The combination of Illumina 16S rRNA sequencing and PMA helps solve the inability to evaluate the efficacy of antibacterial treatments in the bacterial profile of complex ecosystems such as oral biofilms.}, }
@article {pmid39596648, year = {2024}, author = {Wang, Z and Song, X and Yin, W and Shi, K and Lin, Y and Liu, J and Li, X and Tan, J and Rong, J and Xu, K and Wang, G}, title = {Exposure to High Concentrations of Tetrabromobisphenol A Slows the Process of Tissue Regeneration and Induces an Imbalance of Metabolic Homeostasis in the Regenerated Intestines of Apostichopus japonicus.}, journal = {Genes}, volume = {15}, number = {11}, pages = {}, doi = {10.3390/genes15111448}, pmid = {39596648}, issn = {2073-4425}, support = {ZR2023MC141//Natural Science Foundation of Shandong Province/ ; SDAIT-22-03 and SDAIT-22-09//Shandong Modern Agricultural Industrial Technology System/ ; 2023RKY06004//Key R&amp;D Program (Soft Science Project) of Shandong Province/ ; }, mesh = {Animals ; *Regeneration/drug effects ; *Homeostasis/drug effects ; *Polybrominated Biphenyls ; *Gastrointestinal Microbiome/drug effects ; Intestines/drug effects ; Stichopus/genetics/drug effects/microbiology/metabolism ; }, abstract = {BACKGROUND: Tissue regenerative capacity following evisceration, potentially influenced by environmental contaminants and intestinal microflora, is essential for the financial success of Apostichopus japonicus farming. However, the morphological structure, gut microbiome composition, and genes expression pattern of the regenerated gut after exposure to high levels of TBBPA remain poorly unclear.<br><br>METHODS: In this research, the effect of TBBPA exposure on tissue regeneration in A. japonicus was investigated through a comprehensive multi-omics approach.<br><br>RESULTS: Our results showed that the integrity, the intestinal wall thickness, and the villi length of the regenerated intestines in A. japonicus decreased after treatment with high levels of TBBPA. The findings from PCoA and NMDS analyses revealed that the microbial community composition was significantly altered following exposure to high concentrations of TBBPA in the regenerated intestines of A. japonicus. The KEGG pathway enrichment analysis indicated that the DEGs (differentially expressed genes) were predominantly enriched on metabolism and immunity-related signaling pathways after exposure to high levels of TBBPA. These included pathways involved in the PPAR signaling pathway, ECM receptor interaction, glycerolipid metabolism, and fatty acid degradation. Interestingly, the results have demonstrated that there are 77 transcript factors that were significantly different after exposure to TBBPA.<br><br>CONCLUSIONS: These results suggested that high levels of exposure to TBBPA induces an imbalance of the metabolic homeostasis by regulating the expression levels of transcription factors in the regenerated intestines of A. japonicus.}, }
@article {pmid39596522, year = {2024}, author = {Maita, K and Fujihara, H and Matsumura, M and Miyakawa, M and Baba, R and Morimoto, H and Nakayama, R and Ito, Y and Kawaguchi, K and Hamada, Y}, title = {Impact of Reduced Saliva Production on Intestinal Integrity and Microbiome Alterations: A Sialoadenectomy Mouse Model Study.}, journal = {International journal of molecular sciences}, volume = {25}, number = {22}, pages = {}, doi = {10.3390/ijms252212455}, pmid = {39596522}, issn = {1422-0067}, support = {18K09543//Japan Society for the Promotion of Science/ ; 20K10196//Japan Society for the Promotion of Science London/ ; }, mesh = {Animals ; Mice ; *Gastrointestinal Microbiome ; *Saliva/microbiology/metabolism ; *RNA, Ribosomal, 16S/genetics ; Male ; Intestines/microbiology/pathology ; Disease Models, Animal ; Mice, Inbred C57BL ; Intestinal Mucosa/microbiology/metabolism/pathology ; }, abstract = {This study investigates the effect of reduced saliva production on intestinal histological structure and microbiome composition using a sialoadenectomy murine model, evaluating differences in saliva secretion, body weight, intestinal histopathological changes, and microbiome alteration using 16S rRNA gene sequencing across three groups (control, sham, and sialoadenectomy). For statistical analysis, one-way analysis of variance and multiple comparisons using Bonferroni correction were performed. p-values < 0.05 were considered statistically significant. Microbiome analysis was performed using Qiime software. The results show that reduced saliva secretion leads to structural changes in the intestinal tract, including shorter and atrophic villi, deformed Paneth cells, decreased goblet cell density, and immunohistochemical changes in epidermal growth factor and poly(ADP-ribose) polymerase-1, especially at three months after surgery. They also showed significant alterations in the intestinal microbiome, including increased Lactobacillaceae and altered populations of Ruminococcaceae and Peptostreptococcaceae, suggesting potential inflammatory responses and decreased short-chain fatty acid production. However, by 12 months after surgery, these effects appeared to be normalized, indicating potential compensatory mechanisms. Interestingly, sham-operated mice displayed favorable profiles, possibly due to immune activation from minor surgical intervention. This study underscores saliva's essential role in intestinal condition, emphasizing the "oral-gut axis" and highlighting broader implications for the relationship between oral and systemic health.}, }
@article {pmid39596472, year = {2024}, author = {Mihailovich, M and Tolinački, M and Soković Bajić, S and Lestarevic, S and Pejovic-Milovancevic, M and Golić, N}, title = {The Microbiome-Genetics Axis in Autism Spectrum Disorders: A Probiotic Perspective.}, journal = {International journal of molecular sciences}, volume = {25}, number = {22}, pages = {}, doi = {10.3390/ijms252212407}, pmid = {39596472}, issn = {1422-0067}, support = {7744507//Science Fund of the Republic of Serbia, IDEAS program/ ; 451-03-66/2024-03/200042//The Ministry of Science, Technological Development and Innovations of the Republic of Serbia/ ; }, mesh = {Humans ; *Probiotics/therapeutic use ; *Autism Spectrum Disorder/microbiology/therapy ; *Gastrointestinal Microbiome ; Precision Medicine/methods ; Animals ; }, abstract = {Autism spectrum disorder (commonly known as autism) is a complex and prevalent neurodevelopmental condition characterized by challenges in social behavior, restricted interests, and repetitive behaviors. It is projected that the annual cost of autism spectrum disorder in the US will reach USD 461 billion by 2025. However, despite being a major public health problem, effective treatment for the underlying symptoms remains elusive. As numerous literature data indicate the role of gut microbiota in autism prognosis, particularly in terms of alleviating gastrointestinal (GI) symptoms, high hopes have been placed on probiotics for autism treatment. Approximately twenty clinical studies have been conducted using single or mixed probiotic cultures. Ho